diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out index 208b0e2dd..8b9e9c148 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -68,7 +64,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -96,7 +92,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.1 according to the specified width (0.1). colvars: ---------------------------------------------------------------------- @@ -107,28 +102,43 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - alpha colvar component: -colvars: - angle colvar component: -colvars: - hBond colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. +colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/3. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/4. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/5. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/6. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/7. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/8. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/9. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/10. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/11. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/12. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/13. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/14. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/15. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/16. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/17. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/18. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/19. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/20. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/21. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/22. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/23. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/24. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/25. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/26. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/27. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/28. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/29. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 2c3923d92..759c485d6 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 8.42013109670389e-01 + x 8.42013109784351e-01 } restraint { diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj index 1d9d7dbb8..59a13c0cf 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 8.44342403972232e-01 -7.44342403972232e-02 - 1 8.44098854642285e-01 -7.44098854642285e-02 - 2 8.43793147696887e-01 -7.43793147696886e-02 - 3 8.43428641474561e-01 -7.43428641474561e-02 - 4 8.43016163379186e-01 -7.43016163379186e-02 - 5 8.42574360353300e-01 -7.42574360353300e-02 - 6 8.42128240610470e-01 -7.42128240610470e-02 - 7 8.41706134434711e-01 -7.41706134434711e-02 - 8 8.41335763240474e-01 -7.41335763240474e-02 - 9 8.41040339208587e-01 -7.41040339208587e-02 - 10 8.40835525411341e-01 -7.40835525411341e-02 - 11 8.40727764204272e-01 -7.40727764204272e-02 - 12 8.40714100924275e-01 -7.40714100924275e-02 - 13 8.40783338958624e-01 -7.40783338958624e-02 - 14 8.40918192455347e-01 -7.40918192455347e-02 - 15 8.41098021792410e-01 -7.41098021792409e-02 - 16 8.41301655271500e-01 -7.41301655271500e-02 - 17 8.41509729929472e-01 -7.41509729929472e-02 - 18 8.41706023128253e-01 -7.41706023128253e-02 - 19 8.41877486404754e-01 -7.41877486404754e-02 - 20 8.42013109670389e-01 -7.42013109670389e-02 + 0 8.44342403972268e-01 -7.44342403972268e-02 + 1 8.44098854642590e-01 -7.44098854642590e-02 + 2 8.43793147698295e-01 -7.43793147698295e-02 + 3 8.43428641477914e-01 -7.43428641477913e-02 + 4 8.43016163376308e-01 -7.43016163376308e-02 + 5 8.42574360346050e-01 -7.42574360346050e-02 + 6 8.42128240619594e-01 -7.42128240619594e-02 + 7 8.41706134441275e-01 -7.41706134441275e-02 + 8 8.41335763262530e-01 -7.41335763262530e-02 + 9 8.41040339242422e-01 -7.41040339242422e-02 + 10 8.40835525453342e-01 -7.40835525453342e-02 + 11 8.40727764254687e-01 -7.40727764254687e-02 + 12 8.40714100983289e-01 -7.40714100983289e-02 + 13 8.40783339024046e-01 -7.40783339024046e-02 + 14 8.40918192530856e-01 -7.40918192530856e-02 + 15 8.41098021877668e-01 -7.41098021877668e-02 + 16 8.41301655357182e-01 -7.41301655357182e-02 + 17 8.41509730022086e-01 -7.41509730022086e-02 + 18 8.41706023231625e-01 -7.41706023231625e-02 + 19 8.41877486515835e-01 -7.41877486515835e-02 + 20 8.42013109784351e-01 -7.42013109784350e-02 diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out index e2f8eb508..09ba41c2e 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -68,7 +64,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -96,7 +92,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.1 according to the specified width (0.1). colvars: ---------------------------------------------------------------------- @@ -107,33 +102,48 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - alpha colvar component: -colvars: - angle colvar component: -colvars: - hBond colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. +colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/3. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/4. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/5. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/6. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/7. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/8. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/9. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/10. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/11. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/12. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/13. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/14. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/15. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/16. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/17. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/18. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/19. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/20. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/21. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/22. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/23. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/24. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/25. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/26. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/27. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/28. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/29. 2 atoms: total mass = 30.006, total charge = -0.98. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.842013 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 7359bbe19..e09e94eee 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 8.32317621377386e-01 + x 8.32317621580914e-01 } restraint { diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 5d21a33d1..f161a80a9 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 8.42013109670389e-01 -7.42013109670389e-02 - 21 8.42102179859247e-01 -7.42102179859247e-02 - 22 8.42132753897807e-01 -7.42132753897807e-02 - 23 8.42091111194279e-01 -7.42091111194279e-02 - 24 8.41962602226785e-01 -7.41962602226785e-02 - 25 8.41733788173401e-01 -7.41733788173401e-02 - 26 8.41395277535143e-01 -7.41395277535143e-02 - 27 8.40944388629140e-01 -7.40944388629140e-02 - 28 8.40386797315513e-01 -7.40386797315513e-02 - 29 8.39736648516850e-01 -7.39736648516849e-02 - 30 8.39015059742126e-01 -7.39015059742125e-02 - 31 8.38247391201732e-01 -7.38247391201732e-02 - 32 8.37459941069716e-01 -7.37459941069716e-02 - 33 8.36676804346260e-01 -7.36676804346260e-02 - 34 8.35917530408746e-01 -7.35917530408746e-02 - 35 8.35195977166090e-01 -7.35195977166090e-02 - 36 8.34520437212929e-01 -7.34520437212929e-02 - 37 8.33894755921237e-01 -7.33894755921237e-02 - 38 8.33319850305569e-01 -7.33319850305569e-02 - 39 8.32794899843751e-01 -7.32794899843751e-02 - 40 8.32317621377386e-01 -7.32317621377385e-02 + 20 8.42013109784351e-01 -7.42013109784350e-02 + 21 8.42102179978755e-01 -7.42102179978755e-02 + 22 8.42132754021507e-01 -7.42132754021507e-02 + 23 8.42091111321136e-01 -7.42091111321136e-02 + 24 8.41962602356096e-01 -7.41962602356095e-02 + 25 8.41733788301857e-01 -7.41733788301857e-02 + 26 8.41395277661295e-01 -7.41395277661295e-02 + 27 8.40944388762035e-01 -7.40944388762035e-02 + 28 8.40386797451279e-01 -7.40386797451279e-02 + 29 8.39736648652815e-01 -7.39736648652815e-02 + 30 8.39015059877273e-01 -7.39015059877273e-02 + 31 8.38247391341335e-01 -7.38247391341335e-02 + 32 8.37459941212710e-01 -7.37459941212710e-02 + 33 8.36676804493709e-01 -7.36676804493709e-02 + 34 8.35917530561721e-01 -7.35917530561721e-02 + 35 8.35195977325575e-01 -7.35195977325575e-02 + 36 8.34520437356997e-01 -7.34520437356996e-02 + 37 8.33894756096833e-01 -7.33894756096832e-02 + 38 8.33319850486250e-01 -7.33319850486250e-02 + 39 8.32794900028858e-01 -7.32794900028857e-02 + 40 8.32317621580914e-01 -7.32317621580914e-02 diff --git a/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt b/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out index efee19466..4a19c8550 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,42 +55,42 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] @@ -133,7 +129,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -144,27 +139,16 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - angle colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index d398132a2..43525b56b 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.00164524891460e+02 + x 1.00164524892654e+02 } restraint { diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj index 259181bc9..2c8f412a0 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.03254732139588e+02 -4.12618928558351e-01 - 1 1.03132366162310e+02 -4.12129464649240e-01 - 2 1.03006339773933e+02 -4.11625359095731e-01 - 3 1.02876690769855e+02 -4.11106763079420e-01 - 4 1.02743412368037e+02 -4.10573649472149e-01 - 5 1.02606460567606e+02 -4.10025842270424e-01 - 6 1.02465768469001e+02 -4.09463073876003e-01 - 7 1.02321276095485e+02 -4.08885104381940e-01 - 8 1.02172974776860e+02 -4.08291899107440e-01 - 9 1.02020953811828e+02 -4.07683815247310e-01 - 10 1.01865429972566e+02 -4.07061719890263e-01 - 11 1.01706742242777e+02 -4.06426968971107e-01 - 12 1.01545305106535e+02 -4.05781220426139e-01 - 13 1.01381527031664e+02 -4.05126108126656e-01 - 14 1.01215712239860e+02 -4.04462848959438e-01 - 15 1.01047968158544e+02 -4.03791872634177e-01 - 16 1.00878136637506e+02 -4.03112546550023e-01 - 17 1.00705758988893e+02 -4.02423035955572e-01 - 18 1.00530077455794e+02 -4.01720309823177e-01 - 19 1.00350071436460e+02 -4.01000285745841e-01 - 20 1.00164524891460e+02 -4.00258099565841e-01 + 1 1.03132366162315e+02 -4.12129464649258e-01 + 2 1.03006339773950e+02 -4.11625359095801e-01 + 3 1.02876690770137e+02 -4.11106763080547e-01 + 4 1.02743412368775e+02 -4.10573649475101e-01 + 5 1.02606460567804e+02 -4.10025842271217e-01 + 6 1.02465768469158e+02 -4.09463073876632e-01 + 7 1.02321276095597e+02 -4.08885104382386e-01 + 8 1.02172974776925e+02 -4.08291899107700e-01 + 9 1.02020953811854e+02 -4.07683815247416e-01 + 10 1.01865429972567e+02 -4.07061719890269e-01 + 11 1.01706742242773e+02 -4.06426968971090e-01 + 12 1.01545305106549e+02 -4.05781220426196e-01 + 13 1.01381527031724e+02 -4.05126108126898e-01 + 14 1.01215712239996e+02 -4.04462848959984e-01 + 15 1.01047968160132e+02 -4.03791872640529e-01 + 16 1.00878136638138e+02 -4.03112546552552e-01 + 17 1.00705758990434e+02 -4.02423035961734e-01 + 18 1.00530077456623e+02 -4.01720309826491e-01 + 19 1.00350071437758e+02 -4.01000285751032e-01 + 20 1.00164524892654e+02 -4.00258099570617e-01 diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 3752c7683..7b64bde0e 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,42 +55,42 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] @@ -133,7 +129,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -144,32 +139,21 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - angle colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 100.165 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 19ffa9256..186ad215e 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.50832224152502e+01 + x 9.50832224199785e+01 } restraint { diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index f3070f2f5..1173041f5 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.00164524891460e+02 -4.00258099565841e-01 - 21 9.99721208590562e+01 -3.99488483436225e-01 - 22 9.97715541522898e+01 -3.98686216609159e-01 - 23 9.95616505536277e+01 -3.97846602214511e-01 - 24 9.93414788135756e+01 -3.96965915254302e-01 - 25 9.91104429898799e+01 -3.96041771959520e-01 - 26 9.88683487906183e+01 -3.95073395162473e-01 - 27 9.86154431829325e+01 -3.94061772731730e-01 - 28 9.83524306231076e+01 -3.93009722492431e-01 - 29 9.80804706453528e+01 -3.91921882581411e-01 - 30 9.78011567145892e+01 -3.90804626858357e-01 - 31 9.75164710990926e+01 -3.89665884396371e-01 - 32 9.72287071984055e+01 -3.88514828793622e-01 - 33 9.69403528472622e+01 -3.87361411389049e-01 - 34 9.66539367587656e+01 -3.86215747035062e-01 - 35 9.63718539644472e+01 -3.85087415857789e-01 - 36 9.60961965658487e+01 -3.83984786263395e-01 - 37 9.58286196853218e+01 -3.82914478741287e-01 - 38 9.55702653322208e+01 -3.81881061328883e-01 - 39 9.53217520988444e+01 -3.80887008395378e-01 - 40 9.50832224152502e+01 -3.79932889661001e-01 + 20 1.00164524892654e+02 -4.00258099570617e-01 + 21 9.99721208604643e+01 -3.99488483441857e-01 + 22 9.97715541539098e+01 -3.98686216615639e-01 + 23 9.95616505554525e+01 -3.97846602221810e-01 + 24 9.93414788155942e+01 -3.96965915262377e-01 + 25 9.91104429920789e+01 -3.96041771968316e-01 + 26 9.88683487929842e+01 -3.95073395171937e-01 + 27 9.86154431854530e+01 -3.94061772741812e-01 + 28 9.83524306257732e+01 -3.93009722503093e-01 + 29 9.80804706481534e+01 -3.91921882592614e-01 + 30 9.78011567175226e+01 -3.90804626870090e-01 + 31 9.75164711021598e+01 -3.89665884408639e-01 + 32 9.72287072016144e+01 -3.88514828806458e-01 + 33 9.69403528506243e+01 -3.87361411402497e-01 + 34 9.66539367622950e+01 -3.86215747049180e-01 + 35 9.63718539681591e+01 -3.85087415872637e-01 + 36 9.60961965697586e+01 -3.83984786279034e-01 + 37 9.58286196894440e+01 -3.82914478757776e-01 + 38 9.55702653365613e+01 -3.81881061346245e-01 + 39 9.53217521034107e+01 -3.80887008413643e-01 + 40 9.50832224199785e+01 -3.79932889679914e-01 diff --git a/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out index d1e4a4135..23b8999d1 100644 --- a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,29 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - coordNum pairlist: -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out index 43e5df3df..49e0fbd49 100644 --- a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,34 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - coordNum pairlist: -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt index 157cac038..b7bf5455c 100644 --- a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-10-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out index 6b75c3857..6e7b06fa6 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,26 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 952b2b371..309db4bf6 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.50382512265436e-04 + x 4.50382512360039e-04 } restraint { diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj index 9c31c9ffe..112ced7b7 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 4.88336530020493e-04 3.98046653879918e-04 - 1 5.03969504628764e-04 3.97984121981485e-04 - 2 5.19354539513055e-04 3.97922581841948e-04 - 3 5.32983502677849e-04 3.97868065989289e-04 - 4 5.43368523998496e-04 3.97826525904006e-04 - 5 5.49278854725414e-04 3.97802884581098e-04 - 6 5.49958947547140e-04 3.97800164209811e-04 - 7 5.45267296533856e-04 3.97818930813865e-04 - 8 5.35697517312449e-04 3.97857209930750e-04 - 9 5.22279865846730e-04 3.97910880536613e-04 - 10 5.06396380407222e-04 3.97974414478371e-04 - 11 4.89562687024283e-04 3.98041749251903e-04 - 12 4.73229283972216e-04 3.98107082864111e-04 - 13 4.58638307492123e-04 3.98165446770032e-04 - 14 4.46747589785476e-04 3.98213009640858e-04 - 15 4.38212375483778e-04 3.98247150498065e-04 - 16 4.33402944446411e-04 3.98266388222214e-04 - 17 4.32434896997806e-04 3.98270260412009e-04 - 18 4.35195093328268e-04 3.98259219626687e-04 - 19 4.41356151324242e-04 3.98234575394703e-04 - 20 4.50382512265436e-04 3.98198469950938e-04 + 1 5.03969504626528e-04 3.97984121981494e-04 + 2 5.19354539504346e-04 3.97922581841983e-04 + 3 5.32983502659005e-04 3.97868065989364e-04 + 4 5.43368523967091e-04 3.97826525904132e-04 + 5 5.49278854680875e-04 3.97802884581276e-04 + 6 5.49958947491071e-04 3.97800164210036e-04 + 7 5.45267296469905e-04 3.97818930814120e-04 + 8 5.35697517245723e-04 3.97857209931017e-04 + 9 5.22279865782907e-04 3.97910880536868e-04 + 10 5.06396380351657e-04 3.97974414478593e-04 + 11 4.89562686981327e-04 3.98041749252075e-04 + 12 4.73229283944885e-04 3.98107082864221e-04 + 13 4.58638307482096e-04 3.98165446770072e-04 + 14 4.46747589793320e-04 3.98213009640827e-04 + 15 4.38212375509248e-04 3.98247150497963e-04 + 16 4.33402944488714e-04 3.98266388222045e-04 + 17 4.32434897055776e-04 3.98270260411777e-04 + 18 4.35195093400421e-04 3.98259219626398e-04 + 19 4.41356151408746e-04 3.98234575394365e-04 + 20 4.50382512360039e-04 3.98198469950560e-04 diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out index cd3aa273f..27e93bffc 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,31 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.000450383 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 673940f1b..f07d92582 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.07333860034785e-04 + x 5.07333860152640e-04 } restraint { diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 69dbc17d4..7cece45e3 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 4.50382512265436e-04 3.98198469950938e-04 - 21 4.61538871220812e-04 3.98153844515117e-04 - 22 4.73915291286790e-04 3.98104338834853e-04 - 23 4.86481082339776e-04 3.98054075670641e-04 - 24 4.98171600123441e-04 3.98007313599506e-04 - 25 5.08000918764789e-04 3.97967996324941e-04 - 26 5.15183038861356e-04 3.97939267844555e-04 - 27 5.19238454925296e-04 3.97923046180299e-04 - 28 5.20063102812949e-04 3.97919747588748e-04 - 29 5.17943198908027e-04 3.97928227204368e-04 - 30 5.13510005699675e-04 3.97945959977201e-04 - 31 5.07642202407253e-04 3.97969431190371e-04 - 32 5.01335749082877e-04 3.97994657003669e-04 - 33 4.95567637174033e-04 3.98017729451304e-04 - 34 4.91176737636651e-04 3.98035293049453e-04 - 35 4.88775079019952e-04 3.98044899683920e-04 - 36 4.88691484967476e-04 3.98045234060130e-04 - 37 4.90943355320849e-04 3.98036226578717e-04 - 38 4.95233101502291e-04 3.98019067593991e-04 - 39 5.00971349382943e-04 3.97996114602468e-04 - 40 5.07333860034785e-04 3.97970664559861e-04 + 20 4.50382512360039e-04 3.98198469950560e-04 + 21 4.61538871322809e-04 3.98153844514709e-04 + 22 4.73915291393088e-04 3.98104338834428e-04 + 23 4.86481082447120e-04 3.98054075670212e-04 + 24 4.98171600228783e-04 3.98007313599085e-04 + 25 5.08000918865736e-04 3.97967996324537e-04 + 26 5.15183038956578e-04 3.97939267844174e-04 + 27 5.19238455014736e-04 3.97923046179941e-04 + 28 5.20063102897763e-04 3.97919747588409e-04 + 29 5.17943198990256e-04 3.97928227204039e-04 + 30 5.13510005781771e-04 3.97945959976873e-04 + 31 5.07642202491579e-04 3.97969431190034e-04 + 32 5.01335749171320e-04 3.97994657003315e-04 + 33 4.95567637267788e-04 3.98017729450929e-04 + 34 4.91176737736178e-04 3.98035293049055e-04 + 35 4.88775079125039e-04 3.98044899683500e-04 + 36 4.88691485077369e-04 3.98045234059691e-04 + 37 4.90943355434415e-04 3.98036226578262e-04 + 38 4.95233101618235e-04 3.98019067593527e-04 + 39 5.00971349500124e-04 3.97996114602000e-04 + 40 5.07333860152640e-04 3.97970664559389e-04 diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out index 9c06635fa..58f41ca99 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,26 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 91bd082de..3f8e0f234 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.66463134760762e+00 + x 2.66463134738076e+00 } restraint { diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj index d266cabe9..7cf1cd53e 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 2.67119635178005e+00 -1.02847854071202e-02 - 1 2.67227384619314e+00 -1.02890953847726e-02 - 2 2.67273226510484e+00 -1.02909290604194e-02 - 3 2.67255372187147e+00 -1.02902148874859e-02 - 4 2.67175941876139e+00 -1.02870376750455e-02 - 5 2.67040901315621e+00 -1.02816360526248e-02 - 6 2.66859725099990e+00 -1.02743890039996e-02 - 7 2.66644846891371e+00 -1.02657938756549e-02 - 8 2.66410945078046e+00 -1.02564378031219e-02 - 9 2.66174084177962e+00 -1.02469633671185e-02 - 10 2.65950718929972e+00 -1.02380287571989e-02 - 11 2.65756592974274e+00 -1.02302637189710e-02 - 12 2.65605614350359e+00 -1.02242245740144e-02 - 13 2.65508832518654e+00 -1.02203533007461e-02 - 14 2.65473648510148e+00 -1.02189459404059e-02 - 15 2.65503349631646e+00 -1.02201339852658e-02 - 16 2.65596999020253e+00 -1.02238799608101e-02 - 17 2.65749649096805e+00 -1.02299859638722e-02 - 18 2.65952812759685e+00 -1.02381125103874e-02 - 19 2.66195123574845e+00 -1.02478049429938e-02 - 20 2.66463134760762e+00 -1.02585253904305e-02 + 1 2.67227384619251e+00 -1.02890953847700e-02 + 2 2.67273226510223e+00 -1.02909290604089e-02 + 3 2.67255372186561e+00 -1.02902148874625e-02 + 4 2.67175941875083e+00 -1.02870376750033e-02 + 5 2.67040901313963e+00 -1.02816360525585e-02 + 6 2.66859725097598e+00 -1.02743890039039e-02 + 7 2.66644846888120e+00 -1.02657938755248e-02 + 8 2.66410945073814e+00 -1.02564378029526e-02 + 9 2.66174084172640e+00 -1.02469633669056e-02 + 10 2.65950718923457e+00 -1.02380287569383e-02 + 11 2.65756592966473e+00 -1.02302637186589e-02 + 12 2.65605614341187e+00 -1.02242245736475e-02 + 13 2.65508832508033e+00 -1.02203533003213e-02 + 14 2.65473648498004e+00 -1.02189459399202e-02 + 15 2.65503349617912e+00 -1.02201339847165e-02 + 16 2.65596999004862e+00 -1.02238799601945e-02 + 17 2.65749649079691e+00 -1.02299859631876e-02 + 18 2.65952812740781e+00 -1.02381125096312e-02 + 19 2.66195123554084e+00 -1.02478049421634e-02 + 20 2.66463134738076e+00 -1.02585253895231e-02 diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out index c20b26d4f..deed28969 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,31 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 2.66463 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 4c8e4e3f2..59a098582 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.67525299255671e+00 + x 2.67525299195737e+00 } restraint { diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 63f1a55dd..bf12f4d2d 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.66463134760762e+00 -1.02585253904305e-02 - 21 2.66742226053972e+00 -1.02696890421589e-02 - 22 2.67017590948386e+00 -1.02807036379355e-02 - 23 2.67275254986108e+00 -1.02910101994443e-02 - 24 2.67503043669944e+00 -1.03001217467977e-02 - 25 2.67691398874566e+00 -1.03076559549827e-02 - 26 2.67833957672623e+00 -1.03133583069049e-02 - 27 2.67927850954533e+00 -1.03171140381813e-02 - 28 2.67973729619981e+00 -1.03189491847993e-02 - 29 2.67975557122547e+00 -1.03190222849019e-02 - 30 2.67940194174935e+00 -1.03176077669974e-02 - 31 2.67876786491929e+00 -1.03150714596772e-02 - 32 2.67795953937304e+00 -1.03118381574922e-02 - 33 2.67708810619769e+00 -1.03083524247908e-02 - 34 2.67625892947302e+00 -1.03050357178921e-02 - 35 2.67556129291865e+00 -1.03022451716746e-02 - 36 2.67505997743329e+00 -1.03002399097332e-02 - 37 2.67478990214567e+00 -1.02991596085827e-02 - 38 2.67475432209952e+00 -1.02990172883981e-02 - 39 2.67492634553313e+00 -1.02997053821325e-02 - 40 2.67525299255671e+00 -1.03010119702268e-02 + 20 2.66463134738076e+00 -1.02585253895231e-02 + 21 2.66742226029295e+00 -1.02696890411718e-02 + 22 2.67017590921653e+00 -1.02807036368661e-02 + 23 2.67275254957261e+00 -1.02910101982905e-02 + 24 2.67503043638932e+00 -1.03001217455573e-02 + 25 2.67691398841351e+00 -1.03076559536541e-02 + 26 2.67833957637177e+00 -1.03133583054871e-02 + 27 2.67927850916844e+00 -1.03171140366738e-02 + 28 2.67973729580054e+00 -1.03189491832022e-02 + 29 2.67975557080403e+00 -1.03190222832161e-02 + 30 2.67940194130612e+00 -1.03176077652245e-02 + 31 2.67876786445484e+00 -1.03150714578194e-02 + 32 2.67795953888813e+00 -1.03118381555525e-02 + 33 2.67708810569326e+00 -1.03083524227731e-02 + 34 2.67625892895020e+00 -1.03050357158008e-02 + 35 2.67556129237875e+00 -1.03022451695150e-02 + 36 2.67505997687781e+00 -1.03002399075112e-02 + 37 2.67478990157628e+00 -1.02991596063051e-02 + 38 2.67475432151807e+00 -1.02990172860723e-02 + 39 2.67492634494164e+00 -1.02997053797666e-02 + 40 2.67525299195737e+00 -1.03010119678295e-02 diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt index 157cac038..4d05e12c8 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2019-08-05". +colvars: Using NAMD interface, version "2019-08-01". diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out index d0660361f..ec53ee630 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,29 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - coordNum pairlist: -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 3ff2bc585..b646c70df 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01411698412338e+01 + x 1.01411698403566e+01 } restraint { diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj index c8adc634d..8c250f8de 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.01481368521529e+01 -4.01925474086114e-02 - 1 1.01543539600401e+01 -4.02174158401602e-02 - 2 1.01579705670330e+01 -4.02318822681319e-02 - 3 1.01589102870876e+01 -4.02356411483502e-02 - 4 1.01572731010582e+01 -4.02290924042330e-02 - 5 1.01533217576642e+01 -4.02132870306567e-02 - 6 1.01474576215661e+01 -4.01898304862643e-02 - 7 1.01401899753189e+01 -4.01607599012755e-02 - 8 1.01321020978184e+01 -4.01284083912734e-02 - 9 1.01238160001145e+01 -4.00952640004581e-02 - 10 1.01159565520821e+01 -4.00638262083286e-02 - 11 1.01091157350611e+01 -4.00364629402443e-02 - 12 1.01038185758135e+01 -4.00152743032539e-02 - 13 1.01004931566581e+01 -4.00019726266324e-02 - 14 1.00994472487512e+01 -3.99977889950050e-02 - 15 1.01008533190591e+01 -4.00034132762363e-02 - 16 1.01047425600561e+01 -4.00189702402245e-02 - 17 1.01110075583774e+01 -4.00440302335097e-02 - 18 1.01194127100383e+01 -4.00776508401532e-02 - 19 1.01296114941134e+01 -4.01184459764537e-02 - 20 1.01411698412338e+01 -4.01646793649352e-02 + 1 1.01543539600385e+01 -4.02174158401538e-02 + 2 1.01579705670262e+01 -4.02318822681049e-02 + 3 1.01589102870716e+01 -4.02356411482866e-02 + 4 1.01572731010286e+01 -4.02290924041145e-02 + 5 1.01533217576159e+01 -4.02132870304636e-02 + 6 1.01474576214938e+01 -4.01898304859752e-02 + 7 1.01401899752170e+01 -4.01607599008680e-02 + 8 1.01321020976811e+01 -4.01284083907245e-02 + 9 1.01238159999362e+01 -4.00952639997449e-02 + 10 1.01159565518573e+01 -4.00638262074292e-02 + 11 1.01091157347845e+01 -4.00364629391381e-02 + 12 1.01038185754805e+01 -4.00152743019222e-02 + 13 1.01004931562647e+01 -4.00019726250588e-02 + 14 1.00994472482940e+01 -3.99977889931759e-02 + 15 1.01008533185352e+01 -4.00034132741409e-02 + 16 1.01047425594636e+01 -4.00189702378545e-02 + 17 1.01110075577148e+01 -4.00440302308591e-02 + 18 1.01194127093045e+01 -4.00776508372182e-02 + 19 1.01296114933081e+01 -4.01184459732322e-02 + 20 1.01411698403566e+01 -4.01646793614266e-02 diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out index cec376268..25d4265e0 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,34 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - coordNum pairlist: -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 10.1412 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 8264680de..a5a2b6938 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01841922804199e+01 + x 1.01841922784258e+01 } restraint { diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 3d6793224..c07a48c82 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.01411698412338e+01 -4.01646793649352e-02 - 21 1.01535946552464e+01 -4.02143786209857e-02 - 22 1.01663658704350e+01 -4.02654634817400e-02 - 23 1.01789693407977e+01 -4.03158773631909e-02 - 24 1.01909269862300e+01 -4.03637079449202e-02 - 25 1.02018206336654e+01 -4.04072825346614e-02 - 26 1.02113074887461e+01 -4.04452299549842e-02 - 27 1.02191274705721e+01 -4.04765098822886e-02 - 28 1.02251046852595e+01 -4.05004187410379e-02 - 29 1.02291462135776e+01 -4.05165848543106e-02 - 30 1.02312399822203e+01 -4.05249599288811e-02 - 31 1.02314518101113e+01 -4.05258072404452e-02 - 32 1.02299198133700e+01 -4.05196792534798e-02 - 33 1.02268443918197e+01 -4.05073775672787e-02 - 34 1.02224730723386e+01 -4.04898922893544e-02 - 35 1.02170817762737e+01 -4.04683271050948e-02 - 36 1.02109552451751e+01 -4.04438209807005e-02 - 37 1.02043693152234e+01 -4.04174772608938e-02 - 38 1.01975763299143e+01 -4.03903053196573e-02 - 39 1.01907933864549e+01 -4.03631735458195e-02 - 40 1.01841922804199e+01 -4.03367691216797e-02 + 20 1.01411698403566e+01 -4.01646793614266e-02 + 21 1.01535946542976e+01 -4.02143786171906e-02 + 22 1.01663658694150e+01 -4.02654634776601e-02 + 23 1.01789693397072e+01 -4.03158773588289e-02 + 24 1.01909269850700e+01 -4.03637079402800e-02 + 25 1.02018206324370e+01 -4.04072825297481e-02 + 26 1.02113074874510e+01 -4.04452299498039e-02 + 27 1.02191274692122e+01 -4.04765098768487e-02 + 28 1.02251046838367e+01 -4.05004187353467e-02 + 29 1.02291462120943e+01 -4.05165848483772e-02 + 30 1.02312399806787e+01 -4.05249599227147e-02 + 31 1.02314518085137e+01 -4.05258072340550e-02 + 32 1.02299198117186e+01 -4.05196792468743e-02 + 33 1.02268443901165e+01 -4.05073775604658e-02 + 34 1.02224730705855e+01 -4.04898922823419e-02 + 35 1.02170817744726e+01 -4.04683270978904e-02 + 36 1.02109552433282e+01 -4.04438209733127e-02 + 37 1.02043693133334e+01 -4.04174772533334e-02 + 38 1.01975763279845e+01 -4.03903053119382e-02 + 39 1.01907933844900e+01 -4.03631735379599e-02 + 40 1.01841922784258e+01 -4.03367691137030e-02 diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt index 157cac038..b2949c9aa 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-05-08. +colvars: Using NAMD interface, version 2018-04-29. diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out index 28e8e90b2..5f1b09b7b 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,26 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped index bf985d8ad..4b97c242b 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01997380115249e+01 + x 1.01997380106663e+01 } restraint { diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj index 35e491d82..8cadeb993 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.02066554836313e+01 -4.04266219345253e-02 - 1 1.02128103525242e+01 -4.04512414100967e-02 - 2 1.02163905908650e+01 -4.04655623634601e-02 - 3 1.02173205792671e+01 -4.04692823170684e-02 - 4 1.02156993030364e+01 -4.04627972121458e-02 - 5 1.02117868890088e+01 -4.04471475560353e-02 - 6 1.02059806949699e+01 -4.04239227798795e-02 - 7 1.01987849183460e+01 -4.03951396733840e-02 - 8 1.01907770135508e+01 -4.03631080542033e-02 - 9 1.01825727800619e+01 -4.03302911202475e-02 - 10 1.01747908474213e+01 -4.02991633896850e-02 - 11 1.01680172849785e+01 -4.02720691399141e-02 - 12 1.01627718762492e+01 -4.02510875049969e-02 - 13 1.01594784287899e+01 -4.02379137151595e-02 - 14 1.01584416411835e+01 -4.02337665647338e-02 - 15 1.01598322600926e+01 -4.02393290403704e-02 - 16 1.01636811698822e+01 -4.02547246795287e-02 - 17 1.01698820348244e+01 -4.02795281392977e-02 - 18 1.01782016103793e+01 -4.03128064415171e-02 - 19 1.01882968442993e+01 -4.03531873771971e-02 - 20 1.01997380115249e+01 -4.03989520460994e-02 + 1 1.02128103525226e+01 -4.04512414100905e-02 + 2 1.02163905908367e+01 -4.04655623633469e-02 + 3 1.02173205792556e+01 -4.04692823170224e-02 + 4 1.02156993029853e+01 -4.04627972119410e-02 + 5 1.02117868889625e+01 -4.04471475558502e-02 + 6 1.02059806948824e+01 -4.04239227795298e-02 + 7 1.01987849182097e+01 -4.03951396728390e-02 + 8 1.01907770133593e+01 -4.03631080534371e-02 + 9 1.01825727798096e+01 -4.03302911192384e-02 + 10 1.01747908471046e+01 -4.02991633884182e-02 + 11 1.01680172845955e+01 -4.02720691383820e-02 + 12 1.01627718757998e+01 -4.02510875031993e-02 + 13 1.01594784282758e+01 -4.02379137131030e-02 + 14 1.01584416406077e+01 -4.02337665624308e-02 + 15 1.01598322594592e+01 -4.02393290378370e-02 + 16 1.01636811691959e+01 -4.02547246767837e-02 + 17 1.01698820340975e+01 -4.02795281363899e-02 + 18 1.01782016096006e+01 -4.03128064384024e-02 + 19 1.01882968434774e+01 -4.03531873739095e-02 + 20 1.01997380106663e+01 -4.03989520426651e-02 diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out index 56dfff67d..b16bdc9b4 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,31 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 10.1997 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 047e1a4b2..845030b9e 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.02422968531579e+01 + x 1.02422968511954e+01 } restraint { diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 5d7023dd8..d5957567b 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.01997380115249e+01 -4.03989520460994e-02 - 21 1.02120369506585e+01 -4.04481478026342e-02 - 22 1.02246788006083e+01 -4.04987152024332e-02 - 23 1.02371545609629e+01 -4.05486182438517e-02 - 24 1.02489909366769e+01 -4.05959637467076e-02 - 25 1.02597739407961e+01 -4.06390957631846e-02 - 26 1.02691642113129e+01 -4.06766568452516e-02 - 27 1.02769042725010e+01 -4.07076170900039e-02 - 28 1.02828199936102e+01 -4.07312799744409e-02 - 29 1.02868193884911e+01 -4.07472775539644e-02 - 30 1.02888905080147e+01 -4.07555620320589e-02 - 31 1.02890985157159e+01 -4.07563940628635e-02 - 32 1.02875801485946e+01 -4.07503205943785e-02 - 33 1.02845338037653e+01 -4.07381352150613e-02 - 34 1.02802045334771e+01 -4.07208181339083e-02 - 35 1.02748654999713e+01 -4.06994619998850e-02 - 36 1.02687985973514e+01 -4.06751943894056e-02 - 37 1.02622769033932e+01 -4.06491076135727e-02 - 38 1.02555502383063e+01 -4.06222009532253e-02 - 39 1.02488335287781e+01 -4.05953341151125e-02 - 40 1.02422968531579e+01 -4.05691874126314e-02 + 20 1.01997380106663e+01 -4.03989520426651e-02 + 21 1.02120369497625e+01 -4.04481477990502e-02 + 22 1.02246787996745e+01 -4.04987151986978e-02 + 23 1.02371545599893e+01 -4.05486182399573e-02 + 24 1.02489909356603e+01 -4.05959637426412e-02 + 25 1.02597739397322e+01 -4.06390957589289e-02 + 26 1.02691642101966e+01 -4.06766568407865e-02 + 27 1.02769042713270e+01 -4.07076170853082e-02 + 28 1.02828199923736e+01 -4.07312799694943e-02 + 29 1.02868193871873e+01 -4.07472775487492e-02 + 30 1.02888905066404e+01 -4.07555620265616e-02 + 31 1.02890985142689e+01 -4.07563940570755e-02 + 32 1.02875801470742e+01 -4.07503205882967e-02 + 33 1.02845338021721e+01 -4.07381352086885e-02 + 34 1.02802045318133e+01 -4.07208181272531e-02 + 35 1.02748654982405e+01 -4.06994619929619e-02 + 36 1.02687985955587e+01 -4.06751943822348e-02 + 37 1.02622769015451e+01 -4.06491076061802e-02 + 38 1.02555502364106e+01 -4.06222009456423e-02 + 39 1.02488335268439e+01 -4.05953341073754e-02 + 40 1.02422968511954e+01 -4.05691874047814e-02 diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out index 0267e6c70..66c642d91 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,51 +1,48 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Writing to colvar trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] -colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). colvars: # smp = on [default] +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,32 +56,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: Initializing a new "distanceVec" component. @@ -97,45 +94,39 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. -colvars: Warning: Variable r1 is absent from expression "x". -colvars: Warning: Variable r2 is absent from expression "x". -colvars: Warning: Variable r3 is absent from expression "x". -colvars: Warning: Variable r2 is absent from expression "cos(x) + r1 + r3". colvars: Expecting colvar value of type n-dimensional vector of size 2. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -143,17 +134,13 @@ colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] -colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] @@ -161,9 +148,7 @@ colvars: # centers = { ( 20 , -5 ) } colvars: # targetCenters = { ( 20 , -5 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] -colvars: The force constant for colvar "one" will be rescaled to 1 according to the specified width (1). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -172,39 +157,16 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:1/0. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:1/1. 4 atoms: total mass = 54.028. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 318d67a54..0383e1a55 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.25547985268017e+00 , -5.47738843838940e+00 ) + x ( 3.25547985288590e+00 , -5.47738843832200e+00 ) } restraint { diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj index 1e5db1022..4339c71c0 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one 0 ( 3.20554673468334e+00 , -5.48239480832893e+00 ) - 1 ( 3.20450053401175e+00 , -5.47990257545904e+00 ) - 2 ( 3.20435467486190e+00 , -5.47779766549469e+00 ) - 3 ( 3.20511804594360e+00 , -5.47623313988655e+00 ) - 4 ( 3.20675835825949e+00 , -5.47530637697672e+00 ) - 5 ( 3.20920474891228e+00 , -5.47505494785335e+00 ) - 6 ( 3.21235235535399e+00 , -5.47545779404383e+00 ) - 7 ( 3.21606826728072e+00 , -5.47644105785056e+00 ) - 8 ( 3.22019856588528e+00 , -5.47788745971868e+00 ) - 9 ( 3.22457647532480e+00 , -5.47964779043341e+00 ) - 10 ( 3.22903171994837e+00 , -5.48155318035299e+00 ) - 11 ( 3.23340084473853e+00 , -5.48342703484804e+00 ) - 12 ( 3.23753771524510e+00 , -5.48509601107600e+00 ) - 13 ( 3.24132302074078e+00 , -5.48639968497611e+00 ) - 14 ( 3.24467151148181e+00 , -5.48719873296004e+00 ) - 15 ( 3.24753606965591e+00 , -5.48738134516515e+00 ) - 16 ( 3.24990839058944e+00 , -5.48686751976987e+00 ) - 17 ( 3.25181665212772e+00 , -5.48561085839974e+00 ) - 18 ( 3.25332092184557e+00 , -5.48359768716950e+00 ) - 19 ( 3.25450708223514e+00 , -5.48084366848863e+00 ) - 20 ( 3.25547985268017e+00 , -5.47738843838940e+00 ) + 1 ( 3.20450053401237e+00 , -5.47990257545915e+00 ) + 2 ( 3.20435467486442e+00 , -5.47779766549509e+00 ) + 3 ( 3.20511804594931e+00 , -5.47623313988732e+00 ) + 4 ( 3.20675835826968e+00 , -5.47530637697787e+00 ) + 5 ( 3.20920474892822e+00 , -5.47505494785474e+00 ) + 6 ( 3.21235235537689e+00 , -5.47545779404524e+00 ) + 7 ( 3.21606826731175e+00 , -5.47644105785165e+00 ) + 8 ( 3.22019856592551e+00 , -5.47788745971902e+00 ) + 9 ( 3.22457647537524e+00 , -5.47964779043249e+00 ) + 10 ( 3.22903172000991e+00 , -5.48155318035021e+00 ) + 11 ( 3.23340084481198e+00 , -5.48342703484273e+00 ) + 12 ( 3.23753771533118e+00 , -5.48509601106745e+00 ) + 13 ( 3.24132302084013e+00 , -5.48639968496354e+00 ) + 14 ( 3.24467151159499e+00 , -5.48719873294262e+00 ) + 15 ( 3.24753606978343e+00 , -5.48738134514202e+00 ) + 16 ( 3.24990839073177e+00 , -5.48686751974010e+00 ) + 17 ( 3.25181665228529e+00 , -5.48561085836232e+00 ) + 18 ( 3.25332092201882e+00 , -5.48359768712336e+00 ) + 19 ( 3.25450708242444e+00 , -5.48084366843255e+00 ) + 20 ( 3.25547985288590e+00 , -5.47738843832200e+00 ) diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out index c1e36fd05..f79039b3e 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,51 +1,48 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Writing to colvar trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] -colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). colvars: # smp = on [default] +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,32 +56,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: Initializing a new "distanceVec" component. @@ -97,45 +94,39 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. -colvars: Warning: Variable r1 is absent from expression "x". -colvars: Warning: Variable r2 is absent from expression "x". -colvars: Warning: Variable r3 is absent from expression "x". -colvars: Warning: Variable r2 is absent from expression "cos(x) + r1 + r3". colvars: Expecting colvar value of type n-dimensional vector of size 2. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -143,17 +134,13 @@ colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] -colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] @@ -161,9 +148,7 @@ colvars: # centers = { ( 20 , -5 ) } colvars: # targetCenters = { ( 20 , -5 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] -colvars: The force constant for colvar "one" will be rescaled to 1 according to the specified width (1). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -172,44 +157,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 3.25548 , -5.47739 ) -colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:1/0. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:1/1. 4 atoms: total mass = 54.028. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Saving collective variables state to "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Saving collective variables state to "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index c9ce1cfcf..a96c3f221 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.32026945546912e+00 , -5.34818539717392e+00 ) + x ( 3.32026945594503e+00 , -5.34818539676131e+00 ) } restraint { diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj index fd675d4fa..5de5660db 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one - 20 ( 3.25547985268017e+00 , -5.47738843838940e+00 ) - 21 ( 3.25635522894088e+00 , -5.47328901194575e+00 ) - 22 ( 3.25725254105058e+00 , -5.46861283251178e+00 ) - 23 ( 3.25828644104589e+00 , -5.46343113079200e+00 ) - 24 ( 3.25955938734984e+00 , -5.45781309223334e+00 ) - 25 ( 3.26115536827722e+00 , -5.45182122577788e+00 ) - 26 ( 3.26313553184362e+00 , -5.44550828313081e+00 ) - 27 ( 3.26553608582059e+00 , -5.43891612738297e+00 ) - 28 ( 3.26836835302064e+00 , -5.43207683690314e+00 ) - 29 ( 3.27162052061137e+00 , -5.42501611673935e+00 ) - 30 ( 3.27526059063876e+00 , -5.41775865711888e+00 ) - 31 ( 3.27924018683827e+00 , -5.41033456569601e+00 ) - 32 ( 3.28349904494989e+00 , -5.40278559130820e+00 ) - 33 ( 3.28797000642183e+00 , -5.39516984655777e+00 ) - 34 ( 3.29258420352640e+00 , -5.38756403133415e+00 ) - 35 ( 3.29727601922130e+00 , -5.38006282914348e+00 ) - 36 ( 3.30198732290916e+00 , -5.37277582372652e+00 ) - 37 ( 3.30667059698468e+00 , -5.36582266902454e+00 ) - 38 ( 3.31129085392325e+00 , -5.35932721129127e+00 ) - 39 ( 3.31582650736369e+00 , -5.35341088175048e+00 ) - 40 ( 3.32026945546912e+00 , -5.34818539717392e+00 ) + 20 ( 3.25547985288590e+00 , -5.47738843832200e+00 ) + 21 ( 3.25635522916335e+00 , -5.47328901186553e+00 ) + 22 ( 3.25725254129003e+00 , -5.46861283241705e+00 ) + 23 ( 3.25828644130248e+00 , -5.46343113068098e+00 ) + 24 ( 3.25955938762362e+00 , -5.45781309210418e+00 ) + 25 ( 3.26115536856813e+00 , -5.45182122562873e+00 ) + 26 ( 3.26313553215147e+00 , -5.44550828295996e+00 ) + 27 ( 3.26553608614507e+00 , -5.43891612718894e+00 ) + 28 ( 3.26836835336136e+00 , -5.43207683668482e+00 ) + 29 ( 3.27162052096783e+00 , -5.42501611649609e+00 ) + 30 ( 3.27526059101041e+00 , -5.41775865685059e+00 ) + 31 ( 3.27924018722449e+00 , -5.41033456540318e+00 ) + 32 ( 3.28349904535004e+00 , -5.40278559099195e+00 ) + 33 ( 3.28797000683518e+00 , -5.39516984621977e+00 ) + 34 ( 3.29258420395217e+00 , -5.38756403097662e+00 ) + 35 ( 3.29727601965859e+00 , -5.38006282876905e+00 ) + 36 ( 3.30198732335696e+00 , -5.37277582333816e+00 ) + 37 ( 3.30667059744180e+00 , -5.36582266862542e+00 ) + 38 ( 3.31129085438830e+00 , -5.35932721088458e+00 ) + 39 ( 3.31582650783507e+00 , -5.35341088133938e+00 ) + 40 ( 3.32026945594503e+00 , -5.34818539676131e+00 ) diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt b/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt index 157cac038..b7bf5455c 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-10-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt b/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt +++ b/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out index 2695e4d53..2176b6914 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out @@ -192,7 +192,7 @@ colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.07139 colvars: Restarting collective variable "two" from value: -2.07997 -colvars: Restarting metadynamics bias "metadynamics1" from step number 20. +colvars: Restarting metadynamics bias "metadynamics1" from step number 0. colvars: read biasing energy and forces from grids. colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt b/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out index 9ad41eda8..e7f89a4ff 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,56 +55,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -118,10 +114,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -147,7 +143,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -158,27 +153,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 3d5bd5995..66b27ad46 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.98300515486710e+01 + x 5.98300515592260e+01 } restraint { diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj index 1c292a5fb..b78cecb35 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 6.31129478791928e+01 -2.52051791516771e-01 - 1 6.30779645383122e+01 -2.51911858153249e-01 - 2 6.30166636721089e+01 -2.51666654688436e-01 - 3 6.29277968203376e+01 -2.51311187281350e-01 - 4 6.28110919635306e+01 -2.50844367854122e-01 - 5 6.26673366019378e+01 -2.50269346407751e-01 - 6 6.24983825380393e+01 -2.49593530152157e-01 - 7 6.23070775463950e+01 -2.48828310185580e-01 - 8 6.20971375561705e+01 -2.47988550224682e-01 - 9 6.18729765854906e+01 -2.47091906341962e-01 - 10 6.16395107158807e+01 -2.46158042863523e-01 - 11 6.14019498452446e+01 -2.45207799380978e-01 - 12 6.11655875894309e+01 -2.44262350357724e-01 - 13 6.09355955346581e+01 -2.43342382138632e-01 - 14 6.07168266139377e+01 -2.42467306455751e-01 - 15 6.05136310205547e+01 -2.41654524082219e-01 - 16 6.03296902153746e+01 -2.40918760861498e-01 - 17 6.01678777158193e+01 -2.40271510863277e-01 - 18 6.00301578158095e+01 -2.39720631263238e-01 - 19 5.99175335696155e+01 -2.39270134278462e-01 - 20 5.98300515486710e+01 -2.38920206194684e-01 + 0 6.31129478791929e+01 -2.52051791516771e-01 + 1 6.30779645383520e+01 -2.51911858153408e-01 + 2 6.30166636722659e+01 -2.51666654689064e-01 + 3 6.29277968222057e+01 -2.51311187288823e-01 + 4 6.28110919641768e+01 -2.50844367856707e-01 + 5 6.26673366028881e+01 -2.50269346411552e-01 + 6 6.24983825393602e+01 -2.49593530157441e-01 + 7 6.23070775481485e+01 -2.48828310192594e-01 + 8 6.20971375584149e+01 -2.47988550233660e-01 + 9 6.18729765882759e+01 -2.47091906353104e-01 + 10 6.16395107192542e+01 -2.46158042877017e-01 + 11 6.14019498492506e+01 -2.45207799397002e-01 + 12 6.11655875941102e+01 -2.44262350376441e-01 + 13 6.09355955400464e+01 -2.43342382160186e-01 + 14 6.07168266200639e+01 -2.42467306480256e-01 + 15 6.05136310274090e+01 -2.41654524109636e-01 + 16 6.03296902229661e+01 -2.40918760891865e-01 + 17 6.01678777239959e+01 -2.40271510895984e-01 + 18 6.00301578248419e+01 -2.39720631299368e-01 + 19 5.99175335802490e+01 -2.39270134320996e-01 + 20 5.98300515592260e+01 -2.38920206236904e-01 diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out index 9ce9a9ef3..237f53c44 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,56 +55,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -118,10 +114,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -147,7 +143,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -158,32 +153,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 59.8301 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 108bc4cd0..44e24f2b2 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.97551054473693e+01 + x 5.97551054664761e+01 } restraint { diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 3cf42a7dc..71d70ae0b 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.98300515486710e+01 -2.38920206194684e-01 - 21 5.97668650394525e+01 -2.38667460157810e-01 - 22 5.97263508192266e+01 -2.38505403276906e-01 - 23 5.97062661536266e+01 -2.38425064614506e-01 - 24 5.97039266347449e+01 -2.38415706538980e-01 - 25 5.97163827891862e+01 -2.38465531156745e-01 - 26 5.97405738612989e+01 -2.38562295445196e-01 - 27 5.97734430366384e+01 -2.38693772146554e-01 - 28 5.98120052955854e+01 -2.38848021182342e-01 - 29 5.98533709544186e+01 -2.39013483817674e-01 - 30 5.98947361572460e+01 -2.39178944628984e-01 - 31 5.99333583402208e+01 -2.39333433360883e-01 - 32 5.99665373878884e+01 -2.39466149551554e-01 - 33 5.99916207519385e+01 -2.39566483007754e-01 - 34 6.00060426921965e+01 -2.39624170768786e-01 - 35 6.00073965333411e+01 -2.39629586133365e-01 - 36 5.99935248947171e+01 -2.39574099578868e-01 - 37 5.99626029530151e+01 -2.39450411812060e-01 - 38 5.99131916781728e+01 -2.39252766712691e-01 - 39 5.98442490681818e+01 -2.38976996272727e-01 - 40 5.97551054473693e+01 -2.38620421789477e-01 + 20 5.98300515592260e+01 -2.38920206236904e-01 + 21 5.97668650506981e+01 -2.38667460202792e-01 + 22 5.97263508310798e+01 -2.38505403324319e-01 + 23 5.97062661660438e+01 -2.38425064664175e-01 + 24 5.97039266476832e+01 -2.38415706590733e-01 + 25 5.97163828026047e+01 -2.38465531210419e-01 + 26 5.97405738751603e+01 -2.38562295500641e-01 + 27 5.97734430509102e+01 -2.38693772203641e-01 + 28 5.98120053098547e+01 -2.38848021239419e-01 + 29 5.98533709694021e+01 -2.39013483877608e-01 + 30 5.98947361725041e+01 -2.39178944690016e-01 + 31 5.99333583559336e+01 -2.39333433423734e-01 + 32 5.99665374039350e+01 -2.39466149615740e-01 + 33 5.99916207683209e+01 -2.39566483073283e-01 + 34 6.00060427089216e+01 -2.39624170835686e-01 + 35 6.00073965504200e+01 -2.39629586201680e-01 + 36 5.99935249121635e+01 -2.39574099648654e-01 + 37 5.99626029708492e+01 -2.39450411883397e-01 + 38 5.99131916964115e+01 -2.39252766785646e-01 + 39 5.98442490868439e+01 -2.38976996347376e-01 + 40 5.97551054664761e+01 -2.38620421865904e-01 diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt b/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out index f460ff36e..da0de3420 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out @@ -4,9 +4,10 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -170,12 +170,10 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj index 222745310..e603d2abe 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj @@ -16,7 +16,7 @@ 14 6.09757828886766e+01 0.00000000000000e+00 15 6.08031168275266e+01 0.00000000000000e+00 16 6.06502098430779e+01 0.00000000000000e+00 - 17 6.05198025267682e+01 0.00000000000000e+00 + 17 6.05198025267681e+01 0.00000000000000e+00 18 6.04137510819450e+01 0.00000000000000e+00 19 6.03329740983039e+01 0.00000000000000e+00 20 6.02774557419409e+01 0.00000000000000e+00 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat index 29c2e88d8..add429103 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat @@ -1,75 +1,75 @@ # 1 -# -6.00000000000000e+01 5.00000000000000e+00 72 1 +# -60 5 72 1 - -5.75000000000000e+01 0.00000000000000e+00 - -5.25000000000000e+01 0.00000000000000e+00 - -4.75000000000000e+01 0.00000000000000e+00 - -4.25000000000000e+01 0.00000000000000e+00 - -3.75000000000000e+01 0.00000000000000e+00 - -3.25000000000000e+01 0.00000000000000e+00 - -2.75000000000000e+01 0.00000000000000e+00 - -2.25000000000000e+01 0.00000000000000e+00 - -1.75000000000000e+01 0.00000000000000e+00 - -1.25000000000000e+01 0.00000000000000e+00 - -7.50000000000000e+00 0.00000000000000e+00 - -2.50000000000000e+00 0.00000000000000e+00 - 2.50000000000000e+00 0.00000000000000e+00 - 7.50000000000000e+00 0.00000000000000e+00 - 1.25000000000000e+01 0.00000000000000e+00 - 1.75000000000000e+01 0.00000000000000e+00 - 2.25000000000000e+01 0.00000000000000e+00 - 2.75000000000000e+01 0.00000000000000e+00 - 3.25000000000000e+01 0.00000000000000e+00 - 3.75000000000000e+01 0.00000000000000e+00 - 4.25000000000000e+01 0.00000000000000e+00 - 4.75000000000000e+01 0.00000000000000e+00 - 5.25000000000000e+01 0.00000000000000e+00 - 5.75000000000000e+01 0.00000000000000e+00 - 6.25000000000000e+01 2.00000000000000e+01 - 6.75000000000000e+01 0.00000000000000e+00 - 7.25000000000000e+01 0.00000000000000e+00 - 7.75000000000000e+01 0.00000000000000e+00 - 8.25000000000000e+01 0.00000000000000e+00 - 8.75000000000000e+01 0.00000000000000e+00 - 9.25000000000000e+01 0.00000000000000e+00 - 9.75000000000000e+01 0.00000000000000e+00 - 1.02500000000000e+02 0.00000000000000e+00 - 1.07500000000000e+02 0.00000000000000e+00 - 1.12500000000000e+02 0.00000000000000e+00 - 1.17500000000000e+02 0.00000000000000e+00 - 1.22500000000000e+02 0.00000000000000e+00 - 1.27500000000000e+02 0.00000000000000e+00 - 1.32500000000000e+02 0.00000000000000e+00 - 1.37500000000000e+02 0.00000000000000e+00 - 1.42500000000000e+02 0.00000000000000e+00 - 1.47500000000000e+02 0.00000000000000e+00 - 1.52500000000000e+02 0.00000000000000e+00 - 1.57500000000000e+02 0.00000000000000e+00 - 1.62500000000000e+02 0.00000000000000e+00 - 1.67500000000000e+02 0.00000000000000e+00 - 1.72500000000000e+02 0.00000000000000e+00 - 1.77500000000000e+02 0.00000000000000e+00 - 1.82500000000000e+02 0.00000000000000e+00 - 1.87500000000000e+02 0.00000000000000e+00 - 1.92500000000000e+02 0.00000000000000e+00 - 1.97500000000000e+02 0.00000000000000e+00 - 2.02500000000000e+02 0.00000000000000e+00 - 2.07500000000000e+02 0.00000000000000e+00 - 2.12500000000000e+02 0.00000000000000e+00 - 2.17500000000000e+02 0.00000000000000e+00 - 2.22500000000000e+02 0.00000000000000e+00 - 2.27500000000000e+02 0.00000000000000e+00 - 2.32500000000000e+02 0.00000000000000e+00 - 2.37500000000000e+02 0.00000000000000e+00 - 2.42500000000000e+02 0.00000000000000e+00 - 2.47500000000000e+02 0.00000000000000e+00 - 2.52500000000000e+02 0.00000000000000e+00 - 2.57500000000000e+02 0.00000000000000e+00 - 2.62500000000000e+02 0.00000000000000e+00 - 2.67500000000000e+02 0.00000000000000e+00 - 2.72500000000000e+02 0.00000000000000e+00 - 2.77500000000000e+02 0.00000000000000e+00 - 2.82500000000000e+02 0.00000000000000e+00 - 2.87500000000000e+02 0.00000000000000e+00 - 2.92500000000000e+02 0.00000000000000e+00 - 2.97500000000000e+02 0.00000000000000e+00 + -57.5 0 + -52.5 0 + -47.5 0 + -42.5 0 + -37.5 0 + -32.5 0 + -27.5 0 + -22.5 0 + -17.5 0 + -12.5 0 + -7.5 0 + -2.5 0 + 2.5 0 + 7.5 0 + 12.5 0 + 17.5 0 + 22.5 0 + 27.5 0 + 32.5 0 + 37.5 0 + 42.5 0 + 47.5 0 + 52.5 0 + 57.5 0 + 62.5 20 + 67.5 0 + 72.5 0 + 77.5 0 + 82.5 0 + 87.5 0 + 92.5 0 + 97.5 0 + 102.5 0 + 107.5 0 + 112.5 0 + 117.5 0 + 122.5 0 + 127.5 0 + 132.5 0 + 137.5 0 + 142.5 0 + 147.5 0 + 152.5 0 + 157.5 0 + 162.5 0 + 167.5 0 + 172.5 0 + 177.5 0 + 182.5 0 + 187.5 0 + 192.5 0 + 197.5 0 + 202.5 0 + 207.5 0 + 212.5 0 + 217.5 0 + 222.5 0 + 227.5 0 + 232.5 0 + 237.5 0 + 242.5 0 + 247.5 0 + 252.5 0 + 257.5 0 + 262.5 0 + 267.5 0 + 272.5 0 + 277.5 0 + 282.5 0 + 287.5 0 + 292.5 0 + 297.5 0 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out index b917756f8..6b4f434fe 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out @@ -4,9 +4,10 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -170,7 +170,6 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 60.2775 @@ -180,7 +179,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped index 0871d37c1..801e6d28b 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.08972121817132e+01 + x 6.08972121817133e+01 } histogram { diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj index 309eb03b3..26132495a 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj @@ -10,13 +10,13 @@ 28 6.05174152507232e+01 0.00000000000000e+00 29 6.05916134367745e+01 0.00000000000000e+00 30 6.06661106175895e+01 0.00000000000000e+00 - 31 6.07382493916987e+01 0.00000000000000e+00 + 31 6.07382493916988e+01 0.00000000000000e+00 32 6.08054278361141e+01 0.00000000000000e+00 - 33 6.08651028913518e+01 0.00000000000000e+00 - 34 6.09148265769850e+01 0.00000000000000e+00 - 35 6.09523144047667e+01 0.00000000000000e+00 - 36 6.09755306486176e+01 0.00000000000000e+00 - 37 6.09827676263964e+01 0.00000000000000e+00 - 38 6.09726956103267e+01 0.00000000000000e+00 - 39 6.09443715231751e+01 0.00000000000000e+00 - 40 6.08972121817132e+01 0.00000000000000e+00 + 33 6.08651028913519e+01 0.00000000000000e+00 + 34 6.09148265769852e+01 0.00000000000000e+00 + 35 6.09523144047668e+01 0.00000000000000e+00 + 36 6.09755306486177e+01 0.00000000000000e+00 + 37 6.09827676263966e+01 0.00000000000000e+00 + 38 6.09726956103268e+01 0.00000000000000e+00 + 39 6.09443715231752e+01 0.00000000000000e+00 + 40 6.08972121817133e+01 0.00000000000000e+00 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat index 7d3ef8bb5..44f8e383f 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat @@ -1,75 +1,75 @@ # 1 -# -6.00000000000000e+01 5.00000000000000e+00 72 1 +# -60 5 72 1 - -5.75000000000000e+01 0.00000000000000e+00 - -5.25000000000000e+01 0.00000000000000e+00 - -4.75000000000000e+01 0.00000000000000e+00 - -4.25000000000000e+01 0.00000000000000e+00 - -3.75000000000000e+01 0.00000000000000e+00 - -3.25000000000000e+01 0.00000000000000e+00 - -2.75000000000000e+01 0.00000000000000e+00 - -2.25000000000000e+01 0.00000000000000e+00 - -1.75000000000000e+01 0.00000000000000e+00 - -1.25000000000000e+01 0.00000000000000e+00 - -7.50000000000000e+00 0.00000000000000e+00 - -2.50000000000000e+00 0.00000000000000e+00 - 2.50000000000000e+00 0.00000000000000e+00 - 7.50000000000000e+00 0.00000000000000e+00 - 1.25000000000000e+01 0.00000000000000e+00 - 1.75000000000000e+01 0.00000000000000e+00 - 2.25000000000000e+01 0.00000000000000e+00 - 2.75000000000000e+01 0.00000000000000e+00 - 3.25000000000000e+01 0.00000000000000e+00 - 3.75000000000000e+01 0.00000000000000e+00 - 4.25000000000000e+01 0.00000000000000e+00 - 4.75000000000000e+01 0.00000000000000e+00 - 5.25000000000000e+01 0.00000000000000e+00 - 5.75000000000000e+01 0.00000000000000e+00 - 6.25000000000000e+01 4.00000000000000e+01 - 6.75000000000000e+01 0.00000000000000e+00 - 7.25000000000000e+01 0.00000000000000e+00 - 7.75000000000000e+01 0.00000000000000e+00 - 8.25000000000000e+01 0.00000000000000e+00 - 8.75000000000000e+01 0.00000000000000e+00 - 9.25000000000000e+01 0.00000000000000e+00 - 9.75000000000000e+01 0.00000000000000e+00 - 1.02500000000000e+02 0.00000000000000e+00 - 1.07500000000000e+02 0.00000000000000e+00 - 1.12500000000000e+02 0.00000000000000e+00 - 1.17500000000000e+02 0.00000000000000e+00 - 1.22500000000000e+02 0.00000000000000e+00 - 1.27500000000000e+02 0.00000000000000e+00 - 1.32500000000000e+02 0.00000000000000e+00 - 1.37500000000000e+02 0.00000000000000e+00 - 1.42500000000000e+02 0.00000000000000e+00 - 1.47500000000000e+02 0.00000000000000e+00 - 1.52500000000000e+02 0.00000000000000e+00 - 1.57500000000000e+02 0.00000000000000e+00 - 1.62500000000000e+02 0.00000000000000e+00 - 1.67500000000000e+02 0.00000000000000e+00 - 1.72500000000000e+02 0.00000000000000e+00 - 1.77500000000000e+02 0.00000000000000e+00 - 1.82500000000000e+02 0.00000000000000e+00 - 1.87500000000000e+02 0.00000000000000e+00 - 1.92500000000000e+02 0.00000000000000e+00 - 1.97500000000000e+02 0.00000000000000e+00 - 2.02500000000000e+02 0.00000000000000e+00 - 2.07500000000000e+02 0.00000000000000e+00 - 2.12500000000000e+02 0.00000000000000e+00 - 2.17500000000000e+02 0.00000000000000e+00 - 2.22500000000000e+02 0.00000000000000e+00 - 2.27500000000000e+02 0.00000000000000e+00 - 2.32500000000000e+02 0.00000000000000e+00 - 2.37500000000000e+02 0.00000000000000e+00 - 2.42500000000000e+02 0.00000000000000e+00 - 2.47500000000000e+02 0.00000000000000e+00 - 2.52500000000000e+02 0.00000000000000e+00 - 2.57500000000000e+02 0.00000000000000e+00 - 2.62500000000000e+02 0.00000000000000e+00 - 2.67500000000000e+02 0.00000000000000e+00 - 2.72500000000000e+02 0.00000000000000e+00 - 2.77500000000000e+02 0.00000000000000e+00 - 2.82500000000000e+02 0.00000000000000e+00 - 2.87500000000000e+02 0.00000000000000e+00 - 2.92500000000000e+02 0.00000000000000e+00 - 2.97500000000000e+02 0.00000000000000e+00 + -57.5 0 + -52.5 0 + -47.5 0 + -42.5 0 + -37.5 0 + -32.5 0 + -27.5 0 + -22.5 0 + -17.5 0 + -12.5 0 + -7.5 0 + -2.5 0 + 2.5 0 + 7.5 0 + 12.5 0 + 17.5 0 + 22.5 0 + 27.5 0 + 32.5 0 + 37.5 0 + 42.5 0 + 47.5 0 + 52.5 0 + 57.5 0 + 62.5 40 + 67.5 0 + 72.5 0 + 77.5 0 + 82.5 0 + 87.5 0 + 92.5 0 + 97.5 0 + 102.5 0 + 107.5 0 + 112.5 0 + 117.5 0 + 122.5 0 + 127.5 0 + 132.5 0 + 137.5 0 + 142.5 0 + 147.5 0 + 152.5 0 + 157.5 0 + 162.5 0 + 167.5 0 + 172.5 0 + 177.5 0 + 182.5 0 + 187.5 0 + 192.5 0 + 197.5 0 + 202.5 0 + 207.5 0 + 212.5 0 + 217.5 0 + 222.5 0 + 227.5 0 + 232.5 0 + 237.5 0 + 242.5 0 + 247.5 0 + 252.5 0 + 257.5 0 + 262.5 0 + 267.5 0 + 272.5 0 + 277.5 0 + 282.5 0 + 287.5 0 + 292.5 0 + 297.5 0 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt index 157cac038..2c2fdb849 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2021-10-13. +colvars: Using NAMD interface, version "2021-10-13". diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out index 50378ec14..1218eda97 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,56 +55,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -118,10 +114,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -144,7 +140,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { -10 } colvars: # upperWalls = { 10 } @@ -160,27 +155,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped index 84a539af0..e98cccfbb 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.99015240062048e+01 + x 5.99015240169243e+01 } restraint { diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj index bf8a645ef..f83c37fda 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 6.31129478791928e+01 -2.12451791516771e-01 - 1 6.30782207430228e+01 -2.12312882972091e-01 - 2 6.30176844597210e+01 -2.12070737838884e-01 - 3 6.29300795604372e+01 -2.11720318241749e-01 - 4 6.28151165875842e+01 -2.11260466350337e-01 - 5 6.26735597681268e+01 -2.10694239072507e-01 - 6 6.25072326023818e+01 -2.10028930409527e-01 - 7 6.23189505052794e+01 -2.09275802021118e-01 - 8 6.21123940675534e+01 -2.08449576270213e-01 - 9 6.18919401201661e+01 -2.07567760480665e-01 - 10 6.16624668323414e+01 -2.06649867329365e-01 - 11 6.14291465328002e+01 -2.05716586131201e-01 - 12 6.11972365829090e+01 -2.04788946331636e-01 - 13 6.09718744707731e+01 -2.03887497883092e-01 - 14 6.07578818481667e+01 -2.03031527392667e-01 - 15 6.05595809269580e+01 -2.02238323707832e-01 - 16 6.03806287731779e+01 -2.01522515092712e-01 - 17 6.02238782127047e+01 -2.00895512850819e-01 - 18 6.00912764804658e+01 -2.00365105921863e-01 - 19 5.99838130196557e+01 -1.99935252078623e-01 - 20 5.99015240062048e+01 -1.99606096024819e-01 +# step one fa_one + 0 6.31129478791929e+01 -2.12451791516771e-01 + 1 6.30782207430626e+01 -2.12312882972251e-01 + 2 6.30176844598780e+01 -2.12070737839512e-01 + 3 6.29300795621464e+01 -2.11720318248586e-01 + 4 6.28151165882276e+01 -2.11260466352910e-01 + 5 6.26735597690779e+01 -2.10694239076312e-01 + 6 6.25072326037074e+01 -2.10028930414830e-01 + 7 6.23189505070414e+01 -2.09275802028166e-01 + 8 6.21123940698095e+01 -2.08449576279238e-01 + 9 6.18919401229661e+01 -2.07567760491865e-01 + 10 6.16624668357318e+01 -2.06649867342927e-01 + 11 6.14291465368246e+01 -2.05716586147298e-01 + 12 6.11972365876074e+01 -2.04788946350430e-01 + 13 6.09718744761807e+01 -2.03887497904723e-01 + 14 6.07578818543115e+01 -2.03031527417246e-01 + 15 6.05595809338303e+01 -2.02238323735321e-01 + 16 6.03806287808051e+01 -2.01522515123221e-01 + 17 6.02238782208511e+01 -2.00895512883405e-01 + 18 6.00912764895398e+01 -2.00365105958159e-01 + 19 5.99838130302367e+01 -1.99935252120947e-01 + 20 5.99015240167765e+01 -1.99606096067106e-01 diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out index 03cf0c9a7..2b1dab030 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,56 +55,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -118,10 +114,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -144,7 +140,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { -10 } colvars: # upperWalls = { 10 } @@ -160,32 +155,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 59.9015 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped index 77bac4e9f..203f4469d 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 5.99403692539448e+01 + x 5.99403692730741e+01 } diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj index 5b3f70be7..9c2977f98 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 5.99015240062048e+01 -1.99606096024819e-01 - 21 5.98435552188444e+01 -1.99374220875378e-01 - 22 5.98082785181930e+01 -1.99233114072772e-01 - 23 5.97934484948365e+01 -1.99173793979346e-01 - 24 5.97963800349839e+01 -1.99185520139936e-01 - 25 5.98141247089905e+01 -1.99256498835962e-01 - 26 5.98436244176440e+01 -1.99374497670576e-01 - 27 5.98818266354142e+01 -1.99527306541657e-01 - 28 5.99257523474475e+01 -1.99703009389790e-01 - 29 5.99725198410855e+01 -1.99890079364342e-01 - 30 6.00193353623784e+01 -2.00077341449514e-01 - 31 6.00634687212219e+01 -2.00253874884888e-01 - 32 6.01022344101259e+01 -2.00408937640504e-01 - 33 6.01329964922276e+01 -2.00531985968910e-01 - 34 6.01532073938345e+01 -2.00612829575338e-01 - 35 6.01604795350481e+01 -2.00641918140193e-01 - 36 6.01526748742382e+01 -2.00610699496953e-01 - 37 6.01279874115193e+01 -2.00511949646077e-01 - 38 6.00849959389077e+01 -2.00339983755631e-01 - 39 6.00226748752046e+01 -2.00090699500818e-01 - 40 5.99403692539448e+01 -1.99761477015779e-01 +# step one fa_one + 20 5.99015240167765e+01 -1.99606096067106e-01 + 21 5.98435552301064e+01 -1.99374220920425e-01 + 22 5.98082785300632e+01 -1.99233114120253e-01 + 23 5.97934485072713e+01 -1.99173794029085e-01 + 24 5.97963800479404e+01 -1.99185520191762e-01 + 25 5.98141247224277e+01 -1.99256498889711e-01 + 26 5.98436244315244e+01 -1.99374497726098e-01 + 27 5.98818266497052e+01 -1.99527306598821e-01 + 28 5.99257523617425e+01 -1.99703009446970e-01 + 29 5.99725198560893e+01 -1.99890079424357e-01 + 30 6.00193353776544e+01 -2.00077341510617e-01 + 31 6.00634687369522e+01 -2.00253874947809e-01 + 32 6.01022344261894e+01 -2.00408937704758e-01 + 33 6.01329965086264e+01 -2.00531986034505e-01 + 34 6.01532074105757e+01 -2.00612829642303e-01 + 35 6.01604795521431e+01 -2.00641918208573e-01 + 36 6.01526748917010e+01 -2.00610699566804e-01 + 37 6.01279874293707e+01 -2.00511949717483e-01 + 38 6.00849959571649e+01 -2.00339983828660e-01 + 39 6.00226748938869e+01 -2.00090699575548e-01 + 40 5.99403692730741e+01 -1.99761477092296e-01 diff --git a/namd/tests/library/000_dihedralwalls/namd-version.txt b/namd/tests/library/000_dihedralwalls/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_dihedralwalls/namd-version.txt +++ b/namd/tests/library/000_dihedralwalls/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out index c512baba0..c0fccf38e 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,40 +55,40 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -130,7 +126,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -141,28 +136,16 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - dipoleAngle colvar component: -colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 9f4d54156..291b73e90 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.36349055389455e+01 + x 9.36349055337838e+01 } restraint { diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj index 44c231c6c..336b7c00f 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 8.97962480697652e+01 -3.58784992279061e-01 - 1 9.00687365881581e+01 -3.59874946352633e-01 - 2 9.03696531716400e+01 -3.61078612686560e-01 - 3 9.06810803337954e+01 -3.62324321335182e-01 - 4 9.09847043036197e+01 -3.63538817214479e-01 - 5 9.12638043504929e+01 -3.64655217401972e-01 - 6 9.15051697825636e+01 -3.65620679130254e-01 - 7 9.17006524157741e+01 -3.66402609663097e-01 - 8 9.18480994678579e+01 -3.66992397871432e-01 - 9 9.19515174516923e+01 -3.67406069806769e-01 - 10 9.20204550855094e+01 -3.67681820342038e-01 - 11 9.20687188119887e+01 -3.67874875247955e-01 - 12 9.21126240131068e+01 -3.68050496052427e-01 - 13 9.21690190327914e+01 -3.68276076131166e-01 - 14 9.22533018510856e+01 -3.68613207404342e-01 - 15 9.23775997129957e+01 -3.69110398851983e-01 - 16 9.25492271314794e+01 -3.69796908525918e-01 - 17 9.27695098407462e+01 -3.70678039362985e-01 - 18 9.30330692776144e+01 -3.71732277110457e-01 - 19 9.33276898533472e+01 -3.72910759413389e-01 - 20 9.36349055389455e+01 -3.74139622155782e-01 + 1 9.00687365880860e+01 -3.59874946352344e-01 + 2 9.03696531713662e+01 -3.61078612685465e-01 + 3 9.06810803332082e+01 -3.62324321332833e-01 + 4 9.09847043026283e+01 -3.63538817210513e-01 + 5 9.12638043490304e+01 -3.64655217396121e-01 + 6 9.15051697805885e+01 -3.65620679122354e-01 + 7 9.17006524132711e+01 -3.66402609653084e-01 + 8 9.18480994648365e+01 -3.66992397859346e-01 + 9 9.19515174481835e+01 -3.67406069792734e-01 + 10 9.20204550815615e+01 -3.67681820326246e-01 + 11 9.20687188076611e+01 -3.67874875230645e-01 + 12 9.21126240084645e+01 -3.68050496033858e-01 + 13 9.21690190278993e+01 -3.68276076111597e-01 + 14 9.22533018460045e+01 -3.68613207384018e-01 + 15 9.23775997077804e+01 -3.69110398831122e-01 + 16 9.25492271261785e+01 -3.69796908504714e-01 + 17 9.27695098354046e+01 -3.70678039341619e-01 + 18 9.30330692722776e+01 -3.71732277089110e-01 + 19 9.33276898480665e+01 -3.72910759392266e-01 + 20 9.36349055337838e+01 -3.74139622135135e-01 diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 48c3860e5..99d488573 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,40 +55,40 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -130,7 +126,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -141,33 +136,21 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - dipoleAngle colvar component: -colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 93.6349 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 651e66dc5..4da36d6f0 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.01098741923154e+01 + x 9.01098742103920e+01 } restraint { diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index ee86202c8..7e403dd06 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.36349055389455e+01 -3.74139622155782e-01 - 21 9.39314096608430e+01 -3.75325638643372e-01 - 22 9.41912842268812e+01 -3.76365136907525e-01 - 23 9.43888705891540e+01 -3.77155482356616e-01 - 24 9.45019115137236e+01 -3.77607646054895e-01 - 25 9.45144559381111e+01 -3.77657823752444e-01 - 26 9.44189957511575e+01 -3.77275983004630e-01 - 27 9.42174306917003e+01 -3.76469722766801e-01 - 28 9.39206949360476e+01 -3.75282779744190e-01 - 29 9.35471730241369e+01 -3.73788692096548e-01 - 30 9.31202694745324e+01 -3.72081077898130e-01 - 31 9.26656093089659e+01 -3.70262437235864e-01 - 32 9.22083464020604e+01 -3.68433385608242e-01 - 33 9.17709340560258e+01 -3.66683736224103e-01 - 34 9.13715370422709e+01 -3.65086148169084e-01 - 35 9.10230941262197e+01 -3.63692376504879e-01 - 36 9.07329203680483e+01 -3.62531681472193e-01 - 37 9.05026913412928e+01 -3.61610765365171e-01 - 38 9.03286700254905e+01 -3.60914680101962e-01 - 39 9.02021116805683e+01 -3.60408446722273e-01 - 40 9.01098741923154e+01 -3.60039496769262e-01 + 20 9.36349055337838e+01 -3.74139622135135e-01 + 21 9.39314096558801e+01 -3.75325638623520e-01 + 22 9.41912842222173e+01 -3.76365136888869e-01 + 23 9.43888705849112e+01 -3.77155482339645e-01 + 24 9.45019115100439e+01 -3.77607646040175e-01 + 25 9.45144559351512e+01 -3.77657823740605e-01 + 26 9.44189957490813e+01 -3.77275982996325e-01 + 27 9.42174306906690e+01 -3.76469722762676e-01 + 28 9.39206949362101e+01 -3.75282779744841e-01 + 29 9.35471730256220e+01 -3.73788692102488e-01 + 30 9.31202694774434e+01 -3.72081077909774e-01 + 31 9.26656093133783e+01 -3.70262437253513e-01 + 32 9.22083464080232e+01 -3.68433385632093e-01 + 33 9.17709340635645e+01 -3.66683736254258e-01 + 34 9.13715370513921e+01 -3.65086148205568e-01 + 35 9.10230941369154e+01 -3.63692376547662e-01 + 36 9.07329203802995e+01 -3.62531681521198e-01 + 37 9.05026913550711e+01 -3.61610765420284e-01 + 38 9.03286700407576e+01 -3.60914680163030e-01 + 39 9.02021116972737e+01 -3.60408446789095e-01 + 40 9.01098742103920e+01 -3.60039496841568e-01 diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out index 20f72749d..eb22b6e44 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -76,7 +72,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -104,7 +100,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -115,28 +110,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - dipoleMagnitude colvar component: -colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 9fd17e29c..e17335d86 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.25718680414489e+00 + x 1.25718680414711e+00 } restraint { diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj index 8a5faec6e..897dd65db 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.27248491620818e+00 -4.68993966483274e-03 - 1 1.27180733121966e+00 -4.68722932487864e-03 - 2 1.27112801338785e+00 -4.68451205355138e-03 - 3 1.27047853507381e+00 -4.68191414029525e-03 - 4 1.26988621687599e+00 -4.67954486750395e-03 - 5 1.26936978124289e+00 -4.67747912497155e-03 - 6 1.26893615427592e+00 -4.67574461710367e-03 - 7 1.26857880872927e+00 -4.67431523491708e-03 - 8 1.26827782880240e+00 -4.67311131520959e-03 - 9 1.26800167045610e+00 -4.67200668182440e-03 - 10 1.26771038149395e+00 -4.67084152597581e-03 - 11 1.26735983259476e+00 -4.66943933037905e-03 - 12 1.26690635771585e+00 -4.66762543086338e-03 - 13 1.26631116924668e+00 -4.66524467698671e-03 - 14 1.26554403807739e+00 -4.66217615230955e-03 - 15 1.26458596330156e+00 -4.65834385320625e-03 - 16 1.26343080408206e+00 -4.65372321632822e-03 - 17 1.26208600681132e+00 -4.64834402724529e-03 - 18 1.26057258581588e+00 -4.64229034326350e-03 - 19 1.25892442269974e+00 -4.63569769079898e-03 - 20 1.25718680414489e+00 -4.62874721657957e-03 + 1 1.27180733121971e+00 -4.68722932487885e-03 + 2 1.27112801338806e+00 -4.68451205355224e-03 + 3 1.27047853507430e+00 -4.68191414029720e-03 + 4 1.26988621687686e+00 -4.67954486750746e-03 + 5 1.26936978124426e+00 -4.67747912497706e-03 + 6 1.26893615427789e+00 -4.67574461711154e-03 + 7 1.26857880873190e+00 -4.67431523492760e-03 + 8 1.26827782880573e+00 -4.67311131522291e-03 + 9 1.26800167046013e+00 -4.67200668184053e-03 + 10 1.26771038149865e+00 -4.67084152599461e-03 + 11 1.26735983260005e+00 -4.66943933040020e-03 + 12 1.26690635772161e+00 -4.66762543088644e-03 + 13 1.26631116925277e+00 -4.66524467701107e-03 + 14 1.26554403808362e+00 -4.66217615233448e-03 + 15 1.26458596330773e+00 -4.65834385323092e-03 + 16 1.26343080408792e+00 -4.65372321635169e-03 + 17 1.26208600681664e+00 -4.64834402726657e-03 + 18 1.26057258582039e+00 -4.64229034328157e-03 + 19 1.25892442270322e+00 -4.63569769081287e-03 + 20 1.25718680414711e+00 -4.62874721658843e-03 diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out index 4e9d16093..c8da2f965 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -76,7 +72,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -104,7 +100,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -115,33 +110,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - dipoleMagnitude colvar component: -colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 1.25719 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 3e1eeb606..51fc5108c 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.23965387203052e+00 + x 1.23965387204761e+00 } restraint { diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj index f3b3820c2..b874d05f4 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.25718680414489e+00 -4.62874721657957e-03 - 21 1.25541401041628e+00 -4.62165604166510e-03 - 22 1.25366577392698e+00 -4.61466309570791e-03 - 23 1.25200261425621e+00 -4.60801045702483e-03 - 24 1.25048035908344e+00 -4.60192143633375e-03 - 25 1.24914448989145e+00 -4.59657795956581e-03 - 26 1.24802517146902e+00 -4.59210068587607e-03 - 27 1.24713379713557e+00 -4.58853518854227e-03 - 28 1.24646162388823e+00 -4.58584649555294e-03 - 29 1.24598068902163e+00 -4.58392275608653e-03 - 30 1.24564683483206e+00 -4.58258733932823e-03 - 31 1.24540441093114e+00 -4.58161764372455e-03 - 32 1.24519207689764e+00 -4.58076830759057e-03 - 33 1.24494905239874e+00 -4.57979620959498e-03 - 34 1.24462113711495e+00 -4.57848454845980e-03 - 35 1.24416586580795e+00 -4.57666346323180e-03 - 36 1.24355630165299e+00 -4.57422520661195e-03 - 37 1.24278318451547e+00 -4.57113273806189e-03 - 38 1.24185538438953e+00 -4.56742153755813e-03 - 39 1.24079879240046e+00 -4.56319516960184e-03 - 40 1.23965387203052e+00 -4.55861548812208e-03 + 20 1.25718680414711e+00 -4.62874721658843e-03 + 21 1.25541401041707e+00 -4.62165604166829e-03 + 22 1.25366577392626e+00 -4.61466309570505e-03 + 23 1.25200261425396e+00 -4.60801045701586e-03 + 24 1.25048035907975e+00 -4.60192143631898e-03 + 25 1.24914448988648e+00 -4.59657795954592e-03 + 26 1.24802517146302e+00 -4.59210068585208e-03 + 27 1.24713379712889e+00 -4.58853518851555e-03 + 28 1.24646162388128e+00 -4.58584649552511e-03 + 29 1.24598068901487e+00 -4.58392275605946e-03 + 30 1.24564683482598e+00 -4.58258733930391e-03 + 31 1.24540441092625e+00 -4.58161764370501e-03 + 32 1.24519207689444e+00 -4.58076830757776e-03 + 33 1.24494905239767e+00 -4.57979620959067e-03 + 34 1.24462113711636e+00 -4.57848454846545e-03 + 35 1.24416586581212e+00 -4.57666346324848e-03 + 36 1.24355630166006e+00 -4.57422520664022e-03 + 37 1.24278318452544e+00 -4.57113273810176e-03 + 38 1.24185538440224e+00 -4.56742153760896e-03 + 39 1.24079879241559e+00 -4.56319516966238e-03 + 40 1.23965387204761e+00 -4.55861548819043e-03 diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out index 6de123229..0c998afc9 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -120,26 +116,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped index 5268daf85..c1e336541 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253464583e+00 } diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj index 9f55268e7..787f78aa5 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 0.00000000000000e+00 + 11 3.21950367383415e+00 0.00000000000000e+00 + 12 3.22130499858006e+00 0.00000000000000e+00 + 13 3.22263479496347e+00 0.00000000000000e+00 + 14 3.22341769665784e+00 0.00000000000000e+00 + 15 3.22361473677138e+00 0.00000000000000e+00 + 16 3.22322417514557e+00 0.00000000000000e+00 + 17 3.22227942564879e+00 0.00000000000000e+00 + 18 3.22084479803044e+00 0.00000000000000e+00 + 19 3.21900979846930e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat index 23457f54b..54058e8f8 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.94036329632288e-01 - 4 5.63764173125217e-01 - 6 8.25197122357662e-02 - 8 -4.33277918980290e-01 - 10 -8.58922880671951e-01 + 2 8.94036335239450e-01 + 4 5.63764182658574e-01 + 6 8.25197229800656e-02 + 8 -4.33277910141469e-01 + 10 -8.58922876516564e-01 diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out index effa805d2..923c7f755 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -120,30 +116,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped index b307ede0d..139366ade 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878547144e+00 } diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj index 177b1bbb8..3b596ebde 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253444007e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 + 21 3.21458253157603e+00 0.00000000000000e+00 + 22 3.21223315254029e+00 0.00000000000000e+00 + 23 3.20995392032979e+00 0.00000000000000e+00 + 24 3.20785326966943e+00 0.00000000000000e+00 + 25 3.20602244845117e+00 0.00000000000000e+00 + 26 3.20453120146139e+00 0.00000000000000e+00 + 27 3.20342556480347e+00 0.00000000000000e+00 + 28 3.20272769852622e+00 0.00000000000000e+00 + 29 3.20243730776714e+00 0.00000000000000e+00 + 30 3.20253423308456e+00 0.00000000000000e+00 + 31 3.20298183362156e+00 0.00000000000000e+00 + 32 3.20373100914607e+00 0.00000000000000e+00 + 33 3.20472468746373e+00 0.00000000000000e+00 + 34 3.20590256221113e+00 0.00000000000000e+00 + 35 3.20720566184671e+00 0.00000000000000e+00 + 36 3.20858030459458e+00 0.00000000000000e+00 + 37 3.20998111854285e+00 0.00000000000000e+00 + 38 3.21137308334419e+00 0.00000000000000e+00 + 39 3.21273274315657e+00 0.00000000000000e+00 + 40 3.21404878547144e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat index 702a517c3..b55885c02 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.20806872403133e-01 - 4 4.95149534314936e-01 - 6 3.29843583885573e-02 - 8 -5.10193956226866e-01 - 10 -1.03852681816246e+00 + 2 8.20806874278982e-01 + 4 4.95149538768788e-01 + 6 3.29843664998698e-02 + 8 -5.10193943420893e-01 + 10 -1.03852680015666e+00 diff --git a/namd/tests/library/000_distance-autocorrfunc/namd-version.txt b/namd/tests/library/000_distance-autocorrfunc/namd-version.txt index 157cac038..b7bf5455c 100644 --- a/namd/tests/library/000_distance-autocorrfunc/namd-version.txt +++ b/namd/tests/library/000_distance-autocorrfunc/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-10-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out index 9a7a8d5d0..c89a0b8e7 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -97,28 +93,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -129,7 +125,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -157,7 +153,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -168,28 +163,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Linear and polynomial combination of colvar components: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped index ae9aba124..eb4ad3fa9 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.04350737604756e+01 + x 1.04350737609886e+01 } restraint { diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj index d89de7465..31f5eef44 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.04177432613594e+01 -4.12709730454376e-02 - 1 1.04084193931719e+01 -4.12336775726876e-02 - 2 1.04020579749793e+01 -4.12082318999174e-02 - 3 1.03989629510900e+01 -4.11958518043599e-02 - 4 1.03992141619813e+01 -4.11968566479251e-02 - 5 1.04026682614922e+01 -4.12106730459687e-02 - 6 1.04089744651595e+01 -4.12358978606380e-02 - 7 1.04176020660190e+01 -4.12704082640760e-02 - 8 1.04278769153472e+01 -4.13115076613887e-02 - 9 1.04390245452438e+01 -4.13560981809752e-02 - 10 1.04502182762425e+01 -4.14008731049699e-02 - 11 1.04606302346439e+01 -4.14425209385756e-02 - 12 1.04694824773729e+01 -4.14779299094914e-02 - 13 1.04760942601681e+01 -4.15043770406723e-02 - 14 1.04799211557593e+01 -4.15196846230373e-02 - 15 1.04805822766537e+01 -4.15223291066147e-02 - 16 1.04778735079711e+01 -4.15114940318845e-02 - 17 1.04717666626334e+01 -4.14870666505335e-02 - 18 1.04623962952111e+01 -4.14495851808446e-02 - 19 1.04500369407186e+01 -4.14001477628744e-02 - 20 1.04350737604756e+01 -4.13402950419026e-02 + 1 1.04084193931741e+01 -4.12336775726963e-02 + 2 1.04020579749880e+01 -4.12082318999518e-02 + 3 1.03989629511090e+01 -4.11958518044361e-02 + 4 1.03992141620145e+01 -4.11968566480581e-02 + 5 1.04026682615430e+01 -4.12106730461720e-02 + 6 1.04089744652310e+01 -4.12358978609239e-02 + 7 1.04176020661138e+01 -4.12704082644551e-02 + 8 1.04278769154677e+01 -4.13115076618707e-02 + 9 1.04390245453922e+01 -4.13560981815686e-02 + 10 1.04502182764206e+01 -4.14008731056823e-02 + 11 1.04606302348533e+01 -4.14425209394133e-02 + 12 1.04694824776150e+01 -4.14779299104599e-02 + 13 1.04760942604439e+01 -4.15043770417758e-02 + 14 1.04799211560697e+01 -4.15196846242787e-02 + 15 1.04805822769989e+01 -4.15223291079955e-02 + 16 1.04778735083513e+01 -4.15114940334051e-02 + 17 1.04717666630482e+01 -4.14870666521928e-02 + 18 1.04623962956600e+01 -4.14495851826398e-02 + 19 1.04500369412003e+01 -4.14001477648012e-02 + 20 1.04350737609886e+01 -4.13402950439545e-02 diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out index e7657a286..1bd56dbf9 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -97,28 +93,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -129,7 +125,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -157,7 +153,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -168,33 +163,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Linear and polynomial combination of colvar components: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 10.4351 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 11055164f..b8451d7e6 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01168439967474e+01 + x 1.01168439975032e+01 } restraint { diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj index ee78c4b0f..94f67cf85 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.04350737604756e+01 -4.13402950419026e-02 - 21 1.04179692237962e+01 -4.12718768951847e-02 - 22 1.03992281886028e+01 -4.11969127544111e-02 - 23 1.03793633975077e+01 -4.11174535900307e-02 - 24 1.03588635763992e+01 -4.10354543055969e-02 - 25 1.03381666080959e+01 -4.09526664323835e-02 - 26 1.03176399245696e+01 -4.08705596982785e-02 - 27 1.02975696738682e+01 -4.07902786954729e-02 - 28 1.02781591058678e+01 -4.07126364234711e-02 - 29 1.02595353407094e+01 -4.06381413628374e-02 - 30 1.02417631913002e+01 -4.05670527652007e-02 - 31 1.02248638710941e+01 -4.04994554843765e-02 - 32 1.02088361338553e+01 -4.04353445354210e-02 - 33 1.01936770388753e+01 -4.03747081555012e-02 - 34 1.01793996403201e+01 -4.03175985612803e-02 - 35 1.01660453820078e+01 -4.02641815280313e-02 - 36 1.01536901423957e+01 -4.02147605695830e-02 - 37 1.01424440834353e+01 -4.01697763337413e-02 - 38 1.01324465159344e+01 -4.01297860637376e-02 - 39 1.01238570537632e+01 -4.00954282150527e-02 - 40 1.01168439967474e+01 -4.00673759869896e-02 + 20 1.04350737609886e+01 -4.13402950439545e-02 + 21 1.04179692243383e+01 -4.12718768973531e-02 + 22 1.03992281891713e+01 -4.11969127566851e-02 + 23 1.03793633980993e+01 -4.11174535923974e-02 + 24 1.03588635770104e+01 -4.10354543080416e-02 + 25 1.03381666087226e+01 -4.09526664348903e-02 + 26 1.03176399252079e+01 -4.08705597008314e-02 + 27 1.02975696745142e+01 -4.07902786980569e-02 + 28 1.02781591065183e+01 -4.07126364260730e-02 + 29 1.02595353413618e+01 -4.06381413654473e-02 + 30 1.02417631919532e+01 -4.05670527678126e-02 + 31 1.02248638717473e+01 -4.04994554869891e-02 + 32 1.02088361345094e+01 -4.04353445380376e-02 + 33 1.01936770395323e+01 -4.03747081581293e-02 + 34 1.01793996409827e+01 -4.03175985639309e-02 + 35 1.01660453826794e+01 -4.02641815307176e-02 + 36 1.01536901430796e+01 -4.02147605723186e-02 + 37 1.01424440841347e+01 -4.01697763365387e-02 + 38 1.01324465166516e+01 -4.01297860666066e-02 + 39 1.01238570544997e+01 -4.00954282179988e-02 + 40 1.01168439975032e+01 -4.00673759900128e-02 diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt index 157cac038..fc4f9e327 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. +colvars: Using NAMD interface, version 2016-11-23. diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out index 139d30fdd..a8e792240 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,28 +112,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -148,7 +144,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -177,26 +173,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped index b28d17171..7aec83be0 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped @@ -5,11 +5,11 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253464583e+00 } colvar { name two - x 3.24433794495372e+00 + x 3.24433794490785e+00 } diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj index 0cd566be4..5633fa456 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one two fa_two 0 3.20554673468334e+00 0.00000000000000e+00 3.24960869251665e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 3.24790015328133e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 3.24647131781360e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 3.24540254817793e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 3.24474238725799e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 3.24450566303529e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 3.24467445105563e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 3.24520145991688e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 3.24601517427588e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 3.24702592907485e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 3.24813222716439e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 3.24922681805867e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 3.25020238551676e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 3.25095679939459e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 3.25139788925691e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 3.25144751335969e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 3.25104460693083e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 3.25014688214290e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 3.24873101651643e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 3.24679142393386e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 3.24433794495372e+00 0.00000000000000e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 3.24790015328139e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 3.24647131781376e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 3.24540254817816e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 3.24474238725816e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 3.24450566303520e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 3.24467445105498e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 3.24520145991536e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 3.24601517427313e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 3.24702592907053e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 0.00000000000000e+00 3.24813222715817e+00 0.00000000000000e+00 + 11 3.21950367383415e+00 0.00000000000000e+00 3.24922681805023e+00 0.00000000000000e+00 + 12 3.22130499858006e+00 0.00000000000000e+00 3.25020238550581e+00 0.00000000000000e+00 + 13 3.22263479496347e+00 0.00000000000000e+00 3.25095679938081e+00 0.00000000000000e+00 + 14 3.22341769665784e+00 0.00000000000000e+00 3.25139788923999e+00 0.00000000000000e+00 + 15 3.22361473677138e+00 0.00000000000000e+00 3.25144751333927e+00 0.00000000000000e+00 + 16 3.22322417514557e+00 0.00000000000000e+00 3.25104460690651e+00 0.00000000000000e+00 + 17 3.22227942564879e+00 0.00000000000000e+00 3.25014688211417e+00 0.00000000000000e+00 + 18 3.22084479803044e+00 0.00000000000000e+00 3.24873101648273e+00 0.00000000000000e+00 + 19 3.21900979846930e+00 0.00000000000000e+00 3.24679142389449e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 3.24433794490785e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out index ce5cb44d2..0fdca4e94 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,28 +112,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -148,7 +144,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -177,31 +173,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting collective variable "two" from value: 3.24434 colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped index 68f23fd0a..d4fe5f034 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped @@ -5,11 +5,11 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878547144e+00 } colvar { name two - x 3.14863335183754e+00 + x 3.14863335158646e+00 } diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj index af3ea4517..a61269b0f 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one two fa_two - 20 3.21688253444007e+00 0.00000000000000e+00 3.24433794495372e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 3.24139291297126e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 3.23798808487052e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 3.23416173175576e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 3.22995602396352e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 3.22541476812382e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 3.22058155457121e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 3.21549850220181e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 3.21020584536443e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 3.20474257688878e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 3.19914817079401e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 3.19346509302453e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 3.18774148383751e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 3.18203328876528e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 3.17640518192333e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 3.17092997382502e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 3.16568658639959e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 3.16075695183232e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 3.15622225136581e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 3.15215875153341e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 3.14863335183754e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 3.24433794490785e+00 0.00000000000000e+00 + 21 3.21458253157603e+00 0.00000000000000e+00 3.24139291291795e+00 0.00000000000000e+00 + 22 3.21223315254029e+00 0.00000000000000e+00 3.23798808480870e+00 0.00000000000000e+00 + 23 3.20995392032979e+00 0.00000000000000e+00 3.23416173168426e+00 0.00000000000000e+00 + 24 3.20785326966943e+00 0.00000000000000e+00 3.22995602388112e+00 0.00000000000000e+00 + 25 3.20602244845117e+00 0.00000000000000e+00 3.22541476802931e+00 0.00000000000000e+00 + 26 3.20453120146139e+00 0.00000000000000e+00 3.22058155446344e+00 0.00000000000000e+00 + 27 3.20342556480347e+00 0.00000000000000e+00 3.21549850207982e+00 0.00000000000000e+00 + 28 3.20272769852622e+00 0.00000000000000e+00 3.21020584522746e+00 0.00000000000000e+00 + 29 3.20243730776714e+00 0.00000000000000e+00 3.20474257673639e+00 0.00000000000000e+00 + 30 3.20253423308456e+00 0.00000000000000e+00 3.19914817062614e+00 0.00000000000000e+00 + 31 3.20298183362156e+00 0.00000000000000e+00 3.19346509284150e+00 0.00000000000000e+00 + 32 3.20373100914607e+00 0.00000000000000e+00 3.18774148364007e+00 0.00000000000000e+00 + 33 3.20472468746373e+00 0.00000000000000e+00 3.18203328855458e+00 0.00000000000000e+00 + 34 3.20590256221113e+00 0.00000000000000e+00 3.17640518170088e+00 0.00000000000000e+00 + 35 3.20720566184671e+00 0.00000000000000e+00 3.17092997359260e+00 0.00000000000000e+00 + 36 3.20858030459458e+00 0.00000000000000e+00 3.16568658615923e+00 0.00000000000000e+00 + 37 3.20998111854285e+00 0.00000000000000e+00 3.16075695158616e+00 0.00000000000000e+00 + 38 3.21137308334419e+00 0.00000000000000e+00 3.15622225111600e+00 0.00000000000000e+00 + 39 3.21273274315657e+00 0.00000000000000e+00 3.15215875128202e+00 0.00000000000000e+00 + 40 3.21404878547144e+00 0.00000000000000e+00 3.14863335158646e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat index c212baec7..82ce99983 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.20806872403133e-01 - 4 4.95149534314936e-01 - 6 3.29843583885573e-02 - 8 -5.10193956226866e-01 - 10 -1.03852681816246e+00 + 2 8.20806874278982e-01 + 4 4.95149538768788e-01 + 6 3.29843664998698e-02 + 8 -5.10193943420893e-01 + 10 -1.03852680015666e+00 diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat index aafb87afd..d0534bfc8 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.94036329632288e-01 - 4 5.63764173125217e-01 - 6 8.25197122357662e-02 - 8 -4.33277918980290e-01 - 10 -8.58922880671951e-01 + 2 8.94036335239450e-01 + 4 5.63764182658574e-01 + 6 8.25197229800656e-02 + 8 -4.33277910141469e-01 + 10 -8.58922876516564e-01 diff --git a/namd/tests/library/000_distance-corrfunc/namd-version.txt b/namd/tests/library/000_distance-corrfunc/namd-version.txt index 157cac038..b7bf5455c 100644 --- a/namd/tests/library/000_distance-corrfunc/namd-version.txt +++ b/namd/tests/library/000_distance-corrfunc/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-10-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out index 8acf9d14a..b48697538 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -228,12 +229,10 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped index 41807dd58..39cdbdd58 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21688253444007e+00 + x 3.21688253464583e+00 } colvar { name phi - x 6.02774557419409e+01 + x 6.02774557527018e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj index 19662210d..0d258d955 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step r phi 0 3.20554673468334e+00 6.31129478791928e+01 - 1 3.20437148316484e+00 6.30795952608635e+01 - 2 3.20384028588952e+00 6.30231590815800e+01 - 3 3.20396721186862e+00 6.29423176376863e+01 - 4 3.20472817286016e+00 6.28366833855655e+01 - 5 3.20606308065050e+00 6.27068898711517e+01 - 6 3.20787989000757e+00 6.25546017852999e+01 - 7 3.21005997940810e+00 6.23824530243513e+01 - 8 3.21246460651160e+00 6.21939260028577e+01 - 9 3.21494247383722e+00 6.19931890890363e+01 - 10 3.21733851230199e+00 6.17849080653709e+01 - 11 3.21950367376059e+00 6.15740450203887e+01 - 12 3.22130499849384e+00 6.13656547612945e+01 - 13 3.22263479486396e+00 6.11646847382338e+01 - 14 3.22341769654449e+00 6.09757828886766e+01 - 15 3.22361473664369e+00 6.08031168275266e+01 - 16 3.22322417500307e+00 6.06502098430779e+01 - 17 3.22227942549106e+00 6.05198025267682e+01 - 18 3.22084479785707e+00 6.04137510819450e+01 - 19 3.21900979827991e+00 6.03329740983039e+01 - 20 3.21688253444007e+00 6.02774557419409e+01 + 1 3.20437148316546e+00 6.30795952609024e+01 + 2 3.20384028589204e+00 6.30231590817356e+01 + 3 3.20396721187433e+00 6.29423176380356e+01 + 4 3.20472817287036e+00 6.28366833861828e+01 + 5 3.20606308066645e+00 6.27068898721072e+01 + 6 3.20787989003051e+00 6.25546017866590e+01 + 7 3.21005997943917e+00 6.23824530261739e+01 + 8 3.21246460655188e+00 6.21939260051983e+01 + 9 3.21494247388772e+00 6.19931890919450e+01 + 10 3.21733851236362e+00 6.17849080688927e+01 + 11 3.21950367383415e+00 6.15740450245643e+01 + 12 3.22130499858006e+00 6.13656547661594e+01 + 13 3.22263479496346e+00 6.11646847438178e+01 + 14 3.22341769665784e+00 6.09757828950022e+01 + 15 3.22361473677138e+00 6.08031168346083e+01 + 16 3.22322417514557e+00 6.06502098509209e+01 + 17 3.22227942564879e+00 6.05198025353684e+01 + 18 3.22084479803044e+00 6.04137510912894e+01 + 19 3.21900979846930e+00 6.03329741083708e+01 + 20 3.21688253464583e+00 6.02774557527018e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat index 337d77a7b..4ca2d87c5 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat @@ -1,3053 +1,3053 @@ # 2 -# 0.00000000000000e+00 2.00000000000000e-01 50 0 -# 0.00000000000000e+00 6.00000000000000e+00 60 1 +# 0 0.2 50 0 +# 0 6 60 1 - 1.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 - 1.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 - 1.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 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9.5 3 0 + 9.5 9 0 + 9.5 15 0 + 9.5 21 0 + 9.5 27 0 + 9.5 33 0 + 9.5 39 0 + 9.5 45 0 + 9.5 51 0 + 9.5 57 0 + 9.5 63 0 + 9.5 69 0 + 9.5 75 0 + 9.5 81 0 + 9.5 87 0 + 9.5 93 0 + 9.5 99 0 + 9.5 105 0 + 9.5 111 0 + 9.5 117 0 + 9.5 123 0 + 9.5 129 0 + 9.5 135 0 + 9.5 141 0 + 9.5 147 0 + 9.5 153 0 + 9.5 159 0 + 9.5 165 0 + 9.5 171 0 + 9.5 177 0 + 9.5 183 0 + 9.5 189 0 + 9.5 195 0 + 9.5 201 0 + 9.5 207 0 + 9.5 213 0 + 9.5 219 0 + 9.5 225 0 + 9.5 231 0 + 9.5 237 0 + 9.5 243 0 + 9.5 249 0 + 9.5 255 0 + 9.5 261 0 + 9.5 267 0 + 9.5 273 0 + 9.5 279 0 + 9.5 285 0 + 9.5 291 0 + 9.5 297 0 + 9.5 303 0 + 9.5 309 0 + 9.5 315 0 + 9.5 321 0 + 9.5 327 0 + 9.5 333 0 + 9.5 339 0 + 9.5 345 0 + 9.5 351 0 + 9.5 357 0 - 9.70000000000000e+00 3.00000000000000e+00 0.00000000000000e+00 - 9.70000000000000e+00 9.00000000000000e+00 0.00000000000000e+00 - 9.70000000000000e+00 1.50000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 2.10000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 2.70000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 3.30000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 3.90000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 4.50000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 5.10000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 5.70000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 6.30000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 6.90000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 7.50000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 8.10000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 8.70000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 9.30000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 9.90000000000000e+01 0.00000000000000e+00 - 9.70000000000000e+00 1.05000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.11000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.17000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.23000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.29000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.35000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.41000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.47000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.53000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.59000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.65000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.71000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.77000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.83000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.89000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 1.95000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.01000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.07000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.13000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.19000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.25000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.31000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.37000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.43000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.49000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.55000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.61000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.67000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.73000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.79000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.85000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.91000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 2.97000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.03000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 + 9.7 3 0 + 9.7 9 0 + 9.7 15 0 + 9.7 21 0 + 9.7 27 0 + 9.7 33 0 + 9.7 39 0 + 9.7 45 0 + 9.7 51 0 + 9.7 57 0 + 9.7 63 0 + 9.7 69 0 + 9.7 75 0 + 9.7 81 0 + 9.7 87 0 + 9.7 93 0 + 9.7 99 0 + 9.7 105 0 + 9.7 111 0 + 9.7 117 0 + 9.7 123 0 + 9.7 129 0 + 9.7 135 0 + 9.7 141 0 + 9.7 147 0 + 9.7 153 0 + 9.7 159 0 + 9.7 165 0 + 9.7 171 0 + 9.7 177 0 + 9.7 183 0 + 9.7 189 0 + 9.7 195 0 + 9.7 201 0 + 9.7 207 0 + 9.7 213 0 + 9.7 219 0 + 9.7 225 0 + 9.7 231 0 + 9.7 237 0 + 9.7 243 0 + 9.7 249 0 + 9.7 255 0 + 9.7 261 0 + 9.7 267 0 + 9.7 273 0 + 9.7 279 0 + 9.7 285 0 + 9.7 291 0 + 9.7 297 0 + 9.7 303 0 + 9.7 309 0 + 9.7 315 0 + 9.7 321 0 + 9.7 327 0 + 9.7 333 0 + 9.7 339 0 + 9.7 345 0 + 9.7 351 0 + 9.7 357 0 - 9.90000000000000e+00 3.00000000000000e+00 0.00000000000000e+00 - 9.90000000000000e+00 9.00000000000000e+00 0.00000000000000e+00 - 9.90000000000000e+00 1.50000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 2.10000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 2.70000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 3.30000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 3.90000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 4.50000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 5.10000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 5.70000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 6.30000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 6.90000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 7.50000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 8.10000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 8.70000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 9.30000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 9.90000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 1.05000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.11000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.17000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.23000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.29000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.35000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.41000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.47000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.53000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.59000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.65000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.71000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.77000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.83000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.89000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.95000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.01000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.07000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.13000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.19000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.25000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.31000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.37000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.43000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.49000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.55000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.61000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.67000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.73000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.79000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.85000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.91000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.97000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.03000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 + 9.9 3 0 + 9.9 9 0 + 9.9 15 0 + 9.9 21 0 + 9.9 27 0 + 9.9 33 0 + 9.9 39 0 + 9.9 45 0 + 9.9 51 0 + 9.9 57 0 + 9.9 63 0 + 9.9 69 0 + 9.9 75 0 + 9.9 81 0 + 9.9 87 0 + 9.9 93 0 + 9.9 99 0 + 9.9 105 0 + 9.9 111 0 + 9.9 117 0 + 9.9 123 0 + 9.9 129 0 + 9.9 135 0 + 9.9 141 0 + 9.9 147 0 + 9.9 153 0 + 9.9 159 0 + 9.9 165 0 + 9.9 171 0 + 9.9 177 0 + 9.9 183 0 + 9.9 189 0 + 9.9 195 0 + 9.9 201 0 + 9.9 207 0 + 9.9 213 0 + 9.9 219 0 + 9.9 225 0 + 9.9 231 0 + 9.9 237 0 + 9.9 243 0 + 9.9 249 0 + 9.9 255 0 + 9.9 261 0 + 9.9 267 0 + 9.9 273 0 + 9.9 279 0 + 9.9 285 0 + 9.9 291 0 + 9.9 297 0 + 9.9 303 0 + 9.9 309 0 + 9.9 315 0 + 9.9 321 0 + 9.9 327 0 + 9.9 333 0 + 9.9 339 0 + 9.9 345 0 + 9.9 351 0 + 9.9 357 0 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out index 7e5cda273..5c3fb9114 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -228,7 +229,6 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "r" from value: 3.21688 @@ -239,7 +239,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped index ff6d40c16..16d91a903 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21404878499019e+00 + x 3.21404878547144e+00 } colvar { name phi - x 6.08972121817132e+01 + x 6.08972122017851e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj index 00a61ca9a..6e6a9d108 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step r phi - 20 3.21688253444007e+00 6.02774557419409e+01 - 21 3.21458253135360e+00 6.02463068586077e+01 - 22 3.21223315230095e+00 6.02378794547663e+01 - 23 3.20995392007338e+00 6.02499213666401e+01 - 24 3.20785326939589e+00 6.02797520443280e+01 - 25 3.20602244816055e+00 6.03244374884686e+01 - 26 3.20453120115385e+00 6.03809430381167e+01 - 27 3.20342556447929e+00 6.04462482226441e+01 - 28 3.20272769818575e+00 6.05174152507232e+01 - 29 3.20243730741081e+00 6.05916134367745e+01 - 30 3.20253423271288e+00 6.06661106175895e+01 - 31 3.20298183323508e+00 6.07382493916987e+01 - 32 3.20373100874536e+00 6.08054278361141e+01 - 33 3.20472468704943e+00 6.08651028913518e+01 - 34 3.20590256178394e+00 6.09148265769850e+01 - 35 3.20720566140745e+00 6.09523144047667e+01 - 36 3.20858030414420e+00 6.09755306486176e+01 - 37 3.20998111808250e+00 6.09827676263964e+01 - 38 3.21137308287521e+00 6.09726956103267e+01 - 39 3.21273274268056e+00 6.09443715231751e+01 - 40 3.21404878499019e+00 6.08972121817132e+01 + 20 3.21688253464583e+00 6.02774557527018e+01 + 21 3.21458253157603e+00 6.02463068700288e+01 + 22 3.21223315254029e+00 6.02378794668108e+01 + 23 3.20995392032979e+00 6.02499213792704e+01 + 24 3.20785326966943e+00 6.02797520575071e+01 + 25 3.20602244845117e+00 6.03244375021622e+01 + 26 3.20453120146139e+00 6.03809430522940e+01 + 27 3.20342556480347e+00 6.04462482372788e+01 + 28 3.20272769852622e+00 6.05174152657937e+01 + 29 3.20243730776714e+00 6.05916134522643e+01 + 30 3.20253423308456e+00 6.06661106334871e+01 + 31 3.20298183362156e+00 6.07382494079973e+01 + 32 3.20373100914607e+00 6.08054278528112e+01 + 33 3.20472468746373e+00 6.08651029084488e+01 + 34 3.20590256221113e+00 6.09148265944857e+01 + 35 3.20720566184671e+00 6.09523144226767e+01 + 36 3.20858030459458e+00 6.09755306669437e+01 + 37 3.20998111854285e+00 6.09827676451462e+01 + 38 3.21137308334418e+00 6.09726956295080e+01 + 39 3.21273274315657e+00 6.09443715427968e+01 + 40 3.21404878547144e+00 6.08972122017851e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat index 60d272104..bcd93aff0 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat @@ -1,3053 +1,3053 @@ # 2 -# 0.00000000000000e+00 2.00000000000000e-01 50 0 -# 0.00000000000000e+00 6.00000000000000e+00 60 1 +# 0 0.2 50 0 +# 0 6 60 1 - 1.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 - 1.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 - 1.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 5.70000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 8.10000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 8.70000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 9.30000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 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0.00000000000000e+00 - 9.70000000000000e+00 2.97000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.03000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 - 9.70000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 + 9.7 3 0 + 9.7 9 0 + 9.7 15 0 + 9.7 21 0 + 9.7 27 0 + 9.7 33 0 + 9.7 39 0 + 9.7 45 0 + 9.7 51 0 + 9.7 57 0 + 9.7 63 0 + 9.7 69 0 + 9.7 75 0 + 9.7 81 0 + 9.7 87 0 + 9.7 93 0 + 9.7 99 0 + 9.7 105 0 + 9.7 111 0 + 9.7 117 0 + 9.7 123 0 + 9.7 129 0 + 9.7 135 0 + 9.7 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5.10000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 5.70000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 6.30000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 6.90000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 7.50000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 8.10000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 8.70000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 9.30000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 9.90000000000000e+01 0.00000000000000e+00 - 9.90000000000000e+00 1.05000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.11000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.17000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.23000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.29000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.35000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.41000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.47000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.53000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.59000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.65000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.71000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.77000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.83000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.89000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 1.95000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.01000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.07000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.13000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.19000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.25000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.31000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.37000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.43000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.49000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.55000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.61000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.67000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.73000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.79000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.85000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.91000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 2.97000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.03000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 + 9.9 3 0 + 9.9 9 0 + 9.9 15 0 + 9.9 21 0 + 9.9 27 0 + 9.9 33 0 + 9.9 39 0 + 9.9 45 0 + 9.9 51 0 + 9.9 57 0 + 9.9 63 0 + 9.9 69 0 + 9.9 75 0 + 9.9 81 0 + 9.9 87 0 + 9.9 93 0 + 9.9 99 0 + 9.9 105 0 + 9.9 111 0 + 9.9 117 0 + 9.9 123 0 + 9.9 129 0 + 9.9 135 0 + 9.9 141 0 + 9.9 147 0 + 9.9 153 0 + 9.9 159 0 + 9.9 165 0 + 9.9 171 0 + 9.9 177 0 + 9.9 183 0 + 9.9 189 0 + 9.9 195 0 + 9.9 201 0 + 9.9 207 0 + 9.9 213 0 + 9.9 219 0 + 9.9 225 0 + 9.9 231 0 + 9.9 237 0 + 9.9 243 0 + 9.9 249 0 + 9.9 255 0 + 9.9 261 0 + 9.9 267 0 + 9.9 273 0 + 9.9 279 0 + 9.9 285 0 + 9.9 291 0 + 9.9 297 0 + 9.9 303 0 + 9.9 309 0 + 9.9 315 0 + 9.9 321 0 + 9.9 327 0 + 9.9 333 0 + 9.9 339 0 + 9.9 345 0 + 9.9 351 0 + 9.9 357 0 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt index 157cac038..017b69b3a 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2022-04-14. +colvars: Using NAMD interface, version "2022-04-06". diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out index a28b5f43d..0254b6e28 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -225,12 +226,10 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped index 3008cc63c..b2dc7dab5 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21688253444007e+00 + x 3.21688253464583e+00 } colvar { name phi - x 6.02774557419409e+01 + x 6.02774557527018e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj index 19662210d..0d258d955 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step r phi 0 3.20554673468334e+00 6.31129478791928e+01 - 1 3.20437148316484e+00 6.30795952608635e+01 - 2 3.20384028588952e+00 6.30231590815800e+01 - 3 3.20396721186862e+00 6.29423176376863e+01 - 4 3.20472817286016e+00 6.28366833855655e+01 - 5 3.20606308065050e+00 6.27068898711517e+01 - 6 3.20787989000757e+00 6.25546017852999e+01 - 7 3.21005997940810e+00 6.23824530243513e+01 - 8 3.21246460651160e+00 6.21939260028577e+01 - 9 3.21494247383722e+00 6.19931890890363e+01 - 10 3.21733851230199e+00 6.17849080653709e+01 - 11 3.21950367376059e+00 6.15740450203887e+01 - 12 3.22130499849384e+00 6.13656547612945e+01 - 13 3.22263479486396e+00 6.11646847382338e+01 - 14 3.22341769654449e+00 6.09757828886766e+01 - 15 3.22361473664369e+00 6.08031168275266e+01 - 16 3.22322417500307e+00 6.06502098430779e+01 - 17 3.22227942549106e+00 6.05198025267682e+01 - 18 3.22084479785707e+00 6.04137510819450e+01 - 19 3.21900979827991e+00 6.03329740983039e+01 - 20 3.21688253444007e+00 6.02774557419409e+01 + 1 3.20437148316546e+00 6.30795952609024e+01 + 2 3.20384028589204e+00 6.30231590817356e+01 + 3 3.20396721187433e+00 6.29423176380356e+01 + 4 3.20472817287036e+00 6.28366833861828e+01 + 5 3.20606308066645e+00 6.27068898721072e+01 + 6 3.20787989003051e+00 6.25546017866590e+01 + 7 3.21005997943917e+00 6.23824530261739e+01 + 8 3.21246460655188e+00 6.21939260051983e+01 + 9 3.21494247388772e+00 6.19931890919450e+01 + 10 3.21733851236362e+00 6.17849080688927e+01 + 11 3.21950367383415e+00 6.15740450245643e+01 + 12 3.22130499858006e+00 6.13656547661594e+01 + 13 3.22263479496346e+00 6.11646847438178e+01 + 14 3.22341769665784e+00 6.09757828950022e+01 + 15 3.22361473677138e+00 6.08031168346083e+01 + 16 3.22322417514557e+00 6.06502098509209e+01 + 17 3.22227942564879e+00 6.05198025353684e+01 + 18 3.22084479803044e+00 6.04137510912894e+01 + 19 3.21900979846930e+00 6.03329741083708e+01 + 20 3.21688253464583e+00 6.02774557527018e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat index 560cfda3e..d42b8f708 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat @@ -1,7223 +1,7223 @@ # 2 -# 0.00000000000000e+00 1.00000000000000e+00 20 0 -# -1.80000000000000e+02 1.00000000000000e+00 360 1 +# 0 1 20 0 +# -180 1 360 1 - 5.00000000000000e-01 -1.79500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.78500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.77500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.76500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.75500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.74500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.73500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.72500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.71500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.70500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.69500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 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74614ceb4..43174e795 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -225,7 +226,6 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "r" from value: 3.21688 @@ -236,7 +236,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped index 51260c395..1d0bd953f 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21404878499019e+00 + x 3.21404878547144e+00 } colvar { name phi - x 6.08972121817132e+01 + x 6.08972122017851e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj index 00a61ca9a..6e6a9d108 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step r phi - 20 3.21688253444007e+00 6.02774557419409e+01 - 21 3.21458253135360e+00 6.02463068586077e+01 - 22 3.21223315230095e+00 6.02378794547663e+01 - 23 3.20995392007338e+00 6.02499213666401e+01 - 24 3.20785326939589e+00 6.02797520443280e+01 - 25 3.20602244816055e+00 6.03244374884686e+01 - 26 3.20453120115385e+00 6.03809430381167e+01 - 27 3.20342556447929e+00 6.04462482226441e+01 - 28 3.20272769818575e+00 6.05174152507232e+01 - 29 3.20243730741081e+00 6.05916134367745e+01 - 30 3.20253423271288e+00 6.06661106175895e+01 - 31 3.20298183323508e+00 6.07382493916987e+01 - 32 3.20373100874536e+00 6.08054278361141e+01 - 33 3.20472468704943e+00 6.08651028913518e+01 - 34 3.20590256178394e+00 6.09148265769850e+01 - 35 3.20720566140745e+00 6.09523144047667e+01 - 36 3.20858030414420e+00 6.09755306486176e+01 - 37 3.20998111808250e+00 6.09827676263964e+01 - 38 3.21137308287521e+00 6.09726956103267e+01 - 39 3.21273274268056e+00 6.09443715231751e+01 - 40 3.21404878499019e+00 6.08972121817132e+01 + 20 3.21688253464583e+00 6.02774557527018e+01 + 21 3.21458253157603e+00 6.02463068700288e+01 + 22 3.21223315254029e+00 6.02378794668108e+01 + 23 3.20995392032979e+00 6.02499213792704e+01 + 24 3.20785326966943e+00 6.02797520575071e+01 + 25 3.20602244845117e+00 6.03244375021622e+01 + 26 3.20453120146139e+00 6.03809430522940e+01 + 27 3.20342556480347e+00 6.04462482372788e+01 + 28 3.20272769852622e+00 6.05174152657937e+01 + 29 3.20243730776714e+00 6.05916134522643e+01 + 30 3.20253423308456e+00 6.06661106334871e+01 + 31 3.20298183362156e+00 6.07382494079973e+01 + 32 3.20373100914607e+00 6.08054278528112e+01 + 33 3.20472468746373e+00 6.08651029084488e+01 + 34 3.20590256221113e+00 6.09148265944857e+01 + 35 3.20720566184671e+00 6.09523144226767e+01 + 36 3.20858030459458e+00 6.09755306669437e+01 + 37 3.20998111854285e+00 6.09827676451462e+01 + 38 3.21137308334418e+00 6.09726956295080e+01 + 39 3.21273274315657e+00 6.09443715427968e+01 + 40 3.21404878547144e+00 6.08972122017851e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat index 4d18e65a0..3099652d8 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat @@ -1,7223 +1,7223 @@ # 2 -# 0.00000000000000e+00 1.00000000000000e+00 20 0 -# -1.80000000000000e+02 1.00000000000000e+00 360 1 +# 0 1 20 0 +# -180 1 360 1 - 5.00000000000000e-01 -1.79500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.78500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.77500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.76500000000000e+02 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19.5 160.5 0 + 19.5 161.5 0 + 19.5 162.5 0 + 19.5 163.5 0 + 19.5 164.5 0 + 19.5 165.5 0 + 19.5 166.5 0 + 19.5 167.5 0 + 19.5 168.5 0 + 19.5 169.5 0 + 19.5 170.5 0 + 19.5 171.5 0 + 19.5 172.5 0 + 19.5 173.5 0 + 19.5 174.5 0 + 19.5 175.5 0 + 19.5 176.5 0 + 19.5 177.5 0 + 19.5 178.5 0 + 19.5 179.5 0 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt index 157cac038..017b69b3a 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2022-04-14. +colvars: Using NAMD interface, version "2022-04-06". diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out index fd1bac75c..cdf554a37 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out @@ -154,7 +154,7 @@ colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.2155 -colvars: Restarting histogram bias "histogram1" from step number 20. +colvars: Restarting histogram bias "histogram1" from step number 0. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out index b5dee23d8..89726d6e4 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out @@ -153,7 +153,7 @@ colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.2155 -colvars: Restarting histogram bias "histogram1" from step number 20. +colvars: Restarting histogram bias "histogram1" from step number 0. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). diff --git a/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt b/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt +++ b/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-extended/namd-version.txt b/namd/tests/library/000_distance-extended/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_distance-extended/namd-version.txt +++ b/namd/tests/library/000_distance-extended/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out index 04c1af77b..d0cd986cf 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -90,7 +86,7 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 -colvars: # lowerBoundary = 0 [default] +colvars: # lowerBoundary = 0 colvars: # upperBoundary = 0.1 colvars: # hardLowerBoundary = on colvars: # hardUpperBoundary = off [default] @@ -141,27 +137,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped index 10c1037b0..21d01f18d 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688804951235e+00 + x 3.21688804971810e+00 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 2.26845126752189e-07 - 5.71217598091379e-05 1.12710965943565e-03 1.74270241892652e-03 - 2.11141093140343e-04 2.00454018061483e-06 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 2.26845124673292e-07 + 5.71217594827238e-05 1.12710965685979e-03 1.74270242088282e-03 + 2.11141094092476e-04 2.00454019640119e-06 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients grid_parameters { @@ -51,9 +51,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 1.54297695614713e-05 - 2.43078780370765e-03 1.92623445129830e-02 -1.45941325629368e-02 - -7.14477980575610e-03 -1.18875947897555e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.54297694279170e-05 + 2.43078779178197e-03 1.92623445074912e-02 -1.45941325201129e-02 + -7.14477983084629e-03 -1.18875948766480e-04 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj index 06d632fae..f51a5d30c 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 7.26085413750919e-03 - 11 3.21950378525805e+00 7.26085413750919e-03 - 12 3.22130533160336e+00 7.26085413750919e-03 - 13 3.22263545689569e+00 7.26085413750919e-03 - 14 3.22341879070410e+00 7.26085413750919e-03 - 15 3.22361636091569e+00 7.26085413750919e-03 - 16 3.22322642126644e+00 7.26085413750919e-03 - 17 3.22228237889954e+00 7.26085413750919e-03 - 18 3.22084853649908e+00 7.26085413750919e-03 - 19 3.21901439311712e+00 7.26085413750919e-03 - 20 3.21688804951235e+00 1.45941325629368e-02 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 7.26085412753031e-03 + 11 3.21950378533161e+00 7.26085412753031e-03 + 12 3.22130533168958e+00 7.26085412753031e-03 + 13 3.22263545699519e+00 7.26085412753031e-03 + 14 3.22341879081745e+00 7.26085412753031e-03 + 15 3.22361636104338e+00 7.26085412753031e-03 + 16 3.22322642140893e+00 7.26085412753031e-03 + 17 3.22228237905726e+00 7.26085412753031e-03 + 18 3.22084853667244e+00 7.26085412753031e-03 + 19 3.21901439330651e+00 7.26085412753031e-03 + 20 3.21688804971810e+00 1.45941325201129e-02 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf index 80c051dc8..dc034b29d 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf @@ -1,40 +1,40 @@ # 1 # 0.00000000000000e+00 1.00000000000000e-01 37 0 - 5.00000000000000e-02 1.74270241892652e-03 - 1.50000000000000e-01 1.74270241892652e-03 - 2.50000000000000e-01 1.74270241892652e-03 - 3.50000000000000e-01 1.74270241892652e-03 - 4.50000000000000e-01 1.74270241892652e-03 - 5.50000000000000e-01 1.74270241892652e-03 - 6.50000000000000e-01 1.74270241892652e-03 - 7.50000000000000e-01 1.74270241892652e-03 - 8.50000000000000e-01 1.74270241892652e-03 - 9.50000000000000e-01 1.74270241892652e-03 - 1.05000000000000e+00 1.74270241892652e-03 - 1.15000000000000e+00 1.74270241892652e-03 - 1.25000000000000e+00 1.74270241892652e-03 - 1.35000000000000e+00 1.74270241892652e-03 - 1.45000000000000e+00 1.74270241892652e-03 - 1.55000000000000e+00 1.74270241892652e-03 - 1.65000000000000e+00 1.74270241892652e-03 - 1.75000000000000e+00 1.74270241892652e-03 - 1.85000000000000e+00 1.74270241892652e-03 - 1.95000000000000e+00 1.74270241892652e-03 - 2.05000000000000e+00 1.74270241892652e-03 - 2.15000000000000e+00 1.74270241892652e-03 - 2.25000000000000e+00 1.74270241892652e-03 - 2.35000000000000e+00 1.74270241892652e-03 - 2.45000000000000e+00 1.74270241892652e-03 - 2.55000000000000e+00 1.74270241892652e-03 - 2.65000000000000e+00 1.74270241892652e-03 - 2.75000000000000e+00 1.74270241892652e-03 - 2.85000000000000e+00 1.74270241892652e-03 - 2.95000000000000e+00 1.74247557379976e-03 - 3.05000000000000e+00 1.68558065911738e-03 - 3.15000000000000e+00 6.15592759490865e-04 + 5.00000000000000e-02 1.74270242088282e-03 + 1.50000000000000e-01 1.74270242088282e-03 + 2.50000000000000e-01 1.74270242088282e-03 + 3.50000000000000e-01 1.74270242088282e-03 + 4.50000000000000e-01 1.74270242088282e-03 + 5.50000000000000e-01 1.74270242088282e-03 + 6.50000000000000e-01 1.74270242088282e-03 + 7.50000000000000e-01 1.74270242088282e-03 + 8.50000000000000e-01 1.74270242088282e-03 + 9.50000000000000e-01 1.74270242088282e-03 + 1.05000000000000e+00 1.74270242088282e-03 + 1.15000000000000e+00 1.74270242088282e-03 + 1.25000000000000e+00 1.74270242088282e-03 + 1.35000000000000e+00 1.74270242088282e-03 + 1.45000000000000e+00 1.74270242088282e-03 + 1.55000000000000e+00 1.74270242088282e-03 + 1.65000000000000e+00 1.74270242088282e-03 + 1.75000000000000e+00 1.74270242088282e-03 + 1.85000000000000e+00 1.74270242088282e-03 + 1.95000000000000e+00 1.74270242088282e-03 + 2.05000000000000e+00 1.74270242088282e-03 + 2.15000000000000e+00 1.74270242088282e-03 + 2.25000000000000e+00 1.74270242088282e-03 + 2.35000000000000e+00 1.74270242088282e-03 + 2.45000000000000e+00 1.74270242088282e-03 + 2.55000000000000e+00 1.74270242088282e-03 + 2.65000000000000e+00 1.74270242088282e-03 + 2.75000000000000e+00 1.74270242088282e-03 + 2.85000000000000e+00 1.74270242088282e-03 + 2.95000000000000e+00 1.74247557575815e-03 + 3.05000000000000e+00 1.68558066140010e-03 + 3.15000000000000e+00 6.15592764023032e-04 3.25000000000000e+00 -0.00000000000000e+00 - 3.35000000000000e+00 1.53156132578617e-03 - 3.45000000000000e+00 1.74069787874590e-03 - 3.55000000000000e+00 1.74270241892652e-03 - 3.65000000000000e+00 1.74270241892652e-03 + 3.35000000000000e+00 1.53156132679035e-03 + 3.45000000000000e+00 1.74069788068642e-03 + 3.55000000000000e+00 1.74270242088282e-03 + 3.65000000000000e+00 1.74270242088282e-03 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out index e41a5cf1c..5813ff1d2 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -90,7 +86,7 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 -colvars: # lowerBoundary = 0 [default] +colvars: # lowerBoundary = 0 colvars: # upperBoundary = 0.1 colvars: # hardLowerBoundary = on colvars: # hardUpperBoundary = off [default] @@ -141,34 +137,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21689 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped index 16770ad61..34fd5ad0c 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21410417583007e+00 + x 3.21410417631119e+00 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 6.62978157520071e-07 - 1.41194487892242e-04 2.42321240493645e-03 3.34221726380270e-03 - 3.69169353864755e-04 3.25342737556381e-06 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 6.62978143841745e-07 + 1.41194486168262e-04 2.42321239420736e-03 3.34221727286243e-03 + 3.69169357278679e-04 3.25342742518778e-06 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients grid_parameters { @@ -51,9 +51,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 4.38875870035617e-05 - 5.79221287439899e-03 3.83513133503907e-02 -3.14227499478963e-02 - -1.27980744195482e-02 -1.95106962739560e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 4.38875861559355e-05 + 5.79221281512363e-03 3.83513133612739e-02 -3.14227498048830e-02 + -1.27980745147960e-02 -1.95106965527919e-04 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj index bc03d36a4..6941fb0a6 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688804951235e+00 1.45941325629368e-02 - 21 3.21458913699124e+00 1.45941325629368e-02 - 22 3.21224101139884e+00 1.45941325629368e-02 - 23 3.20996318736015e+00 1.45941325629368e-02 - 24 3.20786409091340e+00 1.45941325629368e-02 - 25 3.20603496093235e+00 1.45941325629368e-02 - 26 3.20454553304178e+00 1.45941325629368e-02 - 27 3.20344183417990e+00 1.45941325629368e-02 - 28 3.20274601535548e+00 1.45941325629368e-02 - 29 3.20245777287417e+00 1.45941325629368e-02 - 30 3.20255693872927e+00 2.36650234045914e-02 - 31 3.20300700313402e+00 2.36650234045914e-02 - 32 3.20375885604914e+00 2.36650234045914e-02 - 33 3.20475541396031e+00 2.36650234045914e-02 - 34 3.20593635782781e+00 2.36650234045914e-02 - 35 3.20724270238762e+00 2.36650234045914e-02 - 36 3.20862075136558e+00 2.36650234045914e-02 - 37 3.21002511802444e+00 2.36650234045914e-02 - 38 3.21142076721680e+00 2.36650234045914e-02 - 39 3.21278422862637e+00 2.36650234045914e-02 - 40 3.21410417583007e+00 3.14227499478963e-02 + 20 3.21688804971810e+00 1.45941325201129e-02 + 21 3.21458913721366e+00 1.45941325201129e-02 + 22 3.21224101163817e+00 1.45941325201129e-02 + 23 3.20996318761655e+00 1.45941325201129e-02 + 24 3.20786409118692e+00 1.45941325201129e-02 + 25 3.20603496122295e+00 1.45941325201129e-02 + 26 3.20454553334930e+00 1.45941325201129e-02 + 27 3.20344183450406e+00 1.45941325201129e-02 + 28 3.20274601569592e+00 1.45941325201129e-02 + 29 3.20245777323046e+00 1.45941325201129e-02 + 30 3.20255693910090e+00 2.36650233314395e-02 + 31 3.20300700352046e+00 2.36650233314395e-02 + 32 3.20375885644980e+00 2.36650233314395e-02 + 33 3.20475541437456e+00 2.36650233314395e-02 + 34 3.20593635825493e+00 2.36650233314395e-02 + 35 3.20724270282681e+00 2.36650233314395e-02 + 36 3.20862075181587e+00 2.36650233314395e-02 + 37 3.21002511848469e+00 2.36650233314395e-02 + 38 3.21142076768566e+00 2.36650233314395e-02 + 39 3.21278422910227e+00 2.36650233314395e-02 + 40 3.21410417631119e+00 3.14227498048830e-02 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf index 63d82cbc3..dd7b19d0a 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf @@ -1,40 +1,40 @@ # 1 # 0.00000000000000e+00 1.00000000000000e-01 37 0 - 5.00000000000000e-02 3.34221726380270e-03 - 1.50000000000000e-01 3.34221726380270e-03 - 2.50000000000000e-01 3.34221726380270e-03 - 3.50000000000000e-01 3.34221726380270e-03 - 4.50000000000000e-01 3.34221726380270e-03 - 5.50000000000000e-01 3.34221726380270e-03 - 6.50000000000000e-01 3.34221726380270e-03 - 7.50000000000000e-01 3.34221726380270e-03 - 8.50000000000000e-01 3.34221726380270e-03 - 9.50000000000000e-01 3.34221726380270e-03 - 1.05000000000000e+00 3.34221726380270e-03 - 1.15000000000000e+00 3.34221726380270e-03 - 1.25000000000000e+00 3.34221726380270e-03 - 1.35000000000000e+00 3.34221726380270e-03 - 1.45000000000000e+00 3.34221726380270e-03 - 1.55000000000000e+00 3.34221726380270e-03 - 1.65000000000000e+00 3.34221726380270e-03 - 1.75000000000000e+00 3.34221726380270e-03 - 1.85000000000000e+00 3.34221726380270e-03 - 1.95000000000000e+00 3.34221726380270e-03 - 2.05000000000000e+00 3.34221726380270e-03 - 2.15000000000000e+00 3.34221726380270e-03 - 2.25000000000000e+00 3.34221726380270e-03 - 2.35000000000000e+00 3.34221726380270e-03 - 2.45000000000000e+00 3.34221726380270e-03 - 2.55000000000000e+00 3.34221726380270e-03 - 2.65000000000000e+00 3.34221726380270e-03 - 2.75000000000000e+00 3.34221726380270e-03 - 2.85000000000000e+00 3.34221726380270e-03 - 2.95000000000000e+00 3.34155428564518e-03 - 3.05000000000000e+00 3.20102277591046e-03 - 3.15000000000000e+00 9.19004858866248e-04 + 5.00000000000000e-02 3.34221727286243e-03 + 1.50000000000000e-01 3.34221727286243e-03 + 2.50000000000000e-01 3.34221727286243e-03 + 3.50000000000000e-01 3.34221727286243e-03 + 4.50000000000000e-01 3.34221727286243e-03 + 5.50000000000000e-01 3.34221727286243e-03 + 6.50000000000000e-01 3.34221727286243e-03 + 7.50000000000000e-01 3.34221727286243e-03 + 8.50000000000000e-01 3.34221727286243e-03 + 9.50000000000000e-01 3.34221727286243e-03 + 1.05000000000000e+00 3.34221727286243e-03 + 1.15000000000000e+00 3.34221727286243e-03 + 1.25000000000000e+00 3.34221727286243e-03 + 1.35000000000000e+00 3.34221727286243e-03 + 1.45000000000000e+00 3.34221727286243e-03 + 1.55000000000000e+00 3.34221727286243e-03 + 1.65000000000000e+00 3.34221727286243e-03 + 1.75000000000000e+00 3.34221727286243e-03 + 1.85000000000000e+00 3.34221727286243e-03 + 1.95000000000000e+00 3.34221727286243e-03 + 2.05000000000000e+00 3.34221727286243e-03 + 2.15000000000000e+00 3.34221727286243e-03 + 2.25000000000000e+00 3.34221727286243e-03 + 2.35000000000000e+00 3.34221727286243e-03 + 2.45000000000000e+00 3.34221727286243e-03 + 2.55000000000000e+00 3.34221727286243e-03 + 2.65000000000000e+00 3.34221727286243e-03 + 2.75000000000000e+00 3.34221727286243e-03 + 2.85000000000000e+00 3.34221727286243e-03 + 2.95000000000000e+00 3.34155429471859e-03 + 3.05000000000000e+00 3.20102278669417e-03 + 3.15000000000000e+00 9.19004878655076e-04 3.25000000000000e+00 -0.00000000000000e+00 - 3.35000000000000e+00 2.97304790993794e-03 - 3.45000000000000e+00 3.33896383642714e-03 - 3.55000000000000e+00 3.34221726380270e-03 - 3.65000000000000e+00 3.34221726380270e-03 + 3.35000000000000e+00 2.97304791558375e-03 + 3.45000000000000e+00 3.33896384543724e-03 + 3.55000000000000e+00 3.34221727286243e-03 + 3.65000000000000e+00 3.34221727286243e-03 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt b/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out index 49233a154..7522b04bf 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -133,30 +129,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped index dd78a9c08..20f2914d8 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.19500142870476e+00 + x 3.19500142883077e+00 } abf { @@ -20,7 +20,7 @@ samples 0 0 0 0 gradient - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -2.00127620028148e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -2.00127627059354e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj index 5cab1a630..c883ca64b 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 -7.68950954395538e+00 - 7 3.20994206782701e+00 -1.45081021954275e+01 - 8 3.21200777962688e+00 -2.01168223029416e+01 - 9 3.21384392079195e+00 -2.42708474851834e+01 - 10 3.21523959933526e+00 -2.68357715832755e+01 - 11 3.21601851659179e+00 -2.31658530843961e+01 - 12 3.21612044367303e+00 -1.94776790572418e+01 - 13 3.21551354957116e+00 -1.59170233488103e+01 - 14 3.21419762164954e+00 -1.26130067638535e+01 - 15 3.21220454729786e+00 -9.67058885249113e+00 - 16 3.20959604449940e+00 -7.16540382727106e+00 - 17 3.20645917266472e+00 -5.14219076042560e+00 - 18 3.20290044125515e+00 -3.61665560433892e+00 - 19 3.19903928567179e+00 -2.57951937903240e+00 - 20 3.19500142870476e+00 -2.00127620028148e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 -7.68950956048151e+00 + 7 3.20994206785783e+00 -1.45081022282339e+01 + 8 3.21200777966617e+00 -2.01168223516023e+01 + 9 3.21384392083996e+00 -2.42708475491531e+01 + 10 3.21523959939197e+00 -2.68357716619527e+01 + 11 3.21601851665685e+00 -2.31658531617215e+01 + 12 3.21612044374608e+00 -1.94776791332188e+01 + 13 3.21551354965183e+00 -1.59170234235171e+01 + 14 3.21419762173747e+00 -1.26130068374289e+01 + 15 3.21220454739271e+00 -9.67058892511207e+00 + 16 3.20959604460089e+00 -7.16540389913541e+00 + 17 3.20645917277260e+00 -5.14219083172278e+00 + 18 3.20290044136922e+00 -3.61665567522571e+00 + 19 3.19903928579189e+00 -2.57951944961151e+00 + 20 3.19500142883077e+00 -2.00127627059354e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad index f1d0f6536..a9d8b5547 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -2.00127620028148e+00 + 3.25000000000000e+00 -2.00127627059354e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf index 46f65d7e5..a9c224cc4 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 1.00063810014074e+00 - 5.00000000000000e-01 1.00063810014074e+00 - 1.00000000000000e+00 1.00063810014074e+00 - 1.50000000000000e+00 1.00063810014074e+00 - 2.00000000000000e+00 1.00063810014074e+00 - 2.50000000000000e+00 1.00063810014074e+00 - 3.00000000000000e+00 1.00063810014074e+00 + 0.00000000000000e+00 1.00063813529677e+00 + 5.00000000000000e-01 1.00063813529677e+00 + 1.00000000000000e+00 1.00063813529677e+00 + 1.50000000000000e+00 1.00063813529677e+00 + 2.00000000000000e+00 1.00063813529677e+00 + 2.50000000000000e+00 1.00063813529677e+00 + 3.00000000000000e+00 1.00063813529677e+00 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out index e69be3fb4..1fa514166 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -133,35 +129,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.195 colvars: Restarting abf bias "abf1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped index cf3a7c63e..5ddfe2247 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.16157768304247e+00 + x 3.16157768320120e+00 } abf { @@ -20,7 +20,7 @@ samples 0 0 0 0 gradient - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.06018968543260e+01 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.06018969033008e+01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj index 790f5da38..6b2274e24 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.19500142870476e+00 -2.00127620028148e+00 - 21 3.19091235913242e+00 -1.83655671092344e+00 - 22 3.18689102863460e+00 -2.02779464964507e+00 - 23 3.18304398632164e+00 -2.50868594751815e+00 - 24 3.17946034157703e+00 -3.20793281356371e+00 - 25 3.17620810280522e+00 -4.05360356466712e+00 - 26 3.17333232267116e+00 -4.97767848574970e+00 - 27 3.17085517066390e+00 -5.92001155007172e+00 - 28 3.16877768256299e+00 -6.83099312723649e+00 - 29 3.16708266039313e+00 -7.67258378612514e+00 - 30 3.16573827065657e+00 -8.41821673794446e+00 - 31 3.16470189524569e+00 -9.05180799754020e+00 - 32 3.16392411278234e+00 -9.56669436325192e+00 - 33 3.16335264543312e+00 -9.96442495777829e+00 - 34 3.16293610801839e+00 -1.02534301314753e+01 - 35 3.16262726153762e+00 -1.04473358447738e+01 - 36 3.16238550229189e+00 -1.05630325935795e+01 - 37 3.16217843203474e+00 -1.06187380623063e+01 - 38 3.16198265878694e+00 -1.06325725153697e+01 - 39 3.16178405667746e+00 -1.06216993194485e+01 - 40 3.16157768304247e+00 -1.06018968543260e+01 + 20 3.19500142883077e+00 -2.00127627059354e+00 + 21 3.19091235926421e+00 -1.83655678093969e+00 + 22 3.18689102877202e+00 -2.02779471927389e+00 + 23 3.18304398646448e+00 -2.50868601661760e+00 + 24 3.17946034172504e+00 -3.20793288196262e+00 + 25 3.17620810295805e+00 -4.05360363219171e+00 + 26 3.17333232282842e+00 -4.97767855224492e+00 + 27 3.17085517082510e+00 -5.92001161542199e+00 + 28 3.16877768272762e+00 -6.83099319137926e+00 + 29 3.16708266056064e+00 -7.67258384905857e+00 + 30 3.16573827082641e+00 -8.41821679971556e+00 + 31 3.16470189541734e+00 -9.05180805822893e+00 + 32 3.16392411295527e+00 -9.56669442294402e+00 + 33 3.16335264560683e+00 -9.96442501653096e+00 + 34 3.16293610819235e+00 -1.02534301892968e+01 + 35 3.16262726171125e+00 -1.04473359016060e+01 + 36 3.16238550246452e+00 -1.05630326492936e+01 + 37 3.16217843220556e+00 -1.06187381167053e+01 + 38 3.16198265895496e+00 -1.06325725682142e+01 + 39 3.16178405684152e+00 -1.06216993704827e+01 + 40 3.16157768320120e+00 -1.06018969033008e+01 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad index be93459e2..9b2cd506d 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.06018968543260e+01 + 3.25000000000000e+00 -1.06018969033008e+01 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf index 34e7b0c50..0ddef6258 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 5.30094842716302e+00 - 5.00000000000000e-01 5.30094842716302e+00 - 1.00000000000000e+00 5.30094842716302e+00 - 1.50000000000000e+00 5.30094842716302e+00 - 2.00000000000000e+00 5.30094842716302e+00 - 2.50000000000000e+00 5.30094842716302e+00 - 3.00000000000000e+00 5.30094842716302e+00 + 0.00000000000000e+00 5.30094845165041e+00 + 5.00000000000000e-01 5.30094845165041e+00 + 1.00000000000000e+00 5.30094845165041e+00 + 1.50000000000000e+00 5.30094845165041e+00 + 2.00000000000000e+00 5.30094845165041e+00 + 2.50000000000000e+00 5.30094845165041e+00 + 3.00000000000000e+00 5.30094845165041e+00 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/namd-version.txt b/namd/tests/library/000_distance-grid_abf/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_abf/namd-version.txt +++ b/namd/tests/library/000_distance-grid_abf/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out index 143074633..61f53d955 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,30 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped index 72e414d40..e48d1c4ec 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685457618647e+00 + x 3.21685457639221e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } histogram @@ -29,7 +29,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -1.45777482050594e+00 0.00000000000000e+00 0.00000000000000e+00 + -1.45777476148254e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj index 5eec6dc1f..c0e02c1fa 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788600e+00 -1.23774855515440e-02 1.91502685723351e-02 1.10000000000000e-01 -1.23774855515440e-04 - 2 3.20383990680414e+00 -1.23353596272166e-02 1.90201371415956e-02 1.20000000000000e-01 -2.47128451787606e-04 - 3 3.20396636491103e+00 -1.22958654596441e-02 1.88985384252087e-02 1.30000000000000e-01 -3.70087106384047e-04 - 4 3.20472668059564e+00 -1.22589067223826e-02 1.87850992535096e-02 1.40000000000000e-01 -4.92676173607873e-04 - 5 3.20606077411088e+00 -1.22242430964435e-02 1.86790149101184e-02 1.50000000000000e-01 -6.14918604572308e-04 - 6 3.20787661013578e+00 -1.21915064405431e-02 1.85791036612255e-02 1.60000000000000e-01 -7.36833668977739e-04 - 7 3.21005557808631e+00 -1.21602223123453e-02 1.84838758357074e-02 1.70000000000000e-01 -8.58435892101191e-04 - 8 3.21245894716580e+00 -1.21298357886632e-02 1.83916145324919e-02 1.80000000000000e-01 -9.79734249987824e-04 - 9 3.21493543162121e+00 -1.20997417264848e-02 1.83004687309548e-02 1.90000000000000e-01 -1.10073166725267e-03 - 10 3.21732997387476e+00 -1.20693198954990e-02 1.82085603424861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 11 3.21949353668785e+00 -1.20779741467514e-02 1.82346824361994e-02 2.00000000000000e-01 -1.22142486620766e-03 - 12 3.22129316973139e+00 -1.20851726789256e-02 1.82564248349311e-02 2.00000000000000e-01 -1.22142486620766e-03 - 13 3.22262118961603e+00 -1.20904847584641e-02 1.82724777118316e-02 2.00000000000000e-01 -1.22142486620766e-03 - 14 3.22340223703211e+00 -1.20936089481284e-02 1.82819221737815e-02 2.00000000000000e-01 -1.22142486620766e-03 - 15 3.22359735089020e+00 -1.20943894035608e-02 1.82842818806205e-02 2.00000000000000e-01 -1.22142486620766e-03 - 16 3.22320479573201e+00 -1.20928191829280e-02 1.82795344738740e-02 2.00000000000000e-01 -1.22142486620766e-03 - 17 3.22225798922225e+00 -1.20890319568890e-02 1.82680867068354e-02 2.00000000000000e-01 -1.22142486620766e-03 - 18 3.22082124425633e+00 -1.20832849770253e-02 1.82507219795008e-02 2.00000000000000e-01 -1.22142486620766e-03 - 19 3.21898406979118e+00 -1.20759362791647e-02 1.82285296273058e-02 2.00000000000000e-01 -1.22142486620766e-03 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 + 1 3.20437138788663e+00 -1.23774855515465e-02 1.91502685723428e-02 1.10000000000000e-01 -1.23774855515465e-04 + 2 3.20383990680667e+00 -1.23353596272267e-02 1.90201371416267e-02 1.20000000000000e-01 -2.47128451787732e-04 + 3 3.20396636491675e+00 -1.22958654596670e-02 1.88985384252790e-02 1.30000000000000e-01 -3.70087106384402e-04 + 4 3.20472668060584e+00 -1.22589067224234e-02 1.87850992536346e-02 1.40000000000000e-01 -4.92676173608635e-04 + 5 3.20606077412683e+00 -1.22242430965073e-02 1.86790149103134e-02 1.50000000000000e-01 -6.14918604573709e-04 + 6 3.20787661015870e+00 -1.21915064406348e-02 1.85791036615050e-02 1.60000000000000e-01 -7.36833668980057e-04 + 7 3.21005557811738e+00 -1.21602223124695e-02 1.84838758360852e-02 1.70000000000000e-01 -8.58435892104752e-04 + 8 3.21245894720608e+00 -1.21298357888243e-02 1.83916145329805e-02 1.80000000000000e-01 -9.79734249992995e-04 + 9 3.21493543167171e+00 -1.20997417266868e-02 1.83004687315658e-02 1.90000000000000e-01 -1.10073166725986e-03 + 10 3.21732997393638e+00 -1.20693198957455e-02 1.82085603432298e-02 2.00000000000000e-01 -1.22142486621732e-03 + 11 3.21949353676140e+00 -1.20779741470456e-02 1.82346824370878e-02 2.00000000000000e-01 -1.22142486621732e-03 + 12 3.22129316981759e+00 -1.20851726792704e-02 1.82564248359729e-02 2.00000000000000e-01 -1.22142486621732e-03 + 13 3.22262118971552e+00 -1.20904847588621e-02 1.82724777130345e-02 2.00000000000000e-01 -1.22142486621732e-03 + 14 3.22340223714544e+00 -1.20936089485818e-02 1.82819221751521e-02 2.00000000000000e-01 -1.22142486621732e-03 + 15 3.22359735101788e+00 -1.20943894040715e-02 1.82842818821647e-02 2.00000000000000e-01 -1.22142486621732e-03 + 16 3.22320479587449e+00 -1.20928191834980e-02 1.82795344755970e-02 2.00000000000000e-01 -1.22142486621732e-03 + 17 3.22225798937996e+00 -1.20890319575198e-02 1.82680867087420e-02 2.00000000000000e-01 -1.22142486621732e-03 + 18 3.22082124442969e+00 -1.20832849777187e-02 1.82507219815954e-02 2.00000000000000e-01 -1.22142486621732e-03 + 19 3.21898406998055e+00 -1.20759362799222e-02 1.82285296295926e-02 2.00000000000000e-01 -1.22142486621732e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force index f26fbcd58..29f1a8c10 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.45777482050594e+00 + 3.25000000000000e+00 -1.45777476148234e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf index 34593c780..f89ed6bc3 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf @@ -6,17 +6,17 @@ 2 0 2.5 0 3 0 - 3.5 0.72888741025297 - 4 0.72888741025297 - 4.5 0.72888741025297 - 5 0.72888741025297 - 5.5 0.72888741025297 - 6 0.72888741025297 - 6.5 0.72888741025297 - 7 0.72888741025297 - 7.5 0.72888741025297 - 8 0.72888741025297 - 8.5 0.72888741025297 - 9 0.72888741025297 - 9.5 0.72888741025297 - 10 0.72888741025297 + 3.5 0.72888738074127 + 4 0.72888738074127 + 4.5 0.72888738074127 + 5 0.72888738074127 + 5.5 0.72888738074127 + 6 0.72888738074127 + 6.5 0.72888738074127 + 7 0.72888738074127 + 7.5 0.72888738074127 + 8 0.72888738074127 + 8.5 0.72888738074127 + 9 0.72888738074127 + 9.5 0.72888738074127 + 10 0.72888738074127 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out index 496158813..2a03c4ebb 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,35 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped index f5fbca6c7..e3d52dfab 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397324438969e+00 + x 3.21397324487089e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } histogram @@ -29,7 +29,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 4.72492117878643e+00 0.00000000000000e+00 0.00000000000000e+00 + 4.72492119104379e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj index 9592912c4..82871cb9e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 - 21 3.21455229130029e+00 -1.20582091652012e-02 1.81750510339676e-02 2.00000000000000e-01 -1.22142486620766e-03 - 22 3.21220058167135e+00 -1.20488023266854e-02 1.81467046884425e-02 2.00000000000000e-01 -1.22142486620766e-03 - 23 3.20991897400811e+00 -1.20396758960324e-02 1.81192244601880e-02 2.00000000000000e-01 -1.22142486620766e-03 - 24 3.20781590778578e+00 -1.20312636311431e-02 1.80939130702584e-02 2.00000000000000e-01 -1.22142486620766e-03 - 25 3.20598263662306e+00 -1.20239305464922e-02 1.80718632233586e-02 2.00000000000000e-01 -1.22142486620766e-03 - 26 3.20448891199500e+00 -1.20179556479800e-02 1.80539072446018e-02 2.00000000000000e-01 -1.22142486620766e-03 - 27 3.20338077760483e+00 -1.20135231104193e-02 1.80405921905723e-02 2.00000000000000e-01 -1.22142486620766e-03 - 28 3.20268040182054e+00 -1.20107216072822e-02 1.80321791909543e-02 2.00000000000000e-01 -1.22142486620766e-03 - 29 3.20238749862618e+00 -1.20095499945047e-02 1.80286613838135e-02 2.00000000000000e-01 -1.22142486620766e-03 - 30 3.20248191768589e+00 -1.20099276707435e-02 1.80297953320614e-02 2.00000000000000e-01 -1.22142486620766e-03 - 31 3.20292702714129e+00 -1.20117081085652e-02 1.80351414606713e-02 2.00000000000000e-01 -1.22142486620766e-03 - 32 3.20367373527010e+00 -1.20146949410804e-02 1.80441118159029e-02 2.00000000000000e-01 -1.22142486620766e-03 - 33 3.20466497756289e+00 -1.20186599102516e-02 1.80560232547861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 34 3.20584045419353e+00 -1.20233618167741e-02 1.80701536721327e-02 2.00000000000000e-01 -1.22142486620766e-03 - 35 3.20714119860834e+00 -1.20285647944334e-02 1.80857963767352e-02 2.00000000000000e-01 -1.22142486620766e-03 - 36 3.20851353235803e+00 -1.20340541294321e-02 1.81023073487628e-02 2.00000000000000e-01 -1.22142486620766e-03 - 37 3.20991208499767e+00 -1.20396483399907e-02 1.81191415188300e-02 2.00000000000000e-01 -1.22142486620766e-03 - 38 3.21130183589808e+00 -1.20452073435923e-02 1.81358774937663e-02 2.00000000000000e-01 -1.22142486620766e-03 - 39 3.21265932746957e+00 -1.20506373098783e-02 1.81522324467788e-02 2.00000000000000e-01 -1.22142486620766e-03 - 40 3.21397324438969e+00 -1.20558929775587e-02 1.81680694357938e-02 2.00000000000000e-01 -1.22142486620766e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 + 21 3.21455229152270e+00 -1.20582091660908e-02 1.81750510366495e-02 2.00000000000000e-01 -1.22142486621732e-03 + 22 3.21220058191067e+00 -1.20488023276427e-02 1.81467046913260e-02 2.00000000000000e-01 -1.22142486621732e-03 + 23 3.20991897426449e+00 -1.20396758970580e-02 1.81192244632749e-02 2.00000000000000e-01 -1.22142486621732e-03 + 24 3.20781590805930e+00 -1.20312636322372e-02 1.80939130735492e-02 2.00000000000000e-01 -1.22142486621732e-03 + 25 3.20598263691365e+00 -1.20239305476546e-02 1.80718632268527e-02 2.00000000000000e-01 -1.22142486621732e-03 + 26 3.20448891230251e+00 -1.20179556492100e-02 1.80539072482974e-02 2.00000000000000e-01 -1.22142486621732e-03 + 27 3.20338077792898e+00 -1.20135231117159e-02 1.80405921944666e-02 2.00000000000000e-01 -1.22142486621732e-03 + 28 3.20268040216098e+00 -1.20107216086439e-02 1.80321791950433e-02 2.00000000000000e-01 -1.22142486621732e-03 + 29 3.20238749898247e+00 -1.20095499959299e-02 1.80286613880924e-02 2.00000000000000e-01 -1.22142486621732e-03 + 30 3.20248191805753e+00 -1.20099276722301e-02 1.80297953365248e-02 2.00000000000000e-01 -1.22142486621732e-03 + 31 3.20292702752774e+00 -1.20117081101110e-02 1.80351414653132e-02 2.00000000000000e-01 -1.22142486621732e-03 + 32 3.20367373567078e+00 -1.20146949426831e-02 1.80441118207169e-02 2.00000000000000e-01 -1.22142486621732e-03 + 33 3.20466497797716e+00 -1.20186599119087e-02 1.80560232597650e-02 2.00000000000000e-01 -1.22142486621732e-03 + 34 3.20584045462068e+00 -1.20233618184827e-02 1.80701536772685e-02 2.00000000000000e-01 -1.22142486621732e-03 + 35 3.20714119904756e+00 -1.20285647961903e-02 1.80857963820184e-02 2.00000000000000e-01 -1.22142486621732e-03 + 36 3.20851353280837e+00 -1.20340541312335e-02 1.81023073541822e-02 2.00000000000000e-01 -1.22142486621732e-03 + 37 3.20991208545797e+00 -1.20396483418319e-02 1.81191415243719e-02 2.00000000000000e-01 -1.22142486621732e-03 + 38 3.21130183636701e+00 -1.20452073454680e-02 1.81358774994146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 39 3.21265932794554e+00 -1.20506373117822e-02 1.81522324525146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 40 3.21397324487089e+00 -1.20558929794836e-02 1.81680694415952e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force index 1c62523ef..f7701bacb 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.72492117878643e+00 + 3.25000000000000e+00 4.72492119104315e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf index d82c0a308..19f56570c 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf @@ -1,11 +1,11 @@ # xi A(xi) - 0 2.3624605893932 - 0.5 2.3624605893932 - 1 2.3624605893932 - 1.5 2.3624605893932 - 2 2.3624605893932 - 2.5 2.3624605893932 - 3 2.3624605893932 + 0 2.3624605955218 + 0.5 2.3624605955218 + 1 2.3624605955218 + 1.5 2.3624605955218 + 2 2.3624605955218 + 2.5 2.3624605955218 + 3 2.3624605955218 3.5 0 4 0 4.5 0 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out index b95774d40..4054ca6f6 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,27 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped index 5ef095f44..4109af1f5 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685457618647e+00 + x 3.21685457639221e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } } diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj index 5eec6dc1f..c0e02c1fa 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788600e+00 -1.23774855515440e-02 1.91502685723351e-02 1.10000000000000e-01 -1.23774855515440e-04 - 2 3.20383990680414e+00 -1.23353596272166e-02 1.90201371415956e-02 1.20000000000000e-01 -2.47128451787606e-04 - 3 3.20396636491103e+00 -1.22958654596441e-02 1.88985384252087e-02 1.30000000000000e-01 -3.70087106384047e-04 - 4 3.20472668059564e+00 -1.22589067223826e-02 1.87850992535096e-02 1.40000000000000e-01 -4.92676173607873e-04 - 5 3.20606077411088e+00 -1.22242430964435e-02 1.86790149101184e-02 1.50000000000000e-01 -6.14918604572308e-04 - 6 3.20787661013578e+00 -1.21915064405431e-02 1.85791036612255e-02 1.60000000000000e-01 -7.36833668977739e-04 - 7 3.21005557808631e+00 -1.21602223123453e-02 1.84838758357074e-02 1.70000000000000e-01 -8.58435892101191e-04 - 8 3.21245894716580e+00 -1.21298357886632e-02 1.83916145324919e-02 1.80000000000000e-01 -9.79734249987824e-04 - 9 3.21493543162121e+00 -1.20997417264848e-02 1.83004687309548e-02 1.90000000000000e-01 -1.10073166725267e-03 - 10 3.21732997387476e+00 -1.20693198954990e-02 1.82085603424861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 11 3.21949353668785e+00 -1.20779741467514e-02 1.82346824361994e-02 2.00000000000000e-01 -1.22142486620766e-03 - 12 3.22129316973139e+00 -1.20851726789256e-02 1.82564248349311e-02 2.00000000000000e-01 -1.22142486620766e-03 - 13 3.22262118961603e+00 -1.20904847584641e-02 1.82724777118316e-02 2.00000000000000e-01 -1.22142486620766e-03 - 14 3.22340223703211e+00 -1.20936089481284e-02 1.82819221737815e-02 2.00000000000000e-01 -1.22142486620766e-03 - 15 3.22359735089020e+00 -1.20943894035608e-02 1.82842818806205e-02 2.00000000000000e-01 -1.22142486620766e-03 - 16 3.22320479573201e+00 -1.20928191829280e-02 1.82795344738740e-02 2.00000000000000e-01 -1.22142486620766e-03 - 17 3.22225798922225e+00 -1.20890319568890e-02 1.82680867068354e-02 2.00000000000000e-01 -1.22142486620766e-03 - 18 3.22082124425633e+00 -1.20832849770253e-02 1.82507219795008e-02 2.00000000000000e-01 -1.22142486620766e-03 - 19 3.21898406979118e+00 -1.20759362791647e-02 1.82285296273058e-02 2.00000000000000e-01 -1.22142486620766e-03 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 + 1 3.20437138788663e+00 -1.23774855515465e-02 1.91502685723428e-02 1.10000000000000e-01 -1.23774855515465e-04 + 2 3.20383990680667e+00 -1.23353596272267e-02 1.90201371416267e-02 1.20000000000000e-01 -2.47128451787732e-04 + 3 3.20396636491675e+00 -1.22958654596670e-02 1.88985384252790e-02 1.30000000000000e-01 -3.70087106384402e-04 + 4 3.20472668060584e+00 -1.22589067224234e-02 1.87850992536346e-02 1.40000000000000e-01 -4.92676173608635e-04 + 5 3.20606077412683e+00 -1.22242430965073e-02 1.86790149103134e-02 1.50000000000000e-01 -6.14918604573709e-04 + 6 3.20787661015870e+00 -1.21915064406348e-02 1.85791036615050e-02 1.60000000000000e-01 -7.36833668980057e-04 + 7 3.21005557811738e+00 -1.21602223124695e-02 1.84838758360852e-02 1.70000000000000e-01 -8.58435892104752e-04 + 8 3.21245894720608e+00 -1.21298357888243e-02 1.83916145329805e-02 1.80000000000000e-01 -9.79734249992995e-04 + 9 3.21493543167171e+00 -1.20997417266868e-02 1.83004687315658e-02 1.90000000000000e-01 -1.10073166725986e-03 + 10 3.21732997393638e+00 -1.20693198957455e-02 1.82085603432298e-02 2.00000000000000e-01 -1.22142486621732e-03 + 11 3.21949353676140e+00 -1.20779741470456e-02 1.82346824370878e-02 2.00000000000000e-01 -1.22142486621732e-03 + 12 3.22129316981759e+00 -1.20851726792704e-02 1.82564248359729e-02 2.00000000000000e-01 -1.22142486621732e-03 + 13 3.22262118971552e+00 -1.20904847588621e-02 1.82724777130345e-02 2.00000000000000e-01 -1.22142486621732e-03 + 14 3.22340223714544e+00 -1.20936089485818e-02 1.82819221751521e-02 2.00000000000000e-01 -1.22142486621732e-03 + 15 3.22359735101788e+00 -1.20943894040715e-02 1.82842818821647e-02 2.00000000000000e-01 -1.22142486621732e-03 + 16 3.22320479587449e+00 -1.20928191834980e-02 1.82795344755970e-02 2.00000000000000e-01 -1.22142486621732e-03 + 17 3.22225798937996e+00 -1.20890319575198e-02 1.82680867087420e-02 2.00000000000000e-01 -1.22142486621732e-03 + 18 3.22082124442969e+00 -1.20832849777187e-02 1.82507219815954e-02 2.00000000000000e-01 -1.22142486621732e-03 + 19 3.21898406998055e+00 -1.20759362799222e-02 1.82285296295926e-02 2.00000000000000e-01 -1.22142486621732e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out index 40e76217d..88405593c 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,32 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped index a27db3dc3..100eebdff 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397324438969e+00 + x 3.21397324487089e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } } diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj index 9592912c4..82871cb9e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 - 21 3.21455229130029e+00 -1.20582091652012e-02 1.81750510339676e-02 2.00000000000000e-01 -1.22142486620766e-03 - 22 3.21220058167135e+00 -1.20488023266854e-02 1.81467046884425e-02 2.00000000000000e-01 -1.22142486620766e-03 - 23 3.20991897400811e+00 -1.20396758960324e-02 1.81192244601880e-02 2.00000000000000e-01 -1.22142486620766e-03 - 24 3.20781590778578e+00 -1.20312636311431e-02 1.80939130702584e-02 2.00000000000000e-01 -1.22142486620766e-03 - 25 3.20598263662306e+00 -1.20239305464922e-02 1.80718632233586e-02 2.00000000000000e-01 -1.22142486620766e-03 - 26 3.20448891199500e+00 -1.20179556479800e-02 1.80539072446018e-02 2.00000000000000e-01 -1.22142486620766e-03 - 27 3.20338077760483e+00 -1.20135231104193e-02 1.80405921905723e-02 2.00000000000000e-01 -1.22142486620766e-03 - 28 3.20268040182054e+00 -1.20107216072822e-02 1.80321791909543e-02 2.00000000000000e-01 -1.22142486620766e-03 - 29 3.20238749862618e+00 -1.20095499945047e-02 1.80286613838135e-02 2.00000000000000e-01 -1.22142486620766e-03 - 30 3.20248191768589e+00 -1.20099276707435e-02 1.80297953320614e-02 2.00000000000000e-01 -1.22142486620766e-03 - 31 3.20292702714129e+00 -1.20117081085652e-02 1.80351414606713e-02 2.00000000000000e-01 -1.22142486620766e-03 - 32 3.20367373527010e+00 -1.20146949410804e-02 1.80441118159029e-02 2.00000000000000e-01 -1.22142486620766e-03 - 33 3.20466497756289e+00 -1.20186599102516e-02 1.80560232547861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 34 3.20584045419353e+00 -1.20233618167741e-02 1.80701536721327e-02 2.00000000000000e-01 -1.22142486620766e-03 - 35 3.20714119860834e+00 -1.20285647944334e-02 1.80857963767352e-02 2.00000000000000e-01 -1.22142486620766e-03 - 36 3.20851353235803e+00 -1.20340541294321e-02 1.81023073487628e-02 2.00000000000000e-01 -1.22142486620766e-03 - 37 3.20991208499767e+00 -1.20396483399907e-02 1.81191415188300e-02 2.00000000000000e-01 -1.22142486620766e-03 - 38 3.21130183589808e+00 -1.20452073435923e-02 1.81358774937663e-02 2.00000000000000e-01 -1.22142486620766e-03 - 39 3.21265932746957e+00 -1.20506373098783e-02 1.81522324467788e-02 2.00000000000000e-01 -1.22142486620766e-03 - 40 3.21397324438969e+00 -1.20558929775587e-02 1.81680694357938e-02 2.00000000000000e-01 -1.22142486620766e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 + 21 3.21455229152270e+00 -1.20582091660908e-02 1.81750510366495e-02 2.00000000000000e-01 -1.22142486621732e-03 + 22 3.21220058191067e+00 -1.20488023276427e-02 1.81467046913260e-02 2.00000000000000e-01 -1.22142486621732e-03 + 23 3.20991897426449e+00 -1.20396758970580e-02 1.81192244632749e-02 2.00000000000000e-01 -1.22142486621732e-03 + 24 3.20781590805930e+00 -1.20312636322372e-02 1.80939130735492e-02 2.00000000000000e-01 -1.22142486621732e-03 + 25 3.20598263691365e+00 -1.20239305476546e-02 1.80718632268527e-02 2.00000000000000e-01 -1.22142486621732e-03 + 26 3.20448891230251e+00 -1.20179556492100e-02 1.80539072482974e-02 2.00000000000000e-01 -1.22142486621732e-03 + 27 3.20338077792898e+00 -1.20135231117159e-02 1.80405921944666e-02 2.00000000000000e-01 -1.22142486621732e-03 + 28 3.20268040216098e+00 -1.20107216086439e-02 1.80321791950433e-02 2.00000000000000e-01 -1.22142486621732e-03 + 29 3.20238749898247e+00 -1.20095499959299e-02 1.80286613880924e-02 2.00000000000000e-01 -1.22142486621732e-03 + 30 3.20248191805753e+00 -1.20099276722301e-02 1.80297953365248e-02 2.00000000000000e-01 -1.22142486621732e-03 + 31 3.20292702752774e+00 -1.20117081101110e-02 1.80351414653132e-02 2.00000000000000e-01 -1.22142486621732e-03 + 32 3.20367373567078e+00 -1.20146949426831e-02 1.80441118207169e-02 2.00000000000000e-01 -1.22142486621732e-03 + 33 3.20466497797716e+00 -1.20186599119087e-02 1.80560232597650e-02 2.00000000000000e-01 -1.22142486621732e-03 + 34 3.20584045462068e+00 -1.20233618184827e-02 1.80701536772685e-02 2.00000000000000e-01 -1.22142486621732e-03 + 35 3.20714119904756e+00 -1.20285647961903e-02 1.80857963820184e-02 2.00000000000000e-01 -1.22142486621732e-03 + 36 3.20851353280837e+00 -1.20340541312335e-02 1.81023073541822e-02 2.00000000000000e-01 -1.22142486621732e-03 + 37 3.20991208545797e+00 -1.20396483418319e-02 1.81191415243719e-02 2.00000000000000e-01 -1.22142486621732e-03 + 38 3.21130183636701e+00 -1.20452073454680e-02 1.81358774994146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 39 3.21265932794554e+00 -1.20506373117822e-02 1.81522324525146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 40 3.21397324487089e+00 -1.20558929794836e-02 1.81680694415952e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out index 3d0f629a2..9b0d8d5c9 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,30 +125,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped index 301b9ace6..3f9b13bdc 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685399817416e+00 + x 3.21685399837991e+00 } restraint { @@ -26,7 +26,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -1.45768708516242e+00 0.00000000000000e+00 0.00000000000000e+00 + -1.45768702613562e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj index 2cd06ea2b..ccbac37f2 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.24221869387334e-02 - 1 3.20437138788600e+00 -1.24174855515440e-02 - 2 3.20383990619069e+00 -1.24153596247627e-02 - 3 3.20396636246577e+00 -1.24158654498631e-02 - 4 3.20472667451135e+00 -1.24189066980454e-02 - 5 3.20606076201392e+00 -1.24242430480557e-02 - 6 3.20787658911377e+00 -1.24315063564551e-02 - 7 3.21005554471991e+00 -1.24402221788797e-02 - 8 3.21245889756338e+00 -1.24498355902535e-02 - 9 3.21493536145531e+00 -1.24597414458212e-02 - 10 3.21732987841907e+00 -1.24693195136763e-02 - 11 3.21949341085340e+00 -1.24779736434136e-02 - 12 3.22129300871542e+00 -1.24851720348617e-02 - 13 3.22262098892565e+00 -1.24904839557026e-02 - 14 3.22340199249676e+00 -1.24936079699870e-02 - 15 3.22359705866319e+00 -1.24943882346527e-02 - 16 3.22320445228234e+00 -1.24928178091294e-02 - 17 3.22225759131848e+00 -1.24890303652739e-02 - 18 3.22082078894448e+00 -1.24832831557779e-02 - 19 3.21898355436871e+00 -1.24759342174748e-02 - 20 3.21685399817416e+00 -1.24674159926967e-02 + 1 3.20437138788663e+00 -1.24174855515465e-02 + 2 3.20383990619321e+00 -1.24153596247728e-02 + 3 3.20396636247149e+00 -1.24158654498859e-02 + 4 3.20472667452156e+00 -1.24189066980862e-02 + 5 3.20606076202988e+00 -1.24242430481195e-02 + 6 3.20787658913670e+00 -1.24315063565468e-02 + 7 3.21005554475098e+00 -1.24402221790039e-02 + 8 3.21245889760366e+00 -1.24498355904146e-02 + 9 3.21493536150581e+00 -1.24597414460232e-02 + 10 3.21732987848069e+00 -1.24693195139228e-02 + 11 3.21949341092696e+00 -1.24779736437079e-02 + 12 3.22129300880163e+00 -1.24851720352065e-02 + 13 3.22262098902515e+00 -1.24904839561006e-02 + 14 3.22340199261010e+00 -1.24936079704404e-02 + 15 3.22359705879087e+00 -1.24943882351635e-02 + 16 3.22320445242483e+00 -1.24928178096993e-02 + 17 3.22225759147620e+00 -1.24890303659048e-02 + 18 3.22082078911784e+00 -1.24832831564713e-02 + 19 3.21898355455808e+00 -1.24759342182323e-02 + 20 3.21685399837991e+00 -1.24674159935196e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force index 640855ec6..1b3e03edb 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.45768708516242e+00 + 3.25000000000000e+00 -1.45768702613609e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf index 270f05c0e..af50b46fb 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf @@ -6,17 +6,17 @@ 2 0 2.5 0 3 0 - 3.5 0.72884354258121 - 4 0.72884354258121 - 4.5 0.72884354258121 - 5 0.72884354258121 - 5.5 0.72884354258121 - 6 0.72884354258121 - 6.5 0.72884354258121 - 7 0.72884354258121 - 7.5 0.72884354258121 - 8 0.72884354258121 - 8.5 0.72884354258121 - 9 0.72884354258121 - 9.5 0.72884354258121 - 10 0.72884354258121 + 3.5 0.72884351306783 + 4 0.72884351306783 + 4.5 0.72884351306783 + 5 0.72884351306783 + 5.5 0.72884351306783 + 6 0.72884351306783 + 6.5 0.72884351306783 + 7 0.72884351306783 + 7.5 0.72884351306783 + 8 0.72884351306783 + 8.5 0.72884351306783 + 9 0.72884351306783 + 9.5 0.72884351306783 + 10 0.72884351306783 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out index 618f855ff..d2b2d5ed3 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,35 +125,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped index 17f669708..4f7e0b7d8 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397114716924e+00 + x 3.21397114765047e+00 } restraint { @@ -26,7 +26,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 4.72514253816199e+00 0.00000000000000e+00 0.00000000000000e+00 + 4.72514255041894e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj index 8924671f5..47d79951b 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685399817416e+00 -1.24674159926967e-02 - 21 3.21455164841394e+00 -1.24582065936557e-02 - 22 3.21219987179556e+00 -1.24487994871822e-02 - 23 3.20991819517487e+00 -1.24396727806995e-02 - 24 3.20781505815938e+00 -1.24312602326375e-02 - 25 3.20598171449351e+00 -1.24239268579740e-02 - 26 3.20448791577891e+00 -1.24179516631157e-02 - 27 3.20337970585434e+00 -1.24135188234173e-02 - 28 3.20267925323760e+00 -1.24107170129504e-02 - 29 3.20238627208178e+00 -1.24095450883271e-02 - 30 3.20248061224166e+00 -1.24099224489666e-02 - 31 3.20292564206961e+00 -1.24117025682784e-02 - 32 3.20367227007056e+00 -1.24146890802823e-02 - 33 3.20466343197421e+00 -1.24186537278969e-02 - 34 3.20583882819824e+00 -1.24233553127930e-02 - 35 3.20713949242506e+00 -1.24285579697002e-02 - 36 3.20851174642574e+00 -1.24340469857030e-02 - 37 3.20991021994729e+00 -1.24396408797892e-02 - 38 3.21129989251817e+00 -1.24451995700727e-02 - 39 3.21265730667037e+00 -1.24506292266815e-02 - 40 3.21397114716924e+00 -1.24558845886769e-02 + 20 3.21685399837991e+00 -1.24674159935196e-02 + 21 3.21455164863636e+00 -1.24582065945454e-02 + 22 3.21219987203489e+00 -1.24487994881395e-02 + 23 3.20991819543127e+00 -1.24396727817251e-02 + 24 3.20781505843291e+00 -1.24312602337316e-02 + 25 3.20598171478412e+00 -1.24239268591365e-02 + 26 3.20448791608644e+00 -1.24179516643458e-02 + 27 3.20337970617851e+00 -1.24135188247141e-02 + 28 3.20267925357806e+00 -1.24107170143122e-02 + 29 3.20238627243809e+00 -1.24095450897524e-02 + 30 3.20248061261333e+00 -1.24099224504533e-02 + 31 3.20292564245608e+00 -1.24117025698243e-02 + 32 3.20367227047127e+00 -1.24146890818851e-02 + 33 3.20466343238851e+00 -1.24186537295541e-02 + 34 3.20583882862542e+00 -1.24233553145017e-02 + 35 3.20713949286431e+00 -1.24285579714572e-02 + 36 3.20851174687611e+00 -1.24340469875045e-02 + 37 3.20991022040763e+00 -1.24396408816305e-02 + 38 3.21129989298713e+00 -1.24451995719485e-02 + 39 3.21265730714637e+00 -1.24506292285855e-02 + 40 3.21397114765047e+00 -1.24558845906019e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force index ac92ca14c..1a0e24a9e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.72514253816199e+00 + 3.25000000000000e+00 4.72514255041972e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf index 9c98fb5a6..8cf383c9e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf @@ -1,11 +1,11 @@ # xi A(xi) - 0 2.362571269081 - 0.5 2.362571269081 - 1 2.362571269081 - 1.5 2.362571269081 - 2 2.362571269081 - 2.5 2.362571269081 - 3 2.362571269081 + 0 2.3625712752095 + 0.5 2.3625712752095 + 1 2.3625712752095 + 1.5 2.3625712752095 + 2 2.3625712752095 + 2.5 2.3625712752095 + 3 2.3625712752095 3.5 0 4 0 4.5 0 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out index 001440131..71d7e2285 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,27 +125,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped index fec1e803e..9eef8b44e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685399817416e+00 + x 3.21685399835649e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj index 2cd06ea2b..5a6aa23cd 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.24221869387334e-02 - 1 3.20437138788600e+00 -1.24174855515440e-02 - 2 3.20383990619069e+00 -1.24153596247627e-02 - 3 3.20396636246577e+00 -1.24158654498631e-02 - 4 3.20472667451135e+00 -1.24189066980454e-02 - 5 3.20606076201392e+00 -1.24242430480557e-02 - 6 3.20787658911377e+00 -1.24315063564551e-02 - 7 3.21005554471991e+00 -1.24402221788797e-02 - 8 3.21245889756338e+00 -1.24498355902535e-02 - 9 3.21493536145531e+00 -1.24597414458212e-02 - 10 3.21732987841907e+00 -1.24693195136763e-02 - 11 3.21949341085340e+00 -1.24779736434136e-02 - 12 3.22129300871542e+00 -1.24851720348617e-02 - 13 3.22262098892565e+00 -1.24904839557026e-02 - 14 3.22340199249676e+00 -1.24936079699870e-02 - 15 3.22359705866319e+00 -1.24943882346527e-02 - 16 3.22320445228234e+00 -1.24928178091294e-02 - 17 3.22225759131848e+00 -1.24890303652739e-02 - 18 3.22082078894448e+00 -1.24832831557779e-02 - 19 3.21898355436871e+00 -1.24759342174748e-02 - 20 3.21685399817416e+00 -1.24674159926967e-02 + 1 3.20437138788661e+00 -1.24174855515465e-02 + 2 3.20383990624489e+00 -1.24153596249795e-02 + 3 3.20396636247331e+00 -1.24158654498932e-02 + 4 3.20472667455914e+00 -1.24189066982366e-02 + 5 3.20606076201901e+00 -1.24242430480760e-02 + 6 3.20787658913293e+00 -1.24315063565317e-02 + 7 3.21005554475517e+00 -1.24402221790207e-02 + 8 3.21245889761578e+00 -1.24498355904631e-02 + 9 3.21493536152545e+00 -1.24597414461018e-02 + 10 3.21732987850678e+00 -1.24693195140271e-02 + 11 3.21949341095784e+00 -1.24779736438313e-02 + 12 3.22129300883514e+00 -1.24851720353406e-02 + 13 3.22262098905883e+00 -1.24904839562353e-02 + 14 3.22340199264132e+00 -1.24936079705653e-02 + 15 3.22359705881703e+00 -1.24943882352681e-02 + 16 3.22320445244359e+00 -1.24928178097743e-02 + 17 3.22225759148518e+00 -1.24890303659407e-02 + 18 3.22082078911634e+00 -1.24832831564654e-02 + 19 3.21898355455034e+00 -1.24759342182014e-02 + 20 3.21685399835649e+00 -1.24674159934260e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out index fcf2bfa9e..f795a4bf4 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,32 +125,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 086f80ad0..ba9e5b167 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397114716924e+00 + x 3.21397114764396e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 8924671f5..d18eb0fa7 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685399817416e+00 -1.24674159926967e-02 - 21 3.21455164841394e+00 -1.24582065936557e-02 - 22 3.21219987179556e+00 -1.24487994871822e-02 - 23 3.20991819517487e+00 -1.24396727806995e-02 - 24 3.20781505815938e+00 -1.24312602326375e-02 - 25 3.20598171449351e+00 -1.24239268579740e-02 - 26 3.20448791577891e+00 -1.24179516631157e-02 - 27 3.20337970585434e+00 -1.24135188234173e-02 - 28 3.20267925323760e+00 -1.24107170129504e-02 - 29 3.20238627208178e+00 -1.24095450883271e-02 - 30 3.20248061224166e+00 -1.24099224489666e-02 - 31 3.20292564206961e+00 -1.24117025682784e-02 - 32 3.20367227007056e+00 -1.24146890802823e-02 - 33 3.20466343197421e+00 -1.24186537278969e-02 - 34 3.20583882819824e+00 -1.24233553127930e-02 - 35 3.20713949242506e+00 -1.24285579697002e-02 - 36 3.20851174642574e+00 -1.24340469857030e-02 - 37 3.20991021994729e+00 -1.24396408797892e-02 - 38 3.21129989251817e+00 -1.24451995700727e-02 - 39 3.21265730667037e+00 -1.24506292266815e-02 - 40 3.21397114716924e+00 -1.24558845886769e-02 + 20 3.21685399835649e+00 -1.24674159934260e-02 + 21 3.21455164860269e+00 -1.24582065944107e-02 + 22 3.21219987199261e+00 -1.24487994879705e-02 + 23 3.20991819538261e+00 -1.24396727815305e-02 + 24 3.20781505838050e+00 -1.24312602335220e-02 + 25 3.20598171473079e+00 -1.24239268589232e-02 + 26 3.20448791603500e+00 -1.24179516641400e-02 + 27 3.20337970613153e+00 -1.24135188245261e-02 + 28 3.20267925353770e+00 -1.24107170141508e-02 + 29 3.20238627240592e+00 -1.24095450896237e-02 + 30 3.20248061259023e+00 -1.24099224503609e-02 + 31 3.20292564244219e+00 -1.24117025697688e-02 + 32 3.20367227046597e+00 -1.24146890818639e-02 + 33 3.20466343239054e+00 -1.24186537295621e-02 + 34 3.20583882863293e+00 -1.24233553145317e-02 + 35 3.20713949287508e+00 -1.24285579715003e-02 + 36 3.20851174688770e+00 -1.24340469875508e-02 + 37 3.20991022041763e+00 -1.24396408816705e-02 + 38 3.21129989299330e+00 -1.24451995719732e-02 + 39 3.21265730714688e+00 -1.24506292285875e-02 + 40 3.21397114764396e+00 -1.24558845905758e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out index eebcebec0..f64f6efa8 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,27 +131,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped index 6d65b453d..4507a2d83 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687020497026e+00 + x 3.21687020515258e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj index a79591894..f58ff8ba4 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 - 1 3.20437138788600e+00 -1.12999118519050e-02 1.75395615193440e-02 - 2 3.20383992333029e+00 -1.01805949485234e-02 1.57994685222408e-02 - 3 3.20396643077894e+00 -9.06358197787450e-03 1.40665271009677e-02 - 4 3.20472684448397e+00 -7.94810072187895e-03 1.23383408369400e-02 - 5 3.20606109997218e+00 -6.83333441993879e-03 1.06123771124364e-02 - 6 3.20787717647453e+00 -5.71849400471313e-03 8.88618850052717e-03 - 7 3.21005647713329e+00 -4.60288358615728e-03 7.15761395530948e-03 - 8 3.21246028397626e+00 -3.48595551805342e-03 5.42494905082458e-03 - 9 3.21493732312431e+00 -2.36735236557448e-03 3.68707712025729e-03 - 10 3.21733254790344e+00 -1.24693301916138e-03 1.94355244284363e-03 - 11 3.21949693102052e+00 -1.24779877240821e-03 1.94625222052929e-03 - 12 3.22129751453369e+00 -1.24851900581348e-03 1.94849963484684e-03 - 13 3.22262660677352e+00 -1.24905064270941e-03 1.95015938506598e-03 - 14 3.22340883978115e+00 -1.24936353591246e-03 1.95113655608461e-03 - 15 3.22360524373761e+00 -1.24944209749504e-03 1.95138194374102e-03 - 16 3.22321407463655e+00 -1.24928562985462e-03 1.95089323120157e-03 - 17 3.22226874199272e+00 -1.24890749679709e-03 1.94971241944496e-03 - 18 3.22083355111441e+00 -1.24833342044576e-03 1.94792041075227e-03 - 19 3.21899800404481e+00 -1.24759920161792e-03 1.94562970984710e-03 - 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 + 1 3.20437138788661e+00 -1.12999118519073e-02 1.75395615193509e-02 + 2 3.20383992338449e+00 -1.01805949487011e-02 1.57994685227925e-02 + 3 3.20396643078647e+00 -9.06358197789650e-03 1.40665271010360e-02 + 4 3.20472684453174e+00 -7.94810072200125e-03 1.23383408373197e-02 + 5 3.20606109997726e+00 -6.83333441994998e-03 1.06123771124712e-02 + 6 3.20787717649369e+00 -5.71849400474838e-03 8.88618850063674e-03 + 7 3.21005647716855e+00 -4.60288358620946e-03 7.15761395547176e-03 + 8 3.21246028402867e+00 -3.48595551811211e-03 5.42494905100725e-03 + 9 3.21493732319445e+00 -2.36735236562779e-03 3.68707712042334e-03 + 10 3.21733254799115e+00 -1.24693301919646e-03 1.94355244295300e-03 + 11 3.21949693112495e+00 -1.24779877244998e-03 1.94625222065960e-03 + 12 3.22129751465341e+00 -1.24851900586136e-03 1.94849963499631e-03 + 13 3.22262660690669e+00 -1.24905064276268e-03 1.95015938523232e-03 + 14 3.22340883992570e+00 -1.24936353597028e-03 1.95113655626521e-03 + 15 3.22360524389145e+00 -1.24944209755658e-03 1.95138194393324e-03 + 16 3.22321407479779e+00 -1.24928562991912e-03 1.95089323140301e-03 + 17 3.22226874215941e+00 -1.24890749686377e-03 1.94971241965315e-03 + 18 3.22083355128627e+00 -1.24833342051451e-03 1.94792041096681e-03 + 19 3.21899800422646e+00 -1.24759920169058e-03 1.94562971007373e-03 + 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out index 01867c7f6..c2057ff6d 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,32 +131,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped index 226b212c1..32715071f 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21402990668451e+00 + x 3.21402990715919e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj index 2753d1963..0970380b3 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 - 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 - 21 3.21456967632931e+00 -1.24582787053172e-03 1.94010885374201e-03 - 22 3.21221977994646e+00 -1.24488791197858e-03 1.93718239173800e-03 - 23 3.20994003840243e+00 -1.24397601536097e-03 1.93434540849171e-03 - 24 3.20783888746925e+00 -1.24313555498770e-03 1.93173251009322e-03 - 25 3.20600757726167e+00 -1.24240303090467e-03 1.92945661400138e-03 - 26 3.20451585575643e+00 -1.24180634230257e-03 1.92760373972862e-03 - 27 3.20340976294734e+00 -1.24136390517894e-03 1.92623043135138e-03 - 28 3.20271146313867e+00 -1.24108458525547e-03 1.92536368469842e-03 - 29 3.20242066576110e+00 -1.24096826630444e-03 1.92500279746831e-03 - 30 3.20251721536965e+00 -1.24100688614786e-03 1.92512261433301e-03 - 31 3.20296447447623e+00 -1.24118578979049e-03 1.92567770597231e-03 - 32 3.20371334530005e+00 -1.24148533812002e-03 1.92660730595873e-03 - 33 3.20470675696420e+00 -1.24188270278568e-03 1.92784080934784e-03 - 34 3.20588440315285e+00 -1.24235376126114e-03 1.92930358514962e-03 - 35 3.20718731103156e+00 -1.24287492441263e-03 1.93092259716711e-03 - 36 3.20856179628928e+00 -1.24342471851571e-03 1.93263128826985e-03 - 37 3.20996248338009e+00 -1.24398499335204e-03 1.93437332960633e-03 - 38 3.21135434749032e+00 -1.24454173899613e-03 1.93610517512938e-03 - 39 3.21271392780555e+00 -1.24508557112222e-03 1.93779759927093e-03 - 40 3.21402990668451e+00 -1.24561196267380e-03 1.93943645194510e-03 + 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 + 21 3.21456967651805e+00 -1.24582787060722e-03 1.94010885397715e-03 + 22 3.21221978014351e+00 -1.24488791205741e-03 1.93718239198331e-03 + 23 3.20994003861018e+00 -1.24397601544407e-03 1.93434540875013e-03 + 24 3.20783888769037e+00 -1.24313555507615e-03 1.93173251036810e-03 + 25 3.20600757749894e+00 -1.24240303099958e-03 1.92945661429617e-03 + 26 3.20451585601250e+00 -1.24180634240500e-03 1.92760374004661e-03 + 27 3.20340976322452e+00 -1.24136390528981e-03 1.92623043169546e-03 + 28 3.20271146343875e+00 -1.24108458537550e-03 1.92536368507084e-03 + 29 3.20242066608521e+00 -1.24096826643409e-03 1.92500279787052e-03 + 30 3.20251721571819e+00 -1.24100688628728e-03 1.92512261476555e-03 + 31 3.20296447484878e+00 -1.24118578993951e-03 1.92567770643472e-03 + 32 3.20371334569543e+00 -1.24148533827817e-03 1.92660730644958e-03 + 33 3.20470675738049e+00 -1.24188270295219e-03 1.92784080986481e-03 + 34 3.20588440358750e+00 -1.24235376143500e-03 1.92930358568961e-03 + 35 3.20718731148154e+00 -1.24287492459262e-03 1.93092259772638e-03 + 36 3.20856179675119e+00 -1.24342471870048e-03 1.93263128884420e-03 + 37 3.20996248385038e+00 -1.24398499354015e-03 1.93437333019136e-03 + 38 3.21135434796541e+00 -1.24454173918616e-03 1.93610517572065e-03 + 39 3.21271392828201e+00 -1.24508557131280e-03 1.93779759986417e-03 + 40 3.21402990715919e+00 -1.24561196286367e-03 1.93943645253637e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out index 151617c95..2cb8b2826 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -127,27 +123,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Histogram colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped index f1f122306..48987f05a 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253464583e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj index a3529376d..2d1d01de3 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 0.00000000000000e+00 + 11 3.21950367383415e+00 0.00000000000000e+00 + 12 3.22130499858006e+00 0.00000000000000e+00 + 13 3.22263479496346e+00 0.00000000000000e+00 + 14 3.22341769665784e+00 0.00000000000000e+00 + 15 3.22361473677138e+00 0.00000000000000e+00 + 16 3.22322417514557e+00 0.00000000000000e+00 + 17 3.22227942564879e+00 0.00000000000000e+00 + 18 3.22084479803044e+00 0.00000000000000e+00 + 19 3.21900979846930e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat index 6ff3132f9..1b0ff42d4 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 6.00000000000000e-01 2.00000000000000e-01 24 0 +# 0.6 0.2 24 0 - 7.00000000000000e-01 0.00000000000000e+00 - 9.00000000000000e-01 0.00000000000000e+00 - 1.10000000000000e+00 0.00000000000000e+00 - 1.30000000000000e+00 0.00000000000000e+00 - 1.50000000000000e+00 0.00000000000000e+00 - 1.70000000000000e+00 0.00000000000000e+00 - 1.90000000000000e+00 0.00000000000000e+00 - 2.10000000000000e+00 0.00000000000000e+00 - 2.30000000000000e+00 0.00000000000000e+00 - 2.50000000000000e+00 0.00000000000000e+00 - 2.70000000000000e+00 0.00000000000000e+00 - 2.90000000000000e+00 0.00000000000000e+00 - 3.10000000000000e+00 0.00000000000000e+00 - 3.30000000000000e+00 2.00000000000000e+01 - 3.50000000000000e+00 0.00000000000000e+00 - 3.70000000000000e+00 0.00000000000000e+00 - 3.90000000000000e+00 0.00000000000000e+00 - 4.10000000000000e+00 0.00000000000000e+00 - 4.30000000000000e+00 0.00000000000000e+00 - 4.50000000000000e+00 0.00000000000000e+00 - 4.70000000000000e+00 0.00000000000000e+00 - 4.90000000000000e+00 0.00000000000000e+00 - 5.10000000000000e+00 0.00000000000000e+00 - 5.30000000000000e+00 0.00000000000000e+00 + 0.7 0 + 0.9 0 + 1.1 0 + 1.3 0 + 1.5 0 + 1.7 0 + 1.9 0 + 2.1 0 + 2.3 0 + 2.5 0 + 2.7 0 + 2.9 0 + 3.1 0 + 3.3 20 + 3.5 0 + 3.7 0 + 3.9 0 + 4.1 0 + 4.3 0 + 4.5 0 + 4.7 0 + 4.9 0 + 5.1 0 + 5.3 0 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out index a72b72b3d..231ed2e71 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -127,32 +123,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Histogram colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting histogram bias "histogram1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped index 7ca010783..35abb4af3 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878547144e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj index 9c9860479..58d908160 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253444007e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 + 21 3.21458253157603e+00 0.00000000000000e+00 + 22 3.21223315254029e+00 0.00000000000000e+00 + 23 3.20995392032979e+00 0.00000000000000e+00 + 24 3.20785326966943e+00 0.00000000000000e+00 + 25 3.20602244845117e+00 0.00000000000000e+00 + 26 3.20453120146139e+00 0.00000000000000e+00 + 27 3.20342556480347e+00 0.00000000000000e+00 + 28 3.20272769852622e+00 0.00000000000000e+00 + 29 3.20243730776714e+00 0.00000000000000e+00 + 30 3.20253423308456e+00 0.00000000000000e+00 + 31 3.20298183362156e+00 0.00000000000000e+00 + 32 3.20373100914607e+00 0.00000000000000e+00 + 33 3.20472468746373e+00 0.00000000000000e+00 + 34 3.20590256221113e+00 0.00000000000000e+00 + 35 3.20720566184671e+00 0.00000000000000e+00 + 36 3.20858030459458e+00 0.00000000000000e+00 + 37 3.20998111854285e+00 0.00000000000000e+00 + 38 3.21137308334418e+00 0.00000000000000e+00 + 39 3.21273274315657e+00 0.00000000000000e+00 + 40 3.21404878547144e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat index 686fae912..2a16dc5f6 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 6.00000000000000e-01 2.00000000000000e-01 24 0 +# 0.6 0.2 24 0 - 7.00000000000000e-01 0.00000000000000e+00 - 9.00000000000000e-01 0.00000000000000e+00 - 1.10000000000000e+00 0.00000000000000e+00 - 1.30000000000000e+00 0.00000000000000e+00 - 1.50000000000000e+00 0.00000000000000e+00 - 1.70000000000000e+00 0.00000000000000e+00 - 1.90000000000000e+00 0.00000000000000e+00 - 2.10000000000000e+00 0.00000000000000e+00 - 2.30000000000000e+00 0.00000000000000e+00 - 2.50000000000000e+00 0.00000000000000e+00 - 2.70000000000000e+00 0.00000000000000e+00 - 2.90000000000000e+00 0.00000000000000e+00 - 3.10000000000000e+00 0.00000000000000e+00 - 3.30000000000000e+00 4.00000000000000e+01 - 3.50000000000000e+00 0.00000000000000e+00 - 3.70000000000000e+00 0.00000000000000e+00 - 3.90000000000000e+00 0.00000000000000e+00 - 4.10000000000000e+00 0.00000000000000e+00 - 4.30000000000000e+00 0.00000000000000e+00 - 4.50000000000000e+00 0.00000000000000e+00 - 4.70000000000000e+00 0.00000000000000e+00 - 4.90000000000000e+00 0.00000000000000e+00 - 5.10000000000000e+00 0.00000000000000e+00 - 5.30000000000000e+00 0.00000000000000e+00 + 0.7 0 + 0.9 0 + 1.1 0 + 1.3 0 + 1.5 0 + 1.7 0 + 1.9 0 + 2.1 0 + 2.3 0 + 2.5 0 + 2.7 0 + 2.9 0 + 3.1 0 + 3.3 40 + 3.5 0 + 3.7 0 + 3.9 0 + 4.1 0 + 4.3 0 + 4.5 0 + 4.7 0 + 4.9 0 + 5.1 0 + 5.3 0 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt b/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out index d6add8f3d..5d2854533 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -124,27 +120,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Histogram colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped index ccbc01c61..a717bee50 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253464583e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj index a3529376d..2d1d01de3 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 0.00000000000000e+00 + 11 3.21950367383415e+00 0.00000000000000e+00 + 12 3.22130499858006e+00 0.00000000000000e+00 + 13 3.22263479496346e+00 0.00000000000000e+00 + 14 3.22341769665784e+00 0.00000000000000e+00 + 15 3.22361473677138e+00 0.00000000000000e+00 + 16 3.22322417514557e+00 0.00000000000000e+00 + 17 3.22227942564879e+00 0.00000000000000e+00 + 18 3.22084479803044e+00 0.00000000000000e+00 + 19 3.21900979846930e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat index 69e912676..09d19a2d1 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat @@ -1,23 +1,23 @@ # 1 -# 0.00000000000000e+00 5.00000000000000e-01 20 0 +# 0 0.5 20 0 - 2.50000000000000e-01 0.00000000000000e+00 - 7.50000000000000e-01 0.00000000000000e+00 - 1.25000000000000e+00 0.00000000000000e+00 - 1.75000000000000e+00 0.00000000000000e+00 - 2.25000000000000e+00 0.00000000000000e+00 - 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 2.00000000000000e+01 - 3.75000000000000e+00 0.00000000000000e+00 - 4.25000000000000e+00 0.00000000000000e+00 - 4.75000000000000e+00 0.00000000000000e+00 - 5.25000000000000e+00 0.00000000000000e+00 - 5.75000000000000e+00 0.00000000000000e+00 - 6.25000000000000e+00 0.00000000000000e+00 - 6.75000000000000e+00 0.00000000000000e+00 - 7.25000000000000e+00 0.00000000000000e+00 - 7.75000000000000e+00 0.00000000000000e+00 - 8.25000000000000e+00 0.00000000000000e+00 - 8.75000000000000e+00 0.00000000000000e+00 - 9.25000000000000e+00 0.00000000000000e+00 - 9.75000000000000e+00 0.00000000000000e+00 + 0.25 0 + 0.75 0 + 1.25 0 + 1.75 0 + 2.25 0 + 2.75 0 + 3.25 20 + 3.75 0 + 4.25 0 + 4.75 0 + 5.25 0 + 5.75 0 + 6.25 0 + 6.75 0 + 7.25 0 + 7.75 0 + 8.25 0 + 8.75 0 + 9.25 0 + 9.75 0 diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out index a9d49b469..091d85f52 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -124,32 +120,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Histogram colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting histogram bias "histogram1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped index 0a3fe4f9c..6df06ad1d 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878547144e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj index 9c9860479..58d908160 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253444007e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 + 21 3.21458253157603e+00 0.00000000000000e+00 + 22 3.21223315254029e+00 0.00000000000000e+00 + 23 3.20995392032979e+00 0.00000000000000e+00 + 24 3.20785326966943e+00 0.00000000000000e+00 + 25 3.20602244845117e+00 0.00000000000000e+00 + 26 3.20453120146139e+00 0.00000000000000e+00 + 27 3.20342556480347e+00 0.00000000000000e+00 + 28 3.20272769852622e+00 0.00000000000000e+00 + 29 3.20243730776714e+00 0.00000000000000e+00 + 30 3.20253423308456e+00 0.00000000000000e+00 + 31 3.20298183362156e+00 0.00000000000000e+00 + 32 3.20373100914607e+00 0.00000000000000e+00 + 33 3.20472468746373e+00 0.00000000000000e+00 + 34 3.20590256221113e+00 0.00000000000000e+00 + 35 3.20720566184671e+00 0.00000000000000e+00 + 36 3.20858030459458e+00 0.00000000000000e+00 + 37 3.20998111854285e+00 0.00000000000000e+00 + 38 3.21137308334418e+00 0.00000000000000e+00 + 39 3.21273274315657e+00 0.00000000000000e+00 + 40 3.21404878547144e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat index fe4ddc2fd..544c0ba33 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat @@ -1,23 +1,23 @@ # 1 -# 0.00000000000000e+00 5.00000000000000e-01 20 0 +# 0 0.5 20 0 - 2.50000000000000e-01 0.00000000000000e+00 - 7.50000000000000e-01 0.00000000000000e+00 - 1.25000000000000e+00 0.00000000000000e+00 - 1.75000000000000e+00 0.00000000000000e+00 - 2.25000000000000e+00 0.00000000000000e+00 - 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.00000000000000e+01 - 3.75000000000000e+00 0.00000000000000e+00 - 4.25000000000000e+00 0.00000000000000e+00 - 4.75000000000000e+00 0.00000000000000e+00 - 5.25000000000000e+00 0.00000000000000e+00 - 5.75000000000000e+00 0.00000000000000e+00 - 6.25000000000000e+00 0.00000000000000e+00 - 6.75000000000000e+00 0.00000000000000e+00 - 7.25000000000000e+00 0.00000000000000e+00 - 7.75000000000000e+00 0.00000000000000e+00 - 8.25000000000000e+00 0.00000000000000e+00 - 8.75000000000000e+00 0.00000000000000e+00 - 9.25000000000000e+00 0.00000000000000e+00 - 9.75000000000000e+00 0.00000000000000e+00 + 0.25 0 + 0.75 0 + 1.25 0 + 1.75 0 + 2.25 0 + 2.75 0 + 3.25 40 + 3.75 0 + 4.25 0 + 4.75 0 + 5.25 0 + 5.75 0 + 6.25 0 + 6.75 0 + 7.25 0 + 7.75 0 + 8.25 0 + 8.75 0 + 9.25 0 + 9.75 0 diff --git a/namd/tests/library/000_distance-grid_histogram/namd-version.txt b/namd/tests/library/000_distance-grid_histogram/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_histogram/namd-version.txt +++ b/namd/tests/library/000_distance-grid_histogram/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj index dd7940783..6a779c875 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj @@ -1,2 +1,2 @@ - 10 3.21733851230199e+00 7.50000000000000e-01 1.00000000000000e-02 - 20 3.21688297506098e+00 7.50000000000000e-01 1.00000000000000e-02 + 10 3.21733851236362e+00 7.50000000000000e-01 1.00000000000000e-02 + 20 3.21688297526674e+00 7.50000000000000e-01 1.00000000000000e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out index 2c566b0cb..2404d2e37 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -141,26 +141,10 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped index e88987e94..908bf7241 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688297506098e+00 + x 3.21688297526674e+00 } metadynamics { @@ -22,11 +22,11 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 7.98796537769059e-06 8.94022105552033e-05 6.41564889800856e-04 - 2.95197835228273e-03 8.70895398689607e-03 1.64740003814156e-02 - 1.99807780437246e-02 1.55383881988653e-02 7.74782472299776e-03 - 2.47704476502647e-03 5.07771324547938e-04 6.67394672185917e-05 - 5.62441745710086e-06 3.03915330422993e-07 0.00000000000000e+00 + 7.98796537205394e-06 8.94022105027543e-05 6.41564889500790e-04 + 2.95197835125314e-03 8.70895398489406e-03 1.64740003795870e-02 + 1.99807780438813e-02 1.55383882008336e-02 7.74782472489960e-03 + 2.47704476592871e-03 5.07771324793184e-04 6.67394672587493e-05 + 5.62441746115269e-06 3.03915330677999e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients @@ -37,23 +37,23 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 4.21354234780051e-05 3.92115793470621e-04 2.24360723751294e-03 - 7.69934001123311e-03 1.49733727825032e-02 1.36803233064121e-02 - -1.16827176873810e-03 -1.47204255431243e-02 -1.42269229833801e-02 - -6.75028436894966e-03 -1.83509826691184e-03 -3.00522069155109e-04 - -3.03257488096648e-05 -1.90879841183335e-06 0.00000000000000e+00 + 4.21354234501736e-05 3.92115793261853e-04 2.24360723661620e-03 + 7.69934000924979e-03 1.49733727811320e-02 1.36803233088098e-02 + -1.16827176399835e-03 -1.47204255412967e-02 -1.42269229850317e-02 + -6.75028437082004e-03 -1.83509826767759e-03 -3.00522069320091e-04 + -3.03257488301764e-05 -1.90879841336284e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 hill { step 10 weight 1.00000000000000e-02 - centers 3.21733851230199e+00 + centers 3.21733851236362e+00 widths 1.50000000000000e+00 } hill { step 20 weight 1.00000000000000e-02 - centers 3.21688297506098e+00 + centers 3.21688297526674e+00 widths 1.50000000000000e+00 } } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj index dedaa4935..5824ebe05 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 5.80098335424304e-04 - 11 3.21950368266856e+00 5.80098335424304e-04 - 12 3.22130502510728e+00 5.80098335424304e-04 - 13 3.22263484775629e+00 5.80098335424304e-04 - 14 3.22341778396123e+00 5.80098335424304e-04 - 15 3.22361486641320e+00 5.80098335424304e-04 - 16 3.22322435446593e+00 5.80098335424304e-04 - 17 3.22227966145053e+00 5.80098335424304e-04 - 18 3.22084509655195e+00 5.80098335424304e-04 - 19 3.21901016537961e+00 5.80098335424304e-04 - 20 3.21688297506098e+00 1.16827176873810e-03 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 5.80098334331777e-04 + 11 3.21950368274213e+00 5.80098334331777e-04 + 12 3.22130502519349e+00 5.80098334331777e-04 + 13 3.22263484785580e+00 5.80098334331777e-04 + 14 3.22341778407457e+00 5.80098334331777e-04 + 15 3.22361486654089e+00 5.80098334331777e-04 + 16 3.22322435460843e+00 5.80098334331777e-04 + 17 3.22227966160826e+00 5.80098334331777e-04 + 18 3.22084509672532e+00 5.80098334331777e-04 + 19 3.21901016556900e+00 5.80098334331777e-04 + 20 3.21688297526674e+00 1.16827176399835e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf index 9d98a1715..9da766ced 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.99727900783469e-02 - 7.50000000000000e-01 1.98913758331694e-02 - 1.25000000000000e+00 1.93392131539237e-02 - 1.75000000000000e+00 1.70287996914418e-02 - 2.25000000000000e+00 1.12718240568285e-02 - 2.75000000000000e+00 3.50677766230894e-03 + 2.50000000000000e-01 1.99727900785093e-02 + 7.50000000000000e-01 1.98913758333786e-02 + 1.25000000000000e+00 1.93392131543806e-02 + 1.75000000000000e+00 1.70287996926282e-02 + 2.25000000000000e+00 1.12718240589873e-02 + 2.75000000000000e+00 3.50677766429439e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 4.44238984485923e-03 - 4.25000000000000e+00 1.22329533207268e-02 - 4.75000000000000e+00 1.75037332786981e-02 - 5.25000000000000e+00 1.94730067191766e-02 - 5.75000000000000e+00 1.99140385765060e-02 - 6.25000000000000e+00 1.99751536262675e-02 - 6.75000000000000e+00 1.99804741283941e-02 - 7.25000000000000e+00 1.99807780437246e-02 - 7.75000000000000e+00 1.99807780437246e-02 - 8.25000000000000e+00 1.99807780437246e-02 - 8.75000000000000e+00 1.99807780437246e-02 - 9.25000000000000e+00 1.99807780437246e-02 - 9.75000000000000e+00 1.99807780437246e-02 + 3.75000000000000e+00 4.44238984304775e-03 + 4.25000000000000e+00 1.22329533189817e-02 + 4.75000000000000e+00 1.75037332779526e-02 + 5.25000000000000e+00 1.94730067190882e-02 + 5.75000000000000e+00 1.99140385766226e-02 + 6.25000000000000e+00 1.99751536264202e-02 + 6.75000000000000e+00 1.99804741285507e-02 + 7.25000000000000e+00 1.99807780438813e-02 + 7.75000000000000e+00 1.99807780438813e-02 + 8.25000000000000e+00 1.99807780438813e-02 + 8.75000000000000e+00 1.99807780438813e-02 + 9.25000000000000e+00 1.99807780438813e-02 + 9.75000000000000e+00 1.99807780438813e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj index bf802816e..d357d6751 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj @@ -1,2 +1,2 @@ - 30 3.20253726770953e+00 2.00000000000000e+00 1.00000000000000e-14 - 40 3.21405662873448e+00 2.00000000000000e+00 1.00000000000000e-14 + 30 3.20253726808121e+00 2.00000000000000e+00 1.00000000000000e-14 + 40 3.21405662921571e+00 2.00000000000000e+00 1.00000000000000e-14 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out index 25e53b613..3b6b317a8 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.restart.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -139,28 +139,12 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: This state file/stream contains explicit hills. colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 2 additional explicit hills. +colvars: Read 2 hills. colvars: Rebinning the energy and forces grids from 2 hills (this may take a while)... colvars: 0.00% done. colvars: 100.00% done. @@ -170,7 +154,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped index f3ae76614..23fdc9ae2 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405662873448e+00 + x 3.21405662921571e+00 } metadynamics { @@ -22,25 +22,25 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 3.72168800988033e-04 7.62454155222791e-04 1.45480353465099e-03 - 2.58530507810761e-03 4.27893895388223e-03 6.59594797702447e-03 - 9.46967757657534e-03 1.26622243130771e-02 1.57689092191951e-02 - 1.82898499605756e-02 1.97576583941589e-02 1.98782268062245e-02 - 1.86267313298802e-02 1.62559553963231e-02 1.32131141593403e-02 - 1.00026417641938e-02 7.05246732783860e-03 4.63110140045852e-03 - 2.83233316189597e-03 1.61332262367653e-03 8.55884084142272e-04 - 4.22888150792485e-04 1.94604519590907e-04 8.34059758230608e-05 - 3.32934080094220e-05 1.23775924288879e-05 4.28579055102484e-06 - 1.38210980597084e-06 4.15117455025274e-07 3.64063576668077e-15 - 3.01191095861938e-15 2.46697141353276e-15 2.00052137786274e-15 - 1.60612509381090e-15 1.27665229269180e-15 1.00466895561231e-15 - 7.82763248881975e-16 6.03802577686049e-16 4.61122792884764e-16 - 3.48654526190564e-16 2.60994356544342e-16 1.93430082535114e-16 - 1.41929936582350e-16 1.03105324043511e-16 7.41558240772166e-17 - 5.28039645304659e-17 3.72258726281876e-17 2.59824640226949e-17 - 1.79544817286721e-17 1.22835105542170e-17 8.32011299530226e-18 - 5.57947115673577e-18 3.70436643439502e-18 2.43496058203075e-18 - 1.58462688892833e-18 + 3.72168800800684e-04 7.62454154875249e-04 1.45480353405707e-03 + 2.58530507717515e-03 4.27893895254244e-03 6.59594797527291e-03 + 9.46967757451101e-03 1.26622243109190e-02 1.57689092172573e-02 + 1.82898499591976e-02 1.97576583936095e-02 1.98782268066167e-02 + 1.86267313311331e-02 1.62559553981891e-02 1.32131141614850e-02 + 1.00026417662927e-02 7.05246732965355e-03 4.63110140187036e-03 + 2.83233316289399e-03 1.61332262432165e-03 8.55884084525168e-04 + 4.22888151001758e-04 1.94604519696452e-04 8.34059758722572e-05 + 3.32934080306407e-05 1.23775924373641e-05 4.28579055416322e-06 + 1.38210980704854e-06 4.15117455368664e-07 3.64063576811435e-15 + 3.01191095986970e-15 2.46697141460954e-15 2.00052137877865e-15 + 1.60612509458054e-15 1.27665229333083e-15 1.00466895613666e-15 + 7.82763249307229e-16 6.03802578026978e-16 4.61122793154982e-16 + 3.48654526402326e-16 2.60994356708439e-16 1.93430082660864e-16 + 1.41929936677652e-16 1.03105324114947e-16 7.41558241301806e-17 + 5.28039645693086e-17 3.72258726563668e-17 2.59824640429186e-17 + 1.79544817430310e-17 1.22835105643033e-17 8.32011300231200e-18 + 5.57947116155582e-18 3.70436643767441e-18 2.43496058423845e-18 + 1.58462689039896e-18 hills_energy_gradients grid_parameters { n_colvars 1 @@ -49,47 +49,47 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 1.40075110105780e-03 2.59859363148452e-03 4.44099297579070e-03 - 6.97278888521528e-03 1.00192639073998e-02 1.30993843027639e-02 - 1.54395417665452e-02 1.61426066779483e-02 1.44964828823443e-02 - 1.03109464673752e-02 4.11348240807316e-03 -2.92922895099231e-03 - -9.36764744456861e-03 -1.39552453121627e-02 -1.60410539906239e-02 - -1.56999540158312e-02 -1.35769607030841e-02 -1.05621149930753e-02 - -7.46673071770275e-03 -4.82674321766440e-03 -2.86495075206286e-03 - -1.56591840826989e-03 -7.89796490686730e-04 -3.68156057181895e-04 - -1.58795588263100e-04 -6.34368443091680e-05 -2.34890958399494e-05 - -8.06633422230724e-06 -2.57032529393441e-06 -3.36000867643381e-15 - -2.93034146466045e-15 -2.52350768675858e-15 -2.14639312464089e-15 - -1.80354428877811e-15 -1.49740594580019e-15 -1.22862535955312e-15 - -9.96391242316789e-16 -7.98779361165857e-16 -6.33082111844533e-16 - -4.96105393301648e-16 -3.84422123590172e-16 -2.94577212993405e-16 - -2.23243402354083e-16 -1.67330898960416e-16 -1.24056159737195e-16 - -9.09765563814143e-17 -6.59981612906651e-17 -4.73637102529462e-17 - -3.36271325125033e-17 -2.36200830178057e-17 -1.64148291477159e-17 - -1.12867623434892e-17 -7.67881293566128e-18 -5.16919768249119e-18 - -3.44324803635265e-18 + 1.40075110044120e-03 2.59859363048141e-03 4.44099297432371e-03 + 6.97278888331524e-03 1.00192639052802e-02 1.30993843008538e-02 + 1.54395417654311e-02 1.61426066782075e-02 1.44964828843116e-02 + 1.03109464709461e-02 4.11348241265501e-03 -2.92922894632563e-03 + -9.36764744077205e-03 -1.39552453099017e-02 -1.60410539900880e-02 + -1.56999540167490e-02 -1.35769607049026e-02 -1.05621149951951e-02 + -7.46673071966103e-03 -4.82674321921130e-03 -2.86495075314130e-03 + -1.56591840894438e-03 -7.89796491068873e-04 -3.68156057379246e-04 + -1.58795588356400e-04 -6.34368443496714e-05 -2.34890958561326e-05 + -8.06633422826891e-06 -2.57032529596210e-06 -3.36000867736823e-15 + -2.93034146555533e-15 -2.52350768759663e-15 -2.14639312540996e-15 + -1.80354428947083e-15 -1.49740594641337e-15 -1.22862536008705e-15 + -9.96391242774491e-16 -7.98779361552378e-16 -6.33082112166259e-16 + -4.96105393565718e-16 -3.84422123803986e-16 -2.94577213164243e-16 + -2.23243402488820e-16 -1.67330899065332e-16 -1.24056159817874e-16 + -9.09765564426929e-17 -6.59981613366451e-17 -4.73637102870346e-17 + -3.36271325374767e-17 -2.36200830358874e-17 -1.64148291606559e-17 + -1.12867623526432e-17 -7.67881294206302e-18 -5.16919768691752e-18 + -3.44324803937870e-18 hill { step 10 weight 1.00000000000000e-02 - centers 3.21733851230199e+00 + centers 3.21733851236362e+00 widths 1.50000000000000e+00 } hill { step 20 weight 1.00000000000000e-02 - centers 3.21688297506098e+00 + centers 3.21688297526674e+00 widths 1.50000000000000e+00 } hill { step 30 weight 1.00000000000000e-14 - centers 3.20253726770953e+00 + centers 3.20253726808121e+00 widths 4.00000000000000e+00 } hill { step 40 weight 1.00000000000000e-14 - centers 3.21405662873448e+00 + centers 3.21405662921571e+00 widths 4.00000000000000e+00 } } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj index b775fab7c..05c21c5c1 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688297506098e+00 2.92922895099185e-03 - 21 3.21458307267896e+00 2.92922895099185e-03 - 22 3.21223383426493e+00 2.92922895099185e-03 - 23 3.20995478139232e+00 2.92922895099185e-03 - 24 3.20785434718462e+00 2.92922895099185e-03 - 25 3.20602377760800e+00 2.92922895099185e-03 - 26 3.20453281527191e+00 2.92922895099185e-03 - 27 3.20342749392972e+00 2.92922895099185e-03 - 28 3.20272997118845e+00 2.92922895099185e-03 - 29 3.20243994972914e+00 2.92922895099185e-03 - 30 3.20253726770953e+00 2.92922895099210e-03 - 31 3.20298528199370e+00 2.92922895099210e-03 - 32 3.20373489024518e+00 2.92922895099210e-03 - 33 3.20472901837284e+00 2.92922895099210e-03 - 34 3.20590735833942e+00 2.92922895099210e-03 - 35 3.20721093715982e+00 2.92922895099210e-03 - 36 3.20858607182116e+00 2.92922895099210e-03 - 37 3.20998738936608e+00 2.92922895099210e-03 - 38 3.21137986855483e+00 2.92922895099210e-03 - 39 3.21274005275856e+00 2.92922895099210e-03 - 40 3.21405662873448e+00 2.92922895099231e-03 + 20 3.21688297526674e+00 2.92922894632517e-03 + 21 3.21458307290139e+00 2.92922894632517e-03 + 22 3.21223383450427e+00 2.92922894632517e-03 + 23 3.20995478164873e+00 2.92922894632517e-03 + 24 3.20785434745816e+00 2.92922894632517e-03 + 25 3.20602377789862e+00 2.92922894632517e-03 + 26 3.20453281557945e+00 2.92922894632517e-03 + 27 3.20342749425391e+00 2.92922894632517e-03 + 28 3.20272997152892e+00 2.92922894632517e-03 + 29 3.20243995008546e+00 2.92922894632517e-03 + 30 3.20253726808121e+00 2.92922894632541e-03 + 31 3.20298528238019e+00 2.92922894632541e-03 + 32 3.20373489064589e+00 2.92922894632541e-03 + 33 3.20472901878714e+00 2.92922894632541e-03 + 34 3.20590735876660e+00 2.92922894632541e-03 + 35 3.20721093759908e+00 2.92922894632541e-03 + 36 3.20858607227153e+00 2.92922894632541e-03 + 37 3.20998738982642e+00 2.92922894632541e-03 + 38 3.21137986902379e+00 2.92922894632541e-03 + 39 3.21274005323456e+00 2.92922894632541e-03 + 40 3.21405662921571e+00 2.92922894632563e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf index 775f05da1..35289f537 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf @@ -1,58 +1,58 @@ # 1 # 1.00000000000000e+00 2.00000000000000e-01 55 0 - 1.10000000000000e+00 1.95060580052365e-02 - 1.30000000000000e+00 1.91157726510017e-02 - 1.50000000000000e+00 1.84234232715735e-02 - 1.70000000000000e+00 1.72929217281169e-02 - 1.90000000000000e+00 1.55992878523423e-02 - 2.10000000000000e+00 1.32822788292000e-02 - 2.30000000000000e+00 1.04085492296491e-02 - 2.50000000000000e+00 7.21600249314737e-03 - 2.70000000000000e+00 4.10931758702936e-03 - 2.90000000000000e+00 1.58837684564884e-03 - 3.10000000000000e+00 1.20568412065550e-04 + 1.10000000000000e+00 1.95060580058160e-02 + 1.30000000000000e+00 1.91157726517414e-02 + 1.50000000000000e+00 1.84234232725596e-02 + 1.70000000000000e+00 1.72929217294415e-02 + 1.90000000000000e+00 1.55992878540742e-02 + 2.10000000000000e+00 1.32822788313438e-02 + 2.30000000000000e+00 1.04085492321057e-02 + 2.50000000000000e+00 7.21600249569771e-03 + 2.70000000000000e+00 4.10931758935941e-03 + 2.90000000000000e+00 1.58837684741911e-03 + 3.10000000000000e+00 1.20568413007130e-04 3.30000000000000e+00 -0.00000000000000e+00 - 3.50000000000000e+00 1.25149547634431e-03 - 3.70000000000000e+00 3.62227140990143e-03 - 3.90000000000000e+00 6.66511264688419e-03 - 4.10000000000000e+00 9.87558504203071e-03 - 4.30000000000000e+00 1.28257594783859e-02 - 4.50000000000000e+00 1.52471254057660e-02 - 4.70000000000000e+00 1.70458936443285e-02 - 4.90000000000000e+00 1.82649041825480e-02 - 5.10000000000000e+00 1.90223427220822e-02 - 5.30000000000000e+00 1.94553386554320e-02 - 5.50000000000000e+00 1.96836222866336e-02 - 5.70000000000000e+00 1.97948208304014e-02 - 5.90000000000000e+00 1.98449333982151e-02 - 6.10000000000000e+00 1.98658492137956e-02 - 6.30000000000000e+00 1.98739410156735e-02 - 6.50000000000000e+00 1.98768446964185e-02 - 6.70000000000000e+00 1.98778116887695e-02 - 6.90000000000000e+00 1.98782268062208e-02 - 7.10000000000000e+00 1.98782268062215e-02 - 7.30000000000000e+00 1.98782268062220e-02 - 7.50000000000000e+00 1.98782268062225e-02 - 7.70000000000000e+00 1.98782268062229e-02 - 7.90000000000000e+00 1.98782268062232e-02 - 8.10000000000000e+00 1.98782268062235e-02 - 8.30000000000000e+00 1.98782268062237e-02 - 8.50000000000000e+00 1.98782268062239e-02 - 8.70000000000000e+00 1.98782268062240e-02 - 8.90000000000000e+00 1.98782268062241e-02 - 9.10000000000000e+00 1.98782268062242e-02 - 9.30000000000000e+00 1.98782268062243e-02 - 9.50000000000000e+00 1.98782268062243e-02 - 9.70000000000000e+00 1.98782268062244e-02 - 9.90000000000000e+00 1.98782268062244e-02 - 1.01000000000000e+01 1.98782268062244e-02 - 1.03000000000000e+01 1.98782268062244e-02 - 1.05000000000000e+01 1.98782268062245e-02 - 1.07000000000000e+01 1.98782268062245e-02 - 1.09000000000000e+01 1.98782268062245e-02 - 1.11000000000000e+01 1.98782268062245e-02 - 1.13000000000000e+01 1.98782268062245e-02 - 1.15000000000000e+01 1.98782268062245e-02 - 1.17000000000000e+01 1.98782268062245e-02 - 1.19000000000000e+01 1.98782268062245e-02 + 3.50000000000000e+00 1.25149547548363e-03 + 3.70000000000000e+00 3.62227140842760e-03 + 3.90000000000000e+00 6.66511264513171e-03 + 4.10000000000000e+00 9.87558504032401e-03 + 4.30000000000000e+00 1.28257594769631e-02 + 4.50000000000000e+00 1.52471254047463e-02 + 4.70000000000000e+00 1.70458936437227e-02 + 4.90000000000000e+00 1.82649041822950e-02 + 5.10000000000000e+00 1.90223427220915e-02 + 5.30000000000000e+00 1.94553386556149e-02 + 5.50000000000000e+00 1.96836222869202e-02 + 5.70000000000000e+00 1.97948208307444e-02 + 5.90000000000000e+00 1.98449333985860e-02 + 6.10000000000000e+00 1.98658492141793e-02 + 6.30000000000000e+00 1.98739410160625e-02 + 6.50000000000000e+00 1.98768446968096e-02 + 6.70000000000000e+00 1.98778116891613e-02 + 6.90000000000000e+00 1.98782268066130e-02 + 7.10000000000000e+00 1.98782268066137e-02 + 7.30000000000000e+00 1.98782268066142e-02 + 7.50000000000000e+00 1.98782268066147e-02 + 7.70000000000000e+00 1.98782268066151e-02 + 7.90000000000000e+00 1.98782268066154e-02 + 8.10000000000000e+00 1.98782268066157e-02 + 8.30000000000000e+00 1.98782268066159e-02 + 8.50000000000000e+00 1.98782268066161e-02 + 8.70000000000000e+00 1.98782268066162e-02 + 8.90000000000000e+00 1.98782268066163e-02 + 9.10000000000000e+00 1.98782268066164e-02 + 9.30000000000000e+00 1.98782268066165e-02 + 9.50000000000000e+00 1.98782268066165e-02 + 9.70000000000000e+00 1.98782268066166e-02 + 9.90000000000000e+00 1.98782268066166e-02 + 1.01000000000000e+01 1.98782268066166e-02 + 1.03000000000000e+01 1.98782268066166e-02 + 1.05000000000000e+01 1.98782268066167e-02 + 1.07000000000000e+01 1.98782268066167e-02 + 1.09000000000000e+01 1.98782268066167e-02 + 1.11000000000000e+01 1.98782268066167e-02 + 1.13000000000000e+01 1.98782268066167e-02 + 1.15000000000000e+01 1.98782268066167e-02 + 1.17000000000000e+01 1.98782268066167e-02 + 1.19000000000000e+01 1.98782268066167e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt index 157cac038..49dcaf892 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2021-03-09. +colvars: Using NAMD interface, version "2021-03-02". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out index 25ec7c329..3b35ba0c9 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -139,26 +139,10 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped index a9f5cad12..24be7d8f2 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688254064136e+00 + x 3.21688254084712e+00 } metadynamics { @@ -21,13 +21,13 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 6.65430605259840e-04 9.34557513055957e-04 1.23300798770362e-03 - 1.52820755424302e-03 1.77932544550601e-03 1.94618908285837e-03 - 1.99972957592583e-03 1.93025240787750e-03 1.75030418482405e-03 - 1.49097223014520e-03 1.19311463635811e-03 8.96915206801889e-04 - 6.33398742101442e-04 4.20203437622546e-04 2.61877749852370e-04 - 1.53318370754311e-04 8.43230653239168e-05 4.35667507513804e-05 - 2.11456262451310e-05 9.64145386575516e-06 + 6.65430605193845e-04 9.34557512978891e-04 1.23300798762255e-03 + 1.52820755416809e-03 1.77932544544850e-03 1.94618908282799e-03 + 1.99972957592804e-03 1.93025240791188e-03 1.75030418488448e-03 + 1.49097223022159e-03 1.19311463643918e-03 8.96915206877818e-04 + 6.33398742165647e-04 4.20203437672161e-04 2.61877749887666e-04 + 1.53318370777537e-04 8.43230653380996e-05 4.35667507594360e-05 + 2.11456262493941e-05 9.64145386786002e-06 hills_energy_gradients grid_parameters { n_colvars 1 @@ -36,12 +36,12 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 4.93601531961674e-04 5.76414162023237e-04 6.06365740079512e-04 - 5.60512340082354e-04 4.30201086501742e-04 2.27271348823597e-04 - -1.64425130241460e-05 -2.57152794011114e-04 -4.51967686121292e-04 - -5.71373901803506e-04 -6.06367538361871e-04 -5.67946764108878e-04 - -4.80257088125742e-04 -3.71133070556632e-04 -2.64031001751807e-04 - -1.73743804964989e-04 -1.06097165582428e-04 -6.02625033739621e-05 - -3.18923060819328e-05 -1.57466379126574e-05 + 4.93601531934965e-04 5.76414162006946e-04 6.06365740080861e-04 + 5.60512340105952e-04 4.30201086547313e-04 2.27271348885101e-04 + -1.64425129573257e-05 -2.57152793951181e-04 -4.51967686078399e-04 + -5.71373901782952e-04 -6.06367538363199e-04 -5.67946764126985e-04 + -4.80257088153256e-04 -3.71133070586411e-04 -2.64031001778642e-04 + -1.73743804986186e-04 -1.06097165597456e-04 -6.02625033836491e-05 + -3.18923060876561e-05 -1.57466379157729e-05 } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj index 0738ec8f1..372662fa9 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 8.16428317253262e-06 - 11 3.21950367388596e+00 8.16428317253262e-06 - 12 3.22130499886840e+00 8.16428317253262e-06 - 13 3.22263479560837e+00 8.16428317253262e-06 - 14 3.22341769777479e+00 8.16428317253262e-06 - 15 3.22361473847006e+00 8.16428317253262e-06 - 16 3.22322417752882e+00 8.16428317253262e-06 - 17 3.22227942881194e+00 8.16428317253262e-06 - 18 3.22084480206089e+00 8.16428317253262e-06 - 19 3.21900980344646e+00 8.16428317253262e-06 - 20 3.21688254064136e+00 1.64425130241460e-05 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 8.16428315713133e-06 + 11 3.21950367395952e+00 8.16428315713133e-06 + 12 3.22130499895462e+00 8.16428315713133e-06 + 13 3.22263479570787e+00 8.16428315713133e-06 + 14 3.22341769788814e+00 8.16428315713133e-06 + 15 3.22361473859775e+00 8.16428315713133e-06 + 16 3.22322417767132e+00 8.16428315713133e-06 + 17 3.22227942896967e+00 8.16428315713133e-06 + 18 3.22084480223426e+00 8.16428315713133e-06 + 19 3.21900980363585e+00 8.16428315713133e-06 + 20 3.21688254084712e+00 1.64425129573257e-05 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf index bcac69118..67c5801c2 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.33429897066599e-03 - 7.50000000000000e-01 1.06517206286987e-03 - 1.25000000000000e+00 7.66721588222210e-04 - 1.75000000000000e+00 4.71522021682808e-04 - 2.25000000000000e+00 2.20404130419819e-04 - 2.75000000000000e+00 5.35404930674629e-05 + 2.50000000000000e-01 1.33429897073419e-03 + 7.50000000000000e-01 1.06517206294915e-03 + 1.25000000000000e+00 7.66721588305484e-04 + 1.75000000000000e+00 4.71522021759950e-04 + 2.25000000000000e+00 2.20404130479536e-04 + 2.75000000000000e+00 5.35404931000470e-05 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 6.94771680483336e-05 - 4.25000000000000e+00 2.49425391101783e-04 - 4.75000000000000e+00 5.08757345780628e-04 - 5.25000000000000e+00 8.06614939567721e-04 - 5.75000000000000e+00 1.10281436912394e-03 - 6.25000000000000e+00 1.36633083382439e-03 - 6.75000000000000e+00 1.57952613830328e-03 - 7.25000000000000e+00 1.73785182607346e-03 - 7.75000000000000e+00 1.84641120517152e-03 - 8.25000000000000e+00 1.91540651060191e-03 - 8.75000000000000e+00 1.95616282517445e-03 - 9.25000000000000e+00 1.97858394968070e-03 - 9.75000000000000e+00 1.99008812206007e-03 + 3.75000000000000e+00 6.94771680161525e-05 + 4.25000000000000e+00 2.49425391043558e-04 + 4.75000000000000e+00 5.08757345706442e-04 + 5.25000000000000e+00 8.06614939488859e-04 + 5.75000000000000e+00 1.10281436905022e-03 + 6.25000000000000e+00 1.36633083376239e-03 + 6.75000000000000e+00 1.57952613825587e-03 + 7.25000000000000e+00 1.73785182604037e-03 + 7.75000000000000e+00 1.84641120515050e-03 + 8.25000000000000e+00 1.91540651058994e-03 + 8.75000000000000e+00 1.95616282516860e-03 + 9.25000000000000e+00 1.97858394967864e-03 + 9.75000000000000e+00 1.99008812206018e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out index f80dd081e..2a87d0982 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.restart.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -139,34 +139,17 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. +colvars: Read 0 hills. colvars: Rebinning the energy and forces grids from the grids in the restart file. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped index 81421cf45..ce121d56f 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21404883965667e+00 + x 3.21404884013792e+00 } metadynamics { @@ -21,25 +21,25 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 1.23300798771509e-03 1.23300798771631e-03 1.52820755425691e-03 - 1.52820755425807e-03 1.52820755425917e-03 1.77932544552316e-03 - 1.77932544552405e-03 1.94618908287715e-03 1.94618908287773e-03 - 1.94618908287813e-03 1.99972957594580e-03 1.99972957594581e-03 - 1.93025240789729e-03 1.93025240789690e-03 1.93025240789634e-03 - 1.75030418484216e-03 1.75030418484128e-03 1.49097223016143e-03 - 1.49097223016034e-03 1.49097223015919e-03 1.19311463637090e-03 - 1.19311463636968e-03 8.96915206812262e-04 8.96915206811093e-04 - 8.96915206809974e-04 6.33398742108474e-04 6.33398742107497e-04 - 4.20203437627708e-04 4.20203437626903e-04 4.20203437626187e-04 - 2.61877749855382e-04 2.61877749854837e-04 1.53318370756312e-04 - 1.53318370755917e-04 1.53318370755588e-04 8.43230653249215e-05 - 8.43230653246995e-05 4.35667507519842e-05 4.35667507518415e-05 - 4.35667507517290e-05 2.11456262453920e-05 2.11456262453244e-05 - 9.64145386589709e-06 9.64145386585826e-06 9.64145386582932e-06 - 5.28034713511762e-17 3.72255148064365e-17 2.59822071961412e-17 - 1.79542993629898e-17 1.22833824411128e-17 8.32002395079111e-18 - 5.57940992188942e-18 3.70432476841225e-18 2.43493252970905e-18 - 1.58460820053553e-18 + 1.23300798763402e-03 1.23300798763524e-03 1.52820755418198e-03 + 1.52820755418314e-03 1.52820755418424e-03 1.77932544546565e-03 + 1.77932544546654e-03 1.94618908284677e-03 1.94618908284735e-03 + 1.94618908284775e-03 1.99972957594801e-03 1.99972957594802e-03 + 1.93025240793167e-03 1.93025240793128e-03 1.93025240793072e-03 + 1.75030418490259e-03 1.75030418490171e-03 1.49097223023783e-03 + 1.49097223023673e-03 1.49097223023558e-03 1.19311463645197e-03 + 1.19311463645075e-03 8.96915206888191e-04 8.96915206887022e-04 + 8.96915206885903e-04 6.33398742172679e-04 6.33398742171702e-04 + 4.20203437677323e-04 4.20203437676518e-04 4.20203437675802e-04 + 2.61877749890678e-04 2.61877749890133e-04 1.53318370779538e-04 + 1.53318370779143e-04 1.53318370778814e-04 8.43230653391043e-05 + 8.43230653388823e-05 4.35667507600398e-05 4.35667507598971e-05 + 4.35667507597847e-05 2.11456262496551e-05 2.11456262495875e-05 + 9.64145386800195e-06 9.64145386796312e-06 9.64145386793418e-06 + 5.28034713900195e-17 3.72255148346162e-17 2.59822072163652e-17 + 1.79542993773489e-17 1.22833824511992e-17 8.32002395780095e-18 + 5.57940992670954e-18 3.70432477169169e-18 2.43493253191679e-18 + 1.58460820200618e-18 hills_energy_gradients grid_parameters { n_colvars 1 @@ -48,24 +48,24 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 6.06365740085560e-04 6.06365740085564e-04 5.60512340088285e-04 - 5.60512340088029e-04 5.60512340087635e-04 4.30201086506495e-04 - 4.30201086505838e-04 2.27271348826923e-04 2.27271348826058e-04 - 2.27271348825120e-04 -1.64425130236053e-05 -1.64425130246041e-05 - -2.57152794012557e-04 -2.57152794013499e-04 -2.57152794014372e-04 - -4.51967686125329e-04 -4.51967686125995e-04 -5.71373901808749e-04 - -5.71373901809154e-04 -5.71373901809421e-04 -6.06367538367918e-04 - -6.06367538367924e-04 -5.67946764114821e-04 -5.67946764114611e-04 - -5.67946764114319e-04 -4.80257088130826e-04 -4.80257088130422e-04 - -3.71133070560880e-04 -3.71133070560435e-04 -3.71133070559992e-04 - -2.64031001754737e-04 -2.64031001754330e-04 -1.73743804967135e-04 - -1.73743804966793e-04 -1.73743804966486e-04 -1.06097165583657e-04 - -1.06097165583424e-04 -6.02625033747609e-05 -6.02625033745952e-05 - -6.02625033744582e-05 -3.18923060823172e-05 -3.18923060822274e-05 - -1.57466379128806e-05 -1.57466379128247e-05 -1.57466379127815e-05 - -9.09757785774318e-17 -6.59975776057536e-17 -4.73632774778447e-17 - -3.36268154240955e-17 -2.36198534105275e-17 -1.64146648142998e-17 - -1.12866460797317e-17 -7.67873161883127e-18 -5.16914145223437e-18 - -3.44320959079916e-18 + 6.06365740086909e-04 6.06365740086913e-04 5.60512340111883e-04 + 5.60512340111627e-04 5.60512340111233e-04 4.30201086552066e-04 + 4.30201086551409e-04 2.27271348888427e-04 2.27271348887562e-04 + 2.27271348886624e-04 -1.64425129567850e-05 -1.64425129577838e-05 + -2.57152793952624e-04 -2.57152793953566e-04 -2.57152793954439e-04 + -4.51967686082436e-04 -4.51967686083102e-04 -5.71373901788195e-04 + -5.71373901788600e-04 -5.71373901788867e-04 -6.06367538369246e-04 + -6.06367538369252e-04 -5.67946764132928e-04 -5.67946764132719e-04 + -5.67946764132426e-04 -4.80257088158340e-04 -4.80257088157936e-04 + -3.71133070590659e-04 -3.71133070590214e-04 -3.71133070589771e-04 + -2.64031001781572e-04 -2.64031001781165e-04 -1.73743804988332e-04 + -1.73743804987990e-04 -1.73743804987683e-04 -1.06097165598685e-04 + -1.06097165598452e-04 -6.02625033844479e-05 -6.02625033842822e-05 + -6.02625033841452e-05 -3.18923060880405e-05 -3.18923060879507e-05 + -1.57466379159961e-05 -1.57466379159402e-05 -1.57466379158970e-05 + -9.09757786387114e-17 -6.59975776517344e-17 -4.73632775119337e-17 + -3.36268154490693e-17 -2.36198534286094e-17 -1.64146648272399e-17 + -1.12866460888857e-17 -7.67873162523311e-18 -5.16914145666077e-18 + -3.44320959382525e-18 } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj index 509a07520..fb142e4f6 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688254064136e+00 1.64425130241460e-05 - 21 3.21458253878164e+00 1.64425130241460e-05 - 22 3.21223316113940e+00 1.64425130241460e-05 - 23 3.20995393049671e+00 1.64425130241460e-05 - 24 3.20785328156876e+00 1.64425130241460e-05 - 25 3.20602246223748e+00 1.64425130241460e-05 - 26 3.20453121727901e+00 1.64425130241460e-05 - 27 3.20342558278651e+00 1.64425130241460e-05 - 28 3.20272771879869e+00 1.64425130241460e-05 - 29 3.20243733044315e+00 1.64425130241460e-05 - 30 3.20253425826863e+00 1.64425130243894e-05 - 31 3.20298186140896e+00 1.64425130243894e-05 - 32 3.20373103962324e+00 1.64425130243894e-05 - 33 3.20472472070871e+00 1.64425130243894e-05 - 34 3.20590259829393e+00 1.64425130243894e-05 - 35 3.20720570082978e+00 1.64425130243894e-05 - 36 3.20858034653318e+00 1.64425130243894e-05 - 37 3.20998116348556e+00 1.64425130243894e-05 - 38 3.21137313133328e+00 1.64425130243894e-05 - 39 3.21273279422841e+00 1.64425130243894e-05 - 40 3.21404883965667e+00 1.64425130246041e-05 + 20 3.21688254084712e+00 1.64425129573257e-05 + 21 3.21458253900407e+00 1.64425129573257e-05 + 22 3.21223316137874e+00 1.64425129573257e-05 + 23 3.20995393075312e+00 1.64425129573257e-05 + 24 3.20785328184230e+00 1.64425129573257e-05 + 25 3.20602246252810e+00 1.64425129573257e-05 + 26 3.20453121758655e+00 1.64425129573257e-05 + 27 3.20342558311071e+00 1.64425129573257e-05 + 28 3.20272771913917e+00 1.64425129573257e-05 + 29 3.20243733079947e+00 1.64425129573257e-05 + 30 3.20253425864031e+00 1.64425129575691e-05 + 31 3.20298186179545e+00 1.64425129575691e-05 + 32 3.20373104002396e+00 1.64425129575691e-05 + 33 3.20472472112302e+00 1.64425129575691e-05 + 34 3.20590259872112e+00 1.64425129575691e-05 + 35 3.20720570126905e+00 1.64425129575691e-05 + 36 3.20858034698356e+00 1.64425129575691e-05 + 37 3.20998116394591e+00 1.64425129575691e-05 + 38 3.21137313180225e+00 1.64425129575691e-05 + 39 3.21273279470442e+00 1.64425129575691e-05 + 40 3.21404884013792e+00 1.64425129577838e-05 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf index 9054286e1..225f83d93 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf @@ -1,58 +1,58 @@ # 1 # 1.00000000000000e+00 2.00000000000000e-01 55 0 - 1.10000000000000e+00 7.66721588230714e-04 - 1.30000000000000e+00 7.66721588229502e-04 - 1.50000000000000e+00 4.71522021688902e-04 - 1.70000000000000e+00 4.71522021687739e-04 - 1.90000000000000e+00 4.71522021686641e-04 - 2.10000000000000e+00 2.20404130422646e-04 - 2.30000000000000e+00 2.20404130421759e-04 - 2.50000000000000e+00 5.35404930686546e-05 - 2.70000000000000e+00 5.35404930680746e-05 - 2.90000000000000e+00 5.35404930676752e-05 + 1.10000000000000e+00 7.66721588313994e-04 + 1.30000000000000e+00 7.66721588312782e-04 + 1.50000000000000e+00 4.71522021766042e-04 + 1.70000000000000e+00 4.71522021764879e-04 + 1.90000000000000e+00 4.71522021763781e-04 + 2.10000000000000e+00 2.20404130482366e-04 + 2.30000000000000e+00 2.20404130481479e-04 + 2.50000000000000e+00 5.35404931012447e-05 + 2.70000000000000e+00 5.35404931006646e-05 + 2.90000000000000e+00 5.35404931002652e-05 3.10000000000000e+00 8.23993651088983e-18 3.30000000000000e+00 -0.00000000000000e+00 - 3.50000000000000e+00 6.94771680485205e-05 - 3.70000000000000e+00 6.94771680489045e-05 - 3.90000000000000e+00 6.94771680494700e-05 - 4.10000000000000e+00 2.49425391103651e-04 - 4.30000000000000e+00 2.49425391104527e-04 - 4.50000000000000e+00 5.08757345784374e-04 - 4.70000000000000e+00 5.08757345785465e-04 - 4.90000000000000e+00 5.08757345786624e-04 - 5.10000000000000e+00 8.06614939574912e-04 - 5.30000000000000e+00 8.06614939576124e-04 - 5.50000000000000e+00 1.10281436913355e-03 - 5.70000000000000e+00 1.10281436913472e-03 - 5.90000000000000e+00 1.10281436913583e-03 - 6.10000000000000e+00 1.36633083383733e-03 - 6.30000000000000e+00 1.36633083383831e-03 - 6.50000000000000e+00 1.57952613831810e-03 - 6.70000000000000e+00 1.57952613831891e-03 - 6.90000000000000e+00 1.57952613831962e-03 - 7.10000000000000e+00 1.73785182609043e-03 - 7.30000000000000e+00 1.73785182609097e-03 - 7.50000000000000e+00 1.84641120518950e-03 - 7.70000000000000e+00 1.84641120518989e-03 - 7.90000000000000e+00 1.84641120519022e-03 - 8.10000000000000e+00 1.91540651062089e-03 - 8.30000000000000e+00 1.91540651062111e-03 - 8.50000000000000e+00 1.95616282519382e-03 - 8.70000000000000e+00 1.95616282519397e-03 - 8.90000000000000e+00 1.95616282519408e-03 - 9.10000000000000e+00 1.97858394970042e-03 - 9.30000000000000e+00 1.97858394970048e-03 - 9.50000000000000e+00 1.99008812207991e-03 - 9.70000000000000e+00 1.99008812207995e-03 - 9.90000000000000e+00 1.99008812207998e-03 - 1.01000000000000e+01 1.99972957594576e-03 - 1.03000000000000e+01 1.99972957594577e-03 - 1.05000000000000e+01 1.99972957594578e-03 - 1.07000000000000e+01 1.99972957594579e-03 - 1.09000000000000e+01 1.99972957594580e-03 - 1.11000000000000e+01 1.99972957594580e-03 - 1.13000000000000e+01 1.99972957594580e-03 - 1.15000000000000e+01 1.99972957594580e-03 - 1.17000000000000e+01 1.99972957594581e-03 - 1.19000000000000e+01 1.99972957594581e-03 + 3.50000000000000e+00 6.94771680163505e-05 + 3.70000000000000e+00 6.94771680167345e-05 + 3.90000000000000e+00 6.94771680173000e-05 + 4.10000000000000e+00 2.49425391045431e-04 + 4.30000000000000e+00 2.49425391046307e-04 + 4.50000000000000e+00 5.08757345710194e-04 + 4.70000000000000e+00 5.08757345711285e-04 + 4.90000000000000e+00 5.08757345712444e-04 + 5.10000000000000e+00 8.06614939496052e-04 + 5.30000000000000e+00 8.06614939497264e-04 + 5.50000000000000e+00 1.10281436905983e-03 + 5.70000000000000e+00 1.10281436906100e-03 + 5.90000000000000e+00 1.10281436906212e-03 + 6.10000000000000e+00 1.36633083377534e-03 + 6.30000000000000e+00 1.36633083377632e-03 + 6.50000000000000e+00 1.57952613827070e-03 + 6.70000000000000e+00 1.57952613827150e-03 + 6.90000000000000e+00 1.57952613827222e-03 + 7.10000000000000e+00 1.73785182605734e-03 + 7.30000000000000e+00 1.73785182605789e-03 + 7.50000000000000e+00 1.84641120516848e-03 + 7.70000000000000e+00 1.84641120516888e-03 + 7.90000000000000e+00 1.84641120516921e-03 + 8.10000000000000e+00 1.91540651060891e-03 + 8.30000000000000e+00 1.91540651060914e-03 + 8.50000000000000e+00 1.95616282518798e-03 + 8.70000000000000e+00 1.95616282518812e-03 + 8.90000000000000e+00 1.95616282518823e-03 + 9.10000000000000e+00 1.97858394969836e-03 + 9.30000000000000e+00 1.97858394969843e-03 + 9.50000000000000e+00 1.99008812208002e-03 + 9.70000000000000e+00 1.99008812208006e-03 + 9.90000000000000e+00 1.99008812208008e-03 + 1.01000000000000e+01 1.99972957594797e-03 + 1.03000000000000e+01 1.99972957594798e-03 + 1.05000000000000e+01 1.99972957594799e-03 + 1.07000000000000e+01 1.99972957594800e-03 + 1.09000000000000e+01 1.99972957594801e-03 + 1.11000000000000e+01 1.99972957594801e-03 + 1.13000000000000e+01 1.99972957594801e-03 + 1.15000000000000e+01 1.99972957594801e-03 + 1.17000000000000e+01 1.99972957594802e-03 + 1.19000000000000e+01 1.99972957594802e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt index 157cac038..49dcaf892 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2021-03-09. +colvars: Using NAMD interface, version "2021-03-02". diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out index caed7f14e..a5e27860c 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -138,27 +134,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped index ab45cb882..6de09bffd 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688278576757e+00 + x 3.21688278597333e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.46920493464415e-08 1.70721010337625e-05 6.58298335707084e-04 - 1.98901157282260e-03 4.70902104095221e-04 8.73580075153432e-06 + 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04 + 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 5.18433074964325e-07 1.68175610778412e-04 3.13214891049980e-03 - -6.66334790621162e-04 -2.55603942662786e-03 -9.19086518597186e-05 + 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03 + -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj index 56616ce4c..3ac32bb03 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 3.30884583877525e-04 - 11 3.21950367884164e+00 3.30884583877525e-04 - 12 3.22130501367398e+00 3.30884583877525e-04 - 13 3.22263482503343e+00 3.30884583877525e-04 - 14 3.22341774640647e+00 3.30884583877525e-04 - 15 3.22361481066343e+00 3.30884583877525e-04 - 16 3.22322427736760e+00 3.30884583877525e-04 - 17 3.22227956008091e+00 3.30884583877525e-04 - 18 3.22084496823082e+00 3.30884583877525e-04 - 19 3.21901000767136e+00 3.30884583877525e-04 - 20 3.21688278576757e+00 6.66334790621162e-04 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 3.30884583259955e-04 + 11 3.21950367891521e+00 3.30884583259955e-04 + 12 3.22130501376020e+00 3.30884583259955e-04 + 13 3.22263482513293e+00 3.30884583259955e-04 + 14 3.22341774651982e+00 3.30884583259955e-04 + 15 3.22361481079113e+00 3.30884583259955e-04 + 16 3.22322427751010e+00 3.30884583259955e-04 + 17 3.22227956023865e+00 3.30884583259955e-04 + 18 3.22084496840419e+00 3.30884583259955e-04 + 19 3.21901000786075e+00 3.30884583259955e-04 + 20 3.21688278597333e+00 6.66334787942696e-04 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf index 7a24c6664..3a05a7c71 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.98901157282260e-03 - 7.50000000000000e-01 1.98901157282260e-03 - 1.25000000000000e+00 1.98901157282260e-03 - 1.75000000000000e+00 1.98897688077326e-03 - 2.25000000000000e+00 1.97193947178884e-03 - 2.75000000000000e+00 1.33071323711552e-03 + 2.50000000000000e-01 1.98901157291202e-03 + 7.50000000000000e-01 1.98901157291202e-03 + 1.25000000000000e+00 1.98901157291202e-03 + 1.75000000000000e+00 1.98897688086274e-03 + 2.25000000000000e+00 1.97193947190077e-03 + 2.75000000000000e+00 1.33071323762382e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.51810946872738e-03 - 4.25000000000000e+00 1.98027577207107e-03 - 4.75000000000000e+00 1.98901157282260e-03 - 5.25000000000000e+00 1.98901157282260e-03 - 5.75000000000000e+00 1.98901157282260e-03 - 6.25000000000000e+00 1.98901157282260e-03 - 6.75000000000000e+00 1.98901157282260e-03 - 7.25000000000000e+00 1.98901157282260e-03 - 7.75000000000000e+00 1.98901157282260e-03 - 8.25000000000000e+00 1.98901157282260e-03 - 8.75000000000000e+00 1.98901157282260e-03 - 9.25000000000000e+00 1.98901157282260e-03 - 9.75000000000000e+00 1.98901157282260e-03 + 3.75000000000000e+00 1.51810946847522e-03 + 4.25000000000000e+00 1.98027577214821e-03 + 4.75000000000000e+00 1.98901157291202e-03 + 5.25000000000000e+00 1.98901157291202e-03 + 5.75000000000000e+00 1.98901157291202e-03 + 6.25000000000000e+00 1.98901157291202e-03 + 6.75000000000000e+00 1.98901157291202e-03 + 7.25000000000000e+00 1.98901157291202e-03 + 7.75000000000000e+00 1.98901157291202e-03 + 8.25000000000000e+00 1.98901157291202e-03 + 8.75000000000000e+00 1.98901157291202e-03 + 9.25000000000000e+00 1.98901157291202e-03 + 9.75000000000000e+00 1.98901157291202e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out index 2bb4389fd..adabe2e3d 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -138,34 +134,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped index 5f97bd617..235b1896e 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405136086868e+00 + x 3.21405136134992e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 7.43923406409864e-08 3.57122156643391e-05 1.34466139863962e-03 - 3.97104317611064e-03 9.19770326015385e-04 1.67080044137238e-05 + 7.43923403227782e-08 3.57122155647627e-05 1.34466139685731e-03 + 3.97104317655277e-03 9.19770327415716e-04 1.67080044623168e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.10794466506920e-06 3.50062168801214e-04 6.33510418316085e-03 - -1.50805870086533e-03 -5.03195891344979e-03 -1.76471077412228e-04 + 1.10794466055357e-06 3.50062167930554e-04 6.33510417866273e-03 + -1.50805868972440e-03 -5.03195891853835e-03 -1.76471077879577e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj index e23343a0c..6b959f565 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688278576757e+00 6.66334790621162e-04 - 21 3.21458283239873e+00 6.66334790621162e-04 - 22 3.21223351050617e+00 6.66334790621162e-04 - 23 3.20995434250849e+00 6.66334790621162e-04 - 24 3.20785376273403e+00 6.66334790621162e-04 - 25 3.20602301866294e+00 6.66334790621162e-04 - 26 3.20453185466307e+00 6.66334790621162e-04 - 27 3.20342630641905e+00 6.66334790621162e-04 - 28 3.20272853356652e+00 6.66334790621162e-04 - 29 3.20243824083933e+00 6.66334790621162e-04 - 30 3.20253526840434e+00 1.14429095893840e-03 - 31 3.20298298236841e+00 1.14429095893840e-03 - 32 3.20373228203772e+00 1.14429095893840e-03 - 33 3.20472609467411e+00 1.14429095893840e-03 - 34 3.20590411329665e+00 1.14429095893840e-03 - 35 3.20720736568876e+00 1.14429095893840e-03 - 36 3.20858216935653e+00 1.14429095893840e-03 - 37 3.20998315165031e+00 1.14429095893840e-03 - 38 3.21137529148386e+00 1.14429095893840e-03 - 39 3.21273513229142e+00 1.14429095893840e-03 - 40 3.21405136086868e+00 1.50805870086533e-03 + 20 3.21688278597333e+00 6.66334787942696e-04 + 21 3.21458283262116e+00 6.66334787942696e-04 + 22 3.21223351074552e+00 6.66334787942696e-04 + 23 3.20995434276490e+00 6.66334787942696e-04 + 24 3.20785376300757e+00 6.66334787942696e-04 + 25 3.20602301895356e+00 6.66334787942696e-04 + 26 3.20453185497061e+00 6.66334787942696e-04 + 27 3.20342630674324e+00 6.66334787942696e-04 + 28 3.20272853390700e+00 6.66334787942696e-04 + 29 3.20243824119566e+00 6.66334787942696e-04 + 30 3.20253526877602e+00 1.14429095260314e-03 + 31 3.20298298275490e+00 1.14429095260314e-03 + 32 3.20373228243844e+00 1.14429095260314e-03 + 33 3.20472609508842e+00 1.14429095260314e-03 + 34 3.20590411372385e+00 1.14429095260314e-03 + 35 3.20720736612802e+00 1.14429095260314e-03 + 36 3.20858216980690e+00 1.14429095260314e-03 + 37 3.20998315211066e+00 1.14429095260314e-03 + 38 3.21137529195283e+00 1.14429095260314e-03 + 39 3.21273513276742e+00 1.14429095260314e-03 + 40 3.21405136134992e+00 1.50805868972440e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf index 38a897e10..051812fec 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.97104317611064e-03 - 7.50000000000000e-01 3.97104317611064e-03 - 1.25000000000000e+00 3.97104317611064e-03 - 1.75000000000000e+00 3.97096878377000e-03 - 2.25000000000000e+00 3.93533096044630e-03 - 2.75000000000000e+00 2.62638177747102e-03 + 2.50000000000000e-01 3.97104317655277e-03 + 7.50000000000000e-01 3.97104317655277e-03 + 1.25000000000000e+00 3.97104317655277e-03 + 1.75000000000000e+00 3.97096878421245e-03 + 2.25000000000000e+00 3.93533096098801e-03 + 2.75000000000000e+00 2.62638177969546e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 3.05127285009526e-03 - 4.25000000000000e+00 3.95433517169692e-03 - 4.75000000000000e+00 3.97104317611064e-03 - 5.25000000000000e+00 3.97104317611064e-03 - 5.75000000000000e+00 3.97104317611064e-03 - 6.25000000000000e+00 3.97104317611064e-03 - 6.75000000000000e+00 3.97104317611064e-03 - 7.25000000000000e+00 3.97104317611064e-03 - 7.75000000000000e+00 3.97104317611064e-03 - 8.25000000000000e+00 3.97104317611064e-03 - 8.75000000000000e+00 3.97104317611064e-03 - 9.25000000000000e+00 3.97104317611064e-03 - 9.75000000000000e+00 3.97104317611064e-03 + 3.75000000000000e+00 3.05127284913705e-03 + 4.25000000000000e+00 3.95433517209045e-03 + 4.75000000000000e+00 3.97104317655277e-03 + 5.25000000000000e+00 3.97104317655277e-03 + 5.75000000000000e+00 3.97104317655277e-03 + 6.25000000000000e+00 3.97104317655277e-03 + 6.75000000000000e+00 3.97104317655277e-03 + 7.25000000000000e+00 3.97104317655277e-03 + 7.75000000000000e+00 3.97104317655277e-03 + 8.25000000000000e+00 3.97104317655277e-03 + 8.75000000000000e+00 3.97104317655277e-03 + 9.25000000000000e+00 3.97104317655277e-03 + 9.75000000000000e+00 3.97104317655277e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out index 60aee7ad6..5fcb5a777 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -140,30 +136,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped index 7dc8c95f8..2e2ab665b 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688278576757e+00 + x 3.21688278597333e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.46920493464415e-08 1.70721010337625e-05 6.58298335707084e-04 - 1.98901157282260e-03 4.70902104095221e-04 8.73580075153432e-06 + 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04 + 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 5.18433074964325e-07 1.68175610778412e-04 3.13214891049980e-03 - -6.66334790621162e-04 -2.55603942662786e-03 -9.19086518597186e-05 + 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03 + -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -56,7 +56,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -1.46245128120959e+00 0.00000000000000e+00 0.00000000000000e+00 + -1.46245122218042e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj index 56616ce4c..3ac32bb03 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 3.30884583877525e-04 - 11 3.21950367884164e+00 3.30884583877525e-04 - 12 3.22130501367398e+00 3.30884583877525e-04 - 13 3.22263482503343e+00 3.30884583877525e-04 - 14 3.22341774640647e+00 3.30884583877525e-04 - 15 3.22361481066343e+00 3.30884583877525e-04 - 16 3.22322427736760e+00 3.30884583877525e-04 - 17 3.22227956008091e+00 3.30884583877525e-04 - 18 3.22084496823082e+00 3.30884583877525e-04 - 19 3.21901000767136e+00 3.30884583877525e-04 - 20 3.21688278576757e+00 6.66334790621162e-04 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 3.30884583259955e-04 + 11 3.21950367891521e+00 3.30884583259955e-04 + 12 3.22130501376020e+00 3.30884583259955e-04 + 13 3.22263482513293e+00 3.30884583259955e-04 + 14 3.22341774651982e+00 3.30884583259955e-04 + 15 3.22361481079113e+00 3.30884583259955e-04 + 16 3.22322427751010e+00 3.30884583259955e-04 + 17 3.22227956023865e+00 3.30884583259955e-04 + 18 3.22084496840419e+00 3.30884583259955e-04 + 19 3.21901000786075e+00 3.30884583259955e-04 + 20 3.21688278597333e+00 6.66334787942696e-04 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf index 7a24c6664..3a05a7c71 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.98901157282260e-03 - 7.50000000000000e-01 1.98901157282260e-03 - 1.25000000000000e+00 1.98901157282260e-03 - 1.75000000000000e+00 1.98897688077326e-03 - 2.25000000000000e+00 1.97193947178884e-03 - 2.75000000000000e+00 1.33071323711552e-03 + 2.50000000000000e-01 1.98901157291202e-03 + 7.50000000000000e-01 1.98901157291202e-03 + 1.25000000000000e+00 1.98901157291202e-03 + 1.75000000000000e+00 1.98897688086274e-03 + 2.25000000000000e+00 1.97193947190077e-03 + 2.75000000000000e+00 1.33071323762382e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.51810946872738e-03 - 4.25000000000000e+00 1.98027577207107e-03 - 4.75000000000000e+00 1.98901157282260e-03 - 5.25000000000000e+00 1.98901157282260e-03 - 5.75000000000000e+00 1.98901157282260e-03 - 6.25000000000000e+00 1.98901157282260e-03 - 6.75000000000000e+00 1.98901157282260e-03 - 7.25000000000000e+00 1.98901157282260e-03 - 7.75000000000000e+00 1.98901157282260e-03 - 8.25000000000000e+00 1.98901157282260e-03 - 8.75000000000000e+00 1.98901157282260e-03 - 9.25000000000000e+00 1.98901157282260e-03 - 9.75000000000000e+00 1.98901157282260e-03 + 3.75000000000000e+00 1.51810946847522e-03 + 4.25000000000000e+00 1.98027577214821e-03 + 4.75000000000000e+00 1.98901157291202e-03 + 5.25000000000000e+00 1.98901157291202e-03 + 5.75000000000000e+00 1.98901157291202e-03 + 6.25000000000000e+00 1.98901157291202e-03 + 6.75000000000000e+00 1.98901157291202e-03 + 7.25000000000000e+00 1.98901157291202e-03 + 7.75000000000000e+00 1.98901157291202e-03 + 8.25000000000000e+00 1.98901157291202e-03 + 8.75000000000000e+00 1.98901157291202e-03 + 9.25000000000000e+00 1.98901157291202e-03 + 9.75000000000000e+00 1.98901157291202e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out index 60a73ce49..8704eef89 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -140,37 +136,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped index c9a85fb5b..d3e71c6bd 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405136086868e+00 + x 3.21405136134992e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 7.43923406409864e-08 3.57122156643391e-05 1.34466139863962e-03 - 3.97104317611064e-03 9.19770326015385e-04 1.67080044137238e-05 + 7.43923403227782e-08 3.57122155647627e-05 1.34466139685731e-03 + 3.97104317655277e-03 9.19770327415716e-04 1.67080044623168e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.10794466506920e-06 3.50062168801214e-04 6.33510418316085e-03 - -1.50805870086533e-03 -5.03195891344979e-03 -1.76471077412228e-04 + 1.10794466055357e-06 3.50062167930554e-04 6.33510417866273e-03 + -1.50805868972440e-03 -5.03195891853835e-03 -1.76471077879577e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -56,7 +56,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 4.71618560685502e+00 0.00000000000000e+00 0.00000000000000e+00 + 4.71618561911262e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj index e23343a0c..6b959f565 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688278576757e+00 6.66334790621162e-04 - 21 3.21458283239873e+00 6.66334790621162e-04 - 22 3.21223351050617e+00 6.66334790621162e-04 - 23 3.20995434250849e+00 6.66334790621162e-04 - 24 3.20785376273403e+00 6.66334790621162e-04 - 25 3.20602301866294e+00 6.66334790621162e-04 - 26 3.20453185466307e+00 6.66334790621162e-04 - 27 3.20342630641905e+00 6.66334790621162e-04 - 28 3.20272853356652e+00 6.66334790621162e-04 - 29 3.20243824083933e+00 6.66334790621162e-04 - 30 3.20253526840434e+00 1.14429095893840e-03 - 31 3.20298298236841e+00 1.14429095893840e-03 - 32 3.20373228203772e+00 1.14429095893840e-03 - 33 3.20472609467411e+00 1.14429095893840e-03 - 34 3.20590411329665e+00 1.14429095893840e-03 - 35 3.20720736568876e+00 1.14429095893840e-03 - 36 3.20858216935653e+00 1.14429095893840e-03 - 37 3.20998315165031e+00 1.14429095893840e-03 - 38 3.21137529148386e+00 1.14429095893840e-03 - 39 3.21273513229142e+00 1.14429095893840e-03 - 40 3.21405136086868e+00 1.50805870086533e-03 + 20 3.21688278597333e+00 6.66334787942696e-04 + 21 3.21458283262116e+00 6.66334787942696e-04 + 22 3.21223351074552e+00 6.66334787942696e-04 + 23 3.20995434276490e+00 6.66334787942696e-04 + 24 3.20785376300757e+00 6.66334787942696e-04 + 25 3.20602301895356e+00 6.66334787942696e-04 + 26 3.20453185497061e+00 6.66334787942696e-04 + 27 3.20342630674324e+00 6.66334787942696e-04 + 28 3.20272853390700e+00 6.66334787942696e-04 + 29 3.20243824119566e+00 6.66334787942696e-04 + 30 3.20253526877602e+00 1.14429095260314e-03 + 31 3.20298298275490e+00 1.14429095260314e-03 + 32 3.20373228243844e+00 1.14429095260314e-03 + 33 3.20472609508842e+00 1.14429095260314e-03 + 34 3.20590411372385e+00 1.14429095260314e-03 + 35 3.20720736612802e+00 1.14429095260314e-03 + 36 3.20858216980690e+00 1.14429095260314e-03 + 37 3.20998315211066e+00 1.14429095260314e-03 + 38 3.21137529195283e+00 1.14429095260314e-03 + 39 3.21273513276742e+00 1.14429095260314e-03 + 40 3.21405136134992e+00 1.50805868972440e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf index 38a897e10..051812fec 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.97104317611064e-03 - 7.50000000000000e-01 3.97104317611064e-03 - 1.25000000000000e+00 3.97104317611064e-03 - 1.75000000000000e+00 3.97096878377000e-03 - 2.25000000000000e+00 3.93533096044630e-03 - 2.75000000000000e+00 2.62638177747102e-03 + 2.50000000000000e-01 3.97104317655277e-03 + 7.50000000000000e-01 3.97104317655277e-03 + 1.25000000000000e+00 3.97104317655277e-03 + 1.75000000000000e+00 3.97096878421245e-03 + 2.25000000000000e+00 3.93533096098801e-03 + 2.75000000000000e+00 2.62638177969546e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 3.05127285009526e-03 - 4.25000000000000e+00 3.95433517169692e-03 - 4.75000000000000e+00 3.97104317611064e-03 - 5.25000000000000e+00 3.97104317611064e-03 - 5.75000000000000e+00 3.97104317611064e-03 - 6.25000000000000e+00 3.97104317611064e-03 - 6.75000000000000e+00 3.97104317611064e-03 - 7.25000000000000e+00 3.97104317611064e-03 - 7.75000000000000e+00 3.97104317611064e-03 - 8.25000000000000e+00 3.97104317611064e-03 - 8.75000000000000e+00 3.97104317611064e-03 - 9.25000000000000e+00 3.97104317611064e-03 - 9.75000000000000e+00 3.97104317611064e-03 + 3.75000000000000e+00 3.05127284913705e-03 + 4.25000000000000e+00 3.95433517209045e-03 + 4.75000000000000e+00 3.97104317655277e-03 + 5.25000000000000e+00 3.97104317655277e-03 + 5.75000000000000e+00 3.97104317655277e-03 + 6.25000000000000e+00 3.97104317655277e-03 + 6.75000000000000e+00 3.97104317655277e-03 + 7.25000000000000e+00 3.97104317655277e-03 + 7.75000000000000e+00 3.97104317655277e-03 + 8.25000000000000e+00 3.97104317655277e-03 + 8.75000000000000e+00 3.97104317655277e-03 + 9.25000000000000e+00 3.97104317655277e-03 + 9.75000000000000e+00 3.97104317655277e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj index fa1b525d4..a66046fd3 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj @@ -1,4 +1,4 @@ 5 3.20606308065050e+00 5.00000000000000e-01 1.00000000000000e-01 10 3.21734242206787e+00 5.00000000000000e-01 8.46119581367384e-02 - 15 3.22363050330140e+00 5.00000000000000e-01 7.34385578106080e-02 + 15 3.22363050330139e+00 5.00000000000000e-01 7.34385578106080e-02 20 3.21691895295305e+00 5.00000000000000e-01 6.49380514240066e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out index 689bb1bf4..8e00aed34 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -143,26 +139,16 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped index 87801e244..2b4ef2420 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped @@ -21,10 +21,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.42973919084568e-04 - 4.41360461286583e-03 5.01317117210112e-02 2.09514390772553e-01 - 3.22178897971626e-01 1.82289606890753e-01 3.79496667604973e-02 - 2.90693223696987e-03 8.19298874561864e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.42973919084570e-04 + 4.41360461286586e-03 5.01317117210114e-02 2.09514390772554e-01 + 3.22178897971626e-01 1.82289606890752e-01 3.79496667604971e-02 + 2.90693223696984e-03 8.19298874561855e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -36,10 +36,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.12368805589937e-03 - 2.58626065712127e-02 1.93513466997635e-01 3.89791769357681e-01 - -4.48458537631413e-02 -3.89889393515630e-01 -1.57054622900226e-01 - -1.78431915109616e-02 -6.66729644383008e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.12368805589938e-03 + 2.58626065712129e-02 1.93513466997636e-01 3.89791769357681e-01 + -4.48458537631430e-02 -3.89889393515630e-01 -1.57054622900226e-01 + -1.78431915109615e-02 -6.66729644383001e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj index 89043bf99..b0936f14b 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj @@ -4,19 +4,19 @@ 2 3.20384028588952e+00 0.00000000000000e+00 3 3.20396721186862e+00 0.00000000000000e+00 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 1.75070440392767e-02 - 6 3.20788015841690e+00 1.75070440392767e-02 - 7 3.21006078117990e+00 1.75070440392767e-02 - 8 3.21246619986317e+00 1.75070440392767e-02 - 9 3.21494510727501e+00 1.75070440392767e-02 - 10 3.21734242206787e+00 2.85363794417937e-02 - 11 3.21950925117359e+00 2.85363794417937e-02 - 12 3.22131261706854e+00 2.85363794417937e-02 - 13 3.22264480741010e+00 2.85363794417937e-02 - 14 3.22343043310305e+00 2.85363794417937e-02 - 15 3.22363050330140e+00 3.62717655819525e-02 - 16 3.22324337253598e+00 3.62717655819525e-02 - 17 3.22230242928906e+00 3.62717655819525e-02 - 18 3.22087195749114e+00 3.62717655819525e-02 - 19 3.21904143773479e+00 3.62717655819525e-02 - 20 3.21691895295305e+00 4.48458537631413e-02 + 5 3.20606308065050e+00 1.75070440392768e-02 + 6 3.20788015841690e+00 1.75070440392768e-02 + 7 3.21006078117990e+00 1.75070440392768e-02 + 8 3.21246619986317e+00 1.75070440392768e-02 + 9 3.21494510727501e+00 1.75070440392768e-02 + 10 3.21734242206787e+00 2.85363794417943e-02 + 11 3.21950925117359e+00 2.85363794417943e-02 + 12 3.22131261706854e+00 2.85363794417943e-02 + 13 3.22264480741010e+00 2.85363794417943e-02 + 14 3.22343043310305e+00 2.85363794417943e-02 + 15 3.22363050330139e+00 3.62717655819535e-02 + 16 3.22324337253598e+00 3.62717655819535e-02 + 17 3.22230242928906e+00 3.62717655819535e-02 + 18 3.22087195749114e+00 3.62717655819535e-02 + 19 3.21904143773479e+00 3.62717655819535e-02 + 20 3.21691895295305e+00 4.48458537631430e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf index a4a179906..1433280e7 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.22178897971626e-01 - 7.50000000000000e-01 3.22178897971626e-01 - 1.25000000000000e+00 3.22035924052542e-01 - 1.75000000000000e+00 3.17765293358761e-01 - 2.25000000000000e+00 2.72047186250615e-01 - 2.75000000000000e+00 1.12664507199074e-01 + 2.50000000000000e-01 3.22178897974989e-01 + 7.50000000000000e-01 3.22178897974989e-01 + 1.25000000000000e+00 3.22035924056005e-01 + 1.75000000000000e+00 3.17765293364453e-01 + 2.25000000000000e+00 2.72047186271566e-01 + 2.75000000000000e+00 1.12664507238354e-01 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.39889291080873e-01 - 4.25000000000000e+00 2.84229231211129e-01 - 4.75000000000000e+00 3.19271965734657e-01 - 5.25000000000000e+00 3.22096968084170e-01 - 5.75000000000000e+00 3.22178897971626e-01 - 6.25000000000000e+00 3.22178897971626e-01 - 6.75000000000000e+00 3.22178897971626e-01 - 7.25000000000000e+00 3.22178897971626e-01 - 7.75000000000000e+00 3.22178897971626e-01 - 8.25000000000000e+00 3.22178897971626e-01 - 8.75000000000000e+00 3.22178897971626e-01 - 9.25000000000000e+00 3.22178897971626e-01 - 9.75000000000000e+00 3.22178897971626e-01 + 3.75000000000000e+00 1.39889291048735e-01 + 4.25000000000000e+00 2.84229231200015e-01 + 4.75000000000000e+00 3.19271965736361e-01 + 5.25000000000000e+00 3.22096968087471e-01 + 5.75000000000000e+00 3.22178897974989e-01 + 6.25000000000000e+00 3.22178897974989e-01 + 6.75000000000000e+00 3.22178897974989e-01 + 7.25000000000000e+00 3.22178897974989e-01 + 7.75000000000000e+00 3.22178897974989e-01 + 8.25000000000000e+00 3.22178897974989e-01 + 8.75000000000000e+00 3.22178897974989e-01 + 9.25000000000000e+00 3.22178897974989e-01 + 9.75000000000000e+00 3.22178897974989e-01 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out index 857505a84..817eae3a8 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -143,33 +139,21 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21692 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped index 37445afe6..86220cc57 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped @@ -21,10 +21,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 2.39032008958370e-04 - 7.33347556564710e-03 8.27850280039973e-02 3.43860479556675e-01 - 5.25534912996650e-01 2.95535757364180e-01 6.11516158055121e-02 - 4.65581319200507e-03 1.30428682628954e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 2.39032008958375e-04 + 7.33347556564719e-03 8.27850280039980e-02 3.43860479556677e-01 + 5.25534912996650e-01 2.95535757364178e-01 6.11516158055115e-02 + 4.65581319200500e-03 1.30428682628952e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -36,10 +36,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.87569014992071e-03 - 4.28817998866071e-02 3.18539085938462e-01 6.35512332470773e-01 - -7.95903631638424e-02 -6.35715309684715e-01 -2.53820387793996e-01 - -2.86345787796512e-02 -1.06298017276162e-03 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.87569014992074e-03 + 4.28817998866076e-02 3.18539085938464e-01 6.35512332470772e-01 + -7.95903631638470e-02 -6.35715309684715e-01 -2.53820387793995e-01 + -2.86345787796509e-02 -1.06298017276160e-03 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj index f184c4075..dba722227 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21691895295305e+00 4.48458537631413e-02 - 21 3.21462413660772e+00 4.48458537631413e-02 - 22 3.21228032841215e+00 4.48458537631413e-02 - 23 3.21000702769477e+00 4.48458537631413e-02 - 24 3.20791264597674e+00 4.48458537631413e-02 - 25 3.20608840817769e+00 5.50378747704764e-02 - 26 3.20460419289259e+00 5.50378747704764e-02 - 27 3.20350601131064e+00 5.50378747704764e-02 - 28 3.20281599649048e+00 5.50378747704764e-02 - 29 3.20253382453620e+00 5.50378747704764e-02 - 30 3.20263930510781e+00 6.50046475230887e-02 - 31 3.20309591808115e+00 6.50046475230887e-02 - 32 3.20385452785452e+00 6.50046475230887e-02 - 33 3.20485802441983e+00 6.50046475230887e-02 - 34 3.20604606196811e+00 6.50046475230887e-02 - 35 3.20735962915093e+00 7.32270721427094e-02 - 36 3.20874513121416e+00 7.32270721427094e-02 - 37 3.21015715709204e+00 7.32270721427094e-02 - 38 3.21156064829882e+00 7.32270721427094e-02 - 39 3.21293211249028e+00 7.32270721427094e-02 - 40 3.21426020264931e+00 7.95903631638424e-02 + 20 3.21691895295305e+00 4.48458537631430e-02 + 21 3.21462413660771e+00 4.48458537631430e-02 + 22 3.21228032841214e+00 4.48458537631430e-02 + 23 3.21000702769477e+00 4.48458537631430e-02 + 24 3.20791264597674e+00 4.48458537631430e-02 + 25 3.20608840817769e+00 5.50378747704786e-02 + 26 3.20460419289258e+00 5.50378747704786e-02 + 27 3.20350601131064e+00 5.50378747704786e-02 + 28 3.20281599649047e+00 5.50378747704786e-02 + 29 3.20253382453620e+00 5.50378747704786e-02 + 30 3.20263930510781e+00 6.50046475230917e-02 + 31 3.20309591808115e+00 6.50046475230917e-02 + 32 3.20385452785452e+00 6.50046475230917e-02 + 33 3.20485802441983e+00 6.50046475230917e-02 + 34 3.20604606196811e+00 6.50046475230917e-02 + 35 3.20735962915093e+00 7.32270721427131e-02 + 36 3.20874513121416e+00 7.32270721427131e-02 + 37 3.21015715709204e+00 7.32270721427131e-02 + 38 3.21156064829882e+00 7.32270721427131e-02 + 39 3.21293211249027e+00 7.32270721427131e-02 + 40 3.21426020264931e+00 7.95903631638470e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf index 29265ec37..f2f4c584a 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 5.25534912996650e-01 - 7.50000000000000e-01 5.25534912996650e-01 - 1.25000000000000e+00 5.25295880987692e-01 - 1.75000000000000e+00 5.18201437431003e-01 - 2.25000000000000e+00 4.42749884992653e-01 - 2.75000000000000e+00 1.81674433439975e-01 + 2.50000000000000e-01 5.25534913010848e-01 + 7.50000000000000e-01 5.25534913010848e-01 + 1.25000000000000e+00 5.25295881002282e-01 + 1.75000000000000e+00 5.18201437454156e-01 + 2.25000000000000e+00 4.42749885073309e-01 + 2.75000000000000e+00 1.81674433587149e-01 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 2.29999155632470e-01 - 4.25000000000000e+00 4.64383297191138e-01 - 4.75000000000000e+00 5.20879099804645e-01 - 5.25000000000000e+00 5.25404484314022e-01 - 5.75000000000000e+00 5.25534912996650e-01 - 6.25000000000000e+00 5.25534912996650e-01 - 6.75000000000000e+00 5.25534912996650e-01 - 7.25000000000000e+00 5.25534912996650e-01 - 7.75000000000000e+00 5.25534912996650e-01 - 8.25000000000000e+00 5.25534912996650e-01 - 8.75000000000000e+00 5.25534912996650e-01 - 9.25000000000000e+00 5.25534912996650e-01 - 9.75000000000000e+00 5.25534912996650e-01 + 3.75000000000000e+00 2.29999155517106e-01 + 4.25000000000000e+00 4.64383297153516e-01 + 4.75000000000000e+00 5.20879099813004e-01 + 5.25000000000000e+00 5.25404484328003e-01 + 5.75000000000000e+00 5.25534913010848e-01 + 6.25000000000000e+00 5.25534913010848e-01 + 6.75000000000000e+00 5.25534913010848e-01 + 7.25000000000000e+00 5.25534913010848e-01 + 7.75000000000000e+00 5.25534913010848e-01 + 8.25000000000000e+00 5.25534913010848e-01 + 8.75000000000000e+00 5.25534913010848e-01 + 9.25000000000000e+00 5.25534913010848e-01 + 9.75000000000000e+00 5.25534913010848e-01 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt index 157cac038..617210efd 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-07-07". +colvars: Using NAMD interface, version "2020-05-04". diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out index bc1e4dfcd..0343b9172 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -140,27 +136,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped index ab45cb882..6de09bffd 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688278576757e+00 + x 3.21688278597333e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.46920493464415e-08 1.70721010337625e-05 6.58298335707084e-04 - 1.98901157282260e-03 4.70902104095221e-04 8.73580075153432e-06 + 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04 + 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 5.18433074964325e-07 1.68175610778412e-04 3.13214891049980e-03 - -6.66334790621162e-04 -2.55603942662786e-03 -9.19086518597186e-05 + 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03 + -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj index 56616ce4c..3ac32bb03 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 3.30884583877525e-04 - 11 3.21950367884164e+00 3.30884583877525e-04 - 12 3.22130501367398e+00 3.30884583877525e-04 - 13 3.22263482503343e+00 3.30884583877525e-04 - 14 3.22341774640647e+00 3.30884583877525e-04 - 15 3.22361481066343e+00 3.30884583877525e-04 - 16 3.22322427736760e+00 3.30884583877525e-04 - 17 3.22227956008091e+00 3.30884583877525e-04 - 18 3.22084496823082e+00 3.30884583877525e-04 - 19 3.21901000767136e+00 3.30884583877525e-04 - 20 3.21688278576757e+00 6.66334790621162e-04 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 3.30884583259955e-04 + 11 3.21950367891521e+00 3.30884583259955e-04 + 12 3.22130501376020e+00 3.30884583259955e-04 + 13 3.22263482513293e+00 3.30884583259955e-04 + 14 3.22341774651982e+00 3.30884583259955e-04 + 15 3.22361481079113e+00 3.30884583259955e-04 + 16 3.22322427751010e+00 3.30884583259955e-04 + 17 3.22227956023865e+00 3.30884583259955e-04 + 18 3.22084496840419e+00 3.30884583259955e-04 + 19 3.21901000786075e+00 3.30884583259955e-04 + 20 3.21688278597333e+00 6.66334787942696e-04 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf index 7a24c6664..3a05a7c71 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.98901157282260e-03 - 7.50000000000000e-01 1.98901157282260e-03 - 1.25000000000000e+00 1.98901157282260e-03 - 1.75000000000000e+00 1.98897688077326e-03 - 2.25000000000000e+00 1.97193947178884e-03 - 2.75000000000000e+00 1.33071323711552e-03 + 2.50000000000000e-01 1.98901157291202e-03 + 7.50000000000000e-01 1.98901157291202e-03 + 1.25000000000000e+00 1.98901157291202e-03 + 1.75000000000000e+00 1.98897688086274e-03 + 2.25000000000000e+00 1.97193947190077e-03 + 2.75000000000000e+00 1.33071323762382e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.51810946872738e-03 - 4.25000000000000e+00 1.98027577207107e-03 - 4.75000000000000e+00 1.98901157282260e-03 - 5.25000000000000e+00 1.98901157282260e-03 - 5.75000000000000e+00 1.98901157282260e-03 - 6.25000000000000e+00 1.98901157282260e-03 - 6.75000000000000e+00 1.98901157282260e-03 - 7.25000000000000e+00 1.98901157282260e-03 - 7.75000000000000e+00 1.98901157282260e-03 - 8.25000000000000e+00 1.98901157282260e-03 - 8.75000000000000e+00 1.98901157282260e-03 - 9.25000000000000e+00 1.98901157282260e-03 - 9.75000000000000e+00 1.98901157282260e-03 + 3.75000000000000e+00 1.51810946847522e-03 + 4.25000000000000e+00 1.98027577214821e-03 + 4.75000000000000e+00 1.98901157291202e-03 + 5.25000000000000e+00 1.98901157291202e-03 + 5.75000000000000e+00 1.98901157291202e-03 + 6.25000000000000e+00 1.98901157291202e-03 + 6.75000000000000e+00 1.98901157291202e-03 + 7.25000000000000e+00 1.98901157291202e-03 + 7.75000000000000e+00 1.98901157291202e-03 + 8.25000000000000e+00 1.98901157291202e-03 + 8.75000000000000e+00 1.98901157291202e-03 + 9.25000000000000e+00 1.98901157291202e-03 + 9.75000000000000e+00 1.98901157291202e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out index 625d7c300..1c3db0232 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -140,34 +136,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped index 5f97bd617..235b1896e 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405136086868e+00 + x 3.21405136134992e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 7.43923406409864e-08 3.57122156643391e-05 1.34466139863962e-03 - 3.97104317611064e-03 9.19770326015385e-04 1.67080044137238e-05 + 7.43923403227782e-08 3.57122155647627e-05 1.34466139685731e-03 + 3.97104317655277e-03 9.19770327415716e-04 1.67080044623168e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.10794466506920e-06 3.50062168801214e-04 6.33510418316085e-03 - -1.50805870086533e-03 -5.03195891344979e-03 -1.76471077412228e-04 + 1.10794466055357e-06 3.50062167930554e-04 6.33510417866273e-03 + -1.50805868972440e-03 -5.03195891853835e-03 -1.76471077879577e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj index e23343a0c..6b959f565 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688278576757e+00 6.66334790621162e-04 - 21 3.21458283239873e+00 6.66334790621162e-04 - 22 3.21223351050617e+00 6.66334790621162e-04 - 23 3.20995434250849e+00 6.66334790621162e-04 - 24 3.20785376273403e+00 6.66334790621162e-04 - 25 3.20602301866294e+00 6.66334790621162e-04 - 26 3.20453185466307e+00 6.66334790621162e-04 - 27 3.20342630641905e+00 6.66334790621162e-04 - 28 3.20272853356652e+00 6.66334790621162e-04 - 29 3.20243824083933e+00 6.66334790621162e-04 - 30 3.20253526840434e+00 1.14429095893840e-03 - 31 3.20298298236841e+00 1.14429095893840e-03 - 32 3.20373228203772e+00 1.14429095893840e-03 - 33 3.20472609467411e+00 1.14429095893840e-03 - 34 3.20590411329665e+00 1.14429095893840e-03 - 35 3.20720736568876e+00 1.14429095893840e-03 - 36 3.20858216935653e+00 1.14429095893840e-03 - 37 3.20998315165031e+00 1.14429095893840e-03 - 38 3.21137529148386e+00 1.14429095893840e-03 - 39 3.21273513229142e+00 1.14429095893840e-03 - 40 3.21405136086868e+00 1.50805870086533e-03 + 20 3.21688278597333e+00 6.66334787942696e-04 + 21 3.21458283262116e+00 6.66334787942696e-04 + 22 3.21223351074552e+00 6.66334787942696e-04 + 23 3.20995434276490e+00 6.66334787942696e-04 + 24 3.20785376300757e+00 6.66334787942696e-04 + 25 3.20602301895356e+00 6.66334787942696e-04 + 26 3.20453185497061e+00 6.66334787942696e-04 + 27 3.20342630674324e+00 6.66334787942696e-04 + 28 3.20272853390700e+00 6.66334787942696e-04 + 29 3.20243824119566e+00 6.66334787942696e-04 + 30 3.20253526877602e+00 1.14429095260314e-03 + 31 3.20298298275490e+00 1.14429095260314e-03 + 32 3.20373228243844e+00 1.14429095260314e-03 + 33 3.20472609508842e+00 1.14429095260314e-03 + 34 3.20590411372385e+00 1.14429095260314e-03 + 35 3.20720736612802e+00 1.14429095260314e-03 + 36 3.20858216980690e+00 1.14429095260314e-03 + 37 3.20998315211066e+00 1.14429095260314e-03 + 38 3.21137529195283e+00 1.14429095260314e-03 + 39 3.21273513276742e+00 1.14429095260314e-03 + 40 3.21405136134992e+00 1.50805868972440e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf index 38a897e10..051812fec 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.97104317611064e-03 - 7.50000000000000e-01 3.97104317611064e-03 - 1.25000000000000e+00 3.97104317611064e-03 - 1.75000000000000e+00 3.97096878377000e-03 - 2.25000000000000e+00 3.93533096044630e-03 - 2.75000000000000e+00 2.62638177747102e-03 + 2.50000000000000e-01 3.97104317655277e-03 + 7.50000000000000e-01 3.97104317655277e-03 + 1.25000000000000e+00 3.97104317655277e-03 + 1.75000000000000e+00 3.97096878421245e-03 + 2.25000000000000e+00 3.93533096098801e-03 + 2.75000000000000e+00 2.62638177969546e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 3.05127285009526e-03 - 4.25000000000000e+00 3.95433517169692e-03 - 4.75000000000000e+00 3.97104317611064e-03 - 5.25000000000000e+00 3.97104317611064e-03 - 5.75000000000000e+00 3.97104317611064e-03 - 6.25000000000000e+00 3.97104317611064e-03 - 6.75000000000000e+00 3.97104317611064e-03 - 7.25000000000000e+00 3.97104317611064e-03 - 7.75000000000000e+00 3.97104317611064e-03 - 8.25000000000000e+00 3.97104317611064e-03 - 8.75000000000000e+00 3.97104317611064e-03 - 9.25000000000000e+00 3.97104317611064e-03 - 9.75000000000000e+00 3.97104317611064e-03 + 3.75000000000000e+00 3.05127284913705e-03 + 4.25000000000000e+00 3.95433517209045e-03 + 4.75000000000000e+00 3.97104317655277e-03 + 5.25000000000000e+00 3.97104317655277e-03 + 5.75000000000000e+00 3.97104317655277e-03 + 6.25000000000000e+00 3.97104317655277e-03 + 6.75000000000000e+00 3.97104317655277e-03 + 7.25000000000000e+00 3.97104317655277e-03 + 7.75000000000000e+00 3.97104317655277e-03 + 8.25000000000000e+00 3.97104317655277e-03 + 8.75000000000000e+00 3.97104317655277e-03 + 9.25000000000000e+00 3.97104317655277e-03 + 9.75000000000000e+00 3.97104317655277e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out index dbedf374d..2fccbc3b5 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,26 +111,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped index 5268daf85..c1e336541 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253464583e+00 } diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj index 9f55268e7..787f78aa5 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 0.00000000000000e+00 + 11 3.21950367383415e+00 0.00000000000000e+00 + 12 3.22130499858006e+00 0.00000000000000e+00 + 13 3.22263479496347e+00 0.00000000000000e+00 + 14 3.22341769665784e+00 0.00000000000000e+00 + 15 3.22361473677138e+00 0.00000000000000e+00 + 16 3.22322417514557e+00 0.00000000000000e+00 + 17 3.22227942564879e+00 0.00000000000000e+00 + 18 3.22084479803044e+00 0.00000000000000e+00 + 19 3.21900979846930e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj b/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj index 31a359570..1a1e986ed 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj @@ -1,8 +1,8 @@ # step running average running stddev - 8 3.20722823881721e+00 7.80321480520572e-03 - 10 4.01156286689271e+00 4.58710790766007e-01 - 12 4.01592904504379e+00 4.58975774808969e-01 - 14 4.02060142596487e+00 4.60400083999393e-01 - 16 4.02443749721375e+00 4.62636256583393e-01 - 18 4.02653254505012e+00 4.65172918760069e-01 - 20 4.02641855058464e+00 4.67427978018598e-01 + 8 3.20722823883620e+00 7.80321483722600e-03 + 10 4.01156286692710e+00 4.58710790751680e-01 + 12 4.01592904509911e+00 4.58975774793035e-01 + 14 4.02060142604598e+00 4.60400083982649e-01 + 16 4.02443749732474e+00 4.62636256566416e-01 + 18 4.02653254519438e+00 4.65172918743354e-01 + 20 4.02641855076493e+00 4.67427978002713e-01 diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out index 33058590a..98b6025c4 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,30 +111,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped index b307ede0d..139366ade 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878547144e+00 } diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj index 177b1bbb8..3b596ebde 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253444007e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 + 21 3.21458253157603e+00 0.00000000000000e+00 + 22 3.21223315254029e+00 0.00000000000000e+00 + 23 3.20995392032979e+00 0.00000000000000e+00 + 24 3.20785326966943e+00 0.00000000000000e+00 + 25 3.20602244845117e+00 0.00000000000000e+00 + 26 3.20453120146139e+00 0.00000000000000e+00 + 27 3.20342556480347e+00 0.00000000000000e+00 + 28 3.20272769852622e+00 0.00000000000000e+00 + 29 3.20243730776714e+00 0.00000000000000e+00 + 30 3.20253423308456e+00 0.00000000000000e+00 + 31 3.20298183362156e+00 0.00000000000000e+00 + 32 3.20373100914607e+00 0.00000000000000e+00 + 33 3.20472468746373e+00 0.00000000000000e+00 + 34 3.20590256221113e+00 0.00000000000000e+00 + 35 3.20720566184671e+00 0.00000000000000e+00 + 36 3.20858030459458e+00 0.00000000000000e+00 + 37 3.20998111854285e+00 0.00000000000000e+00 + 38 3.21137308334419e+00 0.00000000000000e+00 + 39 3.21273274315657e+00 0.00000000000000e+00 + 40 3.21404878547144e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-runave/namd-version.txt b/namd/tests/library/000_distance-runave/namd-version.txt index 157cac038..b7bf5455c 100644 --- a/namd/tests/library/000_distance-runave/namd-version.txt +++ b/namd/tests/library/000_distance-runave/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-10-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out index ec75406ef..5b1c03881 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out @@ -130,7 +130,7 @@ colvars: # forceConstant = 0.001 colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } -colvars: # upperWalls = { 0.3 } +colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.001 [default] colvars: # upperWallConstant = 0.001 [default] colvars: The lower wall force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped index 868eb59c6..83b0d62b7 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21549621301549e+00 - v 1.63839888121770e-04 - extended_x 3.20653095017852e+00 - extended_v 1.63839888121770e-04 + x 3.21549617587205e+00 + v 1.63765399419808e-04 + extended_x 3.20653014354441e+00 + extended_v 1.63765399419808e-04 } restraint { diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj index 64538e290..ea3cb4584 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 -1.16221869387334e-02 - 1 3.20437148316484e+00 3.20554661923758e+00 -1.17525151850328e-03 -1.15445759728991e-07 -1.16221864769503e-02 - 2 3.20384207658804e+00 3.20554522853325e+00 -5.29406576805336e-04 -1.39070433041396e-06 -1.16221809141330e-02 - 3 3.20397336375347e+00 3.20554204143963e+00 1.31287165431537e-04 -3.18709362372464e-06 -1.16221681657585e-02 - 4 3.20474099381307e+00 3.20553719067761e+00 7.67630059602453e-04 -4.85076201650243e-06 -1.16221487627105e-02 - 5 3.20608361746435e+00 3.20553143865541e+00 1.34262365128279e-03 -5.75202220486511e-06 -1.16221257546216e-02 - 6 3.20790704408264e+00 3.20552611616669e+00 1.82342661828994e-03 -5.32248871654545e-06 -1.16221044646668e-02 - 7 3.21008979782599e+00 3.20552302811470e+00 2.18275374334675e-03 -3.08805199324812e-06 -1.16220921124588e-02 - 8 3.21248979814124e+00 3.20552433183893e+00 2.40000031525378e-03 1.30372423308412e-06 -1.16220973273557e-02 - 9 3.21495218657788e+00 3.20553239475798e+00 2.46238843663571e-03 8.06291905077686e-06 -1.16221295790319e-02 - 10 3.21731839169077e+00 3.20554963919372e+00 2.36620511289365e-03 1.72444357411129e-05 -1.16221985567749e-02 - 11 3.21943620459394e+00 3.20557838347673e+00 2.11781290316582e-03 2.87442830099992e-05 -1.16223135339069e-02 - 12 3.22117011052185e+00 3.20562068943396e+00 1.73390592791511e-03 4.23059572215591e-05 -1.16224827577358e-02 - 13 3.22241069262564e+00 3.20567822660596e+00 1.24058210378664e-03 5.75371720037448e-05 -1.16227129064238e-02 - 14 3.22308185566108e+00 3.20575216260901e+00 6.71163035445232e-04 7.39360030463537e-05 -1.16230086504360e-02 - 15 3.22314499588221e+00 3.20584308687961e+00 6.31402211261900e-05 9.09242706060132e-05 -1.16233723475184e-02 - 16 3.22259984691011e+00 3.20595097199241e+00 -5.45148972103338e-04 1.07885112795286e-04 -1.16238038879696e-02 - 17 3.22148234906601e+00 3.20607517342430e+00 -1.11749784410220e-03 1.24201431890135e-04 -1.16243006936972e-02 - 18 3.21986026327429e+00 3.20621446566228e+00 -1.62208579171264e-03 1.39292237986185e-04 -1.16248578626491e-02 - 19 3.21782728428053e+00 3.20636711029040e+00 -2.03297899376365e-03 1.52644628112363e-04 -1.16254684411616e-02 - 20 3.21549621301549e+00 3.20653095017852e+00 -2.33107126504306e-03 1.63839888121770e-04 -1.16261238007141e-02 + 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 -1.20221869387334e-02 + 1 3.20437148316484e+00 3.20554661526430e+00 -1.17525151850328e-03 -1.19419048416827e-07 -1.20221864610572e-02 + 2 3.20384207658198e+00 3.20554521661731e+00 -5.29406582859160e-04 -1.39864698615333e-06 -1.20221808664692e-02 + 3 3.20397336372329e+00 3.20554201761950e+00 1.31287141313052e-04 -3.19899781308815e-06 -1.20221680704780e-02 + 4 3.20474099372294e+00 3.20553715100348e+00 7.67629999647745e-04 -4.86661601385684e-06 -1.20221486040139e-02 + 5 3.20608361725515e+00 3.20553137919306e+00 1.34262353221182e-03 -5.77181042148448e-06 -1.20221255167722e-02 + 6 3.20790704366680e+00 3.20552603300132e+00 1.82342641164146e-03 -5.34619173897510e-06 -1.20221041320053e-02 + 7 3.21008979708265e+00 3.20552291735469e+00 2.18275341585361e-03 -3.11564663055446e-06 -1.20220916694188e-02 + 8 3.21248979691190e+00 3.20552418961958e+00 2.39999982925276e-03 1.27226489358961e-06 -1.20220967584783e-02 + 9 3.21495218466242e+00 3.20553221724516e+00 2.46238775052099e-03 8.02762557980444e-06 -1.20221288689807e-02 + 10 3.21731838884401e+00 3.20554942258746e+00 2.36620418158973e-03 1.72053422961567e-05 -1.20221976903498e-02 + 11 3.21943620052261e+00 3.20557812401472e+00 2.11781167860092e-03 2.87014272571360e-05 -1.20223124960589e-02 + 12 3.22117010488210e+00 3.20562038339497e+00 1.73390435948928e-03 4.22593802508272e-05 -1.20224815335799e-02 + 13 3.22241068502092e+00 3.20567787031321e+00 1.24058013882022e-03 5.74869182386481e-05 -1.20227114812528e-02 + 14 3.22308184564051e+00 3.20575175243336e+00 6.71160619590605e-04 7.38821201480224e-05 -1.20230070097334e-02 + 15 3.22314498293928e+00 3.20584261924273e+00 6.31372987673906e-05 9.08668093725243e-05 -1.20233704769709e-02 + 16 3.22259983048180e+00 3.20595044336978e+00 -5.45152457477549e-04 1.07824127056634e-04 -1.20238017734791e-02 + 17 3.22148232853223e+00 3.20607458034818e+00 -1.11750194957105e-03 1.24136978399328e-04 -1.20242983213927e-02 + 18 3.21986023795765e+00 3.20621380472449e+00 -1.62209057458140e-03 1.39224376306895e-04 -1.20248552188980e-02 + 19 3.21782725344634e+00 3.20636637814499e+00 -2.03298451131184e-03 1.52573420503577e-04 -1.20254655125800e-02 + 20 3.21549617587205e+00 3.20653014354441e+00 -2.33107757428819e-03 1.63765399419808e-04 -1.20261205741777e-02 diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out index af642ac95..fd298f3cd 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out @@ -130,7 +130,7 @@ colvars: # forceConstant = 0.001 colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } -colvars: # upperWalls = { 0.3 } +colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.001 [default] colvars: # upperWallConstant = 0.001 [default] colvars: The lower wall force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). @@ -162,7 +162,7 @@ colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.2155 -colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. +colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 0. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped index 67e9debbf..740730ef2 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21130958093225e+00 - v 1.01074979342738e-04 - extended_x 3.20938413437057e+00 - extended_v 1.01074979342738e-04 + x 3.21130917292044e+00 + v 1.00951348854985e-04 + extended_x 3.20938126631322e+00 + extended_v 1.00951348854985e-04 } restraint { diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj index 457fcb155..e35e1b0ba 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 20 3.21549621301549e+00 3.20653095017852e+00 0.00000000000000e+00 1.63839888121770e-04 -1.16261238007141e-02 - 21 3.21299151121102e+00 3.20670352294153e+00 -2.50470180446749e-03 1.72572763011582e-04 -1.16268140917661e-02 - 22 3.21044145238583e+00 3.20688218620849e+00 -2.55005882518766e-03 1.78663266959169e-04 -1.16275287448340e-02 - 23 3.20797018574579e+00 3.20706424683154e+00 -2.47126664004549e-03 1.82060623050948e-04 -1.16282569873262e-02 - 24 3.20569026122289e+00 3.20724708607441e+00 -2.27992452289572e-03 1.82839242865593e-04 -1.16289883442976e-02 - 25 3.20369635095381e+00 3.20742827327941e+00 -1.99391026908335e-03 1.81187205005368e-04 -1.16297130931177e-02 - 26 3.20206080670596e+00 3.20760566170420e+00 -1.63554424784840e-03 1.77388424785744e-04 -1.16304226468168e-02 - 27 3.20083139121777e+00 3.20777746204889e+00 -1.22941548818822e-03 1.71800344689496e-04 -1.16311098481956e-02 - 28 3.20003110175216e+00 3.20794229136206e+00 -8.00289465613613e-04 1.64829313172020e-04 -1.16317691654482e-02 - 29 3.19965963674732e+00 3.20809919710311e+00 -3.71465004831428e-04 1.56905741050733e-04 -1.16323967884124e-02 - 30 3.19969607653556e+00 3.20824765778478e+00 3.64397882326450e-05 1.48460681671230e-04 -1.16329906311391e-02 - 31 3.20010239198518e+00 3.20838756284098e+00 4.06315449623662e-04 1.39905056202667e-04 -1.16335502513639e-02 - 32 3.20082761419017e+00 3.20851917520268e+00 7.25222204989162e-04 1.31612361694413e-04 -1.16340767008107e-02 - 33 3.20181248689262e+00 3.20864308073407e+00 9.84872702445738e-04 1.23905531389011e-04 -1.16345723229363e-02 - 34 3.20299435917704e+00 3.20876012917077e+00 1.18187228442679e-03 1.17048436698551e-04 -1.16350405166831e-02 - 35 3.20431188560568e+00 3.20887137144714e+00 1.31752642863958e-03 1.11242276370810e-04 -1.16354854857885e-02 - 36 3.20570909188769e+00 3.20897799811350e+00 1.39720628201090e-03 1.06626666360912e-04 -1.16359119924540e-02 - 37 3.20713846663531e+00 3.20908128291664e+00 1.42937474761640e-03 1.03284803139886e-04 -1.16363251316666e-02 - 38 3.20856305344034e+00 3.20918253465077e+00 1.42458680502822e-03 1.01251734130282e-04 -1.16367301386031e-02 - 39 3.20995768936497e+00 3.20928305939123e+00 1.39463592463418e-03 1.00524740461639e-04 -1.16371322375649e-02 - 40 3.21130958093225e+00 3.20938413437057e+00 1.35189156727877e-03 1.01074979342738e-04 -1.16375365374823e-02 + 20 3.21549617587205e+00 3.20653014354441e+00 0.00000000000000e+00 1.63765399419808e-04 -1.20261205741776e-02 + 21 3.21299146691002e+00 3.20670263860492e+00 -2.50470896202648e-03 1.72495060509838e-04 -1.20268105544197e-02 + 22 3.21044140002284e+00 3.20688122102521e+00 -2.55006688718051e-03 1.78582420285797e-04 -1.20275248841008e-02 + 23 3.20797012436086e+00 3.20706319772925e+00 -2.47127566198468e-03 1.81976704044760e-04 -1.20282527909170e-02 + 24 3.20569018980129e+00 3.20724595005470e+00 -2.27993455957121e-03 1.82752325450367e-04 -1.20289838002188e-02 + 25 3.20369626842688e+00 3.20742704741977e+00 -1.99392137440801e-03 1.81097365062805e-04 -1.20297081896791e-02 + 26 3.20206071195224e+00 3.20760434315979e+00 -1.63555647464264e-03 1.77295740027368e-04 -1.20304173726392e-02 + 27 3.20083128306446e+00 3.20777604805432e+00 -1.22942888777944e-03 1.71704894527817e-04 -1.20311041922173e-02 + 28 3.20003097897692e+00 3.20794077923291e+00 -8.00304087535064e-04 1.64731178591497e-04 -1.20317631169316e-02 + 29 3.19965949808046e+00 3.20809758423739e+00 -3.71480896461218e-04 1.56805004478955e-04 -1.20323903369496e-02 + 30 3.19969592066247e+00 3.20824594166424e+00 3.64225820090880e-05 1.48357426850803e-04 -1.20329837666570e-02 + 31 3.20010221754926e+00 3.20838574103230e+00 4.06296886787061e-04 1.39799368064253e-04 -1.20335429641292e-02 + 32 3.20082741979556e+00 3.20851724535854e+00 7.25202246302015e-04 1.31504326231438e-04 -1.20340689814341e-02 + 33 3.20181227110765e+00 3.20864104059407e+00 9.84851312094914e-04 1.23795235534061e-04 -1.20345641623763e-02 + 34 3.20299412053733e+00 3.20875797656227e+00 1.18184942967092e-03 1.16935968202223e-04 -1.20350319062491e-02 + 35 3.20431162261699e+00 3.20886910428595e+00 1.31750207966386e-03 1.11127723682791e-04 -1.20354764171438e-02 + 36 3.20570880302891e+00 3.20897561440447e+00 1.39718041191950e-03 1.06510118513249e-04 -1.20359024576179e-02 + 37 3.20713815036053e+00 3.20907878075410e+00 1.42934733162248e-03 1.03166349632568e-04 -1.20363151230164e-02 + 38 3.20856270818102e+00 3.20917991221892e+00 1.42455782049122e-03 1.01131464818439e-04 -1.20367196488757e-02 + 39 3.20995731353255e+00 3.20928031496436e+00 1.39460535153013e-03 1.00402745444511e-04 -1.20371212598575e-02 + 40 3.21130917292044e+00 3.20938126631322e+00 1.35185938788940e-03 1.00951348854985e-04 -1.20375250652529e-02 diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt b/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/test.in b/namd/tests/library/000_distance-wall-bypassExtended-off/test.in index 770d32a5b..5a5def555 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/test.in +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/test.in @@ -30,7 +30,7 @@ colvar { harmonicWalls { colvars one lowerWalls 0.1 - upperWalls 0.3 + upperWalls 0.2 forceConstant 0.001 bypassExtendedLagrangian off } diff --git a/namd/tests/library/000_distance/AutoDiff/test.colvars.out b/namd/tests/library/000_distance/AutoDiff/test.colvars.out index 27f0966fb..1edf5300b 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,26 +108,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped index 5268daf85..283a80870 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253462243e+00 } diff --git a/namd/tests/library/000_distance/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance/AutoDiff/test.colvars.traj index 9f55268e7..d19a63aaf 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 + 1 3.20437148316545e+00 0.00000000000000e+00 + 2 3.20384028594369e+00 0.00000000000000e+00 + 3 3.20396721187615e+00 0.00000000000000e+00 + 4 3.20472817290791e+00 0.00000000000000e+00 + 5 3.20606308065559e+00 0.00000000000000e+00 + 6 3.20787989002674e+00 0.00000000000000e+00 + 7 3.21005997944336e+00 0.00000000000000e+00 + 8 3.21246460656400e+00 0.00000000000000e+00 + 9 3.21494247390735e+00 0.00000000000000e+00 + 10 3.21733851238969e+00 0.00000000000000e+00 + 11 3.21950367386500e+00 0.00000000000000e+00 + 12 3.22130499861355e+00 0.00000000000000e+00 + 13 3.22263479499712e+00 0.00000000000000e+00 + 14 3.22341769668903e+00 0.00000000000000e+00 + 15 3.22361473679752e+00 0.00000000000000e+00 + 16 3.22322417516431e+00 0.00000000000000e+00 + 17 3.22227942565775e+00 0.00000000000000e+00 + 18 3.22084479802894e+00 0.00000000000000e+00 + 19 3.21900979846159e+00 0.00000000000000e+00 + 20 3.21688253462243e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out index f4778ef00..3a7264d71 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,30 +108,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped index b307ede0d..9b4200d28 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878546491e+00 } diff --git a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj index 177b1bbb8..2f8dd9cef 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253444007e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 + 20 3.21688253462243e+00 0.00000000000000e+00 + 21 3.21458253154238e+00 0.00000000000000e+00 + 22 3.21223315249804e+00 0.00000000000000e+00 + 23 3.20995392028117e+00 0.00000000000000e+00 + 24 3.20785326961705e+00 0.00000000000000e+00 + 25 3.20602244839787e+00 0.00000000000000e+00 + 26 3.20453120140997e+00 0.00000000000000e+00 + 27 3.20342556475651e+00 0.00000000000000e+00 + 28 3.20272769848587e+00 0.00000000000000e+00 + 29 3.20243730773497e+00 0.00000000000000e+00 + 30 3.20253423306146e+00 0.00000000000000e+00 + 31 3.20298183360766e+00 0.00000000000000e+00 + 32 3.20373100914076e+00 0.00000000000000e+00 + 33 3.20472468746573e+00 0.00000000000000e+00 + 34 3.20590256221861e+00 0.00000000000000e+00 + 35 3.20720566185745e+00 0.00000000000000e+00 + 36 3.20858030460613e+00 0.00000000000000e+00 + 37 3.20998111855282e+00 0.00000000000000e+00 + 38 3.21137308335033e+00 0.00000000000000e+00 + 39 3.21273274315706e+00 0.00000000000000e+00 + 40 3.21404878546491e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance/namd-version.txt b/namd/tests/library/000_distance/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance/namd-version.txt +++ b/namd/tests/library/000_distance/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out index aa012e652..3ab6145e8 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,27 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped index 7932133bf..4e365695b 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685433498741e+00 + x 3.21685433519314e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22496300314925e-03 + accumulatedWork -1.22496300318146e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj index 036216748..7f6576778 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788600e+00 -1.23974855515440e-02 1.92122060000928e-02 1.05000000000000e-01 -6.19874277577201e-05 - 2 3.20383990649741e+00 -1.23753596259897e-02 1.91436907340719e-02 1.10000000000000e-01 -1.23864225887668e-04 - 3 3.20396636368840e+00 -1.23558654547536e-02 1.90834263919967e-02 1.15000000000000e-01 -1.85643553161436e-04 - 4 3.20472667755350e+00 -1.23389067102140e-02 1.90310773504205e-02 1.20000000000000e-01 -2.47338086712507e-04 - 5 3.20606076806240e+00 -1.23242430722496e-02 1.89858709129865e-02 1.25000000000000e-01 -3.08959302073754e-04 - 6 3.20787659962477e+00 -1.23115063984991e-02 1.89466487250355e-02 1.30000000000000e-01 -3.70516834066250e-04 - 7 3.21005556140311e+00 -1.23002222456125e-02 1.89119334114324e-02 1.35000000000000e-01 -4.32017945294312e-04 - 8 3.21245892236459e+00 -1.22898356894584e-02 1.88800076592355e-02 1.40000000000000e-01 -4.93467123741604e-04 - 9 3.21493539653826e+00 -1.22797415861530e-02 1.88490066778370e-02 1.45000000000000e-01 -5.54865831672369e-04 - 10 3.21732992614691e+00 -1.22693197045876e-02 1.88170257516728e-02 1.50000000000000e-01 -6.16212430195307e-04 - 11 3.21949347377062e+00 -1.22579738950825e-02 1.87822405015655e-02 1.55000000000000e-01 -6.77502299670720e-04 - 12 3.22129308953064e+00 -1.22451723581226e-02 1.87430307600161e-02 1.60000000000000e-01 -7.38728161461332e-04 - 13 3.22262109049609e+00 -1.22304843619843e-02 1.86980934660929e-02 1.65000000000000e-01 -7.99880583271254e-04 - 14 3.22340211781424e+00 -1.22136084712570e-02 1.86465289861450e-02 1.70000000000000e-01 -8.60948625627539e-04 - 15 3.22359721084197e+00 -1.21943888433679e-02 1.85878899079069e-02 1.75000000000000e-01 -9.21920569844378e-04 - 16 3.22320463454852e+00 -1.21728185381941e-02 1.85221888954752e-02 1.80000000000000e-01 -9.82784662535349e-04 - 17 3.22225780700082e+00 -1.21490312280033e-02 1.84498699723748e-02 1.85000000000000e-01 -1.04352981867537e-03 - 18 3.22082104146627e+00 -1.21232841658651e-02 1.83717523707893e-02 1.90000000000000e-01 -1.10414623950469e-03 - 19 3.21898384724052e+00 -1.20959353889621e-02 1.82889566167431e-02 1.95000000000000e-01 -1.16462591644950e-03 - 20 3.21685433498741e+00 -1.20674173399496e-02 1.82028201570646e-02 2.00000000000000e-01 -1.22496300314925e-03 + 1 3.20437138788663e+00 -1.23974855515465e-02 1.92122060001005e-02 1.05000000000000e-01 -6.19874277577326e-05 + 2 3.20383990649994e+00 -1.23753596259998e-02 1.91436907341031e-02 1.10000000000000e-01 -1.23864225887731e-04 + 3 3.20396636369412e+00 -1.23558654547765e-02 1.90834263920673e-02 1.15000000000000e-01 -1.85643553161614e-04 + 4 3.20472667756370e+00 -1.23389067102548e-02 1.90310773505463e-02 1.20000000000000e-01 -2.47338086712888e-04 + 5 3.20606076807835e+00 -1.23242430723134e-02 1.89858709131831e-02 1.25000000000000e-01 -3.08959302074455e-04 + 6 3.20787659964770e+00 -1.23115063985908e-02 1.89466487253177e-02 1.30000000000000e-01 -3.70516834067408e-04 + 7 3.21005556143417e+00 -1.23002222457367e-02 1.89119334118145e-02 1.35000000000000e-01 -4.32017945296092e-04 + 8 3.21245892240487e+00 -1.22898356896195e-02 1.88800076597306e-02 1.40000000000000e-01 -4.93467123744190e-04 + 9 3.21493539658876e+00 -1.22797415863550e-02 1.88490066784571e-02 1.45000000000000e-01 -5.54865831675965e-04 + 10 3.21732992620853e+00 -1.22693197048341e-02 1.88170257524289e-02 1.50000000000000e-01 -6.16212430200135e-04 + 11 3.21949347384418e+00 -1.22579738953767e-02 1.87822405024671e-02 1.55000000000000e-01 -6.77502299677019e-04 + 12 3.22129308961685e+00 -1.22451723584674e-02 1.87430307610718e-02 1.60000000000000e-01 -7.38728161469356e-04 + 13 3.22262109059558e+00 -1.22304843623823e-02 1.86980934673098e-02 1.65000000000000e-01 -7.99880583281267e-04 + 14 3.22340211792757e+00 -1.22136084717103e-02 1.86465289875292e-02 1.70000000000000e-01 -8.60948625639819e-04 + 15 3.22359721096965e+00 -1.21943888438786e-02 1.85878899094638e-02 1.75000000000000e-01 -9.21920569859212e-04 + 16 3.22320463469100e+00 -1.21728185387640e-02 1.85221888972096e-02 1.80000000000000e-01 -9.82784662553032e-04 + 17 3.22225780715853e+00 -1.21490312286341e-02 1.84498699742909e-02 1.85000000000000e-01 -1.04352981869620e-03 + 18 3.22082104163962e+00 -1.21232841665585e-02 1.83717523728909e-02 1.90000000000000e-01 -1.10414623952900e-03 + 19 3.21898384742989e+00 -1.20959353897195e-02 1.82889566190337e-02 1.95000000000000e-01 -1.16462591647759e-03 + 20 3.21685433519314e+00 -1.20674173407726e-02 1.82028201595473e-02 2.00000000000000e-01 -1.22496300318146e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out index fb727736f..baca0fc5b 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,32 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped index 1f650f086..e0888c9dd 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397283795342e+00 + x 3.21397283843462e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22496300314925e-03 + accumulatedWork -1.22496300318146e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj index ad5f71a3c..d650368f1 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685433498741e+00 -1.20674173399496e-02 1.82028201570646e-02 2.00000000000000e-01 -1.22496300314925e-03 - 21 3.21455203283509e+00 -1.20582081313404e-02 1.81750479173404e-02 2.00000000000000e-01 -1.22496300314925e-03 - 22 3.21220030725328e+00 -1.20488012290131e-02 1.81467013820335e-02 2.00000000000000e-01 -1.22496300314925e-03 - 23 3.20991868485870e+00 -1.20396747394348e-02 1.81192209789231e-02 2.00000000000000e-01 -1.22496300314925e-03 - 24 3.20781560502190e+00 -1.20312624200876e-02 1.80939094276265e-02 2.00000000000000e-01 -1.22496300314925e-03 - 25 3.20598232125433e+00 -1.20239292850173e-02 1.80718594313871e-02 2.00000000000000e-01 -1.22496300314925e-03 - 26 3.20448858493049e+00 -1.20179543397220e-02 1.80539033139553e-02 2.00000000000000e-01 -1.22496300314925e-03 - 27 3.20338043966796e+00 -1.20135217586718e-02 1.80405881307602e-02 2.00000000000000e-01 -1.22496300314925e-03 - 28 3.20268005376972e+00 -1.20107202150789e-02 1.80321750106130e-02 2.00000000000000e-01 -1.22496300314925e-03 - 29 3.20238714117950e+00 -1.20095485647180e-02 1.80286570910400e-02 2.00000000000000e-01 -1.22496300314925e-03 - 30 3.20248155154737e+00 -1.20099262061895e-02 1.80297909347646e-02 2.00000000000000e-01 -1.22496300314925e-03 - 31 3.20292665302594e+00 -1.20117066121038e-02 1.80351369669071e-02 2.00000000000000e-01 -1.22496300314925e-03 - 32 3.20367335392557e+00 -1.20146934157023e-02 1.80441072341650e-02 2.00000000000000e-01 -1.22496300314925e-03 - 33 3.20466458978601e+00 -1.20186583591440e-02 1.80560185942279e-02 2.00000000000000e-01 -1.22496300314925e-03 - 34 3.20584006083970e+00 -1.20233602433588e-02 1.80701489426977e-02 2.00000000000000e-01 -1.22496300314925e-03 - 35 3.20714080059199e+00 -1.20285632023680e-02 1.80857915891700e-02 2.00000000000000e-01 -1.22496300314925e-03 - 36 3.20851313064513e+00 -1.20340525225805e-02 1.81023025145283e-02 2.00000000000000e-01 -1.22496300314925e-03 - 37 3.20991168059037e+00 -1.20396467223615e-02 1.81191366499087e-02 2.00000000000000e-01 -1.22496300314925e-03 - 38 3.21130142981427e+00 -1.20452057192571e-02 1.81358726024029e-02 2.00000000000000e-01 -1.22496300314925e-03 - 39 3.21265892071976e+00 -1.20506356828790e-02 1.81522275451847e-02 2.00000000000000e-01 -1.22496300314925e-03 - 40 3.21397283795342e+00 -1.20558913518137e-02 1.81680645358420e-02 2.00000000000000e-01 -1.22496300314925e-03 + 20 3.21685433519314e+00 -1.20674173407726e-02 1.82028201595473e-02 2.00000000000000e-01 -1.22496300318146e-03 + 21 3.21455203305750e+00 -1.20582081322300e-02 1.81750479200222e-02 2.00000000000000e-01 -1.22496300318146e-03 + 22 3.21220030749260e+00 -1.20488012299704e-02 1.81467013849170e-02 2.00000000000000e-01 -1.22496300318146e-03 + 23 3.20991868511508e+00 -1.20396747404603e-02 1.81192209820098e-02 2.00000000000000e-01 -1.22496300318146e-03 + 24 3.20781560529541e+00 -1.20312624211816e-02 1.80939094309172e-02 2.00000000000000e-01 -1.22496300318146e-03 + 25 3.20598232154492e+00 -1.20239292861797e-02 1.80718594348811e-02 2.00000000000000e-01 -1.22496300318146e-03 + 26 3.20448858523800e+00 -1.20179543409520e-02 1.80539033176509e-02 2.00000000000000e-01 -1.22496300318146e-03 + 27 3.20338043999211e+00 -1.20135217599685e-02 1.80405881346544e-02 2.00000000000000e-01 -1.22496300318146e-03 + 28 3.20268005411016e+00 -1.20107202164406e-02 1.80321750147019e-02 2.00000000000000e-01 -1.22496300318146e-03 + 29 3.20238714153578e+00 -1.20095485661431e-02 1.80286570953188e-02 2.00000000000000e-01 -1.22496300318146e-03 + 30 3.20248155191901e+00 -1.20099262076760e-02 1.80297909392280e-02 2.00000000000000e-01 -1.22496300318146e-03 + 31 3.20292665341239e+00 -1.20117066136495e-02 1.80351369715490e-02 2.00000000000000e-01 -1.22496300318146e-03 + 32 3.20367335432625e+00 -1.20146934173050e-02 1.80441072389790e-02 2.00000000000000e-01 -1.22496300318146e-03 + 33 3.20466459020028e+00 -1.20186583608011e-02 1.80560185992068e-02 2.00000000000000e-01 -1.22496300318146e-03 + 34 3.20584006126686e+00 -1.20233602450674e-02 1.80701489478335e-02 2.00000000000000e-01 -1.22496300318146e-03 + 35 3.20714080103121e+00 -1.20285632041248e-02 1.80857915944533e-02 2.00000000000000e-01 -1.22496300318146e-03 + 36 3.20851313109546e+00 -1.20340525243818e-02 1.81023025199476e-02 2.00000000000000e-01 -1.22496300318146e-03 + 37 3.20991168105067e+00 -1.20396467242027e-02 1.81191366554506e-02 2.00000000000000e-01 -1.22496300318146e-03 + 38 3.21130143028320e+00 -1.20452057211328e-02 1.81358726080512e-02 2.00000000000000e-01 -1.22496300318146e-03 + 39 3.21265892119573e+00 -1.20506356847829e-02 1.81522275509204e-02 2.00000000000000e-01 -1.22496300318146e-03 + 40 3.21397283843462e+00 -1.20558913537385e-02 1.81680645416433e-02 2.00000000000000e-01 -1.22496300318146e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt b/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out index 2bce89042..9d06eb030 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 4 colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,27 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped index e298649e7..1cf9a8664 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685409675932e+00 + x 3.21685409696506e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj index 5c980cf93..66081f9e6 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 - 1 3.20437138788600e+00 -1.24174855515440e-02 1.92742434278505e-02 1.00000000000000e-01 - 2 3.20383990619069e+00 -1.24153596247627e-02 1.92676443265236e-02 1.00000000000000e-01 - 3 3.20396636246577e+00 -1.24158654498631e-02 1.92692143586380e-02 1.00000000000000e-01 - 4 3.20472667451135e+00 -1.24189066980454e-02 1.92786554468447e-02 1.00000000000000e-01 - 5 3.20606076201392e+00 -1.24242430480557e-02 1.92952269146450e-02 1.00000000000000e-01 - 6 3.20787658911377e+00 -1.24315063564551e-02 1.93177937863229e-02 1.00000000000000e-01 - 7 3.21005554471991e+00 -1.24402221788797e-02 1.93448909824861e-02 1.00000000000000e-01 - 8 3.21245889756338e+00 -1.24498355902535e-02 1.93748007780429e-02 1.00000000000000e-01 - 9 3.21493536145531e+00 -1.23597414458212e-02 1.90954010759439e-02 1.25000000000000e-01 - 10 3.21732987995403e+00 -1.23693195198161e-02 1.91250081729130e-02 1.25000000000000e-01 - 11 3.21949341543930e+00 -1.23779736617572e-02 1.91517789963944e-02 1.25000000000000e-01 - 12 3.22129301782985e+00 -1.23851720713194e-02 1.91740609045237e-02 1.25000000000000e-01 - 13 3.22262100399005e+00 -1.23904840159602e-02 1.91905117687206e-02 1.25000000000000e-01 - 14 3.22340201486115e+00 -1.23936080594446e-02 1.92001900913912e-02 1.25000000000000e-01 - 15 3.22359708959410e+00 -1.23943883583764e-02 1.92026078472821e-02 1.25000000000000e-01 - 16 3.22320449295439e+00 -1.23928179718176e-02 1.91977421603256e-02 1.25000000000000e-01 - 17 3.22225764280973e+00 -1.22890305712389e-02 1.88775340476056e-02 1.50000000000000e-01 - 18 3.22082085377380e+00 -1.22832834150952e-02 1.88598814319441e-02 1.50000000000000e-01 - 19 3.21898363493937e+00 -1.22759345397575e-02 1.88373211030514e-02 1.50000000000000e-01 - 20 3.21685409675932e+00 -1.22674163870373e-02 1.88111881016189e-02 1.50000000000000e-01 + 1 3.20437138788663e+00 -1.24174855515465e-02 1.92742434278583e-02 1.00000000000000e-01 + 2 3.20383990619321e+00 -1.24153596247728e-02 1.92676443265549e-02 1.00000000000000e-01 + 3 3.20396636247149e+00 -1.24158654498859e-02 1.92692143587090e-02 1.00000000000000e-01 + 4 3.20472667452156e+00 -1.24189066980862e-02 1.92786554469713e-02 1.00000000000000e-01 + 5 3.20606076202988e+00 -1.24242430481195e-02 1.92952269148432e-02 1.00000000000000e-01 + 6 3.20787658913670e+00 -1.24315063565468e-02 1.93177937866079e-02 1.00000000000000e-01 + 7 3.21005554475098e+00 -1.24402221790039e-02 1.93448909828726e-02 1.00000000000000e-01 + 8 3.21245889760366e+00 -1.24498355904147e-02 1.93748007785444e-02 1.00000000000000e-01 + 9 3.21493536150581e+00 -1.23597414460232e-02 1.90954010765681e-02 1.25000000000000e-01 + 10 3.21732988001565e+00 -1.23693195200626e-02 1.91250081736752e-02 1.25000000000000e-01 + 11 3.21949341551286e+00 -1.23779736620515e-02 1.91517789973049e-02 1.25000000000000e-01 + 12 3.22129301791606e+00 -1.23851720716642e-02 1.91740609055915e-02 1.25000000000000e-01 + 13 3.22262100408954e+00 -1.23904840163582e-02 1.91905117699534e-02 1.25000000000000e-01 + 14 3.22340201497448e+00 -1.23936080598979e-02 1.92001900927959e-02 1.25000000000000e-01 + 15 3.22359708972178e+00 -1.23943883588871e-02 1.92026078488646e-02 1.25000000000000e-01 + 16 3.22320449309688e+00 -1.23928179723875e-02 1.91977421620913e-02 1.25000000000000e-01 + 17 3.22225764296745e+00 -1.22890305718698e-02 1.88775340495438e-02 1.50000000000000e-01 + 18 3.22082085394715e+00 -1.22832834157886e-02 1.88598814340734e-02 1.50000000000000e-01 + 19 3.21898363512874e+00 -1.22759345405150e-02 1.88373211053761e-02 1.50000000000000e-01 + 20 3.21685409696506e+00 -1.22674163878602e-02 1.88111881041427e-02 1.50000000000000e-01 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out index abea13011..ac78db1f1 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 4 colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,32 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped index 14415afc1..59699cf48 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397207945158e+00 + x 3.21397207993279e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj index c6b191d7a..cb822a1c2 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one - 20 3.21685409675932e+00 -1.22674163870373e-02 1.88111881016189e-02 1.50000000000000e-01 - 21 3.21455176714650e+00 -1.22582070685860e-02 1.87829550670414e-02 1.50000000000000e-01 - 22 3.21220001266275e+00 -1.22488000506510e-02 1.87541378351035e-02 1.50000000000000e-01 - 23 3.20991836001725e+00 -1.22396734400690e-02 1.87262007399414e-02 1.50000000000000e-01 - 24 3.20781524867392e+00 -1.22312609946957e-02 1.87004681900454e-02 1.50000000000000e-01 - 25 3.20598193223964e+00 -1.21239277289585e-02 1.83737029471263e-02 1.75000000000000e-01 - 26 3.20448816372304e+00 -1.21179526548922e-02 1.83555970682760e-02 1.75000000000000e-01 - 27 3.20337998682136e+00 -1.21135199472854e-02 1.83421706891602e-02 1.75000000000000e-01 - 28 3.20267956990048e+00 -1.21107182796019e-02 1.83336871559855e-02 1.75000000000000e-01 - 29 3.20238662695248e+00 -1.21095465078099e-02 1.83301395781014e-02 1.75000000000000e-01 - 30 3.20248100766347e+00 -1.21099240306539e-02 1.83312825035261e-02 1.75000000000000e-01 - 31 3.20292608021181e+00 -1.21117043208472e-02 1.83366726944537e-02 1.75000000000000e-01 - 32 3.20367275292539e+00 -1.21146910117016e-02 1.83457172886253e-02 1.75000000000000e-01 - 33 3.20466396135575e+00 -1.20186558454230e-02 1.80560110413401e-02 2.00000000000000e-01 - 34 3.20583940727948e+00 -1.20233576291179e-02 1.80701410847085e-02 2.00000000000000e-01 - 35 3.20714012418463e+00 -1.20285604967385e-02 1.80857834529623e-02 2.00000000000000e-01 - 36 3.20851243363315e+00 -1.20340497345326e-02 1.81022941266506e-02 2.00000000000000e-01 - 37 3.20991096515382e+00 -1.20396438606153e-02 1.81191280363064e-02 2.00000000000000e-01 - 38 3.21130069805223e+00 -1.20452027922089e-02 1.81358637881797e-02 2.00000000000000e-01 - 39 3.21265817463677e+00 -1.20506326985471e-02 1.81522185544115e-02 2.00000000000000e-01 - 40 3.21397207945158e+00 -1.20558883178063e-02 1.81680553914274e-02 2.00000000000000e-01 + 20 3.21685409696506e+00 -1.22674163878602e-02 1.88111881041427e-02 1.50000000000000e-01 + 21 3.21455176736891e+00 -1.22582070694756e-02 1.87829550697678e-02 1.50000000000000e-01 + 22 3.21220001290207e+00 -1.22488000516083e-02 1.87541378380349e-02 1.50000000000000e-01 + 23 3.20991836027364e+00 -1.22396734410946e-02 1.87262007430795e-02 1.50000000000000e-01 + 24 3.20781524894743e+00 -1.22312609957897e-02 1.87004681933909e-02 1.50000000000000e-01 + 25 3.20598193253024e+00 -1.21239277301209e-02 1.83737029506495e-02 1.75000000000000e-01 + 26 3.20448816403056e+00 -1.21179526561222e-02 1.83555970720025e-02 1.75000000000000e-01 + 27 3.20337998714552e+00 -1.21135199485821e-02 1.83421706930870e-02 1.75000000000000e-01 + 28 3.20267957024093e+00 -1.21107182809637e-02 1.83336871601086e-02 1.75000000000000e-01 + 29 3.20238662730877e+00 -1.21095465092351e-02 1.83301395824160e-02 1.75000000000000e-01 + 30 3.20248100803512e+00 -1.21099240321405e-02 1.83312825080267e-02 1.75000000000000e-01 + 31 3.20292608059827e+00 -1.21117043223931e-02 1.83366726991344e-02 1.75000000000000e-01 + 32 3.20367275332608e+00 -1.21146910133043e-02 1.83457172934795e-02 1.75000000000000e-01 + 33 3.20466396177004e+00 -1.20186558470801e-02 1.80560110463192e-02 2.00000000000000e-01 + 34 3.20583940770664e+00 -1.20233576308266e-02 1.80701410898444e-02 2.00000000000000e-01 + 35 3.20714012462387e+00 -1.20285604984955e-02 1.80857834582457e-02 2.00000000000000e-01 + 36 3.20851243408350e+00 -1.20340497363340e-02 1.81022941320700e-02 2.00000000000000e-01 + 37 3.20991096561413e+00 -1.20396438624565e-02 1.81191280418484e-02 2.00000000000000e-01 + 38 3.21130069852117e+00 -1.20452027940847e-02 1.81358637938281e-02 2.00000000000000e-01 + 39 3.21265817511275e+00 -1.20506327004510e-02 1.81522185601474e-02 2.00000000000000e-01 + 40 3.21397207993279e+00 -1.20558883197312e-02 1.81680553972288e-02 2.00000000000000e-01 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt b/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out index c5200e63f..437e26dcb 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,27 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped index 5ef095f44..4109af1f5 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685457618647e+00 + x 3.21685457639221e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj index 5eec6dc1f..c0e02c1fa 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788600e+00 -1.23774855515440e-02 1.91502685723351e-02 1.10000000000000e-01 -1.23774855515440e-04 - 2 3.20383990680414e+00 -1.23353596272166e-02 1.90201371415956e-02 1.20000000000000e-01 -2.47128451787606e-04 - 3 3.20396636491103e+00 -1.22958654596441e-02 1.88985384252087e-02 1.30000000000000e-01 -3.70087106384047e-04 - 4 3.20472668059564e+00 -1.22589067223826e-02 1.87850992535096e-02 1.40000000000000e-01 -4.92676173607873e-04 - 5 3.20606077411088e+00 -1.22242430964435e-02 1.86790149101184e-02 1.50000000000000e-01 -6.14918604572308e-04 - 6 3.20787661013578e+00 -1.21915064405431e-02 1.85791036612255e-02 1.60000000000000e-01 -7.36833668977739e-04 - 7 3.21005557808631e+00 -1.21602223123453e-02 1.84838758357074e-02 1.70000000000000e-01 -8.58435892101191e-04 - 8 3.21245894716580e+00 -1.21298357886632e-02 1.83916145324919e-02 1.80000000000000e-01 -9.79734249987824e-04 - 9 3.21493543162121e+00 -1.20997417264848e-02 1.83004687309548e-02 1.90000000000000e-01 -1.10073166725267e-03 - 10 3.21732997387476e+00 -1.20693198954990e-02 1.82085603424861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 11 3.21949353668785e+00 -1.20779741467514e-02 1.82346824361994e-02 2.00000000000000e-01 -1.22142486620766e-03 - 12 3.22129316973139e+00 -1.20851726789256e-02 1.82564248349311e-02 2.00000000000000e-01 -1.22142486620766e-03 - 13 3.22262118961603e+00 -1.20904847584641e-02 1.82724777118316e-02 2.00000000000000e-01 -1.22142486620766e-03 - 14 3.22340223703211e+00 -1.20936089481284e-02 1.82819221737815e-02 2.00000000000000e-01 -1.22142486620766e-03 - 15 3.22359735089020e+00 -1.20943894035608e-02 1.82842818806205e-02 2.00000000000000e-01 -1.22142486620766e-03 - 16 3.22320479573201e+00 -1.20928191829280e-02 1.82795344738740e-02 2.00000000000000e-01 -1.22142486620766e-03 - 17 3.22225798922225e+00 -1.20890319568890e-02 1.82680867068354e-02 2.00000000000000e-01 -1.22142486620766e-03 - 18 3.22082124425633e+00 -1.20832849770253e-02 1.82507219795008e-02 2.00000000000000e-01 -1.22142486620766e-03 - 19 3.21898406979118e+00 -1.20759362791647e-02 1.82285296273058e-02 2.00000000000000e-01 -1.22142486620766e-03 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 + 1 3.20437138788663e+00 -1.23774855515465e-02 1.91502685723428e-02 1.10000000000000e-01 -1.23774855515465e-04 + 2 3.20383990680667e+00 -1.23353596272267e-02 1.90201371416267e-02 1.20000000000000e-01 -2.47128451787732e-04 + 3 3.20396636491675e+00 -1.22958654596670e-02 1.88985384252790e-02 1.30000000000000e-01 -3.70087106384402e-04 + 4 3.20472668060584e+00 -1.22589067224234e-02 1.87850992536346e-02 1.40000000000000e-01 -4.92676173608635e-04 + 5 3.20606077412683e+00 -1.22242430965073e-02 1.86790149103134e-02 1.50000000000000e-01 -6.14918604573709e-04 + 6 3.20787661015870e+00 -1.21915064406348e-02 1.85791036615050e-02 1.60000000000000e-01 -7.36833668980057e-04 + 7 3.21005557811738e+00 -1.21602223124695e-02 1.84838758360852e-02 1.70000000000000e-01 -8.58435892104752e-04 + 8 3.21245894720608e+00 -1.21298357888243e-02 1.83916145329805e-02 1.80000000000000e-01 -9.79734249992995e-04 + 9 3.21493543167171e+00 -1.20997417266868e-02 1.83004687315658e-02 1.90000000000000e-01 -1.10073166725986e-03 + 10 3.21732997393638e+00 -1.20693198957455e-02 1.82085603432298e-02 2.00000000000000e-01 -1.22142486621732e-03 + 11 3.21949353676140e+00 -1.20779741470456e-02 1.82346824370878e-02 2.00000000000000e-01 -1.22142486621732e-03 + 12 3.22129316981759e+00 -1.20851726792704e-02 1.82564248359729e-02 2.00000000000000e-01 -1.22142486621732e-03 + 13 3.22262118971552e+00 -1.20904847588621e-02 1.82724777130345e-02 2.00000000000000e-01 -1.22142486621732e-03 + 14 3.22340223714544e+00 -1.20936089485818e-02 1.82819221751521e-02 2.00000000000000e-01 -1.22142486621732e-03 + 15 3.22359735101788e+00 -1.20943894040715e-02 1.82842818821647e-02 2.00000000000000e-01 -1.22142486621732e-03 + 16 3.22320479587449e+00 -1.20928191834980e-02 1.82795344755970e-02 2.00000000000000e-01 -1.22142486621732e-03 + 17 3.22225798937996e+00 -1.20890319575198e-02 1.82680867087420e-02 2.00000000000000e-01 -1.22142486621732e-03 + 18 3.22082124442969e+00 -1.20832849777187e-02 1.82507219815954e-02 2.00000000000000e-01 -1.22142486621732e-03 + 19 3.21898406998055e+00 -1.20759362799222e-02 1.82285296295926e-02 2.00000000000000e-01 -1.22142486621732e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out index c92a324d4..ec62b7868 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,32 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped index a27db3dc3..100eebdff 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397324438969e+00 + x 3.21397324487089e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj index 9592912c4..82871cb9e 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 - 21 3.21455229130029e+00 -1.20582091652012e-02 1.81750510339676e-02 2.00000000000000e-01 -1.22142486620766e-03 - 22 3.21220058167135e+00 -1.20488023266854e-02 1.81467046884425e-02 2.00000000000000e-01 -1.22142486620766e-03 - 23 3.20991897400811e+00 -1.20396758960324e-02 1.81192244601880e-02 2.00000000000000e-01 -1.22142486620766e-03 - 24 3.20781590778578e+00 -1.20312636311431e-02 1.80939130702584e-02 2.00000000000000e-01 -1.22142486620766e-03 - 25 3.20598263662306e+00 -1.20239305464922e-02 1.80718632233586e-02 2.00000000000000e-01 -1.22142486620766e-03 - 26 3.20448891199500e+00 -1.20179556479800e-02 1.80539072446018e-02 2.00000000000000e-01 -1.22142486620766e-03 - 27 3.20338077760483e+00 -1.20135231104193e-02 1.80405921905723e-02 2.00000000000000e-01 -1.22142486620766e-03 - 28 3.20268040182054e+00 -1.20107216072822e-02 1.80321791909543e-02 2.00000000000000e-01 -1.22142486620766e-03 - 29 3.20238749862618e+00 -1.20095499945047e-02 1.80286613838135e-02 2.00000000000000e-01 -1.22142486620766e-03 - 30 3.20248191768589e+00 -1.20099276707435e-02 1.80297953320614e-02 2.00000000000000e-01 -1.22142486620766e-03 - 31 3.20292702714129e+00 -1.20117081085652e-02 1.80351414606713e-02 2.00000000000000e-01 -1.22142486620766e-03 - 32 3.20367373527010e+00 -1.20146949410804e-02 1.80441118159029e-02 2.00000000000000e-01 -1.22142486620766e-03 - 33 3.20466497756289e+00 -1.20186599102516e-02 1.80560232547861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 34 3.20584045419353e+00 -1.20233618167741e-02 1.80701536721327e-02 2.00000000000000e-01 -1.22142486620766e-03 - 35 3.20714119860834e+00 -1.20285647944334e-02 1.80857963767352e-02 2.00000000000000e-01 -1.22142486620766e-03 - 36 3.20851353235803e+00 -1.20340541294321e-02 1.81023073487628e-02 2.00000000000000e-01 -1.22142486620766e-03 - 37 3.20991208499767e+00 -1.20396483399907e-02 1.81191415188300e-02 2.00000000000000e-01 -1.22142486620766e-03 - 38 3.21130183589808e+00 -1.20452073435923e-02 1.81358774937663e-02 2.00000000000000e-01 -1.22142486620766e-03 - 39 3.21265932746957e+00 -1.20506373098783e-02 1.81522324467788e-02 2.00000000000000e-01 -1.22142486620766e-03 - 40 3.21397324438969e+00 -1.20558929775587e-02 1.81680694357938e-02 2.00000000000000e-01 -1.22142486620766e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 + 21 3.21455229152270e+00 -1.20582091660908e-02 1.81750510366495e-02 2.00000000000000e-01 -1.22142486621732e-03 + 22 3.21220058191067e+00 -1.20488023276427e-02 1.81467046913260e-02 2.00000000000000e-01 -1.22142486621732e-03 + 23 3.20991897426449e+00 -1.20396758970580e-02 1.81192244632749e-02 2.00000000000000e-01 -1.22142486621732e-03 + 24 3.20781590805930e+00 -1.20312636322372e-02 1.80939130735492e-02 2.00000000000000e-01 -1.22142486621732e-03 + 25 3.20598263691365e+00 -1.20239305476546e-02 1.80718632268527e-02 2.00000000000000e-01 -1.22142486621732e-03 + 26 3.20448891230251e+00 -1.20179556492100e-02 1.80539072482974e-02 2.00000000000000e-01 -1.22142486621732e-03 + 27 3.20338077792898e+00 -1.20135231117159e-02 1.80405921944666e-02 2.00000000000000e-01 -1.22142486621732e-03 + 28 3.20268040216098e+00 -1.20107216086439e-02 1.80321791950433e-02 2.00000000000000e-01 -1.22142486621732e-03 + 29 3.20238749898247e+00 -1.20095499959299e-02 1.80286613880924e-02 2.00000000000000e-01 -1.22142486621732e-03 + 30 3.20248191805753e+00 -1.20099276722301e-02 1.80297953365248e-02 2.00000000000000e-01 -1.22142486621732e-03 + 31 3.20292702752774e+00 -1.20117081101110e-02 1.80351414653132e-02 2.00000000000000e-01 -1.22142486621732e-03 + 32 3.20367373567078e+00 -1.20146949426831e-02 1.80441118207169e-02 2.00000000000000e-01 -1.22142486621732e-03 + 33 3.20466497797716e+00 -1.20186599119087e-02 1.80560232597650e-02 2.00000000000000e-01 -1.22142486621732e-03 + 34 3.20584045462068e+00 -1.20233618184827e-02 1.80701536772685e-02 2.00000000000000e-01 -1.22142486621732e-03 + 35 3.20714119904756e+00 -1.20285647961903e-02 1.80857963820184e-02 2.00000000000000e-01 -1.22142486621732e-03 + 36 3.20851353280837e+00 -1.20340541312335e-02 1.81023073541822e-02 2.00000000000000e-01 -1.22142486621732e-03 + 37 3.20991208545797e+00 -1.20396483418319e-02 1.81191415243719e-02 2.00000000000000e-01 -1.22142486621732e-03 + 38 3.21130183636701e+00 -1.20452073454680e-02 1.81358774994146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 39 3.21265932794554e+00 -1.20506373117822e-02 1.81522324525146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 40 3.21397324487089e+00 -1.20558929794836e-02 1.81680694415952e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt b/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out index 99cf50a61..908c0f068 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,27 +125,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped index fec1e803e..9eef8b44e 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685399817416e+00 + x 3.21685399835649e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj index 2cd06ea2b..5a6aa23cd 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.24221869387334e-02 - 1 3.20437138788600e+00 -1.24174855515440e-02 - 2 3.20383990619069e+00 -1.24153596247627e-02 - 3 3.20396636246577e+00 -1.24158654498631e-02 - 4 3.20472667451135e+00 -1.24189066980454e-02 - 5 3.20606076201392e+00 -1.24242430480557e-02 - 6 3.20787658911377e+00 -1.24315063564551e-02 - 7 3.21005554471991e+00 -1.24402221788797e-02 - 8 3.21245889756338e+00 -1.24498355902535e-02 - 9 3.21493536145531e+00 -1.24597414458212e-02 - 10 3.21732987841907e+00 -1.24693195136763e-02 - 11 3.21949341085340e+00 -1.24779736434136e-02 - 12 3.22129300871542e+00 -1.24851720348617e-02 - 13 3.22262098892565e+00 -1.24904839557026e-02 - 14 3.22340199249676e+00 -1.24936079699870e-02 - 15 3.22359705866319e+00 -1.24943882346527e-02 - 16 3.22320445228234e+00 -1.24928178091294e-02 - 17 3.22225759131848e+00 -1.24890303652739e-02 - 18 3.22082078894448e+00 -1.24832831557779e-02 - 19 3.21898355436871e+00 -1.24759342174748e-02 - 20 3.21685399817416e+00 -1.24674159926967e-02 + 1 3.20437138788661e+00 -1.24174855515465e-02 + 2 3.20383990624489e+00 -1.24153596249795e-02 + 3 3.20396636247331e+00 -1.24158654498932e-02 + 4 3.20472667455914e+00 -1.24189066982366e-02 + 5 3.20606076201901e+00 -1.24242430480760e-02 + 6 3.20787658913293e+00 -1.24315063565317e-02 + 7 3.21005554475517e+00 -1.24402221790207e-02 + 8 3.21245889761578e+00 -1.24498355904631e-02 + 9 3.21493536152545e+00 -1.24597414461018e-02 + 10 3.21732987850678e+00 -1.24693195140271e-02 + 11 3.21949341095784e+00 -1.24779736438313e-02 + 12 3.22129300883514e+00 -1.24851720353406e-02 + 13 3.22262098905883e+00 -1.24904839562353e-02 + 14 3.22340199264132e+00 -1.24936079705653e-02 + 15 3.22359705881703e+00 -1.24943882352681e-02 + 16 3.22320445244359e+00 -1.24928178097743e-02 + 17 3.22225759148518e+00 -1.24890303659407e-02 + 18 3.22082078911634e+00 -1.24832831564654e-02 + 19 3.21898355455034e+00 -1.24759342182014e-02 + 20 3.21685399835649e+00 -1.24674159934260e-02 diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out index a71fdf83a..8752f5403 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,32 +125,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 086f80ad0..ba9e5b167 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397114716924e+00 + x 3.21397114764396e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 8924671f5..d18eb0fa7 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685399817416e+00 -1.24674159926967e-02 - 21 3.21455164841394e+00 -1.24582065936557e-02 - 22 3.21219987179556e+00 -1.24487994871822e-02 - 23 3.20991819517487e+00 -1.24396727806995e-02 - 24 3.20781505815938e+00 -1.24312602326375e-02 - 25 3.20598171449351e+00 -1.24239268579740e-02 - 26 3.20448791577891e+00 -1.24179516631157e-02 - 27 3.20337970585434e+00 -1.24135188234173e-02 - 28 3.20267925323760e+00 -1.24107170129504e-02 - 29 3.20238627208178e+00 -1.24095450883271e-02 - 30 3.20248061224166e+00 -1.24099224489666e-02 - 31 3.20292564206961e+00 -1.24117025682784e-02 - 32 3.20367227007056e+00 -1.24146890802823e-02 - 33 3.20466343197421e+00 -1.24186537278969e-02 - 34 3.20583882819824e+00 -1.24233553127930e-02 - 35 3.20713949242506e+00 -1.24285579697002e-02 - 36 3.20851174642574e+00 -1.24340469857030e-02 - 37 3.20991021994729e+00 -1.24396408797892e-02 - 38 3.21129989251817e+00 -1.24451995700727e-02 - 39 3.21265730667037e+00 -1.24506292266815e-02 - 40 3.21397114716924e+00 -1.24558845886769e-02 + 20 3.21685399835649e+00 -1.24674159934260e-02 + 21 3.21455164860269e+00 -1.24582065944107e-02 + 22 3.21219987199261e+00 -1.24487994879705e-02 + 23 3.20991819538261e+00 -1.24396727815305e-02 + 24 3.20781505838050e+00 -1.24312602335220e-02 + 25 3.20598171473079e+00 -1.24239268589232e-02 + 26 3.20448791603500e+00 -1.24179516641400e-02 + 27 3.20337970613153e+00 -1.24135188245261e-02 + 28 3.20267925353770e+00 -1.24107170141508e-02 + 29 3.20238627240592e+00 -1.24095450896237e-02 + 30 3.20248061259023e+00 -1.24099224503609e-02 + 31 3.20292564244219e+00 -1.24117025697688e-02 + 32 3.20367227046597e+00 -1.24146890818639e-02 + 33 3.20466343239054e+00 -1.24186537295621e-02 + 34 3.20583882863293e+00 -1.24233553145317e-02 + 35 3.20713949287508e+00 -1.24285579715003e-02 + 36 3.20851174688770e+00 -1.24340469875508e-02 + 37 3.20991022041763e+00 -1.24396408816705e-02 + 38 3.21129989299330e+00 -1.24451995719732e-02 + 39 3.21265730714688e+00 -1.24506292285875e-02 + 40 3.21397114764396e+00 -1.24558845905758e-02 diff --git a/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out index 8085f9903..db180cf49 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out @@ -1,174 +1,118 @@ colvars: ---------------------------------------------------------------------- -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] -colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) -colvars: # smp = on [default] +colvars: # indexFile = index.ndx +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] +colvars: # colvarsTrajAppend = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = "one" +colvars: # name = one colvars: Initializing a new "distance" component. -colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # scalable = on [default] +colvars: # oneSiteSystemForce = off [default] colvars: Initializing atom group "group1". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] -colvars: # indexGroup = "group1" +colvars: # indexGroup = group1 colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Enabling scalable calculation for group "group1". -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028. colvars: Initializing atom group "group2". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] -colvars: # indexGroup = "group2" +colvars: # indexGroup = group2 colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Enabling scalable calculation for group "group2". -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028. colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerWallConstant = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputTotalForce = off [default] +colvars: # outputSystemForce = off [default] colvars: # outputAppliedForce = on -colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = on -colvars: # outputFreq = 10 [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] +colvars: # forceConstant = 0.001 colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] -colvars: # outputCenters = off [default] -colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 -colvars: # targetNumSteps = 8 -colvars: # targetNumStages = 4 -colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: # targetNumSteps = 8 +colvars: # targetNumStages = 4 +colvars: # targetForceExponent = 1 [default] +colvars: # outputCenters = off [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- -colvars: Updating NAMD interface: -colvars: updating atomic data (0 atoms). -colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). -colvars: Updating NAMD interface: -colvars: updating atomic data (0 atoms). -colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Restraint harmonic1, stage 0 : lambda = 0, k = 0.001 -colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Restraint harmonic1 Lambda= 0 dA/dLambda= -0.0195425 -colvars: Restraint harmonic1, stage 1 : lambda = 0.25, k = 0.000775 +colvars: Writing to colvar trajectory file "test.colvars.traj". +colvars: Restraint harmonic1, stage 0 : lambda = 0 +colvars: Setting force constant to 0.001 +colvars: Lambda= 0 dA/dLambda= -0.0195425 +colvars: Restraint harmonic1, stage 1 : lambda = 0.25 +colvars: Setting force constant to 0.000775 +colvars: Writing the state file "test.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.tmp.colvars.state". -colvars: Restraint harmonic1 Lambda= 0.25 dA/dLambda= -0.0175302 -colvars: Restraint harmonic1, stage 2 : lambda = 0.5, k = 0.00055 +colvars: Lambda= 0.25 dA/dLambda= -0.0175302 +colvars: Restraint harmonic1, stage 2 : lambda = 0.5 +colvars: Setting force constant to 0.00055 +colvars: Writing the state file "test.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.tmp.colvars.state". colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped index 199ba99ec..57c7b11d1 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685733295311e+00 + x 3.21685733313543e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj index b1edac98e..ec772e9bf 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 - 1 3.20437138788600e+00 -1.24174855515440e-02 1.92742434278505e-02 - 2 3.20383990619069e+00 -1.24153596247627e-02 1.92676443265236e-02 - 3 3.20396636246577e+00 -1.24158654498631e-02 1.92692143586380e-02 - 4 3.20472667451135e+00 -1.24189066980454e-02 1.92786554468447e-02 - 5 3.20606076201392e+00 -1.24242430480557e-02 1.92952269146450e-02 - 6 3.20787658911377e+00 -1.24315063564551e-02 1.93177937863229e-02 - 7 3.21005554471991e+00 -1.24402221788797e-02 1.93448909824861e-02 - 8 3.21245889756338e+00 -9.64862258244647e-03 1.50154706029832e-02 - 9 3.21493540443572e+00 -9.65629975375074e-03 1.50393749894011e-02 - 10 3.21733000686193e+00 -9.66372302127197e-03 1.50625068761068e-02 - 11 3.21949366620235e+00 -9.67043036522729e-03 1.50834231368887e-02 - 12 3.22129343087844e+00 -9.67600963572316e-03 1.51008326565496e-02 - 13 3.22262161584524e+00 -9.68012700912024e-03 1.51136869214031e-02 - 14 3.22340285980675e+00 -9.68254886540093e-03 1.51212504082059e-02 - 15 3.22359819944574e+00 -9.68315441828180e-03 1.51231418529500e-02 - 16 3.22320589693159e+00 -6.87105297324950e-03 1.07298565820911e-02 - 17 3.22225941074492e+00 -6.86897070363883e-03 1.07233542107838e-02 - 18 3.22082305081454e+00 -6.86581071179198e-03 1.07134901659449e-02 - 19 3.21898632267996e+00 -6.86176990989590e-03 1.07008832491711e-02 - 20 3.21685733295311e+00 -6.85708613249684e-03 1.06862795973819e-02 + 1 3.20437138788661e+00 -1.24174855515465e-02 1.92742434278581e-02 + 2 3.20383990624489e+00 -1.24153596249795e-02 1.92676443271965e-02 + 3 3.20396636247331e+00 -1.24158654498932e-02 1.92692143587316e-02 + 4 3.20472667455914e+00 -1.24189066982366e-02 1.92786554474381e-02 + 5 3.20606076201901e+00 -1.24242430480760e-02 1.92952269147082e-02 + 6 3.20787658913293e+00 -1.24315063565317e-02 1.93177937865610e-02 + 7 3.21005554475517e+00 -1.24402221790207e-02 1.93448909829248e-02 + 8 3.21245889761578e+00 -9.64862258260892e-03 1.50154706034888e-02 + 9 3.21493540450586e+00 -9.65629975396818e-03 1.50393749900784e-02 + 10 3.21733000694964e+00 -9.66372302154388e-03 1.50625068769544e-02 + 11 3.21949366630678e+00 -9.67043036555102e-03 1.50834231378986e-02 + 12 3.22129343099816e+00 -9.67600963609430e-03 1.51008326577080e-02 + 13 3.22262161597842e+00 -9.68012700953309e-03 1.51136869226923e-02 + 14 3.22340285995130e+00 -9.68254886584905e-03 1.51212504096056e-02 + 15 3.22359819959959e+00 -9.68315441875872e-03 1.51231418544397e-02 + 16 3.22320589709283e+00 -6.87105297360423e-03 1.07298565831990e-02 + 17 3.22225941091162e+00 -6.86897070400556e-03 1.07233542119288e-02 + 18 3.22082305098640e+00 -6.86581071217007e-03 1.07134901671248e-02 + 19 3.21898632286159e+00 -6.86176991029550e-03 1.07008832504174e-02 + 20 3.21685733313543e+00 -6.85708613289795e-03 1.06862795986321e-02 diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out index e5fe4122e..cd19260d0 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out @@ -1,179 +1,123 @@ colvars: ---------------------------------------------------------------------- -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] -colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) -colvars: # smp = on [default] +colvars: # indexFile = index.ndx +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] +colvars: # colvarsTrajAppend = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = "one" +colvars: # name = one colvars: Initializing a new "distance" component. -colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # scalable = on [default] +colvars: # oneSiteSystemForce = off [default] colvars: Initializing atom group "group1". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] -colvars: # indexGroup = "group1" +colvars: # indexGroup = group1 colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Enabling scalable calculation for group "group1". -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028. colvars: Initializing atom group "group2". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] -colvars: # indexGroup = "group2" +colvars: # indexGroup = group2 colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Enabling scalable calculation for group "group2". -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028. colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerWallConstant = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputTotalForce = off [default] +colvars: # outputSystemForce = off [default] colvars: # outputAppliedForce = on -colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = on -colvars: # outputFreq = 10 [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] +colvars: # forceConstant = 0.001 colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] -colvars: # outputCenters = off [default] -colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 -colvars: # targetNumSteps = 8 -colvars: # targetNumStages = 4 -colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: # targetNumSteps = 8 +colvars: # targetNumStages = 4 +colvars: # targetForceExponent = 1 [default] +colvars: # outputCenters = off [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- -colvars: Updating NAMD interface: -colvars: updating atomic data (0 atoms). -colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). -colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21686 -colvars: Restarting harmonic bias "harmonic1" from step number 20. +colvars: Restarting restraint bias "harmonic1". +colvars: # forceConstant = 0.00055 +colvars: # stage = 2 colvars: ---------------------------------------------------------------------- -colvars: Updating NAMD interface: -colvars: updating atomic data (0 atoms). -colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Writing to colvar trajectory file "test.restart.colvars.traj". +colvars: Lambda= 0.5 dA/dLambda= -0.010897 +colvars: Restraint harmonic1, stage 3 : lambda = 0.75 +colvars: Setting force constant to 0.000325 +colvars: Writing the state file "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Restraint harmonic1 Lambda= 0.5 dA/dLambda= -0.010897 -colvars: Restraint harmonic1, stage 3 : lambda = 0.75, k = 0.000325 -colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "test.restart.tmp.colvars.state". -colvars: Restraint harmonic1 Lambda= 0.75 dA/dLambda= -0.0173372 -colvars: Restraint harmonic1, stage 4 : lambda = 1, k = 0.0001 -colvars: Restraint harmonic1 Lambda= 1 dA/dLambda= -0.0174016 +colvars: Lambda= 0.75 dA/dLambda= -0.0173372 +colvars: Restraint harmonic1, stage 4 : lambda = 1 +colvars: Setting force constant to 0.0001 +colvars: Lambda= 1 dA/dLambda= -0.0174016 +colvars: Writing the state file "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "test.restart.tmp.colvars.state". colvars: Saving collective variables state to "test.restart.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped index 74a01de19..b91f1692e 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21399913220478e+00 + x 3.21399913267948e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj index d899a4145..9b8f32622 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 - 20 3.21685733295311e+00 -6.85708613249684e-03 1.06862795973819e-02 - 21 3.21455560554461e+00 -6.85202233219815e-03 1.06705022820323e-02 - 22 3.21220450297830e+00 -6.84684990655226e-03 1.06543985551943e-02 - 23 3.20992354800290e+00 -6.84183180560639e-03 1.06387869218653e-02 - 24 3.20782117629534e+00 -4.04016752918394e-03 6.27805910148934e-03 - 25 3.20598868088311e+00 -4.03778528514804e-03 6.27065769575309e-03 - 26 3.20449580932365e+00 -4.03584455212074e-03 6.26463124957027e-03 - 27 3.20338860114077e+00 -4.03440518148300e-03 6.26016352629879e-03 - 28 3.20268922031311e+00 -4.03349598640704e-03 6.25734225860066e-03 - 29 3.20239737626966e+00 -4.03311658915055e-03 6.25616516218516e-03 - 30 3.20249291400027e+00 -4.03324078820035e-03 6.25655048292422e-03 - 31 3.20293919691480e+00 -4.03382095598924e-03 6.25835057883767e-03 - 32 3.20368712856237e+00 -1.24147485142495e-03 1.92657475840075e-03 - 33 3.20467968265656e+00 -1.24187187306262e-03 1.92780718638008e-03 - 34 3.20585655419651e+00 -1.24234262167861e-03 1.92926898704909e-03 - 35 3.20715877104842e+00 -1.24286350841937e-03 1.93088712570063e-03 - 36 3.20853264885916e+00 -1.24341305954367e-03 1.93259504580467e-03 - 37 3.20993281112190e+00 -1.24397312444876e-03 1.93433641793852e-03 - 38 3.21132423111018e+00 -1.24452969244407e-03 1.93606769421867e-03 - 39 3.21268344520547e+00 -1.24507337808219e-03 1.93775964601125e-03 - 40 3.21399913220478e+00 -1.24559965288191e-03 1.93939811907443e-03 + 20 3.21685733313543e+00 -6.85708613289795e-03 1.06862795986321e-02 + 21 3.21455560573336e+00 -6.85202233261338e-03 1.06705022833256e-02 + 22 3.21220450317535e+00 -6.84684990698578e-03 1.06543985565434e-02 + 23 3.20992354821064e+00 -6.84183180606342e-03 1.06387869232866e-02 + 24 3.20782117651646e+00 -4.04016752947140e-03 6.27805910238270e-03 + 25 3.20598868112038e+00 -4.03778528545649e-03 6.27065769671115e-03 + 26 3.20449580957973e+00 -4.03584455245364e-03 6.26463125060375e-03 + 27 3.20338860141795e+00 -4.03440518184334e-03 6.26016352741707e-03 + 28 3.20268922061319e+00 -4.03349598679715e-03 6.25734225981105e-03 + 29 3.20239737659378e+00 -4.03311658957192e-03 6.25616516349240e-03 + 30 3.20249291434882e+00 -4.03324078865346e-03 6.25655048433000e-03 + 31 3.20293919728737e+00 -4.03382095647358e-03 6.25835058034053e-03 + 32 3.20368712895776e+00 -1.24147485158310e-03 1.92657475889161e-03 + 33 3.20467968307286e+00 -1.24187187322914e-03 1.92780718689708e-03 + 34 3.20585655463118e+00 -1.24234262185247e-03 1.92926898758910e-03 + 35 3.20715877149842e+00 -1.24286350859937e-03 1.93088712625992e-03 + 36 3.20853264932110e+00 -1.24341305972844e-03 1.93259504637905e-03 + 37 3.20993281159222e+00 -1.24397312463689e-03 1.93433641852358e-03 + 38 3.21132423158529e+00 -1.24452969263412e-03 1.93606769480996e-03 + 39 3.21268344568196e+00 -1.24507337827279e-03 1.93775964660451e-03 + 40 3.21399913267948e+00 -1.24559965307179e-03 1.93939811966572e-03 diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt b/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt index 157cac038..494519348 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2015-09-16. +colvars: Using NAMD interface, version 2015-07-24. diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out index d2be0212a..11f61358e 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,27 +131,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped index 6d65b453d..4507a2d83 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687020497026e+00 + x 3.21687020515258e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj index a79591894..f58ff8ba4 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 - 1 3.20437138788600e+00 -1.12999118519050e-02 1.75395615193440e-02 - 2 3.20383992333029e+00 -1.01805949485234e-02 1.57994685222408e-02 - 3 3.20396643077894e+00 -9.06358197787450e-03 1.40665271009677e-02 - 4 3.20472684448397e+00 -7.94810072187895e-03 1.23383408369400e-02 - 5 3.20606109997218e+00 -6.83333441993879e-03 1.06123771124364e-02 - 6 3.20787717647453e+00 -5.71849400471313e-03 8.88618850052717e-03 - 7 3.21005647713329e+00 -4.60288358615728e-03 7.15761395530948e-03 - 8 3.21246028397626e+00 -3.48595551805342e-03 5.42494905082458e-03 - 9 3.21493732312431e+00 -2.36735236557448e-03 3.68707712025729e-03 - 10 3.21733254790344e+00 -1.24693301916138e-03 1.94355244284363e-03 - 11 3.21949693102052e+00 -1.24779877240821e-03 1.94625222052929e-03 - 12 3.22129751453369e+00 -1.24851900581348e-03 1.94849963484684e-03 - 13 3.22262660677352e+00 -1.24905064270941e-03 1.95015938506598e-03 - 14 3.22340883978115e+00 -1.24936353591246e-03 1.95113655608461e-03 - 15 3.22360524373761e+00 -1.24944209749504e-03 1.95138194374102e-03 - 16 3.22321407463655e+00 -1.24928562985462e-03 1.95089323120157e-03 - 17 3.22226874199272e+00 -1.24890749679709e-03 1.94971241944496e-03 - 18 3.22083355111441e+00 -1.24833342044576e-03 1.94792041075227e-03 - 19 3.21899800404481e+00 -1.24759920161792e-03 1.94562970984710e-03 - 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 + 1 3.20437138788661e+00 -1.12999118519073e-02 1.75395615193509e-02 + 2 3.20383992338449e+00 -1.01805949487011e-02 1.57994685227925e-02 + 3 3.20396643078647e+00 -9.06358197789650e-03 1.40665271010360e-02 + 4 3.20472684453174e+00 -7.94810072200125e-03 1.23383408373197e-02 + 5 3.20606109997726e+00 -6.83333441994998e-03 1.06123771124712e-02 + 6 3.20787717649369e+00 -5.71849400474838e-03 8.88618850063674e-03 + 7 3.21005647716855e+00 -4.60288358620946e-03 7.15761395547176e-03 + 8 3.21246028402867e+00 -3.48595551811211e-03 5.42494905100725e-03 + 9 3.21493732319445e+00 -2.36735236562779e-03 3.68707712042334e-03 + 10 3.21733254799115e+00 -1.24693301919646e-03 1.94355244295300e-03 + 11 3.21949693112495e+00 -1.24779877244998e-03 1.94625222065960e-03 + 12 3.22129751465341e+00 -1.24851900586136e-03 1.94849963499631e-03 + 13 3.22262660690669e+00 -1.24905064276268e-03 1.95015938523232e-03 + 14 3.22340883992570e+00 -1.24936353597028e-03 1.95113655626521e-03 + 15 3.22360524389145e+00 -1.24944209755658e-03 1.95138194393324e-03 + 16 3.22321407479779e+00 -1.24928562991912e-03 1.95089323140301e-03 + 17 3.22226874215941e+00 -1.24890749686377e-03 1.94971241965315e-03 + 18 3.22083355128627e+00 -1.24833342051451e-03 1.94792041096681e-03 + 19 3.21899800422646e+00 -1.24759920169058e-03 1.94562971007373e-03 + 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out index 4e433433c..126710c7e 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,32 +131,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped index 226b212c1..32715071f 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21402990668451e+00 + x 3.21402990715919e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj index 2753d1963..0970380b3 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 - 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 - 21 3.21456967632931e+00 -1.24582787053172e-03 1.94010885374201e-03 - 22 3.21221977994646e+00 -1.24488791197858e-03 1.93718239173800e-03 - 23 3.20994003840243e+00 -1.24397601536097e-03 1.93434540849171e-03 - 24 3.20783888746925e+00 -1.24313555498770e-03 1.93173251009322e-03 - 25 3.20600757726167e+00 -1.24240303090467e-03 1.92945661400138e-03 - 26 3.20451585575643e+00 -1.24180634230257e-03 1.92760373972862e-03 - 27 3.20340976294734e+00 -1.24136390517894e-03 1.92623043135138e-03 - 28 3.20271146313867e+00 -1.24108458525547e-03 1.92536368469842e-03 - 29 3.20242066576110e+00 -1.24096826630444e-03 1.92500279746831e-03 - 30 3.20251721536965e+00 -1.24100688614786e-03 1.92512261433301e-03 - 31 3.20296447447623e+00 -1.24118578979049e-03 1.92567770597231e-03 - 32 3.20371334530005e+00 -1.24148533812002e-03 1.92660730595873e-03 - 33 3.20470675696420e+00 -1.24188270278568e-03 1.92784080934784e-03 - 34 3.20588440315285e+00 -1.24235376126114e-03 1.92930358514962e-03 - 35 3.20718731103156e+00 -1.24287492441263e-03 1.93092259716711e-03 - 36 3.20856179628928e+00 -1.24342471851571e-03 1.93263128826985e-03 - 37 3.20996248338009e+00 -1.24398499335204e-03 1.93437332960633e-03 - 38 3.21135434749032e+00 -1.24454173899613e-03 1.93610517512938e-03 - 39 3.21271392780555e+00 -1.24508557112222e-03 1.93779759927093e-03 - 40 3.21402990668451e+00 -1.24561196267380e-03 1.93943645194510e-03 + 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 + 21 3.21456967651805e+00 -1.24582787060722e-03 1.94010885397715e-03 + 22 3.21221978014351e+00 -1.24488791205741e-03 1.93718239198331e-03 + 23 3.20994003861018e+00 -1.24397601544407e-03 1.93434540875013e-03 + 24 3.20783888769037e+00 -1.24313555507615e-03 1.93173251036810e-03 + 25 3.20600757749894e+00 -1.24240303099958e-03 1.92945661429617e-03 + 26 3.20451585601250e+00 -1.24180634240500e-03 1.92760374004661e-03 + 27 3.20340976322452e+00 -1.24136390528981e-03 1.92623043169546e-03 + 28 3.20271146343875e+00 -1.24108458537550e-03 1.92536368507084e-03 + 29 3.20242066608521e+00 -1.24096826643409e-03 1.92500279787052e-03 + 30 3.20251721571819e+00 -1.24100688628728e-03 1.92512261476555e-03 + 31 3.20296447484878e+00 -1.24118578993951e-03 1.92567770643472e-03 + 32 3.20371334569543e+00 -1.24148533827817e-03 1.92660730644958e-03 + 33 3.20470675738049e+00 -1.24188270295219e-03 1.92784080986481e-03 + 34 3.20588440358750e+00 -1.24235376143500e-03 1.92930358568961e-03 + 35 3.20718731148154e+00 -1.24287492459262e-03 1.93092259772638e-03 + 36 3.20856179675119e+00 -1.24342471870048e-03 1.93263128884420e-03 + 37 3.20996248385038e+00 -1.24398499354015e-03 1.93437333019136e-03 + 38 3.21135434796541e+00 -1.24454173918616e-03 1.93610517572065e-03 + 39 3.21271392828201e+00 -1.24508557131280e-03 1.93779759986417e-03 + 40 3.21402990715919e+00 -1.24561196286367e-03 1.93943645253637e-03 diff --git a/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out index e8ce74ce1..454648299 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -132,27 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped index a0bbaca3d..ed4ff587f 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491521323e+00 + x 3.21685491541898e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj index d5d525eb6..dfbf0ebd2 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095402e+00 -1.20174855638161e-02 - 2 3.20383991841948e+00 -1.20153596736779e-02 - 3 3.20396638982490e+00 -1.20158655592996e-02 - 4 3.20472672277551e+00 -1.20189068911021e-02 - 5 3.20606083670179e+00 -1.20242433468072e-02 - 6 3.20787669543948e+00 -1.20315067817579e-02 - 7 3.21005568755800e+00 -1.20402227502320e-02 - 8 3.21245908142754e+00 -1.20498363257101e-02 - 9 3.21493559049101e+00 -1.20597423619640e-02 - 10 3.21733015640955e+00 -1.20693206256382e-02 - 11 3.21949374123820e+00 -1.20779749649528e-02 - 12 3.22129339461899e+00 -1.20851735784760e-02 - 13 3.22262143319445e+00 -1.20904857327778e-02 - 14 3.22340249773966e+00 -1.20936099909586e-02 - 15 3.22359762729192e+00 -1.20943905091677e-02 - 16 3.22320508654863e+00 -1.20928203461945e-02 - 17 3.22225829334495e+00 -1.20890331733798e-02 - 18 3.22082156074746e+00 -1.20832862429898e-02 - 19 3.21898439787187e+00 -1.20759375914875e-02 - 20 3.21685491521323e+00 -1.20674196608529e-02 + 1 3.20437139095465e+00 -1.20174855638186e-02 + 2 3.20383991842200e+00 -1.20153596736880e-02 + 3 3.20396638983062e+00 -1.20158655593225e-02 + 4 3.20472672278571e+00 -1.20189068911429e-02 + 5 3.20606083671774e+00 -1.20242433468710e-02 + 6 3.20787669546241e+00 -1.20315067818496e-02 + 7 3.21005568758906e+00 -1.20402227503562e-02 + 8 3.21245908146782e+00 -1.20498363258713e-02 + 9 3.21493559054151e+00 -1.20597423621660e-02 + 10 3.21733015647118e+00 -1.20693206258847e-02 + 11 3.21949374131176e+00 -1.20779749652470e-02 + 12 3.22129339470521e+00 -1.20851735788208e-02 + 13 3.22262143329394e+00 -1.20904857331758e-02 + 14 3.22340249785300e+00 -1.20936099914120e-02 + 15 3.22359762741961e+00 -1.20943905096784e-02 + 16 3.22320508669112e+00 -1.20928203467645e-02 + 17 3.22225829350267e+00 -1.20890331740107e-02 + 18 3.22082156092082e+00 -1.20832862436833e-02 + 19 3.21898439806125e+00 -1.20759375922450e-02 + 20 3.21685491541898e+00 -1.20674196616759e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out index 5da67b4d9..57651fe22 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -132,32 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped index f58df11b7..8719ed7ca 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397364200070e+00 + x 3.21397364248195e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj index 8b5e494a7..fec7bdbdb 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685491521323e+00 -1.20674196608529e-02 - 21 3.21455264073267e+00 -1.20582105629307e-02 - 22 3.21220094103318e+00 -1.20488037641327e-02 - 23 3.20991934284523e+00 -1.20396773713809e-02 - 24 3.20781628562398e+00 -1.20312651424959e-02 - 25 3.20598302292944e+00 -1.20239320917178e-02 - 26 3.20448930614687e+00 -1.20179572245875e-02 - 27 3.20338117886792e+00 -1.20135247154717e-02 - 28 3.20268080933861e+00 -1.20107232373544e-02 - 29 3.20238791142161e+00 -1.20095516456865e-02 - 30 3.20248233467135e+00 -1.20099293386854e-02 - 31 3.20292744714189e+00 -1.20117097885676e-02 - 32 3.20367415705454e+00 -1.20146966282182e-02 - 33 3.20466539988114e+00 -1.20186615995246e-02 - 34 3.20584087581816e+00 -1.20233635032726e-02 - 35 3.20714161837695e+00 -1.20285664735078e-02 - 36 3.20851394921166e+00 -1.20340557968466e-02 - 37 3.20991249801338e+00 -1.20396499920535e-02 - 38 3.21130224431234e+00 -1.20452089772494e-02 - 39 3.21265973069097e+00 -1.20506389227639e-02 - 40 3.21397364200070e+00 -1.20558945680028e-02 + 20 3.21685491541898e+00 -1.20674196616759e-02 + 21 3.21455264095509e+00 -1.20582105638204e-02 + 22 3.21220094127252e+00 -1.20488037650901e-02 + 23 3.20991934310164e+00 -1.20396773724066e-02 + 24 3.20781628589752e+00 -1.20312651435901e-02 + 25 3.20598302322006e+00 -1.20239320928802e-02 + 26 3.20448930645441e+00 -1.20179572258176e-02 + 27 3.20338117919211e+00 -1.20135247167684e-02 + 28 3.20268080967909e+00 -1.20107232387163e-02 + 29 3.20238791177794e+00 -1.20095516471117e-02 + 30 3.20248233504303e+00 -1.20099293401721e-02 + 31 3.20292744752838e+00 -1.20117097901135e-02 + 32 3.20367415745526e+00 -1.20146966298210e-02 + 33 3.20466540029545e+00 -1.20186616011818e-02 + 34 3.20584087624535e+00 -1.20233635049814e-02 + 35 3.20714161881621e+00 -1.20285664752649e-02 + 36 3.20851394966204e+00 -1.20340557986482e-02 + 37 3.20991249847373e+00 -1.20396499938949e-02 + 38 3.21130224478131e+00 -1.20452089791253e-02 + 39 3.21265973116698e+00 -1.20506389246679e-02 + 40 3.21397364248195e+00 -1.20558945699278e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out index 9064d17fa..a58050110 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.002 @@ -138,27 +133,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped index bf89cca29..75c48b998 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687111229972e+00 + x 3.21687111250546e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.37880405391244e-02 + accumulatedWork -3.37880405409319e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj index dfafafb40..260962906 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 0 3.20554673468334e+00 -1.20221869387334e-02 1.80666223487314e-02 0.00000000000000e+00 - 1 3.20437139095402e+00 -1.09007134627843e-02 1.63748958342883e-02 -1.67759907527770e-03 - 2 3.20383993554679e+00 -9.78221064079167e-03 1.46920974903704e-02 -3.35460468847827e-03 - 3 3.20396645808888e+00 -8.66600108900544e-03 1.30161882985670e-02 -5.03175157650461e-03 - 4 3.20472689262560e+00 -7.55129058412370e-03 1.13447829460735e-02 -6.70974768961999e-03 - 5 3.20606117441688e+00 -6.43724359705212e-03 9.67537402368102e-03 -8.38923439861843e-03 - 6 3.20787728237960e+00 -5.32305735341078e-03 8.00555164306400e-03 -1.00707510400595e-02 - 7 3.21005661930852e+00 -4.20802874840541e-03 6.33320239418913e-03 -1.17547052270162e-02 - 8 3.21246046686444e+00 -3.09161036522795e-03 4.65667700209877e-03 -1.34413501178592e-02 - 9 3.21493755079559e+00 -1.97345282364599e-03 2.97491851136694e-03 -1.51307699355289e-02 - 10 3.21733282406293e+00 -8.53430600396662e-04 1.28754208181829e-03 -1.68228752015806e-02 - 11 3.21949725902808e+00 -8.54042795053181e-04 1.28938993937788e-03 -1.85174089470984e-02 - 12 3.22129789744302e+00 -8.54552092506647e-04 1.29092822017293e-03 -2.02139643220999e-02 - 13 3.22262704736871e+00 -8.54928032876915e-04 1.29206429786374e-03 -2.19120127458105e-02 - 14 3.22340934061631e+00 -8.55149298821016e-04 1.29273318883847e-03 -2.36109402351118e-02 - 15 3.22360580717604e+00 -8.55204867955681e-04 1.29290120253801e-03 -2.53100885302957e-02 - 16 3.22321470288645e+00 -8.55094246957553e-04 1.29256674987784e-03 -2.70087972832577e-02 - 17 3.22226943713660e+00 -8.54826885428858e-04 1.29175858493715e-03 -2.87064439348940e-02 - 18 3.22083431513039e+00 -8.54420971627888e-04 1.29053209533029e-03 -3.04024787172548e-02 - 19 3.21899883881885e+00 -8.53901820529248e-04 1.28896430232155e-03 -3.20964530847806e-02 - 20 3.21687111229972e+00 -8.53300008589174e-04 1.28714807301889e-03 -3.37880405391244e-02 + 1 3.20437139095465e+00 -1.09007134627866e-02 1.63748958342951e-02 -1.67759907527840e-03 + 2 3.20383993554932e+00 -9.78221064079988e-03 1.46920974903951e-02 -3.35460468848178e-03 + 3 3.20396645809459e+00 -8.66600108902194e-03 1.30161882986166e-02 -5.03175157651451e-03 + 4 3.20472689263580e+00 -7.55129058414933e-03 1.13447829461505e-02 -6.70974768964128e-03 + 5 3.20606117443283e+00 -6.43724359708628e-03 9.67537402378371e-03 -8.38923439865754e-03 + 6 3.20787728240253e+00 -5.32305735345136e-03 8.00555164318605e-03 -1.00707510401243e-02 + 7 3.21005661933959e+00 -4.20802874844884e-03 6.33320239431985e-03 -1.17547052271157e-02 + 8 3.21246046690473e+00 -3.09161036526929e-03 4.65667700222331e-03 -1.34413501180038e-02 + 9 3.21493755084609e+00 -1.97345282367904e-03 2.97491851146660e-03 -1.51307699357301e-02 + 10 3.21733282412455e+00 -8.53430600414092e-04 1.28754208187088e-03 -1.68228752018509e-02 + 11 3.21949725910164e+00 -8.54042795073986e-04 1.28938993944070e-03 -1.85174089474513e-02 + 12 3.22129789752922e+00 -8.54552092531030e-04 1.29092822024660e-03 -2.02139643225496e-02 + 13 3.22262704746820e+00 -8.54928032905055e-04 1.29206429794880e-03 -2.19120127463720e-02 + 14 3.22340934072964e+00 -8.55149298853072e-04 1.29273318893539e-03 -2.36109402358007e-02 + 15 3.22360580730372e+00 -8.55204867991794e-04 1.29290120264720e-03 -2.53100885311281e-02 + 16 3.22321470302893e+00 -8.55094246997852e-04 1.29256674999968e-03 -2.70087972842502e-02 + 17 3.22226943729432e+00 -8.54826885473466e-04 1.29175858507197e-03 -2.87064439360637e-02 + 18 3.22083431530374e+00 -8.54420971676919e-04 1.29053209547840e-03 -3.04024787186191e-02 + 19 3.21899883900822e+00 -8.53901820582810e-04 1.28896430248325e-03 -3.20964530863574e-02 + 20 3.21687111250546e+00 -8.53300008647365e-04 1.28714807319445e-03 -3.37880405409319e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out index 9014734ce..942b809b4 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.002 @@ -138,32 +133,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped index fc7a79383..520580d86 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403236488325e+00 + x 3.21403236536445e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.37880405391244e-02 + accumulatedWork -3.37880405409319e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj index d0e1dbfa0..2e304633f 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 - 20 3.21687111229972e+00 -8.53300008589174e-04 1.28714807301889e-03 -3.37880405391244e-02 - 21 3.21457065791810e+00 -8.52649341831951e-04 1.28518584368989e-03 -3.37880405391244e-02 - 22 3.21222083739193e+00 -8.51984712220503e-04 1.28318305164498e-03 -3.37880405391244e-02 - 23 3.20994117317441e+00 -8.51339925809688e-04 1.28124154753091e-03 -3.37880405391244e-02 - 24 3.20784010088332e+00 -8.50745652823771e-04 1.27945344510775e-03 -3.37880405391244e-02 - 25 3.20600887044777e+00 -8.50227702640212e-04 1.27789600801845e-03 -3.37880405391244e-02 - 26 3.20451722962774e+00 -8.49805802904639e-04 1.27662808833231e-03 -3.37880405391244e-02 - 27 3.20341121817082e+00 -8.49492975624134e-04 1.27568836637342e-03 -3.37880405391244e-02 - 28 3.20271300011156e+00 -8.49295489734355e-04 1.27509530398073e-03 -3.37880405391244e-02 - 29 3.20242228459368e+00 -8.49213262968719e-04 1.27484841255490e-03 -3.37880405391244e-02 - 30 3.20251891587653e+00 -8.49240594422870e-04 1.27493047444245e-03 -3.37880405391244e-02 - 31 3.20296625617950e+00 -8.49367121367561e-04 1.27531040228755e-03 -3.37880405391244e-02 - 32 3.20371520744477e+00 -8.49578956774942e-04 1.27594661619498e-03 -3.37880405391244e-02 - 33 3.20470869854482e+00 -8.49859958492498e-04 1.27679080491367e-03 -3.37880405391244e-02 - 34 3.20588642295006e+00 -8.50193069257824e-04 1.27779190188417e-03 -3.37880405391244e-02 - 35 3.20718940766233e+00 -8.50561608988155e-04 1.27889993055670e-03 -3.37880405391244e-02 - 36 3.20856396826048e+00 -8.50950393436199e-04 1.28006934623462e-03 -3.37880405391244e-02 - 37 3.20996472914883e+00 -8.51346588445386e-04 1.28126160175090e-03 -3.37880405391244e-02 - 38 3.21135666552061e+00 -8.51740287504375e-04 1.28244689603437e-03 -3.37880405391244e-02 - 39 3.21271631661605e+00 -8.52124854908226e-04 1.28360522708805e-03 -3.37880405391244e-02 - 40 3.21403236488325e+00 -8.52497089569868e-04 1.28472690946618e-03 -3.37880405391244e-02 + 20 3.21687111250546e+00 -8.53300008647364e-04 1.28714807319444e-03 -3.37880405409319e-02 + 21 3.21457065814050e+00 -8.52649341894857e-04 1.28518584387952e-03 -3.37880405409319e-02 + 22 3.21222083763125e+00 -8.51984712288192e-04 1.28318305184888e-03 -3.37880405409319e-02 + 23 3.20994117343080e+00 -8.51339925882205e-04 1.28124154774919e-03 -3.37880405409319e-02 + 24 3.20784010115684e+00 -8.50745652901133e-04 1.27945344534044e-03 -3.37880405409319e-02 + 25 3.20600887073836e+00 -8.50227702722403e-04 1.27789600826552e-03 -3.37880405409319e-02 + 26 3.20451722993525e+00 -8.49805802991615e-04 1.27662808859363e-03 -3.37880405409319e-02 + 27 3.20341121849498e+00 -8.49492975715819e-04 1.27568836664879e-03 -3.37880405409319e-02 + 28 3.20271300045200e+00 -8.49295489830646e-04 1.27509530426987e-03 -3.37880405409319e-02 + 29 3.20242228494997e+00 -8.49213263069492e-04 1.27484841285746e-03 -3.37880405409319e-02 + 30 3.20251891624817e+00 -8.49240594527986e-04 1.27493047475806e-03 -3.37880405409319e-02 + 31 3.20296625656595e+00 -8.49367121476866e-04 1.27531040261579e-03 -3.37880405409319e-02 + 32 3.20371520784545e+00 -8.49578956888271e-04 1.27594661653539e-03 -3.37880405409319e-02 + 33 3.20470869895909e+00 -8.49859958609671e-04 1.27679080526574e-03 -3.37880405409319e-02 + 34 3.20588642337721e+00 -8.50193069378641e-04 1.27779190224733e-03 -3.37880405409319e-02 + 35 3.20718940810155e+00 -8.50561609112386e-04 1.27889993093029e-03 -3.37880405409319e-02 + 36 3.20856396871082e+00 -8.50950393563573e-04 1.28006934661783e-03 -3.37880405409319e-02 + 37 3.20996472960913e+00 -8.51346588575580e-04 1.28126160214278e-03 -3.37880405409319e-02 + 38 3.21135666598954e+00 -8.51740287637006e-04 1.28244689643377e-03 -3.37880405409319e-02 + 39 3.21271631709201e+00 -8.52124855042849e-04 1.28360522749363e-03 -3.37880405409319e-02 + 40 3.21403236536445e+00 -8.52497089705972e-04 1.28472690987640e-03 -3.37880405409319e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out index a29b506dc..333ed7f0a 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.001 [default] @@ -138,27 +133,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped index 99d5623d0..af765be67 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687060179954e+00 + x 3.21687060200527e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063080692e-02 + accumulatedWork -3.27231063098198e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj index f2c850ae5..6c0216a7f 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 0 3.20554673468334e+00 -1.20221869387334e-02 1.80666223487314e-02 0.00000000000000e+00 - 1 3.20437139095402e+00 -1.09359118630726e-02 1.64277703677051e-02 -1.62472454186094e-03 - 2 3.20383993500698e+00 -9.85259498682288e-03 1.47978091424340e-02 -3.24887432578663e-03 - 3 3.20396645593733e+00 -8.77158205133702e-03 1.31747691238592e-02 -4.87316093009804e-03 - 4 3.20472688727227e+00 -7.69210083141700e-03 1.15563310938840e-02 -6.49826999017548e-03 - 5 3.20606116377278e+00 -6.61333456030012e-03 9.94004409237728e-03 -8.12482265983721e-03 - 6 3.20787726388044e+00 -5.53449416554000e-03 8.32353958380334e-03 -9.75334127405960e-03 - 7 3.21005658994163e+00 -4.45488375311361e-03 6.70472609924175e-03 -1.13842205954968e-02 - 8 3.21246042319826e+00 -3.37395567398206e-03 5.08195396874809e-03 -1.30177057997372e-02 - 9 3.21493748901074e+00 -2.29135249164817e-03 3.45414226380412e-03 -1.46538784510129e-02 - 10 3.21733273998387e+00 -1.20693309599355e-03 1.82085937275571e-03 -1.62926518864930e-02 - 11 3.21949714815442e+00 -1.20779885926177e-03 1.82347260554254e-03 -1.79337772314813e-02 - 12 3.22129775552305e+00 -1.20851910220922e-03 1.82564802550573e-03 -1.95768604544364e-02 - 13 3.22262687042120e+00 -1.20905074816848e-03 1.82725463955845e-03 -2.12213896300391e-02 - 14 3.22340912494254e+00 -1.20936364997702e-03 1.82820054735717e-03 -2.28667701226605e-02 - 15 3.22360554936245e+00 -1.20944221974498e-03 1.82843810362708e-03 -2.45123644159249e-02 - 16 3.22321439979867e+00 -1.20928575991947e-03 1.82796506143001e-03 -2.61575329712119e-02 - 17 3.22226908590648e+00 -1.20890763436259e-03 1.82682208552520e-03 -2.78016728481846e-02 - 18 3.22083391313757e+00 -1.20833356525503e-03 1.82508750615241e-03 -2.94442516037217e-02 - 19 3.21899838366880e+00 -1.20759935346752e-03 1.82287024811897e-03 -3.10848348270288e-02 - 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 + 1 3.20437139095465e+00 -1.09359118630749e-02 1.64277703677119e-02 -1.62472454186161e-03 + 2 3.20383993500950e+00 -9.85259498683116e-03 1.47978091424589e-02 -3.24887432579003e-03 + 3 3.20396645594305e+00 -8.77158205135371e-03 1.31747691239093e-02 -4.87316093010762e-03 + 4 3.20472688728247e+00 -7.69210083144311e-03 1.15563310939625e-02 -6.49826999019610e-03 + 5 3.20606116378874e+00 -6.61333456033522e-03 9.94004409248278e-03 -8.12482265987509e-03 + 6 3.20787726390336e+00 -5.53449416558219e-03 8.32353958393024e-03 -9.75334127412231e-03 + 7 3.21005658997269e+00 -4.45488375315958e-03 6.70472609938014e-03 -1.13842205955932e-02 + 8 3.21246042323855e+00 -3.37395567402717e-03 5.08195396888400e-03 -1.30177057998773e-02 + 9 3.21493748906124e+00 -2.29135249168655e-03 3.45414226391983e-03 -1.46538784512077e-02 + 10 3.21733274004549e+00 -1.20693309601820e-03 1.82085937283009e-03 -1.62926518867548e-02 + 11 3.21949714822798e+00 -1.20779885929119e-03 1.82347260563138e-03 -1.79337772318231e-02 + 12 3.22129775560926e+00 -1.20851910224370e-03 1.82564802560991e-03 -1.95768604548720e-02 + 13 3.22262687052069e+00 -1.20905074820828e-03 1.82725463967874e-03 -2.12213896305829e-02 + 14 3.22340912505588e+00 -1.20936365002235e-03 1.82820054749423e-03 -2.28667701233277e-02 + 15 3.22360554949013e+00 -1.20944221979605e-03 1.82843810378150e-03 -2.45123644167310e-02 + 16 3.22321439994115e+00 -1.20928575997646e-03 1.82796506160231e-03 -2.61575329721731e-02 + 17 3.22226908606420e+00 -1.20890763442568e-03 1.82682208571586e-03 -2.78016728493174e-02 + 18 3.22083391331092e+00 -1.20833356532437e-03 1.82508750636188e-03 -2.94442516050430e-02 + 19 3.21899838385817e+00 -1.20759935354327e-03 1.82287024834765e-03 -3.10848348285559e-02 + 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out index 959f0c552..35f57cbba 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.001 [default] @@ -138,32 +133,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped index a9bad9be9..1cdd044fd 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403051403523e+00 + x 3.21403051451645e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063080692e-02 + accumulatedWork -3.27231063098198e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj index 7cdbd31e7..476fdf462 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 - 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 - 21 3.21457009005187e+00 -1.20582803602075e-03 1.81752656556706e-03 -3.27231063080692e-02 - 22 3.21222021029772e+00 -1.20488808411909e-03 1.81469411906520e-03 -3.27231063080692e-02 - 23 3.20994048512507e+00 -1.20397619405003e-03 1.81194834479899e-03 -3.27231063080692e-02 - 24 3.20783935027265e+00 -1.20313574010906e-03 1.80941951140972e-03 -3.27231063080692e-02 - 25 3.20600805578400e+00 -1.20240322231360e-03 1.80721688628766e-03 -3.27231063080692e-02 - 26 3.20451634953337e+00 -1.20180653981335e-03 1.80542369892267e-03 -3.27231063080692e-02 - 27 3.20341027138948e+00 -1.20136410855579e-03 1.80409465165757e-03 -3.27231063080692e-02 - 28 3.20271198551962e+00 -1.20108479420785e-03 1.80325585359664e-03 -3.27231063080692e-02 - 29 3.20242120121622e+00 -1.20096848048649e-03 1.80290661390253e-03 -3.27231063080692e-02 - 30 3.20251776290552e+00 -1.20100710516221e-03 1.80302258331263e-03 -3.27231063080692e-02 - 31 3.20296503299079e+00 -1.20118601319632e-03 1.80355979787307e-03 -3.27231063080692e-02 - 32 3.20371391361211e+00 -1.20148556544484e-03 1.80445945496540e-03 -3.27231063080692e-02 - 33 3.20470733384994e+00 -1.20188293353998e-03 1.80565323241832e-03 -3.27231063080692e-02 - 34 3.20588498738668e+00 -1.20235399495467e-03 1.80706891147932e-03 -3.27231063080692e-02 - 35 3.20718790142930e+00 -1.20287516057172e-03 1.80863581490056e-03 -3.27231063080692e-02 - 36 3.20856239174816e+00 -1.20342495669926e-03 1.81028953300828e-03 -3.27231063080692e-02 - 37 3.20996308291416e+00 -1.20398523316567e-03 1.81197555210123e-03 -3.27231063080692e-02 - 38 3.21135495025727e+00 -1.20454198010291e-03 1.81365172728779e-03 -3.27231063080692e-02 - 39 3.21271453312301e+00 -1.20508581324920e-03 1.81528977161812e-03 -3.27231063080692e-02 - 40 3.21403051403523e+00 -1.20561220561409e-03 1.81687598790710e-03 -3.27231063080692e-02 + 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 + 21 3.21457009027428e+00 -1.20582803610971e-03 1.81752656583525e-03 -3.27231063098198e-02 + 22 3.21222021053704e+00 -1.20488808421481e-03 1.81469411935356e-03 -3.27231063098198e-02 + 23 3.20994048538146e+00 -1.20397619415258e-03 1.81194834510767e-03 -3.27231063098198e-02 + 24 3.20783935054617e+00 -1.20313574021847e-03 1.80941951173880e-03 -3.27231063098198e-02 + 25 3.20600805607460e+00 -1.20240322242984e-03 1.80721688663708e-03 -3.27231063098198e-02 + 26 3.20451634984089e+00 -1.20180653993636e-03 1.80542369929224e-03 -3.27231063098198e-02 + 27 3.20341027171365e+00 -1.20136410868546e-03 1.80409465204701e-03 -3.27231063098198e-02 + 28 3.20271198586007e+00 -1.20108479434403e-03 1.80325585400555e-03 -3.27231063098198e-02 + 29 3.20242120157252e+00 -1.20096848062901e-03 1.80290661433043e-03 -3.27231063098198e-02 + 30 3.20251776327717e+00 -1.20100710531087e-03 1.80302258375899e-03 -3.27231063098198e-02 + 31 3.20296503337725e+00 -1.20118601335090e-03 1.80355979833728e-03 -3.27231063098198e-02 + 32 3.20371391401280e+00 -1.20148556560512e-03 1.80445945544681e-03 -3.27231063098198e-02 + 33 3.20470733426422e+00 -1.20188293370569e-03 1.80565323291624e-03 -3.27231063098198e-02 + 34 3.20588498781384e+00 -1.20235399512554e-03 1.80706891199292e-03 -3.27231063098198e-02 + 35 3.20718790186854e+00 -1.20287516074742e-03 1.80863581542890e-03 -3.27231063098198e-02 + 36 3.20856239219851e+00 -1.20342495687940e-03 1.81028953355024e-03 -3.27231063098198e-02 + 37 3.20996308337448e+00 -1.20398523334979e-03 1.81197555265544e-03 -3.27231063098198e-02 + 38 3.21135495072621e+00 -1.20454198029048e-03 1.81365172785265e-03 -3.27231063098198e-02 + 39 3.21271453359899e+00 -1.20508581343960e-03 1.81528977219172e-03 -3.27231063098198e-02 + 40 3.21403051451645e+00 -1.20561220580658e-03 1.81687598848726e-03 -3.27231063098198e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out index 29a8ea10b..2432c858b 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -131,27 +126,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped index a0bbaca3d..ed4ff587f 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491521323e+00 + x 3.21685491541898e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj index d5d525eb6..dfbf0ebd2 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095402e+00 -1.20174855638161e-02 - 2 3.20383991841948e+00 -1.20153596736779e-02 - 3 3.20396638982490e+00 -1.20158655592996e-02 - 4 3.20472672277551e+00 -1.20189068911021e-02 - 5 3.20606083670179e+00 -1.20242433468072e-02 - 6 3.20787669543948e+00 -1.20315067817579e-02 - 7 3.21005568755800e+00 -1.20402227502320e-02 - 8 3.21245908142754e+00 -1.20498363257101e-02 - 9 3.21493559049101e+00 -1.20597423619640e-02 - 10 3.21733015640955e+00 -1.20693206256382e-02 - 11 3.21949374123820e+00 -1.20779749649528e-02 - 12 3.22129339461899e+00 -1.20851735784760e-02 - 13 3.22262143319445e+00 -1.20904857327778e-02 - 14 3.22340249773966e+00 -1.20936099909586e-02 - 15 3.22359762729192e+00 -1.20943905091677e-02 - 16 3.22320508654863e+00 -1.20928203461945e-02 - 17 3.22225829334495e+00 -1.20890331733798e-02 - 18 3.22082156074746e+00 -1.20832862429898e-02 - 19 3.21898439787187e+00 -1.20759375914875e-02 - 20 3.21685491521323e+00 -1.20674196608529e-02 + 1 3.20437139095465e+00 -1.20174855638186e-02 + 2 3.20383991842200e+00 -1.20153596736880e-02 + 3 3.20396638983062e+00 -1.20158655593225e-02 + 4 3.20472672278571e+00 -1.20189068911429e-02 + 5 3.20606083671774e+00 -1.20242433468710e-02 + 6 3.20787669546241e+00 -1.20315067818496e-02 + 7 3.21005568758906e+00 -1.20402227503562e-02 + 8 3.21245908146782e+00 -1.20498363258713e-02 + 9 3.21493559054151e+00 -1.20597423621660e-02 + 10 3.21733015647118e+00 -1.20693206258847e-02 + 11 3.21949374131176e+00 -1.20779749652470e-02 + 12 3.22129339470521e+00 -1.20851735788208e-02 + 13 3.22262143329394e+00 -1.20904857331758e-02 + 14 3.22340249785300e+00 -1.20936099914120e-02 + 15 3.22359762741961e+00 -1.20943905096784e-02 + 16 3.22320508669112e+00 -1.20928203467645e-02 + 17 3.22225829350267e+00 -1.20890331740107e-02 + 18 3.22082156092082e+00 -1.20832862436833e-02 + 19 3.21898439806125e+00 -1.20759375922450e-02 + 20 3.21685491541898e+00 -1.20674196616759e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out index 95f077f0b..57b080e73 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -131,32 +126,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped index f58df11b7..8719ed7ca 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397364200070e+00 + x 3.21397364248195e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj index 8b5e494a7..fec7bdbdb 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685491521323e+00 -1.20674196608529e-02 - 21 3.21455264073267e+00 -1.20582105629307e-02 - 22 3.21220094103318e+00 -1.20488037641327e-02 - 23 3.20991934284523e+00 -1.20396773713809e-02 - 24 3.20781628562398e+00 -1.20312651424959e-02 - 25 3.20598302292944e+00 -1.20239320917178e-02 - 26 3.20448930614687e+00 -1.20179572245875e-02 - 27 3.20338117886792e+00 -1.20135247154717e-02 - 28 3.20268080933861e+00 -1.20107232373544e-02 - 29 3.20238791142161e+00 -1.20095516456865e-02 - 30 3.20248233467135e+00 -1.20099293386854e-02 - 31 3.20292744714189e+00 -1.20117097885676e-02 - 32 3.20367415705454e+00 -1.20146966282182e-02 - 33 3.20466539988114e+00 -1.20186615995246e-02 - 34 3.20584087581816e+00 -1.20233635032726e-02 - 35 3.20714161837695e+00 -1.20285664735078e-02 - 36 3.20851394921166e+00 -1.20340557968466e-02 - 37 3.20991249801338e+00 -1.20396499920535e-02 - 38 3.21130224431234e+00 -1.20452089772494e-02 - 39 3.21265973069097e+00 -1.20506389227639e-02 - 40 3.21397364200070e+00 -1.20558945680028e-02 + 20 3.21685491541898e+00 -1.20674196616759e-02 + 21 3.21455264095509e+00 -1.20582105638204e-02 + 22 3.21220094127252e+00 -1.20488037650901e-02 + 23 3.20991934310164e+00 -1.20396773724066e-02 + 24 3.20781628589752e+00 -1.20312651435901e-02 + 25 3.20598302322006e+00 -1.20239320928802e-02 + 26 3.20448930645441e+00 -1.20179572258176e-02 + 27 3.20338117919211e+00 -1.20135247167684e-02 + 28 3.20268080967909e+00 -1.20107232387163e-02 + 29 3.20238791177794e+00 -1.20095516471117e-02 + 30 3.20248233504303e+00 -1.20099293401721e-02 + 31 3.20292744752838e+00 -1.20117097901135e-02 + 32 3.20367415745526e+00 -1.20146966298210e-02 + 33 3.20466540029545e+00 -1.20186616011818e-02 + 34 3.20584087624535e+00 -1.20233635049814e-02 + 35 3.20714161881621e+00 -1.20285664752649e-02 + 36 3.20851394966204e+00 -1.20340557986482e-02 + 37 3.20991249847373e+00 -1.20396499938949e-02 + 38 3.21130224478131e+00 -1.20452089791253e-02 + 39 3.21265973116698e+00 -1.20506389246679e-02 + 40 3.21397364248195e+00 -1.20558945699278e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out index 188ad78a8..be491208e 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -152,12 +153,10 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out index abd39e0f9..27cae7081 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -152,7 +153,6 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.1979 @@ -162,7 +162,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt index 157cac038..d885e1c46 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2022-05-24. +colvars: Using NAMD interface, version "2022-05-09". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out index c92a480be..0dd351c58 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. colvars: # upperWalls = { 0.2 } @@ -137,27 +132,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped index 99d5623d0..af765be67 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687060179954e+00 + x 3.21687060200527e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063080692e-02 + accumulatedWork -3.27231063098198e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj index f2c850ae5..6c0216a7f 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 0 3.20554673468334e+00 -1.20221869387334e-02 1.80666223487314e-02 0.00000000000000e+00 - 1 3.20437139095402e+00 -1.09359118630726e-02 1.64277703677051e-02 -1.62472454186094e-03 - 2 3.20383993500698e+00 -9.85259498682288e-03 1.47978091424340e-02 -3.24887432578663e-03 - 3 3.20396645593733e+00 -8.77158205133702e-03 1.31747691238592e-02 -4.87316093009804e-03 - 4 3.20472688727227e+00 -7.69210083141700e-03 1.15563310938840e-02 -6.49826999017548e-03 - 5 3.20606116377278e+00 -6.61333456030012e-03 9.94004409237728e-03 -8.12482265983721e-03 - 6 3.20787726388044e+00 -5.53449416554000e-03 8.32353958380334e-03 -9.75334127405960e-03 - 7 3.21005658994163e+00 -4.45488375311361e-03 6.70472609924175e-03 -1.13842205954968e-02 - 8 3.21246042319826e+00 -3.37395567398206e-03 5.08195396874809e-03 -1.30177057997372e-02 - 9 3.21493748901074e+00 -2.29135249164817e-03 3.45414226380412e-03 -1.46538784510129e-02 - 10 3.21733273998387e+00 -1.20693309599355e-03 1.82085937275571e-03 -1.62926518864930e-02 - 11 3.21949714815442e+00 -1.20779885926177e-03 1.82347260554254e-03 -1.79337772314813e-02 - 12 3.22129775552305e+00 -1.20851910220922e-03 1.82564802550573e-03 -1.95768604544364e-02 - 13 3.22262687042120e+00 -1.20905074816848e-03 1.82725463955845e-03 -2.12213896300391e-02 - 14 3.22340912494254e+00 -1.20936364997702e-03 1.82820054735717e-03 -2.28667701226605e-02 - 15 3.22360554936245e+00 -1.20944221974498e-03 1.82843810362708e-03 -2.45123644159249e-02 - 16 3.22321439979867e+00 -1.20928575991947e-03 1.82796506143001e-03 -2.61575329712119e-02 - 17 3.22226908590648e+00 -1.20890763436259e-03 1.82682208552520e-03 -2.78016728481846e-02 - 18 3.22083391313757e+00 -1.20833356525503e-03 1.82508750615241e-03 -2.94442516037217e-02 - 19 3.21899838366880e+00 -1.20759935346752e-03 1.82287024811897e-03 -3.10848348270288e-02 - 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 + 1 3.20437139095465e+00 -1.09359118630749e-02 1.64277703677119e-02 -1.62472454186161e-03 + 2 3.20383993500950e+00 -9.85259498683116e-03 1.47978091424589e-02 -3.24887432579003e-03 + 3 3.20396645594305e+00 -8.77158205135371e-03 1.31747691239093e-02 -4.87316093010762e-03 + 4 3.20472688728247e+00 -7.69210083144311e-03 1.15563310939625e-02 -6.49826999019610e-03 + 5 3.20606116378874e+00 -6.61333456033522e-03 9.94004409248278e-03 -8.12482265987509e-03 + 6 3.20787726390336e+00 -5.53449416558219e-03 8.32353958393024e-03 -9.75334127412231e-03 + 7 3.21005658997269e+00 -4.45488375315958e-03 6.70472609938014e-03 -1.13842205955932e-02 + 8 3.21246042323855e+00 -3.37395567402717e-03 5.08195396888400e-03 -1.30177057998773e-02 + 9 3.21493748906124e+00 -2.29135249168655e-03 3.45414226391983e-03 -1.46538784512077e-02 + 10 3.21733274004549e+00 -1.20693309601820e-03 1.82085937283009e-03 -1.62926518867548e-02 + 11 3.21949714822798e+00 -1.20779885929119e-03 1.82347260563138e-03 -1.79337772318231e-02 + 12 3.22129775560926e+00 -1.20851910224370e-03 1.82564802560991e-03 -1.95768604548720e-02 + 13 3.22262687052069e+00 -1.20905074820828e-03 1.82725463967874e-03 -2.12213896305829e-02 + 14 3.22340912505588e+00 -1.20936365002235e-03 1.82820054749423e-03 -2.28667701233277e-02 + 15 3.22360554949013e+00 -1.20944221979605e-03 1.82843810378150e-03 -2.45123644167310e-02 + 16 3.22321439994115e+00 -1.20928575997646e-03 1.82796506160231e-03 -2.61575329721731e-02 + 17 3.22226908606420e+00 -1.20890763442568e-03 1.82682208571586e-03 -2.78016728493174e-02 + 18 3.22083391331092e+00 -1.20833356532437e-03 1.82508750636188e-03 -2.94442516050430e-02 + 19 3.21899838385817e+00 -1.20759935354327e-03 1.82287024834765e-03 -3.10848348285559e-02 + 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out index 0187122c8..0bd2a2834 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. colvars: # upperWalls = { 0.2 } @@ -137,32 +132,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped index a9bad9be9..1cdd044fd 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403051403523e+00 + x 3.21403051451645e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063080692e-02 + accumulatedWork -3.27231063098198e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj index 7cdbd31e7..476fdf462 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 - 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 - 21 3.21457009005187e+00 -1.20582803602075e-03 1.81752656556706e-03 -3.27231063080692e-02 - 22 3.21222021029772e+00 -1.20488808411909e-03 1.81469411906520e-03 -3.27231063080692e-02 - 23 3.20994048512507e+00 -1.20397619405003e-03 1.81194834479899e-03 -3.27231063080692e-02 - 24 3.20783935027265e+00 -1.20313574010906e-03 1.80941951140972e-03 -3.27231063080692e-02 - 25 3.20600805578400e+00 -1.20240322231360e-03 1.80721688628766e-03 -3.27231063080692e-02 - 26 3.20451634953337e+00 -1.20180653981335e-03 1.80542369892267e-03 -3.27231063080692e-02 - 27 3.20341027138948e+00 -1.20136410855579e-03 1.80409465165757e-03 -3.27231063080692e-02 - 28 3.20271198551962e+00 -1.20108479420785e-03 1.80325585359664e-03 -3.27231063080692e-02 - 29 3.20242120121622e+00 -1.20096848048649e-03 1.80290661390253e-03 -3.27231063080692e-02 - 30 3.20251776290552e+00 -1.20100710516221e-03 1.80302258331263e-03 -3.27231063080692e-02 - 31 3.20296503299079e+00 -1.20118601319632e-03 1.80355979787307e-03 -3.27231063080692e-02 - 32 3.20371391361211e+00 -1.20148556544484e-03 1.80445945496540e-03 -3.27231063080692e-02 - 33 3.20470733384994e+00 -1.20188293353998e-03 1.80565323241832e-03 -3.27231063080692e-02 - 34 3.20588498738668e+00 -1.20235399495467e-03 1.80706891147932e-03 -3.27231063080692e-02 - 35 3.20718790142930e+00 -1.20287516057172e-03 1.80863581490056e-03 -3.27231063080692e-02 - 36 3.20856239174816e+00 -1.20342495669926e-03 1.81028953300828e-03 -3.27231063080692e-02 - 37 3.20996308291416e+00 -1.20398523316567e-03 1.81197555210123e-03 -3.27231063080692e-02 - 38 3.21135495025727e+00 -1.20454198010291e-03 1.81365172728779e-03 -3.27231063080692e-02 - 39 3.21271453312301e+00 -1.20508581324920e-03 1.81528977161812e-03 -3.27231063080692e-02 - 40 3.21403051403523e+00 -1.20561220561409e-03 1.81687598790710e-03 -3.27231063080692e-02 + 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 + 21 3.21457009027428e+00 -1.20582803610971e-03 1.81752656583525e-03 -3.27231063098198e-02 + 22 3.21222021053704e+00 -1.20488808421481e-03 1.81469411935356e-03 -3.27231063098198e-02 + 23 3.20994048538146e+00 -1.20397619415258e-03 1.81194834510767e-03 -3.27231063098198e-02 + 24 3.20783935054617e+00 -1.20313574021847e-03 1.80941951173880e-03 -3.27231063098198e-02 + 25 3.20600805607460e+00 -1.20240322242984e-03 1.80721688663708e-03 -3.27231063098198e-02 + 26 3.20451634984089e+00 -1.20180653993636e-03 1.80542369929224e-03 -3.27231063098198e-02 + 27 3.20341027171365e+00 -1.20136410868546e-03 1.80409465204701e-03 -3.27231063098198e-02 + 28 3.20271198586007e+00 -1.20108479434403e-03 1.80325585400555e-03 -3.27231063098198e-02 + 29 3.20242120157252e+00 -1.20096848062901e-03 1.80290661433043e-03 -3.27231063098198e-02 + 30 3.20251776327717e+00 -1.20100710531087e-03 1.80302258375899e-03 -3.27231063098198e-02 + 31 3.20296503337725e+00 -1.20118601335090e-03 1.80355979833728e-03 -3.27231063098198e-02 + 32 3.20371391401280e+00 -1.20148556560512e-03 1.80445945544681e-03 -3.27231063098198e-02 + 33 3.20470733426422e+00 -1.20188293370569e-03 1.80565323291624e-03 -3.27231063098198e-02 + 34 3.20588498781384e+00 -1.20235399512554e-03 1.80706891199292e-03 -3.27231063098198e-02 + 35 3.20718790186854e+00 -1.20287516074742e-03 1.80863581542890e-03 -3.27231063098198e-02 + 36 3.20856239219851e+00 -1.20342495687940e-03 1.81028953355024e-03 -3.27231063098198e-02 + 37 3.20996308337448e+00 -1.20398523334979e-03 1.81197555265544e-03 -3.27231063098198e-02 + 38 3.21135495072621e+00 -1.20454198029048e-03 1.81365172785265e-03 -3.27231063098198e-02 + 39 3.21271453359899e+00 -1.20508581343960e-03 1.81528977219172e-03 -3.27231063098198e-02 + 40 3.21403051451645e+00 -1.20561220580658e-03 1.81687598848726e-03 -3.27231063098198e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out index c19bd65ec..a86d5ad83 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out @@ -4,9 +4,10 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -142,12 +142,10 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat index 6ff3132f9..1b0ff42d4 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 6.00000000000000e-01 2.00000000000000e-01 24 0 +# 0.6 0.2 24 0 - 7.00000000000000e-01 0.00000000000000e+00 - 9.00000000000000e-01 0.00000000000000e+00 - 1.10000000000000e+00 0.00000000000000e+00 - 1.30000000000000e+00 0.00000000000000e+00 - 1.50000000000000e+00 0.00000000000000e+00 - 1.70000000000000e+00 0.00000000000000e+00 - 1.90000000000000e+00 0.00000000000000e+00 - 2.10000000000000e+00 0.00000000000000e+00 - 2.30000000000000e+00 0.00000000000000e+00 - 2.50000000000000e+00 0.00000000000000e+00 - 2.70000000000000e+00 0.00000000000000e+00 - 2.90000000000000e+00 0.00000000000000e+00 - 3.10000000000000e+00 0.00000000000000e+00 - 3.30000000000000e+00 2.00000000000000e+01 - 3.50000000000000e+00 0.00000000000000e+00 - 3.70000000000000e+00 0.00000000000000e+00 - 3.90000000000000e+00 0.00000000000000e+00 - 4.10000000000000e+00 0.00000000000000e+00 - 4.30000000000000e+00 0.00000000000000e+00 - 4.50000000000000e+00 0.00000000000000e+00 - 4.70000000000000e+00 0.00000000000000e+00 - 4.90000000000000e+00 0.00000000000000e+00 - 5.10000000000000e+00 0.00000000000000e+00 - 5.30000000000000e+00 0.00000000000000e+00 + 0.7 0 + 0.9 0 + 1.1 0 + 1.3 0 + 1.5 0 + 1.7 0 + 1.9 0 + 2.1 0 + 2.3 0 + 2.5 0 + 2.7 0 + 2.9 0 + 3.1 0 + 3.3 20 + 3.5 0 + 3.7 0 + 3.9 0 + 4.1 0 + 4.3 0 + 4.5 0 + 4.7 0 + 4.9 0 + 5.1 0 + 5.3 0 diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out index a44f3ed1b..cc179e493 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out @@ -4,9 +4,10 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -142,7 +142,6 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 @@ -152,7 +151,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out index 6e8a55a99..2f8db54b9 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,27 +125,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped index e2cb5b6df..54969f08b 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687794922887e+00 + x 3.21687794941120e+00 } restraint { diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj index 31625d56a..60f1c7042 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -2.00000000000000e-03 - 1 3.20437146782473e+00 -2.00000000000000e-03 - 2 3.20384022474555e+00 -2.00000000000000e-03 - 3 3.20396707507294e+00 -2.00000000000000e-03 - 4 3.20472793153934e+00 -2.00000000000000e-03 - 5 3.20606270721111e+00 -2.00000000000000e-03 - 6 3.20787935837892e+00 -2.00000000000000e-03 - 7 3.21005926521749e+00 -2.00000000000000e-03 - 8 3.21246368719045e+00 -2.00000000000000e-03 - 9 3.21494132865815e+00 -2.00000000000000e-03 - 10 3.21733712234869e+00 -2.00000000000000e-03 - 11 3.21950202183533e+00 -2.00000000000000e-03 - 12 3.22130306897412e+00 -2.00000000000000e-03 - 13 3.22263257351741e+00 -2.00000000000000e-03 - 14 3.22341517032649e+00 -2.00000000000000e-03 - 15 3.22361189349532e+00 -2.00000000000000e-03 - 16 3.22322100366549e+00 -2.00000000000000e-03 - 17 3.22227591535082e+00 -2.00000000000000e-03 - 18 3.22084093883207e+00 -2.00000000000000e-03 - 19 3.21900558075137e+00 -2.00000000000000e-03 - 20 3.21687794922887e+00 -2.00000000000000e-03 + 1 3.20437146782535e+00 -2.00000000000000e-03 + 2 3.20384022479972e+00 -2.00000000000000e-03 + 3 3.20396707508047e+00 -2.00000000000000e-03 + 4 3.20472793158710e+00 -2.00000000000000e-03 + 5 3.20606270721620e+00 -2.00000000000000e-03 + 6 3.20787935839808e+00 -2.00000000000000e-03 + 7 3.21005926525274e+00 -2.00000000000000e-03 + 8 3.21246368724284e+00 -2.00000000000000e-03 + 9 3.21494132872828e+00 -2.00000000000000e-03 + 10 3.21733712243639e+00 -2.00000000000000e-03 + 11 3.21950202193975e+00 -2.00000000000000e-03 + 12 3.22130306909382e+00 -2.00000000000000e-03 + 13 3.22263257365056e+00 -2.00000000000000e-03 + 14 3.22341517047102e+00 -2.00000000000000e-03 + 15 3.22361189364914e+00 -2.00000000000000e-03 + 16 3.22322100382672e+00 -2.00000000000000e-03 + 17 3.22227591551750e+00 -2.00000000000000e-03 + 18 3.22084093900392e+00 -2.00000000000000e-03 + 19 3.21900558093302e+00 -2.00000000000000e-03 + 20 3.21687794941120e+00 -2.00000000000000e-03 diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out index f25f2a600..ae73096ad 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,32 +125,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting linear bias "linear1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped index 8bd282397..7819eca62 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403631049857e+00 + x 3.21403631097325e+00 } restraint { diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj index feadd768c..22b58b046 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21687794922887e+00 -2.00000000000000e-03 - 21 3.21457756974034e+00 -2.00000000000000e-03 - 22 3.21222780608884e+00 -2.00000000000000e-03 - 23 3.20994818169250e+00 -2.00000000000000e-03 - 24 3.20784713203794e+00 -2.00000000000000e-03 - 25 3.20601590593918e+00 -2.00000000000000e-03 - 26 3.20452424926460e+00 -2.00000000000000e-03 - 27 3.20341819935304e+00 -2.00000000000000e-03 - 28 3.20271991761219e+00 -2.00000000000000e-03 - 29 3.20242911063155e+00 -2.00000000000000e-03 - 30 3.20252562047120e+00 -2.00000000000000e-03 - 31 3.20297280776558e+00 -2.00000000000000e-03 - 32 3.20372157370085e+00 -2.00000000000000e-03 - 33 3.20471484737174e+00 -2.00000000000000e-03 - 34 3.20589232352072e+00 -2.00000000000000e-03 - 35 3.20719503146155e+00 -2.00000000000000e-03 - 36 3.20856929000306e+00 -2.00000000000000e-03 - 37 3.20996972751317e+00 -2.00000000000000e-03 - 38 3.21136132363592e+00 -2.00000000000000e-03 - 39 3.21272062227744e+00 -2.00000000000000e-03 - 40 3.21403631049857e+00 -2.00000000000000e-03 + 20 3.21687794941120e+00 -2.00000000000000e-03 + 21 3.21457756992910e+00 -2.00000000000000e-03 + 22 3.21222780628590e+00 -2.00000000000000e-03 + 23 3.20994818190026e+00 -2.00000000000000e-03 + 24 3.20784713225907e+00 -2.00000000000000e-03 + 25 3.20601590617646e+00 -2.00000000000000e-03 + 26 3.20452424952068e+00 -2.00000000000000e-03 + 27 3.20341819963022e+00 -2.00000000000000e-03 + 28 3.20271991791227e+00 -2.00000000000000e-03 + 29 3.20242911095567e+00 -2.00000000000000e-03 + 30 3.20252562081973e+00 -2.00000000000000e-03 + 31 3.20297280813812e+00 -2.00000000000000e-03 + 32 3.20372157409621e+00 -2.00000000000000e-03 + 33 3.20471484778801e+00 -2.00000000000000e-03 + 34 3.20589232395536e+00 -2.00000000000000e-03 + 35 3.20719503191152e+00 -2.00000000000000e-03 + 36 3.20856929046496e+00 -2.00000000000000e-03 + 37 3.20996972798345e+00 -2.00000000000000e-03 + 38 3.21136132411101e+00 -2.00000000000000e-03 + 39 3.21272062275390e+00 -2.00000000000000e-03 + 40 3.21403631097325e+00 -2.00000000000000e-03 diff --git a/namd/tests/library/000_distance_linear-fixed/namd-version.txt b/namd/tests/library/000_distance_linear-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance_linear-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_linear-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out index 3d1d47403..5461163f6 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -0.1 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,27 +131,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped index 7978e66e5..d40e34747 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21716984757735e+00 + x 3.21716984778310e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name linear1 firstStep 0 forceConstant -1.00000000000000e-01 - accumulatedWork -1.25846317029250e+00 + accumulatedWork -1.25846317032503e+00 } } diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj index ab81a1e48..d7a3f40f3 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_linear1 W_linear1 0 3.20554673468334e+00 -2.00000000000000e-03 6.21109346936669e-03 0.00000000000000e+00 - 1 3.20437146782473e+00 1.82000000000000e-02 -5.64995607144102e-02 -6.27083036500596e-02 - 2 3.20384053454173e+00 3.84000000000000e-02 -1.19187476526403e-01 -1.25405882447803e-01 - 3 3.20396830993065e+00 5.86000000000000e-02 -1.81892542961936e-01 -1.88106042308402e-01 - 4 3.20473100410431e+00 7.88000000000000e-02 -2.44652803123419e-01 -2.50821608591309e-01 - 5 3.20606881617484e+00 9.90000000000000e-02 -3.07500812801309e-01 -3.13564198678041e-01 - 6 3.20788997449316e+00 1.19200000000000e-01 -3.70460484959585e-01 -3.76343576162802e-01 - 7 3.21007611525328e+00 1.39400000000000e-01 -4.33544610466307e-01 -4.39167113690919e-01 - 8 3.21248873642126e+00 1.59600000000000e-01 -4.96753202332834e-01 -5.02039386166628e-01 - 9 3.21497676245318e+00 1.79800000000000e-01 -5.60072821889081e-01 -5.64961916768182e-01 - 10 3.21738532749986e+00 2.00000000000000e-01 -6.23477065499971e-01 -6.27933100383679e-01 - 11 3.21956556827726e+00 2.00000000000000e-01 -6.23913113655452e-01 -6.90948324862880e-01 - 12 3.22138438212180e+00 2.00000000000000e-01 -6.24276876424360e-01 -7.54000289381740e-01 - 13 3.22273392229575e+00 2.00000000000000e-01 -6.24546784459149e-01 -8.17079514612114e-01 - 14 3.22353866090033e+00 2.00000000000000e-01 -6.24707732180065e-01 -8.80174995562301e-01 - 15 3.22375946848086e+00 2.00000000000000e-01 -6.24751893696173e-01 -9.43274936825614e-01 - 16 3.22339444626381e+00 2.00000000000000e-01 -6.24678889252761e-01 -1.00636750464014e+00 - 17 3.22247685750743e+00 2.00000000000000e-01 -6.24495371501486e-01 -1.06944153716179e+00 - 18 3.22107087240991e+00 2.00000000000000e-01 -6.24214174481982e-01 -1.13248716878447e+00 - 19 3.21926587064193e+00 2.00000000000000e-01 -6.23853174128386e-01 -1.19549633937144e+00 - 20 3.21716984757735e+00 2.00000000000000e-01 -6.23433969515469e-01 -1.25846317029250e+00 + 1 3.20437146782536e+00 1.82000000000000e-02 -5.64995607144215e-02 -6.27083036500722e-02 + 2 3.20384053454426e+00 3.84000000000000e-02 -1.19187476526499e-01 -1.25405882447866e-01 + 3 3.20396830993637e+00 5.86000000000000e-02 -1.81892542962271e-01 -1.88106042308581e-01 + 4 3.20473100411451e+00 7.88000000000000e-02 -2.44652803124223e-01 -2.50821608591694e-01 + 5 3.20606881619079e+00 9.90000000000000e-02 -3.07500812802888e-01 -3.13564198678748e-01 + 6 3.20788997451609e+00 1.19200000000000e-01 -3.70460484962318e-01 -3.76343576163973e-01 + 7 3.21007611528435e+00 1.39400000000000e-01 -4.33544610470638e-01 -4.39167113692717e-01 + 8 3.21248873646155e+00 1.59600000000000e-01 -4.96753202339263e-01 -5.02039386169240e-01 + 9 3.21497676250368e+00 1.79800000000000e-01 -5.60072821898162e-01 -5.64961916771815e-01 + 10 3.21738532756148e+00 2.00000000000000e-01 -6.23477065512297e-01 -6.27933100388556e-01 + 11 3.21956556835082e+00 2.00000000000000e-01 -6.23913113670165e-01 -6.90948324869243e-01 + 12 3.22138438220801e+00 2.00000000000000e-01 -6.24276876441603e-01 -7.54000289389845e-01 + 13 3.22273392239524e+00 2.00000000000000e-01 -6.24546784479049e-01 -8.17079514622229e-01 + 14 3.22353866101367e+00 2.00000000000000e-01 -6.24707732202734e-01 -8.80174995574705e-01 + 15 3.22375946860855e+00 2.00000000000000e-01 -6.24751893721710e-01 -9.43274936840598e-01 + 16 3.22339444640630e+00 2.00000000000000e-01 -6.24678889281260e-01 -1.00636750465800e+00 + 17 3.22247685766515e+00 2.00000000000000e-01 -6.24495371533031e-01 -1.06944153718284e+00 + 18 3.22107087258327e+00 2.00000000000000e-01 -6.24214174516655e-01 -1.13248716880902e+00 + 19 3.21926587083132e+00 2.00000000000000e-01 -6.23853174166263e-01 -1.19549633939982e+00 + 20 3.21716984778310e+00 2.00000000000000e-01 -6.23433969556620e-01 -1.25846317032503e+00 diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out index 1abc5a030..bffe886e1 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -0.1 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,32 +131,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21717 colvars: Restarting linear bias "linear1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped index 329d673d2..c2d3e24ea 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21509555082278e+00 + x 3.21509555130398e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name linear1 firstStep 0 forceConstant -1.00000000000000e-01 - accumulatedWork -1.25846317029250e+00 + accumulatedWork -1.25846317032503e+00 } } diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj index cd6a6f61c..105936f55 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_linear1 W_linear1 - 20 3.21716984757735e+00 2.00000000000000e-01 -6.23433969515469e-01 -1.25846317029250e+00 - 21 3.21490223025136e+00 2.00000000000000e-01 -6.22980446050271e-01 -1.25846317029250e+00 - 22 3.21258629724258e+00 2.00000000000000e-01 -6.22517259448516e-01 -1.25846317029250e+00 - 23 3.21034149757330e+00 2.00000000000000e-01 -6.22068299514661e-01 -1.25846317029250e+00 - 24 3.20827619999141e+00 2.00000000000000e-01 -6.21655239998281e-01 -1.25846317029250e+00 - 25 3.20648158985175e+00 2.00000000000000e-01 -6.21296317970351e-01 -1.25846317029250e+00 - 26 3.20502734915530e+00 2.00000000000000e-01 -6.21005469831060e-01 -1.25846317029250e+00 - 27 3.20395944688168e+00 2.00000000000000e-01 -6.20791889376335e-01 -1.25846317029250e+00 - 28 3.20329996891376e+00 2.00000000000000e-01 -6.20659993782751e-01 -1.25846317029250e+00 - 29 3.20304853658376e+00 2.00000000000000e-01 -6.20609707316753e-01 -1.25846317029250e+00 - 30 3.20318489575175e+00 2.00000000000000e-01 -6.20636979150349e-01 -1.25846317029250e+00 - 31 3.20367230075533e+00 2.00000000000000e-01 -6.20734460151066e-01 -1.25846317029250e+00 - 32 3.20446153809111e+00 2.00000000000000e-01 -6.20892307618221e-01 -1.25846317029250e+00 - 33 3.20549541623088e+00 2.00000000000000e-01 -6.21099083246176e-01 -1.25846317029250e+00 - 34 3.20671350699132e+00 2.00000000000000e-01 -6.21342701398263e-01 -1.25846317029250e+00 - 35 3.20805672062037e+00 2.00000000000000e-01 -6.21611344124074e-01 -1.25846317029250e+00 - 36 3.20947126470013e+00 2.00000000000000e-01 -6.21894252940025e-01 -1.25846317029250e+00 - 37 3.21091167068192e+00 2.00000000000000e-01 -6.22182334136383e-01 -1.25846317029250e+00 - 38 3.21234283861993e+00 2.00000000000000e-01 -6.22468567723985e-01 -1.25846317029250e+00 - 39 3.21374125101100e+00 2.00000000000000e-01 -6.22748250202200e-01 -1.25846317029250e+00 - 40 3.21509555082278e+00 2.00000000000000e-01 -6.23019110164555e-01 -1.25846317029250e+00 + 20 3.21716984778310e+00 2.00000000000000e-01 -6.23433969556620e-01 -1.25846317032503e+00 + 21 3.21490223047378e+00 2.00000000000000e-01 -6.22980446094756e-01 -1.25846317032503e+00 + 22 3.21258629748191e+00 2.00000000000000e-01 -6.22517259496383e-01 -1.25846317032503e+00 + 23 3.21034149782971e+00 2.00000000000000e-01 -6.22068299565942e-01 -1.25846317032503e+00 + 24 3.20827620026494e+00 2.00000000000000e-01 -6.21655240052988e-01 -1.25846317032503e+00 + 25 3.20648159014237e+00 2.00000000000000e-01 -6.21296318028474e-01 -1.25846317032503e+00 + 26 3.20502734946283e+00 2.00000000000000e-01 -6.21005469892566e-01 -1.25846317032503e+00 + 27 3.20395944720586e+00 2.00000000000000e-01 -6.20791889441172e-01 -1.25846317032503e+00 + 28 3.20329996925422e+00 2.00000000000000e-01 -6.20659993850845e-01 -1.25846317032503e+00 + 29 3.20304853694008e+00 2.00000000000000e-01 -6.20609707388016e-01 -1.25846317032503e+00 + 30 3.20318489612342e+00 2.00000000000000e-01 -6.20636979224683e-01 -1.25846317032503e+00 + 31 3.20367230114181e+00 2.00000000000000e-01 -6.20734460228362e-01 -1.25846317032503e+00 + 32 3.20446153849181e+00 2.00000000000000e-01 -6.20892307698363e-01 -1.25846317032503e+00 + 33 3.20549541664518e+00 2.00000000000000e-01 -6.21099083329035e-01 -1.25846317032503e+00 + 34 3.20671350741850e+00 2.00000000000000e-01 -6.21342701483699e-01 -1.25846317032503e+00 + 35 3.20805672105962e+00 2.00000000000000e-01 -6.21611344211924e-01 -1.25846317032503e+00 + 36 3.20947126515048e+00 2.00000000000000e-01 -6.21894253030096e-01 -1.25846317032503e+00 + 37 3.21091167114224e+00 2.00000000000000e-01 -6.22182334228447e-01 -1.25846317032503e+00 + 38 3.21234283908886e+00 2.00000000000000e-01 -6.22468567817772e-01 -1.25846317032503e+00 + 39 3.21374125148697e+00 2.00000000000000e-01 -6.22748250297394e-01 -1.25846317032503e+00 + 40 3.21509555130398e+00 2.00000000000000e-01 -6.23019110260796e-01 -1.25846317032503e+00 diff --git a/namd/tests/library/000_distance_linear-k-moving/namd-version.txt b/namd/tests/library/000_distance_linear-k-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_linear-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_linear-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out index b7fa6abce..abb32eebd 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -152,7 +148,6 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -163,28 +158,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index 26945fa08..f4d2ca8a0 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.17274648853048e-01 , -1.89053561545958e-03 , 9.48331810639220e-01 ) + x ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index 84fccc97a..653638305 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.39806527406457e-01 , 7.75672148823424e-03 , 9.40463373664131e-01 ) ( 2.67961305481292e-03 , -1.55134429764685e-05 , -1.88092674732826e-03 ) - 1 ( -3.39402299530748e-01 , 6.96783241211861e-03 , 9.40615505073522e-01 ) ( 2.67880459906150e-03 , -1.39356648242372e-05 , -1.88123101014704e-03 ) - 2 ( -3.38852268621315e-01 , 6.28615128621521e-03 , 9.40818592690533e-01 ) ( 2.67770453724263e-03 , -1.25723025724304e-05 , -1.88163718538107e-03 ) - 3 ( -3.38144430390545e-01 , 5.71702991523034e-03 , 9.41076861773151e-01 ) ( 2.67628886078109e-03 , -1.14340598304607e-05 , -1.88215372354630e-03 ) - 4 ( -3.37272058702922e-01 , 5.26001267429506e-03 , 9.41392527421457e-01 ) ( 2.67454411740584e-03 , -1.05200253485901e-05 , -1.88278505484291e-03 ) - 5 ( -3.36235002706895e-01 , 4.90828501062859e-03 , 9.41765327293880e-01 ) ( 2.67247000541379e-03 , -9.81657002125718e-06 , -1.88353065458776e-03 ) - 6 ( -3.35040319467782e-01 , 4.64847236791525e-03 , 9.42192324334884e-01 ) ( 2.67008063893556e-03 , -9.29694473583050e-06 , -1.88438464866977e-03 ) - 7 ( -3.33702304344449e-01 , 4.46100232397236e-03 , 9.42667954018524e-01 ) ( 2.66740460868890e-03 , -8.92200464794472e-06 , -1.88533590803705e-03 ) - 8 ( -3.32242055264741e-01 , 4.32116578678476e-03 , 9.43184257841332e-01 ) ( 2.66448411052948e-03 , -8.64233157356951e-06 , -1.88636851568266e-03 ) - 9 ( -3.30686722575443e-01 , 4.20085972855961e-03 , 9.43731235198800e-01 ) ( 2.66137344515089e-03 , -8.40171945711923e-06 , -1.88746247039760e-03 ) - 10 ( -3.29068550292791e-01 , 4.07080426882692e-03 , 9.44297261332895e-01 ) ( 2.65813710058558e-03 , -8.14160853765385e-06 , -1.88859452266579e-03 ) - 11 ( -3.27423742833967e-01 , 3.90288351107626e-03 , 9.44869546619476e-01 ) ( 2.65484748566793e-03 , -7.80576702215252e-06 , -1.88973909323895e-03 ) - 12 ( -3.25791132203644e-01 , 3.67221267471163e-03 , 9.45434637101656e-01 ) ( 2.65158226440729e-03 , -7.34442534942325e-06 , -1.89086927420331e-03 ) - 13 ( -3.24210587610799e-01 , 3.35858640839648e-03 , 9.45978971636472e-01 ) ( 2.64842117522160e-03 , -6.71717281679296e-06 , -1.89195794327294e-03 ) - 14 ( -3.22721152621232e-01 , 2.94710471653878e-03 , 9.46489499268013e-01 ) ( 2.64544230524246e-03 , -5.89420943307757e-06 , -1.89297899853603e-03 ) - 15 ( -3.21358984318630e-01 , 2.42796439219500e-03 , 9.46954332682738e-01 ) ( 2.64271796863726e-03 , -4.85592878438999e-06 , -1.89390866536548e-03 ) - 16 ( -3.20155244148942e-01 , 1.79559469694439e-03 , 9.47363391462651e-01 ) ( 2.64031048829788e-03 , -3.59118939388878e-06 , -1.89472678292530e-03 ) - 17 ( -3.19134137387790e-01 , 1.04747308610593e-03 , 9.47708977035611e-01 ) ( 2.63826827477558e-03 , -2.09494617221186e-06 , -1.89541795407122e-03 ) - 18 ( -3.18311310715357e-01 , 1.83029983452565e-04 , 9.47986221403400e-01 ) ( 2.63662262143071e-03 , -3.66059966905130e-07 , -1.89597244280680e-03 ) - 19 ( -3.17692796752311e-01 , -7.96993693460030e-04 , 9.48193361974628e-01 ) ( 2.63538559350462e-03 , 1.59398738692006e-06 , -1.89638672394926e-03 ) - 20 ( -3.17274648853048e-01 , -1.89053561545958e-03 , 9.48331810639220e-01 ) ( 2.63454929770610e-03 , 3.78107123091915e-06 , -1.89666362127844e-03 ) + 0 ( -3.39806527406457e-01 , 7.75672148823417e-03 , 9.40463373664131e-01 ) ( 2.67961305481292e-03 , -1.55134429764683e-05 , -1.88092674732826e-03 ) + 1 ( -3.39402299531197e-01 , 6.96783241200742e-03 , 9.40615505073361e-01 ) ( 2.67880459906239e-03 , -1.39356648240148e-05 , -1.88123101014672e-03 ) + 2 ( -3.38852268623157e-01 , 6.28615128581265e-03 , 9.40818592689872e-01 ) ( 2.67770453724631e-03 , -1.25723025716253e-05 , -1.88163718537974e-03 ) + 3 ( -3.38144430394757e-01 , 5.71702991439356e-03 , 9.41076861771643e-01 ) ( 2.67628886078951e-03 , -1.14340598287871e-05 , -1.88215372354329e-03 ) + 4 ( -3.37272058710501e-01 , 5.26001267291420e-03 , 9.41392527418750e-01 ) ( 2.67454411742100e-03 , -1.05200253458284e-05 , -1.88278505483750e-03 ) + 5 ( -3.36235002718839e-01 , 4.90828500862304e-03 , 9.41765327289626e-01 ) ( 2.67247000543768e-03 , -9.81657001724609e-06 , -1.88353065457925e-03 ) + 6 ( -3.35040319485078e-01 , 4.64847236523130e-03 , 9.42192324328747e-01 ) ( 2.67008063897016e-03 , -9.29694473046260e-06 , -1.88438464865749e-03 ) + 7 ( -3.33702304368059e-01 , 4.46100232057914e-03 , 9.42667954010182e-01 ) ( 2.66740460873612e-03 , -8.92200464115828e-06 , -1.88533590802036e-03 ) + 8 ( -3.32242055295591e-01 , 4.32116578267109e-03 , 9.43184257830484e-01 ) ( 2.66448411059118e-03 , -8.64233156534219e-06 , -1.88636851566097e-03 ) + 9 ( -3.30686722614415e-01 , 4.20085972373069e-03 , 9.43731235185166e-01 ) ( 2.66137344522883e-03 , -8.40171944746138e-06 , -1.88746247037033e-03 ) + 10 ( -3.29068550340716e-01 , 4.07080426330041e-03 , 9.44297261316218e-01 ) ( 2.65813710068143e-03 , -8.14160852660083e-06 , -1.88859452263244e-03 ) + 11 ( -3.27423742891617e-01 , 3.90288350488177e-03 , 9.44869546599525e-01 ) ( 2.65484748578323e-03 , -7.80576700976354e-06 , -1.88973909319905e-03 ) + 12 ( -3.25791132271727e-01 , 3.67221266789039e-03 , 9.45434637078221e-01 ) ( 2.65158226454345e-03 , -7.34442533578077e-06 , -1.89086927415644e-03 ) + 13 ( -3.24210587689955e-01 , 3.35858640100320e-03 , 9.45978971609370e-01 ) ( 2.64842117537991e-03 , -6.71717280200640e-06 , -1.89195794321874e-03 ) + 14 ( -3.22721152712020e-01 , 2.94710470864841e-03 , 9.46489499237081e-01 ) ( 2.64544230542404e-03 , -5.89420941729682e-06 , -1.89297899847416e-03 ) + 15 ( -3.21358984421525e-01 , 2.42796438390647e-03 , 9.46954332647840e-01 ) ( 2.64271796884305e-03 , -4.85592876781293e-06 , -1.89390866529568e-03 ) + 16 ( -3.20155244264332e-01 , 1.79559468838712e-03 , 9.47363391423672e-01 ) ( 2.64031048852866e-03 , -3.59118937677423e-06 , -1.89472678284734e-03 ) + 17 ( -3.19134137515970e-01 , 1.04747307744542e-03 , 9.47708976992457e-01 ) ( 2.63826827503194e-03 , -2.09494615489084e-06 , -1.89541795398491e-03 ) + 18 ( -3.18311310856538e-01 , 1.83029974893031e-04 , 9.47986221355997e-01 ) ( 2.63662262171308e-03 , -3.66059949786063e-07 , -1.89597244271199e-03 ) + 19 ( -3.17692796906620e-01 , -7.96993701676326e-04 , 9.48193361922919e-01 ) ( 2.63538559381324e-03 , 1.59398740335265e-06 , -1.89638672384584e-03 ) + 20 ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) ( 2.63454929804108e-03 , 3.78107124610862e-06 , -1.89666362116634e-03 ) diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 6785f7248..9097222e0 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -152,7 +148,6 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -163,33 +158,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -0.317275 , -0.00189054 , 0.948332 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index 0236b3b01..f3e20f202 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.11598263481038e-01 , -2.44590603951106e-02 , 9.49899087566774e-01 ) + x ( -3.11598263889815e-01 , -2.44590603702029e-02 , 9.49899087433323e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index 2bb02cd37..7d738d1c8 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.17274648853048e-01 , -1.89053561545958e-03 , 9.48331810639220e-01 ) ( 2.63454929770610e-03 , 3.78107123091915e-06 , -1.89666362127844e-03 ) - 21 ( -3.17043326102425e-01 , -3.09358621457674e-03 , 9.48406009627862e-01 ) ( 2.63408665220485e-03 , 6.18717242915348e-06 , -1.89681201925572e-03 ) - 22 ( -3.16976780285387e-01 , -4.39920684988128e-03 , 9.48423095321387e-01 ) ( 2.63395356057077e-03 , 8.79841369976256e-06 , -1.89684619064277e-03 ) - 23 ( -3.17046097459336e-01 , -5.79657340367589e-03 , 9.48392414469127e-01 ) ( 2.63409219491867e-03 , 1.15931468073518e-05 , -1.89678482893825e-03 ) - 24 ( -3.17217482639898e-01 , -7.27041161938927e-03 , 9.48324949488565e-01 ) ( 2.63443496527980e-03 , 1.45408232387785e-05 , -1.89664989897713e-03 ) - 25 ( -3.17454368922200e-01 , -8.80106277368526e-03 , 9.48232706115045e-01 ) ( 2.63490873784440e-03 , 1.76021255473705e-05 , -1.89646541223009e-03 ) - 26 ( -3.17719471221428e-01 , -1.03652349433106e-02 , 9.48128102901367e-01 ) ( 2.63543894244286e-03 , 2.07304698866213e-05 , -1.89625620580273e-03 ) - 27 ( -3.17976645861785e-01 , -1.19373246190291e-02 , 9.48023392626695e-01 ) ( 2.63595329172357e-03 , 2.38746492380582e-05 , -1.89604678525339e-03 ) - 28 ( -3.18192455511519e-01 , -1.34910475095471e-02 , 9.47930141356759e-01 ) ( 2.63638491102304e-03 , 2.69820950190943e-05 , -1.89586028271352e-03 ) - 29 ( -3.18337378603559e-01 , -1.50010625514700e-02 , 9.47858787745380e-01 ) ( 2.63667475720712e-03 , 3.00021251029400e-05 , -1.89571757549076e-03 ) - 30 ( -3.18386627540012e-01 , -1.64443011671489e-02 , 9.47818305564322e-01 ) ( 2.63677325508002e-03 , 3.28886023342977e-05 , -1.89563661112864e-03 ) - 31 ( -3.18320580486092e-01 , -1.78008340716119e-02 , 9.47815983377233e-01 ) ( 2.63664116097219e-03 , 3.56016681432239e-05 , -1.89563196675447e-03 ) - 32 ( -3.18124861284371e-01 , -1.90542515899086e-02 , 9.47857324774751e-01 ) ( 2.63624972256874e-03 , 3.81085031798172e-05 , -1.89571464954950e-03 ) - 33 ( -3.17790139572305e-01 , -2.01916660342723e-02 , 9.47946055328770e-01 ) ( 2.63558027914461e-03 , 4.03833320685447e-05 , -1.89589211065754e-03 ) - 34 ( -3.17311724625781e-01 , -2.12034927642144e-02 , 9.48084216359291e-01 ) ( 2.63462344925156e-03 , 4.24069855284288e-05 , -1.89616843271858e-03 ) - 35 ( -3.16689032700701e-01 , -2.20831582361305e-02 , 9.48272318845917e-01 ) ( 2.63337806540140e-03 , 4.41663164722610e-05 , -1.89654463769183e-03 ) - 36 ( -3.15924961738176e-01 , -2.28268525331288e-02 , 9.48509543101261e-01 ) ( 2.63184992347635e-03 , 4.56537050662576e-05 , -1.89701908620252e-03 ) - 37 ( -3.15025223717057e-01 , -2.34334010090392e-02 , 9.48793962954638e-01 ) ( 2.63005044743411e-03 , 4.68668020180783e-05 , -1.89758792590928e-03 ) - 38 ( -3.13997687895431e-01 , -2.39042792710176e-02 , 9.49122772579426e-01 ) ( 2.62799537579086e-03 , 4.78085585420352e-05 , -1.89824554515885e-03 ) - 39 ( -3.12851812803389e-01 , -2.42437511921662e-02 , 9.49492487465681e-01 ) ( 2.62570362560678e-03 , 4.84875023843323e-05 , -1.89898497493136e-03 ) - 40 ( -3.11598263481038e-01 , -2.44590603951106e-02 , 9.49899087566774e-01 ) ( 2.62319652696208e-03 , 4.89181207902213e-05 , -1.89979817513355e-03 ) + 20 ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) ( 2.63454929804108e-03 , 3.78107124610862e-06 , -1.89666362116634e-03 ) + 21 ( -3.17043326283096e-01 , -3.09358622124357e-03 , 9.48406009567444e-01 ) ( 2.63408665256619e-03 , 6.18717244248714e-06 , -1.89681201913489e-03 ) + 22 ( -3.16976780479176e-01 , -4.39920685529361e-03 , 9.48423095256595e-01 ) ( 2.63395356095835e-03 , 8.79841371058722e-06 , -1.89684619051319e-03 ) + 23 ( -3.17046097666149e-01 , -5.79657340749948e-03 , 9.48392414399967e-01 ) ( 2.63409219533230e-03 , 1.15931468149990e-05 , -1.89678482879993e-03 ) + 24 ( -3.17217482859608e-01 , -7.27041162129638e-03 , 9.48324949415057e-01 ) ( 2.63443496571922e-03 , 1.45408232425928e-05 , -1.89664989883011e-03 ) + 25 ( -3.17454369154660e-01 , -8.80106277336966e-03 , 9.48232706037224e-01 ) ( 2.63490873830932e-03 , 1.76021255467393e-05 , -1.89646541207445e-03 ) + 26 ( -3.17719471466479e-01 , -1.03652349405030e-02 , 9.48128102819281e-01 ) ( 2.63543894293296e-03 , 2.07304698810060e-05 , -1.89625620563856e-03 ) + 27 ( -3.17976646119255e-01 , -1.19373246135143e-02 , 9.48023392540407e-01 ) ( 2.63595329223851e-03 , 2.38746492270286e-05 , -1.89604678508081e-03 ) + 28 ( -3.18192455781236e-01 , -1.34910475011762e-02 , 9.47930141266342e-01 ) ( 2.63638491156247e-03 , 2.69820950023524e-05 , -1.89586028253268e-03 ) + 29 ( -3.18337378885354e-01 , -1.50010625401725e-02 , 9.47858787650918e-01 ) ( 2.63667475777071e-03 , 3.00021250803450e-05 , -1.89571757530184e-03 ) + 30 ( -3.18386627833720e-01 , -1.64443011529380e-02 , 9.47818305465907e-01 ) ( 2.63677325566744e-03 , 3.28886023058761e-05 , -1.89563661093181e-03 ) + 31 ( -3.18320580791560e-01 , -1.78008340545886e-02 , 9.47815983274963e-01 ) ( 2.63664116158312e-03 , 3.56016681091771e-05 , -1.89563196654993e-03 ) + 32 ( -3.18124861601468e-01 , -1.90542515702588e-02 , 9.47857324668720e-01 ) ( 2.63624972320294e-03 , 3.81085031405176e-05 , -1.89571464933744e-03 ) + 33 ( -3.17790139900921e-01 , -2.01916660122652e-02 , 9.47946055219073e-01 ) ( 2.63558027980184e-03 , 4.03833320245304e-05 , -1.89589211043815e-03 ) + 34 ( -3.17311724965833e-01 , -2.12034927401992e-02 , 9.48084216246017e-01 ) ( 2.63462344993167e-03 , 4.24069854803984e-05 , -1.89616843249203e-03 ) + 35 ( -3.16689033052138e-01 , -2.20831582105308e-02 , 9.48272318729146e-01 ) ( 2.63337806610428e-03 , 4.41663164210616e-05 , -1.89654463745829e-03 ) + 36 ( -3.15924962100982e-01 , -2.28268525064398e-02 , 9.48509542981062e-01 ) ( 2.63184992420196e-03 , 4.56537050128795e-05 , -1.89701908596212e-03 ) + 37 ( -3.15025224091246e-01 , -2.34334009818228e-02 , 9.48793962831070e-01 ) ( 2.63005044818249e-03 , 4.68668019636457e-05 , -1.89758792566214e-03 ) + 38 ( -3.13997688281053e-01 , -2.39042792438929e-02 , 9.49122772452534e-01 ) ( 2.62799537656211e-03 , 4.78085584877859e-05 , -1.89824554490507e-03 ) + 39 ( -3.12851813200530e-01 , -2.42437511657998e-02 , 9.49492487335498e-01 ) ( 2.62570362640106e-03 , 4.84875023315996e-05 , -1.89898497467100e-03 ) + 40 ( -3.11598263889815e-01 , -2.44590603702029e-02 , 9.49899087433323e-01 ) ( 2.62319652777963e-03 , 4.89181207404057e-05 , -1.89979817486665e-03 ) diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out index 6d5786be0..1d23f8568 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -117,7 +113,6 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,28 +123,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index ae8e82001..e64cb9b15 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.10901432109335e-01 , 2.11904534160048e-01 , 9.26518627937279e-01 ) + x ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index b16b4e9e6..8935a8e9e 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.31000066838099e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223396e-04 , -1.83760097863971e-03 ) - 1 ( -3.30748902386493e-01 , 2.14640582517095e-01 , 9.18985627693302e-01 ) ( 2.66149780477299e-03 , -4.29281165034190e-04 , -1.83797125538660e-03 ) - 2 ( -3.30335278565548e-01 , 2.14351255511183e-01 , 9.19201905457012e-01 ) ( 2.66067055713110e-03 , -4.28702511022365e-04 , -1.83840381091402e-03 ) - 3 ( -3.29748301584291e-01 , 2.14175295386331e-01 , 9.19453642359664e-01 ) ( 2.65949660316858e-03 , -4.28350590772662e-04 , -1.83890728471933e-03 ) - 4 ( -3.28983003247068e-01 , 2.14104941845713e-01 , 9.19744126076260e-01 ) ( 2.65796600649414e-03 , -4.28209883691426e-04 , -1.83948825215252e-03 ) - 5 ( -3.28041624976885e-01 , 2.14126988072693e-01 , 9.20075173701281e-01 ) ( 2.65608324995377e-03 , -4.28253976145385e-04 , -1.84015034740256e-03 ) - 6 ( -3.26934234935534e-01 , 2.14223081735800e-01 , 9.20446889982651e-01 ) ( 2.65386846987107e-03 , -4.28446163471600e-04 , -1.84089377996530e-03 ) - 7 ( -3.25678693135581e-01 , 2.14370527640576e-01 , 9.20857570809189e-01 ) ( 2.65135738627116e-03 , -4.28741055281152e-04 , -1.84171514161838e-03 ) - 8 ( -3.24300051430000e-01 , 2.14543670061471e-01 , 9.21303690581479e-01 ) ( 2.64860010286000e-03 , -4.29087340122942e-04 , -1.84260738116296e-03 ) - 9 ( -3.22829511472042e-01 , 2.14715764661014e-01 , 9.21779934110501e-01 ) ( 2.64565902294409e-03 , -4.29431529322028e-04 , -1.84355986822100e-03 ) - 10 ( -3.21303059745326e-01 , 2.14861065905351e-01 , 9.22279277744170e-01 ) ( 2.64260611949065e-03 , -4.29722131810702e-04 , -1.84455855548834e-03 ) - 11 ( -3.19759878990855e-01 , 2.14956751283305e-01 , 9.22793159307914e-01 ) ( 2.63951975798171e-03 , -4.29913502566610e-04 , -1.84558631861583e-03 ) - 12 ( -3.18240618841290e-01 , 2.14984320901043e-01 , 9.23311783898716e-01 ) ( 2.63648123768258e-03 , -4.29968641802086e-04 , -1.84662356779743e-03 ) - 13 ( -3.16785580563842e-01 , 2.14930240619444e-01 , 9.23824597861573e-01 ) ( 2.63357116112768e-03 , -4.29860481238888e-04 , -1.84764919572315e-03 ) - 14 ( -3.15432869408985e-01 , 2.14785792597053e-01 , 9.24320922729152e-01 ) ( 2.63086573881797e-03 , -4.29571585194106e-04 , -1.84864184545830e-03 ) - 15 ( -3.14216581806419e-01 , 2.14546290789039e-01 , 9.24790694604220e-01 ) ( 2.62843316361284e-03 , -4.29092581578078e-04 , -1.84958138920844e-03 ) - 16 ( -3.13165103198593e-01 , 2.14209940595846e-01 , 9.25225226357636e-01 ) ( 2.62633020639719e-03 , -4.28419881191692e-04 , -1.85045045271527e-03 ) - 17 ( -3.12299612081994e-01 , 2.13776666346595e-01 , 9.25617895904770e-01 ) ( 2.62459922416399e-03 , -4.27553332693190e-04 , -1.85123579180954e-03 ) - 18 ( -3.11632908920174e-01 , 2.13247200166255e-01 , 9.25964665470127e-01 ) ( 2.62326581784035e-03 , -4.26494400332510e-04 , -1.85192933094025e-03 ) - 19 ( -3.11168697452754e-01 , 2.12622637200253e-01 , 9.26264355287175e-01 ) ( 2.62233739490551e-03 , -4.25245274400506e-04 , -1.85252871057435e-03 ) - 20 ( -3.10901432109335e-01 , 2.11904534160048e-01 , 9.26518627937279e-01 ) ( 2.62180286421867e-03 , -4.23809068320096e-04 , -1.85303725587456e-03 ) + 0 ( -3.31000066838100e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223397e-04 , -1.83760097863971e-03 ) + 1 ( -3.30748902386919e-01 , 2.14640582516973e-01 , 9.18985627693177e-01 ) ( 2.66149780477384e-03 , -4.29281165033946e-04 , -1.83797125538635e-03 ) + 2 ( -3.30335278614263e-01 , 2.14351255518651e-01 , 9.19201905437763e-01 ) ( 2.66067055722853e-03 , -4.28702511037302e-04 , -1.83840381087553e-03 ) + 3 ( -3.29748301598012e-01 , 2.14175295385314e-01 , 9.19453642354981e-01 ) ( 2.65949660319602e-03 , -4.28350590770628e-04 , -1.83890728470996e-03 ) + 4 ( -3.28983003286818e-01 , 2.14104941848711e-01 , 9.19744126061344e-01 ) ( 2.65796600657364e-03 , -4.28209883697422e-04 , -1.83948825212269e-03 ) + 5 ( -3.28041624986510e-01 , 2.14126988066820e-01 , 9.20075173699216e-01 ) ( 2.65608324997302e-03 , -4.28253976133641e-04 , -1.84015034739843e-03 ) + 6 ( -3.26934234947895e-01 , 2.14223081728789e-01 , 9.20446889979892e-01 ) ( 2.65386846989579e-03 , -4.28446163457579e-04 , -1.84089377995978e-03 ) + 7 ( -3.25678693151725e-01 , 2.14370527632503e-01 , 9.20857570805359e-01 ) ( 2.65135738630345e-03 , -4.28741055265006e-04 , -1.84171514161072e-03 ) + 8 ( -3.24300051451023e-01 , 2.14543670052469e-01 , 9.21303690576175e-01 ) ( 2.64860010290205e-03 , -4.29087340104938e-04 , -1.84260738115235e-03 ) + 9 ( -3.22829511499202e-01 , 2.14715764651319e-01 , 9.21779934103247e-01 ) ( 2.64565902299840e-03 , -4.29431529302638e-04 , -1.84355986820649e-03 ) + 10 ( -3.21303059779930e-01 , 2.14861065895251e-01 , 9.22279277734468e-01 ) ( 2.64260611955986e-03 , -4.29722131790503e-04 , -1.84455855546894e-03 ) + 11 ( -3.19759879034225e-01 , 2.14956751273127e-01 , 9.22793159295257e-01 ) ( 2.63951975806845e-03 , -4.29913502546255e-04 , -1.84558631859051e-03 ) + 12 ( -3.18240618894718e-01 , 2.14984320891132e-01 , 9.23311783882609e-01 ) ( 2.63648123778944e-03 , -4.29968641782263e-04 , -1.84662356776522e-03 ) + 13 ( -3.16785580628539e-01 , 2.14930240610141e-01 , 9.23824597841553e-01 ) ( 2.63357116125708e-03 , -4.29860481220281e-04 , -1.84764919568311e-03 ) + 14 ( -3.15432869486022e-01 , 2.14785792588681e-01 , 9.24320922704807e-01 ) ( 2.63086573897204e-03 , -4.29571585177362e-04 , -1.84864184540961e-03 ) + 15 ( -3.14216581896700e-01 , 2.14546290781891e-01 , 9.24790694575203e-01 ) ( 2.62843316379340e-03 , -4.29092581563783e-04 , -1.84958138915041e-03 ) + 16 ( -3.13165103302749e-01 , 2.14209940590278e-01 , 9.25225226323671e-01 ) ( 2.62633020660550e-03 , -4.28419881180556e-04 , -1.85045045264734e-03 ) + 17 ( -3.12299612195620e-01 , 2.13776666349982e-01 , 9.25617895865650e-01 ) ( 2.62459922439124e-03 , -4.27553332699964e-04 , -1.85123579173130e-03 ) + 18 ( -3.11632909053414e-01 , 2.13247200164350e-01 , 9.25964665425724e-01 ) ( 2.62326581810683e-03 , -4.26494400328700e-04 , -1.85192933085145e-03 ) + 19 ( -3.11168697605864e-01 , 2.12622637201006e-01 , 9.26264355235566e-01 ) ( 2.62233739521173e-03 , -4.25245274402012e-04 , -1.85252871047113e-03 ) + 20 ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) ( 2.62180286454399e-03 , -4.23809068324612e-04 , -1.85303725576436e-03 ) diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 7b60a6e6d..42c1974d9 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -117,7 +113,6 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,33 +123,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -0.310901 , 0.211905 , 0.926519 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index 99b9e8168..6b8d538b6 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.08478218972664e-01 , 1.95662054911782e-01 , 9.30890728650335e-01 ) + x ( -3.08478219385086e-01 , 1.95662054939033e-01 , 9.30890728507939e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index 3c70716e5..0b3f5ab28 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.10901432109335e-01 , 2.11904534160048e-01 , 9.26518627937279e-01 ) ( 2.62180286421867e-03 , -4.23809068320096e-04 , -1.85303725587456e-03 ) - 21 ( -3.10816792043180e-01 , 2.11095479023442e-01 , 9.26731687447802e-01 ) ( 2.62163358408636e-03 , -4.22190958046885e-04 , -1.85346337489560e-03 ) - 22 ( -3.10892759556907e-01 , 2.10199933225375e-01 , 9.26909747562911e-01 ) ( 2.62178551911381e-03 , -4.20399866450750e-04 , -1.85381949512582e-03 ) - 23 ( -3.11101193001973e-01 , 2.09225066821485e-01 , 9.27060364337886e-01 ) ( 2.62220238600395e-03 , -4.18450133642970e-04 , -1.85412072867577e-03 ) - 24 ( -3.11409710822334e-01 , 2.08181314892433e-01 , 9.27191745074992e-01 ) ( 2.62281942164467e-03 , -4.16362629784866e-04 , -1.85438349014998e-03 ) - 25 ( -3.11783673220749e-01 , 2.07082466717213e-01 , 9.27312133583558e-01 ) ( 2.62356734644150e-03 , -4.14164933434426e-04 , -1.85462426716712e-03 ) - 26 ( -3.12188067196429e-01 , 2.05945244391887e-01 , 9.27429332624607e-01 ) ( 2.62437613439286e-03 , -4.11890488783774e-04 , -1.85485866524921e-03 ) - 27 ( -3.12589140107981e-01 , 2.04788460679522e-01 , 9.27550384539333e-01 ) ( 2.62517828021596e-03 , -4.09576921359045e-04 , -1.85510076907867e-03 ) - 28 ( -3.12955684858097e-01 , 2.03631959607588e-01 , 9.27681391611028e-01 ) ( 2.62591136971619e-03 , -4.07263919215175e-04 , -1.85536278322206e-03 ) - 29 ( -3.13259948406249e-01 , 2.02495576402221e-01 , 9.27827433449802e-01 ) ( 2.62651989681250e-03 , -4.04991152804443e-04 , -1.85565486689960e-03 ) - 30 ( -3.13478176635625e-01 , 2.01398322556721e-01 , 9.27992536847437e-01 ) ( 2.62695635327125e-03 , -4.02796645113443e-04 , -1.85598507369487e-03 ) - 31 ( -3.13590843690062e-01 , 2.00357900910451e-01 , 9.28179667034628e-01 ) ( 2.62718168738012e-03 , -4.00715801820901e-04 , -1.85635933406926e-03 ) - 32 ( -3.13582620933990e-01 , 1.99390533243234e-01 , 9.28390734066831e-01 ) ( 2.62716524186798e-03 , -3.98781066486467e-04 , -1.85678146813366e-03 ) - 33 ( -3.13442157096821e-01 , 1.98510960961320e-01 , 9.28626627085776e-01 ) ( 2.62688431419364e-03 , -3.97021921922641e-04 , -1.85725325417155e-03 ) - 34 ( -3.13161736228558e-01 , 1.97732440178262e-01 , 9.28887296211691e-01 ) ( 2.62632347245712e-03 , -3.95464880356523e-04 , -1.85777459242338e-03 ) - 35 ( -3.12736895260678e-01 , 1.97066585086681e-01 , 9.29171886889065e-01 ) ( 2.62547379052136e-03 , -3.94133170173362e-04 , -1.85834377377813e-03 ) - 36 ( -3.12166050940956e-01 , 1.96522999337743e-01 , 9.29478922499712e-01 ) ( 2.62433210188191e-03 , -3.93045998675485e-04 , -1.85895784499942e-03 ) - 37 ( -3.11450199233999e-01 , 1.96108732486406e-01 , 9.29806505913826e-01 ) ( 2.62290039846800e-03 , -3.92217464972813e-04 , -1.85961301182765e-03 ) - 38 ( -3.10592727274054e-01 , 1.95827676700691e-01 , 9.30152502981352e-01 ) ( 2.62118545454811e-03 , -3.91655353401382e-04 , -1.86030500596270e-03 ) - 39 ( -3.09599356904062e-01 , 1.95680044103037e-01 , 9.30514674008113e-01 ) ( 2.61919871380812e-03 , -3.91360088206074e-04 , -1.86102934801623e-03 ) - 40 ( -3.08478218972664e-01 , 1.95662054911782e-01 , 9.30890728650335e-01 ) ( 2.61695643794533e-03 , -3.91324109823565e-04 , -1.86178145730067e-03 ) + 20 ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) ( 2.62180286454399e-03 , -4.23809068324612e-04 , -1.85303725576436e-03 ) + 21 ( -3.10816792220306e-01 , 2.11095479027854e-01 , 9.26731687387390e-01 ) ( 2.62163358444061e-03 , -4.22190958055708e-04 , -1.85346337477478e-03 ) + 22 ( -3.10892759748286e-01 , 2.10199933231990e-01 , 9.26909747497221e-01 ) ( 2.62178551949657e-03 , -4.20399866463979e-04 , -1.85381949499444e-03 ) + 23 ( -3.11101193207355e-01 , 2.09225066830326e-01 , 9.27060364266969e-01 ) ( 2.62220238641471e-03 , -4.18450133660652e-04 , -1.85412072853394e-03 ) + 24 ( -3.11409711041452e-01 , 2.08181314903498e-01 , 9.27191744998913e-01 ) ( 2.62281942208290e-03 , -4.16362629806997e-04 , -1.85438348999783e-03 ) + 25 ( -3.11783673453337e-01 , 2.07082466730478e-01 , 9.27312133502395e-01 ) ( 2.62356734690667e-03 , -4.14164933460955e-04 , -1.85462426700479e-03 ) + 26 ( -3.12188067442232e-01 , 2.05945244407307e-01 , 9.27429332538441e-01 ) ( 2.62437613488447e-03 , -4.11890488814613e-04 , -1.85485866507688e-03 ) + 27 ( -3.12589140366756e-01 , 2.04788460697038e-01 , 9.27550384448258e-01 ) ( 2.62517828073351e-03 , -4.09576921394075e-04 , -1.85510076889652e-03 ) + 28 ( -3.12955685129617e-01 , 2.03631959627123e-01 , 9.27681391515142e-01 ) ( 2.62591137025923e-03 , -4.07263919254245e-04 , -1.85536278303028e-03 ) + 29 ( -3.13259948690306e-01 , 2.02495576423685e-01 , 9.27827433349212e-01 ) ( 2.62651989738061e-03 , -4.04991152847370e-04 , -1.85565486669842e-03 ) + 30 ( -3.13478176932022e-01 , 2.01398322580004e-01 , 9.27992536742261e-01 ) ( 2.62695635386404e-03 , -4.02796645160007e-04 , -1.85598507348452e-03 ) + 31 ( -3.13590843998619e-01 , 2.00357900935419e-01 , 9.28179666924991e-01 ) ( 2.62718168799724e-03 , -4.00715801870839e-04 , -1.85635933384998e-03 ) + 32 ( -3.13582621254546e-01 , 1.99390533269725e-01 , 9.28390733952867e-01 ) ( 2.62716524250909e-03 , -3.98781066539451e-04 , -1.85678146790573e-03 ) + 33 ( -3.13442157429236e-01 , 1.98510960989129e-01 , 9.28626626967630e-01 ) ( 2.62688431485847e-03 , -3.97021921978259e-04 , -1.85725325393526e-03 ) + 34 ( -3.13161736572708e-01 , 1.97732440207133e-01 , 9.28887296089519e-01 ) ( 2.62632347314542e-03 , -3.95464880414266e-04 , -1.85777459217904e-03 ) + 35 ( -3.12736895616453e-01 , 1.97066585116309e-01 , 9.29171886763036e-01 ) ( 2.62547379123291e-03 , -3.94133170232619e-04 , -1.85834377352607e-03 ) + 36 ( -3.12166051308255e-01 , 1.96522999367774e-01 , 9.29478922370005e-01 ) ( 2.62433210261651e-03 , -3.93045998735549e-04 , -1.85895784474001e-03 ) + 37 ( -3.11450199612716e-01 , 1.96108732516444e-01 , 9.29806505780634e-01 ) ( 2.62290039922543e-03 , -3.92217465032889e-04 , -1.85961301156127e-03 ) + 38 ( -3.10592727664091e-01 , 1.95827676730295e-01 , 9.30152502844880e-01 ) ( 2.62118545532818e-03 , -3.91655353460590e-04 , -1.86030500568976e-03 ) + 39 ( -3.09599357305329e-01 , 1.95680044131724e-01 , 9.30514673868571e-01 ) ( 2.61919871461066e-03 , -3.91360088263449e-04 , -1.86102934773714e-03 ) + 40 ( -3.08478219385086e-01 , 1.95662054939033e-01 , 9.30890728507939e-01 ) ( 2.61695643877017e-03 , -3.91324109878067e-04 , -1.86178145701588e-03 ) diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out index 74c288689..5b55b80fb 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -120,7 +120,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,27 +131,10 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped index a3cdd7bbc..41cb47258 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.10902612073187e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) + x ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj index 41394b2d9..4806fa83f 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 ( -3.31000066838099e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223396e-04 , -1.83760097863971e-03 ) 5.32400026735240e-03 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 1 ( -3.30748902386493e-01 , 2.14640582517095e-01 , 9.18985627693302e-01 ) ( 2.65426681755214e-03 , -2.59364533396170e-04 , -1.83797125538660e-03 ) 5.24527031778478e-03 ( 9.96384506389575e-01 , 8.49583158190100e-02 , 0.00000000000000e+00 ) -4.11137793191958e-05 - 2 ( -3.30335278534755e-01 , 2.14351256281980e-01 , 9.19201905288334e-01 ) ( 2.61609431372619e-03 , -8.80022404594749e-06 , -1.83840381057667e-03 ) 5.11187773649830e-03 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -1.11474667340389e-04 - 3 ( -3.29748301559332e-01 , 2.14175298816286e-01 , 9.19453641569650e-01 ) ( 2.49361536951405e-03 , 3.69150719454903e-04 , -1.83890728313930e-03 ) 4.86798493036677e-03 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -2.40880322518690e-04 - 4 ( -3.28983003639495e-01 , 2.14104951472765e-01 , 9.19744123694835e-01 ) ( 2.15062069976169e-03 , 9.02948227784763e-04 , -1.83948824738967e-03 ) 4.41210095429392e-03 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -4.77813021182742e-04 + 2 ( -3.30335278534755e-01 , 2.14351256281980e-01 , 9.19201905288334e-01 ) ( 2.61609431372619e-03 , -8.80022404594755e-06 , -1.83840381057667e-03 ) 5.11187773649830e-03 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -1.11474667340389e-04 + 3 ( -3.29748301559333e-01 , 2.14175298816286e-01 , 9.19453641569650e-01 ) ( 2.49361536951405e-03 , 3.69150719454903e-04 , -1.83890728313930e-03 ) 4.86798493036677e-03 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -2.40880322518690e-04 + 4 ( -3.28983003639496e-01 , 2.14104951472765e-01 , 9.19744123694835e-01 ) ( 2.15062069976169e-03 , 9.02948227784763e-04 , -1.83948824738967e-03 ) 4.41210095429392e-03 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -4.77813021182742e-04 5 ( -3.28041627441930e-01 , 2.14127009680035e-01 , 9.20075167793771e-01 ) ( 1.42145011961404e-03 , 1.41950504566250e-03 , -1.84015033558754e-03 ) 3.71083413738751e-03 ( 3.82683432365090e-01 , 9.23879532511287e-01 , 0.00000000000000e+00 ) -8.12629094252072e-04 - 6 ( -3.26934243989618e-01 , 2.14223123081484e-01 , 9.20446877144005e-01 ) ( 5.39673174025795e-04 , 1.56829094993247e-03 , -1.84089375428801e-03 ) 3.06983672648989e-03 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -1.08583725325208e-03 - 7 ( -3.25678716875358e-01 , 2.14370596669932e-01 , 9.20857546343514e-01 ) ( -8.16417941512113e-05 , 1.43209521319758e-03 , -1.84171509268703e-03 ) 2.72473828242342e-03 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -1.22624326781898e-03 - 8 ( -3.24300100426940e-01 , 2.14543773657555e-01 , 9.21303649210103e-01 ) ( -4.37177441924497e-04 , 1.25052160675694e-03 , -1.84260729842021e-03 ) 2.57506503044251e-03 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -1.28775963537044e-03 - 9 ( -3.22829597532926e-01 , 2.14715908506054e-01 , 9.21779870463197e-01 ) ( -6.43292084741086e-04 , 1.09981786773007e-03 , -1.84355974092639e-03 ) 2.51106828341672e-03 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -1.31512027126455e-03 - 10 ( -3.21303195136168e-01 , 2.14861254665660e-01 , 9.22279186601751e-01 ) ( -7.71607172100759e-04 , 9.84491053041776e-04 , -1.84455837320350e-03 ) 2.48349792685589e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 11 ( -3.19760075975256e-01 , 2.14956988805007e-01 , 9.22793035721544e-01 ) ( -7.74693410422583e-04 , 9.84299584763081e-04 , -1.84558607144309e-03 ) 2.48759174991084e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 12 ( -3.18240889009190e-01 , 2.14984610793561e-01 , 9.23311623280343e-01 ) ( -7.77731784354715e-04 , 9.84244340785974e-04 , -1.84662324656069e-03 ) 2.49181053275156e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 13 ( -3.16785934761419e-01 , 2.14930586280875e-01 , 9.23824395985673e-01 ) ( -7.80641692850257e-04 , 9.84352389811345e-04 , -1.84764879197135e-03 ) 2.49607856920830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 6 ( -3.26934243989619e-01 , 2.14223123081484e-01 , 9.20446877144005e-01 ) ( 5.39673174025796e-04 , 1.56829094993247e-03 , -1.84089375428801e-03 ) 3.06983672648989e-03 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -1.08583725325208e-03 + 7 ( -3.25678716875359e-01 , 2.14370596669932e-01 , 9.20857546343514e-01 ) ( -8.16417941512103e-05 , 1.43209521319758e-03 , -1.84171509268703e-03 ) 2.72473828242341e-03 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -1.22624326781898e-03 + 8 ( -3.24300100426941e-01 , 2.14543773657555e-01 , 9.21303649210103e-01 ) ( -4.37177441924495e-04 , 1.25052160675694e-03 , -1.84260729842021e-03 ) 2.57506503044251e-03 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -1.28775963537044e-03 + 9 ( -3.22829597532927e-01 , 2.14715908506054e-01 , 9.21779870463197e-01 ) ( -6.43292084741085e-04 , 1.09981786773007e-03 , -1.84355974092639e-03 ) 2.51106828341672e-03 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -1.31512027126455e-03 + 10 ( -3.21303195136169e-01 , 2.14861254665660e-01 , 9.22279186601751e-01 ) ( -7.71607172100758e-04 , 9.84491053041776e-04 , -1.84455837320350e-03 ) 2.48349792685589e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 11 ( -3.19760075975256e-01 , 2.14956988805007e-01 , 9.22793035721544e-01 ) ( -7.74693410422582e-04 , 9.84299584763081e-04 , -1.84558607144309e-03 ) 2.48759174991084e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 12 ( -3.18240889009191e-01 , 2.14984610793561e-01 , 9.23311623280342e-01 ) ( -7.77731784354714e-04 , 9.84244340785974e-04 , -1.84662324656068e-03 ) 2.49181053275155e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 13 ( -3.16785934761420e-01 , 2.14930586280875e-01 , 9.23824395985673e-01 ) ( -7.80641692850256e-04 , 9.84352389811345e-04 , -1.84764879197135e-03 ) 2.49607856920830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 14 ( -3.15433317695425e-01 , 2.14786197242876e-01 , 9.24320675718985e-01 ) ( -7.83346926982245e-04 , 9.84641167887343e-04 , -1.84864135143797e-03 ) 2.50031274187874e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 15 ( -3.14217133435043e-01 , 2.14546757480910e-01 , 9.24790398906851e-01 ) ( -7.85779295503009e-04 , 9.85120047411276e-04 , -1.84958079781370e-03 ) 2.50442986834698e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 16 ( -3.13165766618894e-01 , 2.14210472267861e-01 , 9.25224878712619e-01 ) ( -7.87882029135307e-04 , 9.85792617837373e-04 , -1.85044975742524e-03 ) 2.50835474098607e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 17 ( -3.12300394959219e-01 , 2.13777265827329e-01 , 9.25617493311199e-01 ) ( -7.89612772454658e-04 , 9.86659030718436e-04 , -1.85123498662240e-03 ) 2.51202767450830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 18 ( -3.11633818168871e-01 , 2.13247870196032e-01 , 9.25964205156089e-01 ) ( -7.90945926035354e-04 , 9.87717821981030e-04 , -1.85192841031218e-03 ) 2.51541039534613e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 19 ( -3.11169739281378e-01 , 2.12623380444018e-01 , 9.26263834684329e-01 ) ( -7.91874083810338e-04 , 9.88966801485060e-04 , -1.85252766936866e-03 ) 2.51848933241326e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 20 ( -3.10902612073187e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226722e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 16 ( -3.13165766618895e-01 , 2.14210472267861e-01 , 9.25224878712619e-01 ) ( -7.87882029135306e-04 , 9.85792617837373e-04 , -1.85044975742524e-03 ) 2.50835474098607e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 17 ( -3.12300394959219e-01 , 2.13777265827330e-01 , 9.25617493311199e-01 ) ( -7.89612772454658e-04 , 9.86659030718436e-04 , -1.85123498662240e-03 ) 2.51202767450830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 18 ( -3.11633818168871e-01 , 2.13247870196033e-01 , 9.25964205156089e-01 ) ( -7.90945926035354e-04 , 9.87717821981030e-04 , -1.85192841031218e-03 ) 2.51541039534613e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 19 ( -3.11169739281378e-01 , 2.12623380444018e-01 , 9.26263834684329e-01 ) ( -7.91874083810339e-04 , 9.88966801485059e-04 , -1.85252766936866e-03 ) 2.51848933241326e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 20 ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226723e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out index 28afcc8be..a610a83f9 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -120,7 +120,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,22 +131,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -0.310903 , 0.211905 , 0.926518 ) @@ -157,7 +140,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped index dc793f2a2..e86a2eb4b 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.08482822701286e-01 , 1.95664885198602e-01 , 9.30888608158068e-01 ) + x ( -3.08482822701290e-01 , 1.95664885198602e-01 , 9.30888608158067e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj index 43f39b9f0..d4530bcd2 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( -3.10902612073187e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226722e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 21 ( -3.10818115103370e-01 , 2.11096376432417e-01 , 9.26731039288472e-01 ) ( -7.92577332166354e-04 , 9.92020809508262e-04 , -1.85346207857694e-03 ) 2.52380289534206e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 22 ( -3.10894230143356e-01 , 2.10200911472952e-01 , 9.26909032472718e-01 ) ( -7.92425102086383e-04 , 9.93811739427192e-04 , -1.85381806494544e-03 ) 2.52612036687898e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 23 ( -3.11102815077491e-01 , 2.09226128345936e-01 , 9.27059580430638e-01 ) ( -7.92007932218113e-04 , 9.95761305681223e-04 , -1.85411916086128e-03 ) 2.52828750263065e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 24 ( -3.11411487946956e-01 , 2.08182462090056e-01 , 9.27190890622198e-01 ) ( -7.91390586479183e-04 , 9.97848638192983e-04 , -1.85438178124440e-03 ) 2.53036637786130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 20 ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226723e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 21 ( -3.10818115103370e-01 , 2.11096376432417e-01 , 9.26731039288472e-01 ) ( -7.92577332166356e-04 , 9.92020809508261e-04 , -1.85346207857694e-03 ) 2.52380289534207e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 22 ( -3.10894230143356e-01 , 2.10200911472952e-01 , 9.26909032472718e-01 ) ( -7.92425102086384e-04 , 9.93811739427191e-04 , -1.85381806494544e-03 ) 2.52612036687898e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 23 ( -3.11102815077490e-01 , 2.09226128345936e-01 , 9.27059580430638e-01 ) ( -7.92007932218114e-04 , 9.95761305681222e-04 , -1.85411916086128e-03 ) 2.52828750263065e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 24 ( -3.11411487946955e-01 , 2.08182462090057e-01 , 9.27190890622198e-01 ) ( -7.91390586479184e-04 , 9.97848638192982e-04 , -1.85438178124440e-03 ) 2.53036637786130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 25 ( -3.11785608613730e-01 , 2.07083701948798e-01 , 9.27311207011189e-01 ) ( -7.90642345145636e-04 , 1.00004615847550e-03 , -1.85462241402238e-03 ) 2.53241596780659e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 26 ( -3.12190163793984e-01 , 2.05946569990115e-01 , 9.27428332508552e-01 ) ( -7.89833234785128e-04 , 1.00232042239287e-03 , -1.85485666501710e-03 ) 2.53448800783766e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 26 ( -3.12190163793984e-01 , 2.05946569990115e-01 , 9.27428332508551e-01 ) ( -7.89833234785128e-04 , 1.00232042239286e-03 , -1.85485666501710e-03 ) 2.53448800783766e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 27 ( -3.12591400614140e-01 , 2.04789878956263e-01 , 9.27549309599856e-01 ) ( -7.89030761144815e-04 , 1.00463380446057e-03 , -1.85509861919971e-03 ) 2.53662475502718e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 28 ( -3.12958111790193e-01 , 2.03633472860108e-01 , 9.27680240705626e-01 ) ( -7.88297338792708e-04 , 1.00694661665288e-03 , -1.85536048141125e-03 ) 2.53885834955947e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 29 ( -3.13262544129310e-01 , 2.02497186917752e-01 , 9.27826205566554e-01 ) ( -7.87688474114474e-04 , 1.00921918853759e-03 , -1.85565241113311e-03 ) 2.54121118685469e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 30 ( -3.13480943392435e-01 , 2.01400032613720e-01 , 9.27991231097030e-01 ) ( -7.87251675588225e-04 , 1.01141349714566e-03 , -1.85598246219406e-03 ) 2.54369668144840e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 31 ( -3.13593783631660e-01 , 2.00359712776967e-01 , 9.28178282639446e-01 ) ( -7.87025995109775e-04 , 1.01349413681916e-03 , -1.85635656527889e-03 ) 2.54631998989970e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 32 ( -3.13585736154326e-01 , 1.99392449174349e-01 , 9.28389270345583e-01 ) ( -7.87042090064442e-04 , 1.01542866402440e-03 , -1.85677854069117e-03 ) 2.54907858621330e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 33 ( -3.13445449674931e-01 , 1.98512983197192e-01 , 9.28625083432615e-01 ) ( -7.87322663023234e-04 , 1.01718759597871e-03 , -1.85725016686523e-03 ) 2.55196288172194e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 34 ( -3.13165208280151e-01 , 1.97734570946912e-01 , 9.28885672069114e-01 ) ( -7.87883145812792e-04 , 1.01874442047927e-03 , -1.85777134413823e-03 ) 2.55495720640733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 35 ( -3.12740549003456e-01 , 1.97068826614834e-01 , 9.29170181713592e-01 ) ( -7.88732464366183e-04 , 1.02007590914343e-03 , -1.85834036342718e-03 ) 2.55804133355131e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 36 ( -3.12169888759600e-01 , 1.96525353868791e-01 , 9.29477135726622e-01 ) ( -7.89873784853896e-04 , 1.02116285463551e-03 , -1.85895427145324e-03 ) 2.56119257752052e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 37 ( -3.11454223752150e-01 , 1.96111202307429e-01 , 9.29804636919219e-01 ) ( -7.91305114868796e-04 , 1.02199115775824e-03 , -1.85960927383844e-03 ) 2.56438818134973e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 38 ( -3.10596941423872e-01 , 1.95830264173119e-01 , 9.30150551046454e-01 ) ( -7.93019679525352e-04 , 1.02255303402686e-03 , -1.86030110209291e-03 ) 2.56760755498005e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 39 ( -3.09603763986270e-01 , 1.95682751690521e-01 , 9.30512638289433e-01 ) ( -7.95006034400556e-04 , 1.02284805899205e-03 , -1.86102527657887e-03 ) 2.57083391329128e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 40 ( -3.08482822701286e-01 , 1.95664885198602e-01 , 9.30888608158068e-01 ) ( -7.97247916970524e-04 , 1.02288379197589e-03 , -1.86177721631614e-03 ) 2.57405494809734e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 28 ( -3.12958111790194e-01 , 2.03633472860108e-01 , 9.27680240705626e-01 ) ( -7.88297338792708e-04 , 1.00694661665288e-03 , -1.85536048141125e-03 ) 2.53885834955947e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 29 ( -3.13262544129311e-01 , 2.02497186917752e-01 , 9.27826205566553e-01 ) ( -7.87688474114472e-04 , 1.00921918853759e-03 , -1.85565241113311e-03 ) 2.54121118685469e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 30 ( -3.13480943392436e-01 , 2.01400032613720e-01 , 9.27991231097030e-01 ) ( -7.87251675588223e-04 , 1.01141349714565e-03 , -1.85598246219406e-03 ) 2.54369668144840e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 31 ( -3.13593783631662e-01 , 2.00359712776967e-01 , 9.28178282639445e-01 ) ( -7.87025995109772e-04 , 1.01349413681916e-03 , -1.85635656527889e-03 ) 2.54631998989969e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 32 ( -3.13585736154328e-01 , 1.99392449174349e-01 , 9.28389270345582e-01 ) ( -7.87042090064439e-04 , 1.01542866402440e-03 , -1.85677854069116e-03 ) 2.54907858621329e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 33 ( -3.13445449674932e-01 , 1.98512983197192e-01 , 9.28625083432615e-01 ) ( -7.87322663023230e-04 , 1.01718759597871e-03 , -1.85725016686523e-03 ) 2.55196288172193e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 34 ( -3.13165208280154e-01 , 1.97734570946912e-01 , 9.28885672069113e-01 ) ( -7.87883145812788e-04 , 1.01874442047927e-03 , -1.85777134413823e-03 ) 2.55495720640733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 35 ( -3.12740549003459e-01 , 1.97068826614834e-01 , 9.29170181713591e-01 ) ( -7.88732464366178e-04 , 1.02007590914343e-03 , -1.85834036342718e-03 ) 2.55804133355130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 36 ( -3.12169888759603e-01 , 1.96525353868791e-01 , 9.29477135726621e-01 ) ( -7.89873784853888e-04 , 1.02116285463551e-03 , -1.85895427145324e-03 ) 2.56119257752050e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 37 ( -3.11454223752153e-01 , 1.96111202307429e-01 , 9.29804636919218e-01 ) ( -7.91305114868789e-04 , 1.02199115775824e-03 , -1.85960927383844e-03 ) 2.56438818134972e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 38 ( -3.10596941423876e-01 , 1.95830264173120e-01 , 9.30150551046453e-01 ) ( -7.93019679525344e-04 , 1.02255303402686e-03 , -1.86030110209291e-03 ) 2.56760755498004e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 39 ( -3.09603763986273e-01 , 1.95682751690521e-01 , 9.30512638289431e-01 ) ( -7.95006034400549e-04 , 1.02284805899205e-03 , -1.86102527657886e-03 ) 2.57083391329127e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 40 ( -3.08482822701290e-01 , 1.95664885198602e-01 , 9.30888608158067e-01 ) ( -7.97247916970515e-04 , 1.02288379197589e-03 , -1.86177721631613e-03 ) 2.57405494809733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt b/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt index 157cac038..617210efd 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-07-07". +colvars: Using NAMD interface, version "2020-05-04". diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out index 99a22e5fd..2724e6331 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -88,7 +84,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,26 +122,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceInv colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 469850fcd..9745bfb6a 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.42783836136749e+00 + x 2.42783836132997e+00 } restraint { diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj index 9b364a5cf..0f1bd304e 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 2.39061650308305e+00 -9.16246601233221e-03 - 1 2.38234770114191e+00 -9.12939080456763e-03 - 2 2.37511792679912e+00 -9.10047170719648e-03 - 3 2.36945079734406e+00 -9.07780318937623e-03 - 4 2.36577204845768e+00 -9.06308819383071e-03 - 5 2.36436521236120e+00 -9.05746084944482e-03 - 6 2.36534500808037e+00 -9.06138003232147e-03 - 7 2.36864872147381e+00 -9.07459488589523e-03 - 8 2.37404299848291e+00 -9.09617199393162e-03 - 9 2.38114314200753e+00 -9.12457256803010e-03 - 10 2.38944311901955e+00 -9.15777247607821e-03 - 11 2.39835525129330e+00 -9.19342100517319e-03 - 12 2.40725780808025e+00 -9.22903123232098e-03 - 13 2.41554677330587e+00 -9.26218709322349e-03 - 14 2.42268616657072e+00 -9.29074466628286e-03 - 15 2.42825074174393e+00 -9.31300296697570e-03 - 16 2.43195609325616e+00 -9.32782437302463e-03 - 17 2.43367350232427e+00 -9.33469400929707e-03 - 18 2.43342929444717e+00 -9.33371717778869e-03 - 19 2.43139031964034e+00 -9.32556127856135e-03 - 20 2.42783836136749e+00 -9.31135344546996e-03 + 1 2.38234770114368e+00 -9.12939080457472e-03 + 2 2.37511792680581e+00 -9.10047170722326e-03 + 3 2.36945079735818e+00 -9.07780318943272e-03 + 4 2.36577204848084e+00 -9.06308819392336e-03 + 5 2.36436521239393e+00 -9.05746084957573e-03 + 6 2.36534500812203e+00 -9.06138003248811e-03 + 7 2.36864872152266e+00 -9.07459488609063e-03 + 8 2.37404299853629e+00 -9.09617199414514e-03 + 9 2.38114314206215e+00 -9.12457256824860e-03 + 10 2.38944311907187e+00 -9.15777247628748e-03 + 11 2.39835525133988e+00 -9.19342100535952e-03 + 12 2.40725780811812e+00 -9.22903123247246e-03 + 13 2.41554677333277e+00 -9.26218709333110e-03 + 14 2.42268616658529e+00 -9.29074466634115e-03 + 15 2.42825074174577e+00 -9.31300296698308e-03 + 16 2.43195609324583e+00 -9.32782437298332e-03 + 17 2.43367350230322e+00 -9.33469400921286e-03 + 18 2.43342929441762e+00 -9.33371717767048e-03 + 19 2.43139031960514e+00 -9.32556127842056e-03 + 20 2.42783836132997e+00 -9.31135344531990e-03 diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out index fe78368a1..fd5a4f5e9 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -88,7 +84,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,31 +122,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceInv colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 2.42784 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index d50294abc..8b74c0b18 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.39535776160792e+00 + x 2.39535776180124e+00 } restraint { diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 8afdaf44b..a892a5839 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.42783836136749e+00 -9.31135344546996e-03 - 21 2.42313713931922e+00 -9.29254855727687e-03 - 22 2.41769617213041e+00 -9.27078468852164e-03 - 23 2.41193587332118e+00 -9.24774349328473e-03 - 24 2.40625738446726e+00 -9.22502953786906e-03 - 25 2.40101869519248e+00 -9.20407478076994e-03 - 26 2.39651622530201e+00 -9.18606490120804e-03 - 27 2.39296966655697e+00 -9.17187866622788e-03 - 28 2.39050847169341e+00 -9.16203388677364e-03 - 29 2.38916060732936e+00 -9.15664242931743e-03 - 30 2.38884732554973e+00 -9.15538930219891e-03 - 31 2.38938907295485e+00 -9.15755629181939e-03 - 32 2.39052656449122e+00 -9.16210625796488e-03 - 33 2.39195711452612e+00 -9.16782845810448e-03 - 34 2.39338167011611e+00 -9.17352668046446e-03 - 35 2.39455393665551e+00 -9.17821574662203e-03 - 36 2.39532170766483e+00 -9.18128683065931e-03 - 37 2.39565155143393e+00 -9.18260620573574e-03 - 38 2.39563139473288e+00 -9.18252557893151e-03 - 39 2.39545006610174e+00 -9.18180026440696e-03 - 40 2.39535776160792e+00 -9.18143104643170e-03 + 20 2.42783836132997e+00 -9.31135344531990e-03 + 21 2.42313713928297e+00 -9.29254855713189e-03 + 22 2.41769617209907e+00 -9.27078468839628e-03 + 23 2.41193587329818e+00 -9.24774349319270e-03 + 24 2.40625738445557e+00 -9.22502953782229e-03 + 25 2.40101869519443e+00 -9.20407478077773e-03 + 26 2.39651622531912e+00 -9.18606490127647e-03 + 27 2.39296966658990e+00 -9.17187866635958e-03 + 28 2.39050847174201e+00 -9.16203388696806e-03 + 29 2.38916060739287e+00 -9.15664242957147e-03 + 30 2.38884732562697e+00 -9.15538930250787e-03 + 31 2.38938907304455e+00 -9.15755629217820e-03 + 32 2.39052656459227e+00 -9.16210625836907e-03 + 33 2.39195711463777e+00 -9.16782845855110e-03 + 34 2.39338167023812e+00 -9.17352668095248e-03 + 35 2.39455393678809e+00 -9.17821574715235e-03 + 36 2.39532170780857e+00 -9.18128683123430e-03 + 37 2.39565155158960e+00 -9.18260620635839e-03 + 38 2.39563139490110e+00 -9.18252557960440e-03 + 39 2.39545006628275e+00 -9.18180026513099e-03 + 40 2.39535776180124e+00 -9.18143104720494e-03 diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out index 18bfc4768..9b43c99fa 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -124,28 +120,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - distancePairs colvar component: -colvars: - histogramRestraint colvar bias implementation: -colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped index 76f57335f..2fdfb6c4c 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.04650863844542e+00 , 4.49435411373106e+00 , 5.18841527687423e+00 , 6.16645837246753e+00 , 2.49717925475228e+00 , 3.86424835988508e+00 , 4.55750848670402e+00 , 5.34080670712767e+00 , 1.36568581550375e+00 , 2.47047097074510e+00 , 3.12336009876006e+00 , 3.85074280234761e+00 , 2.22178524374518e+00 , 2.73185149420872e+00 , 2.91864419945045e+00 , 3.29101397434784e+00 ) + x ( 3.04650863884945e+00 , 4.49435411437724e+00 , 5.18841527762764e+00 , 6.16645837340779e+00 , 2.49717925480425e+00 , 3.86424836018692e+00 , 4.55750848697779e+00 , 5.34080670765490e+00 , 1.36568581546352e+00 , 2.47047097097987e+00 , 3.12336009885461e+00 , 3.85074280281206e+00 , 2.22178524357949e+00 , 2.73185149414085e+00 , 2.91864419906098e+00 , 3.29101397431997e+00 ) } histogramrestraint { diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj index e0a6a3b8e..703c0aa24 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hr 0 ( 2.95543971137580e+00 , 4.40149446295507e+00 , 5.19438956774262e+00 , 6.22241603343745e+00 , 2.46985074910253e+00 , 3.82984200895935e+00 , 4.58947829164686e+00 , 5.41000980054028e+00 , 1.34023744154865e+00 , 2.42537620134385e+00 , 3.12639105039661e+00 , 3.90388793384236e+00 , 2.19602098164167e+00 , 2.66815420835178e+00 , 2.96116058328487e+00 , 3.36815290626777e+00 ) ( -5.92960352862036e-03 , 1.10620242770031e-02 , 1.68173891728727e-02 , 1.87723003472394e-02 , -1.12008206156859e-02 , 4.95828158263673e-03 , 1.27336187454413e-02 , 1.77621382788059e-02 , -1.61490029424512e-02 , -1.16075543291348e-02 , -3.82398122724722e-03 , 5.82475954854570e-03 , -1.34483793610802e-02 , -9.21377746348792e-03 , -5.86053342506391e-03 , -7.62252484367914e-04 ) 3.78092070171140e-01 - 1 ( 2.95875719071828e+00 , 4.40108157301207e+00 , 5.19334777145334e+00 , 6.22377033112801e+00 , 2.46917672947451e+00 , 3.82473616688607e+00 , 4.58659307892583e+00 , 5.40932559983924e+00 , 1.33333768535497e+00 , 2.41676016397270e+00 , 3.12170836496912e+00 , 3.90418294782421e+00 , 2.19936580917941e+00 , 2.66448894985246e+00 , 2.96000465033399e+00 , 3.36551108557249e+00 ) ( -5.86283106865521e-03 , 1.10731958752829e-02 , 1.68140327966110e-02 , 1.87597892711689e-02 , -1.11822547405590e-02 , 4.92033089418465e-03 , 1.27214365048558e-02 , 1.77580366645080e-02 , -1.61363624056552e-02 , -1.16601244086846e-02 , -3.85595598392256e-03 , 5.84982545350766e-03 , -1.34023678457379e-02 , -9.22688145618673e-03 , -5.84776463391588e-03 , -7.69953161976424e-04 ) 3.77945851131380e-01 - 2 ( 2.96294215660827e+00 , 4.40226828651185e+00 , 5.19286012272654e+00 , 6.22443374457976e+00 , 2.46935518847865e+00 , 3.82150874456602e+00 , 4.58422849105882e+00 , 5.40818433918403e+00 , 1.32707626478422e+00 , 2.41052101094634e+00 , 3.11822280908445e+00 , 3.90473321715676e+00 , 2.20349735093127e+00 , 2.66304418493398e+00 , 2.95871521201740e+00 , 3.36219610857201e+00 ) ( -5.79800647502922e-03 , 1.10923908557419e-02 , 1.68129107062924e-02 , 1.87535308678630e-02 , -1.11672628469244e-02 , 4.89409954504780e-03 , 1.27081525944472e-02 , 1.77533370847938e-02 , -1.61279245724598e-02 , -1.17024782043052e-02 , -3.88536413831673e-03 , 5.86771262483623e-03 , -1.33609408182681e-02 , -9.22837266280075e-03 , -5.84907998228004e-03 , -7.98316100680052e-04 ) 3.77862223359593e-01 - 3 ( 2.96775402992694e+00 , 4.40516830459548e+00 , 5.19308580986083e+00 , 6.22426614571086e+00 , 2.47031640871780e+00 , 3.82049095747998e+00 , 4.58271436795677e+00 , 5.40668366046462e+00 , 1.32191637302337e+00 , 2.40699048525175e+00 , 3.11597732152133e+00 , 3.90507762174690e+00 , 2.20806859148285e+00 , 2.66384305029386e+00 , 2.95730260671757e+00 , 3.35823946236147e+00 ) ( -5.73812439859379e-03 , 1.11203452480056e-02 , 1.68145007712454e-02 , 1.87535589647976e-02 , -1.11565343480424e-02 , 4.88326606493625e-03 , 1.26961984974043e-02 , 1.77480942241991e-02 , -1.61238345657143e-02 , -1.17319756039677e-02 , -3.91183713328302e-03 , 5.87286048563701e-03 , -1.33265703304845e-02 , -9.21811206393306e-03 , -5.86446396094804e-03 , -8.47126580670137e-04 ) 3.77840179115355e-01 - 4 ( 2.97293625444857e+00 , 4.40980004758125e+00 , 5.19408774075846e+00 , 6.22316886249381e+00 , 2.47196059702068e+00 , 3.82188498631687e+00 , 4.58227967128769e+00 , 5.40493151507430e+00 , 1.31824010722335e+00 , 2.40633376724167e+00 , 3.11491133209983e+00 , 3.90477299810360e+00 , 2.21271348718989e+00 , 2.66679770357475e+00 , 2.95576116726311e+00 , 3.35371179659075e+00 ) ( -5.68562536211738e-03 , 1.11574404636562e-02 , 1.68189720084544e-02 , 1.87595928078326e-02 , -1.11503656066572e-02 , 4.89069779983769e-03 , 1.26876273223686e-02 , 1.77424383833725e-02 , -1.61240913055969e-02 , -1.17467229287332e-02 , -3.93551745856113e-03 , 5.86059410516952e-03 , -1.33013307602559e-02 , -9.19636281522561e-03 , -5.89333166754952e-03 , -9.14911497713965e-04 ) 3.77876668465000e-01 - 5 ( 2.97824318820620e+00 , 4.41608136345158e+00 , 5.19583111697961e+00 , 6.22109580805119e+00 , 2.47416649816765e+00 , 3.82573442794791e+00 , 4.58302854469209e+00 , 5.40302751449250e+00 , 1.31631479781056e+00 , 2.40854057670679e+00 , 3.11487986891832e+00 , 3.90345112760315e+00 , 2.21707823699791e+00 , 2.67171151319462e+00 , 2.95407669276953e+00 , 3.34871521635490e+00 ) ( -5.64215660564444e-03 , 1.12036160407990e-02 , 1.68261920493138e-02 , 1.87710646714446e-02 , -1.11486629033573e-02 , 4.91802392897703e-03 , 1.26838914739109e-02 , 1.77365452169039e-02 , -1.61285450767192e-02 , -1.17456807872873e-02 , -3.95690439720719e-03 , 5.82769711943081e-03 , -1.32867339927808e-02 , -9.16386239601504e-03 , -5.93452419993883e-03 , -9.99112313017295e-04 ) 3.77966928510290e-01 - 6 ( 2.98346272349810e+00 , 4.42383057898326e+00 , 5.19819070218742e+00 , 6.21805993368695e+00 , 2.47679966397792e+00 , 3.83190740551774e+00 , 4.58492741116317e+00 , 5.40104621783311e+00 , 1.31627480642875e+00 , 2.41343034363858e+00 , 3.11567915001139e+00 , 3.90086651022608e+00 , 2.22085290399274e+00 , 2.67829022321015e+00 , 2.95223463734567e+00 , 3.34337409763593e+00 ) ( -5.60843111665177e-03 , 1.12583138089623e-02 , 1.68357668482585e-02 , 1.87871810209162e-02 , -1.11509975020431e-02 , 4.96532034611288e-03 , 1.26856803073333e-02 , 1.77306125297607e-02 , -1.61369024575768e-02 , -1.17287330746808e-02 , -3.97667165949540e-03 , 5.77284958036822e-03 , -1.32835970604198e-02 , -9.12186140006743e-03 , -5.98634736725953e-03 , -1.09632452077415e-03 ) 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1.32170353599299e+00 , 2.42978572116422e+00 , 3.11883162759681e+00 , 3.89171382371156e+00 , 2.22577247715835e+00 , 2.69489401029209e+00 , 2.94805450436009e+00 , 3.33220883826211e+00 ) ( -5.56820917282278e-03 , 1.13885155084319e-02 , 1.68595280947096e-02 , 1.88295545639784e-02 , -1.11650126061194e-02 , 5.11152770905446e-03 , 1.27043773431331e-02 , 1.77194261761126e-02 , -1.61635185303969e-02 , -1.16514770997870e-02 , -4.01376337777638e-03 , 5.60281550584254e-03 , -1.33110285193897e-02 , -9.01681060037427e-03 , -6.11297722345335e-03 , -1.31358022351808e-03 ) 3.78500459333923e-01 - 9 ( 2.99727803932683e+00 , 4.45276689003159e+00 , 5.20671940496760e+00 , 6.20418842997876e+00 , 2.48582792210202e+00 , 3.86044838529561e+00 , 4.59519142345580e+00 , 5.39478097747158e+00 , 1.32677703124828e+00 , 2.44021023612503e+00 , 3.12073277454684e+00 , 3.88545705707712e+00 , 2.22673027072218e+00 , 2.70403228030061e+00 , 2.94572999620193e+00 , 3.32665870422601e+00 ) ( -5.55846922909315e-03 , 1.14605208114470e-02 , 1.68723226152897e-02 , 1.88538732088346e-02 , -1.11751436044541e-02 , 5.20218321504213e-03 , 1.27185877234887e-02 , 1.77145300274814e-02 , -1.61806180975511e-02 , -1.15957536333710e-02 , -4.03166013215670e-03 , 5.49565596179502e-03 , -1.33392618858410e-02 , -8.95847435004462e-03 , -6.18265891926579e-03 , -1.42505162862931e-03 ) 3.78746600048281e-01 - 10 ( 3.00113590351193e+00 , 4.46295283628442e+00 , 5.20913451135400e+00 , 6.19856492361509e+00 , 2.48872700417910e+00 , 3.87127405643474e+00 , 4.59883180779499e+00 , 5.39241395041393e+00 , 1.33297408008389e+00 , 2.45129095459194e+00 , 3.12259990733059e+00 , 3.87852252716797e+00 , 2.22673463302703e+00 , 2.71311302779813e+00 , 2.94327377818026e+00 , 3.32129591623069e+00 ) ( -5.55224417164072e-03 , 1.15342512228427e-02 , 1.68848695705750e-02 , 1.88791062752049e-02 , -1.11863975635185e-02 , 5.29683799032226e-03 , 1.27332368515994e-02 , 1.77102817912748e-02 , -1.61993578794913e-02 , -1.15331925419960e-02 , 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5.21179795342402e+00 , 6.18720282644011e+00 , 2.49355503432457e+00 , 3.89041360009451e+00 , 4.60360319942864e+00 , 5.38662146956213e+00 , 1.34691612070145e+00 , 2.47263280494077e+00 , 3.12573989585393e+00 , 3.86445347573540e+00 , 2.22457351043668e+00 , 2.72936720512052e+00 , 2.93807666861132e+00 , 3.31151936864297e+00 ) ( -5.53721626795029e-03 , 1.16774905532618e-02 , 1.69074760243028e-02 , 1.89295470420789e-02 , -1.12098518648447e-02 , 5.47099418188079e-03 , 1.27539142271434e-02 , 1.77039734250454e-02 , -1.62389653920810e-02 , -1.14054942040387e-02 , -4.07841190427115e-03 , 5.16538673702184e-03 , -1.34542775132188e-02 , -8.79243550204225e-03 , -6.38585394534860e-03 , -1.72351102574743e-03 ) 3.79629555593815e-01 - 13 ( 3.01147358102753e+00 , 4.48893928194997e+00 , 5.21171292451106e+00 , 6.18194650016787e+00 , 2.49529420874019e+00 , 3.89726774753210e+00 , 4.60388154116292e+00 , 5.38295779117939e+00 , 1.35366684255277e+00 , 2.48151732623380e+00 , 3.12686979147052e+00 , 3.85826315071113e+00 , 2.22290718088401e+00 , 2.73578615464733e+00 , 2.93539988719616e+00 , 3.30724327376658e+00 ) ( -5.52138817482320e-03 , 1.17425495705784e-02 , 1.69171191446419e-02 , 1.89536788062538e-02 , -1.12208703478021e-02 , 5.53719445578204e-03 , 1.27553319589290e-02 , 1.77018696730068e-02 , -1.62585085963099e-02 , -1.13502429741435e-02 , -4.08878426817147e-03 , 5.07741732348955e-03 , -1.34928430954218e-02 , -8.74878890446318e-03 , -6.44401748260910e-03 , -1.80072599449384e-03 ) 3.79960806988138e-01 - 14 ( 3.01500498355936e+00 , 4.49484105603145e+00 , 5.21058888397878e+00 , 6.17725979125500e+00 , 2.49652507990531e+00 , 3.90150978133327e+00 , 4.60234863260006e+00 , 5.37865915135750e+00 , 1.35963468851140e+00 , 2.48838344220267e+00 , 3.12766033460393e+00 , 3.85317752048532e+00 , 2.22122742538576e+00 , 2.74066674507216e+00 , 2.93271867782830e+00 , 3.30343100744147e+00 ) ( -5.49549732867158e-03 , 1.18007441986952e-02 , 1.69256728814974e-02 , 1.89765088186476e-02 , -1.12304979163713e-02 , 5.58188833376368e-03 , 1.27484793036664e-02 , 1.77003118142817e-02 , -1.62771022173966e-02 , -1.13072324040326e-02 , -4.09500221423765e-03 , 5.01132420994778e-03 , -1.35265575664752e-02 , -8.71473341320642e-03 , -6.49440390633471e-03 , -1.86333145708674e-03 ) 3.80303913164440e-01 - 15 ( 3.01885935134200e+00 , 4.49895836101355e+00 , 5.20845880435748e+00 , 6.17330861970770e+00 , 2.49726571448041e+00 , 3.90273958726481e+00 , 4.59886715923434e+00 , 5.37368145631357e+00 , 1.36442685860666e+00 , 2.49273626173455e+00 , 3.12809348126300e+00 , 3.84947011778950e+00 , 2.21980329429498e+00 , 2.74380165828177e+00 , 2.93007263674742e+00 , 3.30010253658084e+00 ) ( -5.45664327434154e-03 , 1.18507598188582e-02 , 1.69333270288283e-02 , 1.89976486937448e-02 , -1.12378675651178e-02 , 5.60103026326155e-03 , 1.27324557193522e-02 , 1.76990895586115e-02 , -1.62942676689069e-02 , -1.12806824591946e-02 , -4.09652022589830e-03 , 4.97117341132816e-03 , -1.35529004612138e-02 , -8.69192881828445e-03 , -6.53579293927686e-03 , -1.91029892067540e-03 ) 3.80653281337756e-01 - 16 ( 3.02318574233431e+00 , 4.50121671715298e+00 , 5.20543347930304e+00 , 6.17020596649946e+00 , 2.49758367078486e+00 , 3.90075791018026e+00 , 4.59345084620333e+00 , 5.36803107326493e+00 , 1.36776218077457e+00 , 2.49422221697351e+00 , 3.12814676409148e+00 , 3.84727076112079e+00 , 2.21885835313521e+00 , 2.74506502298711e+00 , 2.92750329382881e+00 , 3.29726720552320e+00 ) ( -5.40260775227740e-03 , 1.18918393995497e-02 , 1.69403563723388e-02 , 1.90167057123976e-02 , -1.12419666467266e-02 , 5.59228671198299e-03 , 1.27071500736935e-02 , 1.76979317995731e-02 , -1.63096075137775e-02 , -1.12738072092257e-02 , -4.09333242371338e-03 , 4.95876082069397e-03 , -1.35699155635357e-02 , -8.68152857719622e-03 , -6.56737454138995e-03 , -1.94123960773835e-03 ) 3.81001871240511e-01 - 17 ( 3.02809415710879e+00 , 4.50166506104922e+00 , 5.20168811881594e+00 , 6.16800533349194e+00 , 2.49758857964583e+00 , 3.89558236005592e+00 , 4.58626174925325e+00 , 5.36177010617776e+00 , 1.36949463578708e+00 , 2.49265415188493e+00 , 3.12778059652950e+00 , 3.84655116097139e+00 , 2.21854897895857e+00 , 2.74441563397565e+00 , 2.92505081205027e+00 , 3.29493032180216e+00 ) ( -5.33207795486475e-03 , 1.19238375475688e-02 , 1.69470627883182e-02 , 1.90332731864346e-02 , -1.12416911796005e-02 , 5.55523293564110e-03 , 1.26732473366659e-02 , 1.76965367632408e-02 , -1.63227936088094e-02 , -1.12884863427824e-02 , -4.08612201263206e-03 , 4.97341853049439e-03 , -1.35763317145022e-02 , -8.68411432067984e-03 , -6.58877216935854e-03 , -1.95630818933365e-03 ) 3.81341269972205e-01 - 18 ( 3.03363892679024e+00 , 4.50047208564501e+00 , 5.19744285787811e+00 , 6.16669911720665e+00 , 2.49741999764829e+00 , 3.88744865212165e+00 , 4.57759477230416e+00 , 5.35501860432485e+00 , 1.36962096542427e+00 , 2.48802587288390e+00 , 3.12692927006197e+00 , 3.84712592421505e+00 , 2.21895140215167e+00 , 2.74189783528608e+00 , 2.92274822946829e+00 , 3.29309909618837e+00 ) ( -5.24483234477642e-03 , 1.19472351637181e-02 , 1.69537131714762e-02 , 1.90469452610655e-02 , -1.12359373173825e-02 , 5.49144095224124e-03 , 1.26321668666295e-02 , 1.76946183386180e-02 , -1.63335559240562e-02 , -1.13250482267429e-02 , -4.07634438280624e-03 , 5.01204954188020e-03 , -1.35716288069538e-02 , -8.69964479496807e-03 , -6.60008084392255e-03 , -1.95609218069161e-03 ) 3.81662024543382e-01 - 19 ( 3.03980638894298e+00 , 4.49791396519392e+00 , 5.19293926689468e+00 , 6.16622192395595e+00 , 2.49723246064096e+00 , 3.87679761673723e+00 , 4.56785187518058e+00 , 5.34795393847889e+00 , 1.36827142975610e+00 , 2.48051460680503e+00 , 3.12549701697292e+00 , 3.84866874555677e+00 , 2.22005841870842e+00 , 2.73764013703583e+00 , 2.92061396081615e+00 , 3.29178674652695e+00 ) ( -5.14186565350286e-03 , 1.19631117657520e-02 , 1.69604787022727e-02 , 1.90573528747551e-02 , -1.12237144458926e-02 , 5.40445708215642e-03 , 1.25859420489657e-02 , 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3.82208090962526e-01 + 1 ( 2.95875719071982e+00 , 4.40108157301290e+00 , 5.19334777145356e+00 , 6.22377033113224e+00 , 2.46917672947515e+00 , 3.82473616688567e+00 , 4.58659307892474e+00 , 5.40932559984203e+00 , 1.33333768535653e+00 , 2.41676016397346e+00 , 3.12170836496849e+00 , 3.90418294782770e+00 , 2.19936580917918e+00 , 2.66448894985085e+00 , 2.96000465033168e+00 , 3.36551108557328e+00 ) ( -5.86283106863594e-03 , 1.10731958752850e-02 , 1.68140327966034e-02 , 1.87597892711556e-02 , -1.11822547405509e-02 , 4.92033089417690e-03 , 1.27214365048402e-02 , 1.77580366645092e-02 , -1.61363624056526e-02 , -1.16601244086755e-02 , -3.85595598393038e-03 , 5.84982545354479e-03 , -1.34023678457367e-02 , -9.22688145620218e-03 , -5.84776463394309e-03 , -7.69953161967240e-04 ) 3.77945851131251e-01 + 2 ( 2.96294215661432e+00 , 4.40226828651527e+00 , 5.19286012272764e+00 , 6.22443374459694e+00 , 2.46935518848109e+00 , 3.82150874456456e+00 , 4.58422849105476e+00 , 5.40818433919542e+00 , 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5.19819070221187e+00 , 6.21805993383684e+00 , 2.47679966399307e+00 , 3.83190740551612e+00 , 4.58492741114084e+00 , 5.40104621793262e+00 , 1.31627480646442e+00 , 2.41343034366284e+00 , 3.11567914999535e+00 , 3.90086651034176e+00 , 2.22085290398016e+00 , 2.67829022316575e+00 , 2.95223463727300e+00 , 3.34337409766356e+00 ) ( -5.60843111606338e-03 , 1.12583138090471e-02 , 1.68357668480079e-02 , 1.87871810204228e-02 , -1.11509975018142e-02 , 4.96532034592246e-03 , 1.26856803068378e-02 , 1.77306125297571e-02 , -1.61369024574342e-02 , -1.17287330743696e-02 , -3.97667165972031e-03 , 5.77284958152370e-03 , -1.32835970603912e-02 , -9.12186140048792e-03 , -5.98634736812786e-03 , -1.09632452049312e-03 ) 3.78105088301569e-01 + 7 ( 2.98843276398744e+00 , 4.43277362483451e+00 , 5.20096598215456e+00 , 6.21413473649645e+00 , 2.47971835574389e+00 , 3.84009332258054e+00 , 4.58780406792093e+00 , 5.39902438402581e+00 , 1.31811662219982e+00 , 2.42066789068249e+00 , 3.11707520826167e+00 , 3.89692854958901e+00 , 2.22379944065945e+00 , 2.68616059173228e+00 , 2.95022670924909e+00 , 3.33782534397885e+00 ) ( -5.58418350392305e-03 , 1.13204634820250e-02 , 1.68471093234050e-02 , 1.88070063165611e-02 , -1.11567058554382e-02 , 5.03094217833919e-03 , 1.26928382670779e-02 , 1.77248424341677e-02 , -1.61487389919253e-02 , -1.16967256674628e-02 , -3.99547330134301e-03 , 5.69688275344288e-03 , -1.32919546974225e-02 , -9.07211334097645e-03 , -6.04665602071449e-03 , -1.20257089380199e-03 ) 3.78284907038721e-01 + 8 ( 2.99305095207488e+00 , 4.44255706235088e+00 , 5.20390279809292e+00 , 6.20945090058357e+00 , 2.48277685515950e+00 , 3.84981382800082e+00 , 4.59135934528309e+00 , 5.39695380947607e+00 , 1.32170353603877e+00 , 2.42978572120870e+00 , 3.11883162757640e+00 , 3.89171382389852e+00 , 2.22577247713240e+00 , 2.69489401022899e+00 , 2.94805450424125e+00 , 3.33220883830515e+00 ) ( -5.56820917188656e-03 , 1.13885155086110e-02 , 1.68595280943234e-02 , 1.88295545631365e-02 , 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-8.95847435071736e-03 , -6.18265892101870e-03 , -1.42505162821923e-03 ) 3.78746600035240e-01 + 10 ( 3.00113590362578e+00 , 4.46295283642265e+00 , 5.20913451147704e+00 , 6.19856492398371e+00 , 2.48872700419815e+00 , 3.87127405646959e+00 , 4.59883180778555e+00 , 5.39241395065204e+00 , 1.33297408012915e+00 , 2.45129095466347e+00 , 3.12259990731229e+00 , 3.87852252742574e+00 , 2.22673463298190e+00 , 2.71311302772409e+00 , 2.94327377801210e+00 , 3.32129591628587e+00 ) ( -5.55224417034228e-03 , 1.15342512231714e-02 , 1.68848695700858e-02 , 1.88791062739624e-02 , -1.11863975631308e-02 , 5.29683799008538e-03 , 1.27332368505308e-02 , 1.77102817911029e-02 , -1.61993578790013e-02 , -1.15331925411162e-02 , -4.04888243585471e-03 , 5.38197720759974e-03 , -1.33744234726094e-02 , -8.89981537283595e-03 , -6.25302646254240e-03 , -1.53289195744994e-03 ) 3.79019107024581e-01 + 11 ( 3.00470125503232e+00 , 4.47265711228424e+00 , 5.21089460531976e+00 , 6.19282083273147e+00 , 2.49134008905727e+00 , 3.88151734630328e+00 , 4.60179016418754e+00 , 5.38973566951884e+00 , 1.33985118526983e+00 , 2.46233295679202e+00 , 3.12429892039402e+00 , 3.87136030320866e+00 , 2.22594006156255e+00 , 2.72169287069741e+00 , 2.94071248075728e+00 , 3.31622273015255e+00 ) ( -5.54632287865549e-03 , 1.16073489553701e-02 , 1.68966879651642e-02 , 1.89045283462007e-02 , -1.11981583558499e-02 , 5.38873432377074e-03 , 1.27458325711537e-02 , 1.77067581962933e-02 , -1.62190359535014e-02 , -1.14681548196382e-02 , -4.06477383520721e-03 , 5.26930541316280e-03 , -1.34137735934670e-02 , -8.84358548360923e-03 , -6.32152819384059e-03 , -1.63341748079868e-03 ) 3.79314492509373e-01 + 12 ( 3.00809583960727e+00 , 4.48144568626711e+00 , 5.21179795363804e+00 , 6.18720282692826e+00 , 2.49355503433962e+00 , 3.89041360016790e+00 , 4.60360319945111e+00 , 5.38662146987011e+00 , 1.34691612073454e+00 , 2.47263280504502e+00 , 3.12573989584620e+00 , 3.86445347605522e+00 , 2.22457351036754e+00 , 2.72936720504478e+00 , 2.93807666839465e+00 , 3.31151936870328e+00 ) ( -5.53721626627702e-03 , 1.16774905538055e-02 , 1.69074760237742e-02 , 1.89295470404025e-02 , -1.12098518644332e-02 , 5.47099418171554e-03 , 1.27539142258515e-02 , 1.77039734246792e-02 , -1.62389653913332e-02 , -1.14054942027861e-02 , -4.07841190467654e-03 , 5.16538673979658e-03 , -1.34542775132534e-02 , -8.79243550280625e-03 , -6.38585394807292e-03 , -1.72351102546992e-03 ) 3.79629555570475e-01 + 13 ( 3.01147358120148e+00 , 4.48893928221114e+00 , 5.21171292478083e+00 , 6.18194650071545e+00 , 2.49529420875273e+00 , 3.89726774762925e+00 , 4.60388154120812e+00 , 5.38295779152011e+00 , 1.35366684257626e+00 , 2.48151732635576e+00 , 3.12686979147126e+00 , 3.85826315105735e+00 , 2.22290718080169e+00 , 2.73578615457354e+00 , 2.93539988695624e+00 , 3.30724327382593e+00 ) ( -5.52138817294984e-03 , 1.17425495712558e-02 , 1.69171191441226e-02 , 1.89536788043514e-02 , -1.12208703473856e-02 , 5.53719445567561e-03 , 1.27553319575538e-02 , 1.77018696725139e-02 , -1.62585085954183e-02 , -1.13502429726935e-02 , -4.08878426855555e-03 , 5.07741732638636e-03 , -1.34928430954787e-02 , -8.74878890522558e-03 , -6.44401748565672e-03 , -1.80072599434109e-03 ) 3.79960806960900e-01 + 14 ( 3.01500498375669e+00 , 4.49484105634166e+00 , 5.21058888431015e+00 , 6.17725979186124e+00 , 2.49652507991581e+00 , 3.90150978145652e+00 , 4.60234863267193e+00 , 5.37865915172911e+00 , 1.35963468852382e+00 , 2.48838344234272e+00 , 3.12766033461501e+00 , 3.85317752085478e+00 , 2.22122742528990e+00 , 2.74066674500144e+00 , 2.93271867756587e+00 , 3.30343100749719e+00 ) ( -5.49549732658235e-03 , 1.18007441995238e-02 , 1.69256728810072e-02 , 1.89765088165145e-02 , -1.12304979159479e-02 , 5.58188833372983e-03 , 1.27484793022279e-02 , 1.77003118136450e-02 , -1.62771022163553e-02 , -1.13072324023837e-02 , -4.09500221458595e-03 , 5.01132421291456e-03 , -1.35265575665557e-02 , -8.71473341395976e-03 , -6.49440390970358e-03 , -1.86333145710300e-03 ) 3.80303913133154e-01 + 15 ( 3.01885935156514e+00 , 4.49895836137591e+00 , 5.20845880475518e+00 , 6.17330862037168e+00 , 2.49726571449010e+00 , 3.90273958741594e+00 , 4.59886715933612e+00 , 5.37368145671421e+00 , 1.36442685860736e+00 , 2.49273626189266e+00 , 3.12809348128601e+00 , 3.84947011817928e+00 , 2.21980329418561e+00 , 2.74380165821453e+00 , 2.93007263646310e+00 , 3.30010253663009e+00 ) ( -5.45664327201426e-03 , 1.18507598198550e-02 , 1.69333270283853e-02 , 1.89976486913772e-02 , -1.12378675646792e-02 , 5.60103026331286e-03 , 1.27324557178694e-02 , 1.76990895578171e-02 , -1.62942676677129e-02 , -1.12806824573500e-02 , -4.09652022619895e-03 , 4.97117341431712e-03 , -1.35529004613194e-02 , -8.69192881902856e-03 , -6.53579294296637e-03 , -1.91029892090598e-03 ) 3.80653281302327e-01 + 16 ( 3.02318574258621e+00 , 4.50121671756992e+00 , 5.20543347977050e+00 , 6.17020596722025e+00 , 2.49758367079577e+00 , 3.90075791036053e+00 , 4.59345084633747e+00 , 5.36803107369289e+00 , 1.36776218076375e+00 , 2.49422221714921e+00 , 3.12814676412765e+00 , 3.84727076152845e+00 , 2.21885835301271e+00 , 2.74506502292299e+00 , 2.92750329352306e+00 , 3.29726720556305e+00 ) ( -5.40260774968335e-03 , 1.18918394007310e-02 , 1.69403563719583e-02 , 1.90167057097929e-02 , -1.12419666462581e-02 , 5.59228671213132e-03 , 1.27071500721839e-02 , 1.76979317986111e-02 , -1.63096075124309e-02 , -1.12738072071936e-02 , -4.09333242395765e-03 , 4.95876082366399e-03 , -1.35699155636684e-02 , -8.68152857793866e-03 , -6.56737454540186e-03 , -1.94123960822893e-03 ) 3.81001871200905e-01 + 17 ( 3.02809415739285e+00 , 4.50166506152248e+00 , 5.20168811935516e+00 , 6.16800533426867e+00 , 2.49758857966083e+00 , 3.89558236026613e+00 , 4.58626174942138e+00 , 5.36177010663164e+00 , 1.36949463576574e+00 , 2.49265415207740e+00 , 3.12778059657973e+00 , 3.84655116139501e+00 , 2.21854897882363e+00 , 2.74441563391359e+00 , 2.92505081172337e+00 , 3.29493032182962e+00 ) ( -5.33207795196924e-03 , 1.19238375489492e-02 , 1.69470627880117e-02 , 1.90332731835913e-02 , -1.12416911790806e-02 , 5.55523293589804e-03 , 1.26732473351448e-02 , 1.76965367621060e-02 , -1.63227936073129e-02 , -1.12884863405751e-02 , -4.08612201281463e-03 , 4.97341853341229e-03 , -1.35763317146644e-02 , -8.68411432143570e-03 , -6.58877217369707e-03 , -1.95630819012991e-03 ) 3.81341269928444e-01 + 18 ( 3.03363892711023e+00 , 4.50047208617566e+00 , 5.19744285848972e+00 , 6.16669911803858e+00 , 2.49741999767105e+00 , 3.88744865236222e+00 , 4.57759477250720e+00 , 5.35501860480364e+00 , 1.36962096539415e+00 , 2.48802587309199e+00 , 3.12692927012681e+00 , 3.84712592465320e+00 , 2.21895140200526e+00 , 2.74189783522437e+00 , 2.92274822912038e+00 , 3.29309909620042e+00 ) ( -5.24483234153983e-03 , 1.19472351653105e-02 , 1.69537131712506e-02 , 1.90469452579835e-02 , -1.12359373167835e-02 , 5.49144095261838e-03 , 1.26321668651098e-02 , 1.76946183373094e-02 , -1.63335559224151e-02 , -1.13250482243768e-02 , -4.07634438292505e-03 , 5.01204954472087e-03 , -1.35716288071488e-02 , -8.69964479575904e-03 , -6.60008084859376e-03 , -1.95609218183908e-03 ) 3.81662024495540e-01 + 19 ( 3.03980638930293e+00 , 4.49791396578241e+00 , 5.19293926757803e+00 , 6.16622192484240e+00 , 2.49723246067585e+00 , 3.87679761700838e+00 , 4.56785187541893e+00 , 5.34795393898199e+00 , 1.36827142971955e+00 , 2.48051460702728e+00 , 3.12549701705262e+00 , 3.84866874600845e+00 , 2.22005841855173e+00 , 2.73764013697229e+00 , 2.92061396044736e+00 , 3.29178674652055e+00 ) ( -5.14186564988213e-03 , 1.19631117675662e-02 , 1.69604787021299e-02 , 1.90573528714360e-02 , -1.12237144451809e-02 , 5.40445708266560e-03 , 1.25859420474585e-02 , 1.76919640583354e-02 , -1.63416796379246e-02 , -1.13821966907384e-02 , -4.06622804413393e-03 , 5.06938813592078e-03 , -1.35560499548848e-02 , -8.72742264831989e-03 , -6.60191447726332e-03 , -1.94150498787041e-03 ) 3.81954197395723e-01 + 20 ( 3.04650863884945e+00 , 4.49435411437724e+00 , 5.18841527762764e+00 , 6.16645837340779e+00 , 2.49717925480425e+00 , 3.86424836018692e+00 , 4.55750848697779e+00 , 5.34080670765490e+00 , 1.36568581546352e+00 , 2.47047097097987e+00 , 3.12336009885461e+00 , 3.85074280281206e+00 , 2.22178524357949e+00 , 2.73185149414085e+00 , 2.91864419906098e+00 , 3.29101397431997e+00 ) ( -5.02542974750439e-03 , 1.19730728164444e-02 , 1.69673824742426e-02 , 1.90642123537368e-02 , -1.12042672914772e-02 , 5.29965572263668e-03 , 1.25370495916030e-02 , 1.76884949726336e-02 , -1.63470133927038e-02 , -1.14570941759426e-02 , -4.05868153495143e-03 , 5.13846947912402e-03 , -1.35305636185385e-02 , -8.76608365877139e-03 , -6.59544443572543e-03 , -1.91369494935530e-03 ) 3.82208090906906e-01 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat index 03221b542..1a12c5a95 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat @@ -1,10 +1,10 @@ # one p(one ) - 2.00000000000000 0.09030392972369 - 4.00000000000000 0.19798865120683 - 6.00000000000000 0.14853769410307 - 8.00000000000000 0.04657771648442 - 10.00000000000000 0.00481731601539 - 12.00000000000000 0.00011856440761 + 2.00000000000000 0.09030392971801 + 4.00000000000000 0.19798865118667 + 6.00000000000000 0.14853769410362 + 8.00000000000000 0.04657771650417 + 10.00000000000000 0.00481731602070 + 12.00000000000000 0.00011856440783 14.00000000000000 0.00000057948069 16.00000000000000 0.00000000051553 18.00000000000000 0.00000000000008 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out index 852f8a3ae..c7b2aef1d 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -124,33 +120,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - distancePairs colvar component: -colvars: - histogramRestraint colvar bias implementation: -colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 3.04651 , 4.49435 , 5.18842 , 6.16646 , 2.49718 , 3.86425 , 4.55751 , 5.34081 , 1.36569 , 2.47047 , 3.12336 , 3.85074 , 2.22179 , 2.73185 , 2.91864 , 3.29101 ) colvars: Restarting histogramrestraint bias "hr" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped index 7bec45097..0ecc9386e 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.03953158571266e+00 , 4.51209497787138e+00 , 5.09894673253801e+00 , 6.16578599788259e+00 , 2.46957015768712e+00 , 3.86055335003907e+00 , 4.47595360314062e+00 , 5.36499714872809e+00 , 1.33944926913138e+00 , 2.47813660022930e+00 , 3.01476283614106e+00 , 3.86080601681174e+00 , 2.22155937137345e+00 , 2.76529935955117e+00 , 2.86078736612033e+00 , 3.36901381742548e+00 ) + x ( 3.03953158726547e+00 , 4.51209497961311e+00 , 5.09894673434180e+00 , 6.16578599928733e+00 , 2.46957015850689e+00 , 3.86055335115988e+00 , 4.47595360418285e+00 , 5.36499714940424e+00 , 1.33944926924420e+00 , 2.47813660080028e+00 , 3.01476283660714e+00 , 3.86080601707240e+00 , 2.22155937101033e+00 , 2.76529935945446e+00 , 2.86078736535835e+00 , 3.36901381632414e+00 ) } histogramrestraint { diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj index c3e1e1b2e..2c3a7993e 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hr - 20 ( 3.04650863844542e+00 , 4.49435411373106e+00 , 5.18841527687423e+00 , 6.16645837246753e+00 , 2.49717925475228e+00 , 3.86424835988508e+00 , 4.55750848670402e+00 , 5.34080670712767e+00 , 1.36568581550375e+00 , 2.47047097074510e+00 , 3.12336009876006e+00 , 3.85074280234761e+00 , 2.22178524374518e+00 , 2.73185149420872e+00 , 2.91864419945045e+00 , 3.29101397434784e+00 ) ( -5.02542975155399e-03 , 1.19730728144022e-02 , 1.69673824743050e-02 , 1.90642123572900e-02 , -1.12042672923401e-02 , 5.29965572198335e-03 , 1.25370495930876e-02 , 1.76884949742769e-02 , -1.63470133946114e-02 , -1.14570941785658e-02 , -4.05868153495528e-03 , 5.13846947648582e-03 , -1.35305636182661e-02 , -8.76608365782640e-03 , -6.59544443037070e-03 , -1.91369494736973e-03 ) 3.82208090962526e-01 - 21 ( 3.05358451385306e+00 , 4.49021607823814e+00 , 5.18408103497026e+00 , 6.16725452583661e+00 , 2.49739586880410e+00 , 3.85055803143711e+00 , 4.54707448734276e+00 , 5.33385181822192e+00 , 1.36217943433076e+00 , 2.45839729703337e+00 , 3.12037538151779e+00 , 3.85284349899673e+00 , 2.22398282808873e+00 , 2.72481510491786e+00 , 2.91680739909571e+00 , 3.29080759711060e+00 ) ( -4.89897222682100e-03 , 1.19791313892808e-02 , 1.69742633770304e-02 , 1.90673755298261e-02 , -1.11771991099852e-02 , 5.18394936419736e-03 , 1.24881958022913e-02 , 1.76843138080640e-02 , -1.63494863620738e-02 , -1.15455916073648e-02 , -4.05710100270291e-03 , 5.21127645896876e-03 , -1.34967807331177e-02 , -8.81361359377299e-03 , -6.58240414263767e-03 , -1.87397588595395e-03 ) 3.82415073675832e-01 - 22 ( 3.06080810157937e+00 , 4.48595132736801e+00 , 5.18009807716127e+00 , 6.16843183886407e+00 , 2.49798391776076e+00 , 3.83656952216095e+00 , 4.53705219467757e+00 , 5.32739339712202e+00 , 1.35810535034214e+00 , 2.44491630836693e+00 , 3.11639519244157e+00 , 3.85445062126223e+00 , 2.22645629784030e+00 , 2.71687952046412e+00 , 2.91504287509639e+00 , 3.29119674282126e+00 ) ( -4.76696535704344e-03 , 1.19835479428934e-02 , 1.69807629788419e-02 , 1.90668703443345e-02 , -1.11425894939780e-02 , 5.06534159075236e-03 , 1.24420691537260e-02 , 1.76797272308617e-02 , -1.63491285200756e-02 , -1.16425743101174e-02 , -4.06508397900589e-03 , 5.27951326523871e-03 , -1.34568327359927e-02 , -8.86739837013206e-03 , -6.56503633186065e-03 , -1.82377839047625e-03 ) 3.82568429560664e-01 - 23 ( 3.06790413948872e+00 , 4.48200450053951e+00 , 5.17656382698377e+00 , 6.16980236968489e+00 , 2.49899682551938e+00 , 3.82315020141056e+00 , 4.52789434427541e+00 , 5.32174323321216e+00 , 1.35381897118564e+00 , 2.43073302835376e+00 , 3.11128737624436e+00 , 3.85508563435849e+00 , 2.22898609581243e+00 , 2.70844682608125e+00 , 2.91326470584562e+00 , 3.29220745968855e+00 ) ( -4.63463283787862e-03 , 1.19886381009935e-02 , 1.69863384513460e-02 , 1.90629238582122e-02 , -1.11010960470692e-02 , 4.95233310116970e-03 , 1.24010752264571e-02 , 1.76752321496742e-02 , -1.63460880185607e-02 , -1.17423776658788e-02 , -4.08607045622158e-03 , 5.33543540458643e-03 , -1.34132176175144e-02 , -8.92431330337852e-03 , -6.54597178283978e-03 , -1.76461824947690e-03 ) 3.82664136179363e-01 - 24 ( 3.07456896189780e+00 , 4.47877932702159e+00 , 5.17350292321320e+00 , 6.17118403121453e+00 , 2.50042929754554e+00 , 3.81112677805404e+00 , 4.51996576437108e+00 , 5.31719422066849e+00 , 1.34964937408689e+00 , 2.41659320666385e+00 , 3.10495847659781e+00 , 3.85436853999778e+00 , 2.23134971001298e+00 , 2.69995765874844e+00 , 2.91137078731589e+00 , 3.29385683034138e+00 ) ( -4.50759628033739e-03 , 1.19965650752233e-02 , 1.69902999511294e-02 , 1.90559636503187e-02 , -1.10540221258452e-02 , 4.85322332152704e-03 , 1.23670789601672e-02 , 1.76714640602726e-02 , -1.63406409728297e-02 , -1.18392197142181e-02 , -4.12294937353427e-03 , 5.37265037296092e-03 , -1.33686231651157e-02 , -8.98085589401957e-03 , -6.52804678895842e-03 , -1.69807764903222e-03 ) 3.82701469869588e-01 - 25 ( 3.08049503044240e+00 , 4.47660862577235e+00 , 5.17086621112506e+00 , 6.17241473688239e+00 , 2.50221287162265e+00 , 3.80122270018355e+00 , 4.51351282021268e+00 , 5.31399204853792e+00 , 1.34587887726960e+00 , 2.40324136970565e+00 , 3.09737705582823e+00 , 3.85206778233211e+00 , 2.23334232029070e+00 , 2.69187293457495e+00 , 2.90925556253781e+00 , 3.29614768342963e+00 ) ( -4.39147561366562e-03 , 1.20091384936196e-02 , 1.69918666389837e-02 , 1.90465983751812e-02 , -1.10033293365613e-02 , 4.77538069587196e-03 , 1.23411865325813e-02 , 1.76691155106009e-02 , -1.63331907134106e-02 , -1.19276016529115e-02 , -4.17768182194874e-03 , 5.38679797685642e-03 , -1.33257388617823e-02 , -9.03332249666318e-03 , -6.51408372908440e-03 , -1.62579454103830e-03 ) 3.82683339848463e-01 - 26 ( 3.08539660284712e+00 , 4.47573108402803e+00 , 5.16853739588371e+00 , 6.17336434712941e+00 , 2.50421915051295e+00 , 3.79400439209675e+00 , 4.50864423648805e+00 , 5.31230947905661e+00 , 1.34272952084715e+00 , 2.39138079552345e+00 , 3.08859350083748e+00 , 3.84813653868004e+00 , 2.23479506275618e+00 , 2.68465243792059e+00 , 2.90682401319677e+00 , 3.29906482230846e+00 ) ( -4.29148411756531e-03 , 1.20276418269237e-02 , 1.69902333320655e-02 , 1.90355816653891e-02 , -1.09515770462413e-02 , 4.72457054126106e-03 , 1.23236006628952e-02 , 1.76688416349909e-02 , -1.63242548568613e-02 , -1.20026405122825e-02 , -4.25099682948340e-03 , 5.37602868783482e-03 , -1.32870692578888e-02 , -9.07802146171702e-03 , -6.50666848591685e-03 , -1.54945341319546e-03 ) 3.82616280448582e-01 - 27 ( 3.08903403409934e+00 , 4.47627640260616e+00 , 5.16634667844742e+00 , 6.17394349813873e+00 , 2.50627068458191e+00 , 3.78984102049283e+00 , 4.50532543258662e+00 , 5.31222723639859e+00 , 1.34035363315651e+00 , 2.38163676655146e+00 , 3.07875275662228e+00 , 3.84272979858715e+00 , 2.23558983282953e+00 , 2.67873088564368e+00 , 2.90400432206480e+00 , 3.30257333791634e+00 ) ( -4.21205605492461e-03 , 1.20527080280103e-02 , 1.69846407370455e-02 , 1.90237651466753e-02 , -1.09017840062163e-02 , 4.70442293946673e-03 , 1.23135748682848e-02 , 1.76711728222598e-02 , -1.63144400090597e-02 , -1.20603163406075e-02 , -4.34220656326890e-03 , 5.34122227042115e-03 , -1.32547619860300e-02 , -9.11150666597606e-03 , -6.50795643020656e-03 , -1.47076879228184e-03 ) 3.82510078913831e-01 - 28 ( 3.09123422921692e+00 , 4.47825901442763e+00 , 5.16409003425862e+00 , 6.17410853348936e+00 , 2.50815760679602e+00 , 3.78888026398353e+00 , 4.50338659978164e+00 , 5.31372412141838e+00 , 1.33882620806712e+00 , 2.37452389462613e+00 , 3.06809741606238e+00 , 3.83619894758952e+00 , 2.23566954506562e+00 , 2.67449273825598e+00 , 2.90075730703912e+00 , 3.30661925645080e+00 ) ( -4.15653937678158e-03 , 1.20842556425878e-02 , 1.69744443916726e-02 , 1.90120465148651e-02 , -1.08572245330596e-02 , 4.71610016144383e-03 , 1.23094771136140e-02 , 1.76764515744409e-02 , -1.63044061247141e-02 , -1.20976332906350e-02 , -4.44916678162194e-03 , 5.28592246110960e-03 , -1.32304641404146e-02 , -9.13080845840673e-03 , -6.51952625382809e-03 , -1.39145151027727e-03 ) 3.82377079925851e-01 - 29 ( 3.09190509421309e+00 , 4.48157956404059e+00 , 5.16155211354150e+00 , 6.17386201037197e+00 , 2.50965699766396e+00 , 3.79104075049304e+00 , 4.50254293446649e+00 , 5.31667718768969e+00 , 1.33813889021320e+00 , 2.37041835800957e+00 , 3.05696001570915e+00 , 3.82906376008603e+00 , 2.23504287481449e+00 , 2.67224775269306e+00 , 2.89708163089409e+00 , 3.31113228156639e+00 ) ( -4.12697760466075e-03 , 1.21214889662362e-02 , 1.69591787208369e-02 , 1.90013176269185e-02 , -1.08211850017392e-02 , 4.75819485382931e-03 , 1.23089551817022e-02 , 1.76848031284823e-02 , -1.62948248999482e-02 , -1.21127058785823e-02 , -4.56838460845013e-03 , 5.21600003410379e-03 , -1.32152197145269e-02 , -9.13363621823788e-03 , -6.54228804046270e-03 , -1.31315219908283e-03 ) 3.82231264856908e-01 - 30 ( 3.09104253687721e+00 , 4.48603307826026e+00 , 5.15853060452976e+00 , 6.17324867828692e+00 , 2.51055204362215e+00 , 3.79602095739377e+00 , 4.50242469586112e+00 , 5.32087138875897e+00 , 1.33819822704847e+00 , 2.36953676664519e+00 , 3.04574554871881e+00 , 3.82196513028943e+00 , 2.23378273956030e+00 , 2.67220981860937e+00 , 2.89301507576693e+00 , 3.31603007026754e+00 ) ( -4.12399775228976e-03 , 1.21629569237827e-02 , 1.69386135407473e-02 , 1.89924164921859e-02 , -1.07967128795658e-02 , 4.82686270427262e-03 , 1.23091825422540e-02 , 1.76961399144551e-02 , -1.62863384458131e-02 , -1.21047856641569e-02 , -4.69525042105293e-03 , 5.13908728020596e-03 , -1.32094206825129e-02 , -9.11853167377214e-03 , -6.57644050305645e-03 , -1.23738605053167e-03 ) 3.82087235611880e-01 - 31 ( 3.08872930034045e+00 , 4.49132288916588e+00 , 5.15485959375857e+00 , 6.17234728763030e+00 , 2.51064912969521e+00 , 3.80332415543735e+00 , 4.50261440796340e+00 , 5.32601736250928e+00 , 1.33883231975609e+00 , 2.37192384271979e+00 , 3.03490626617957e+00 , 3.81560419549194e+00 , 2.23201834770136e+00 , 2.67448174873522e+00 , 2.88863286961083e+00 , 3.32122334543885e+00 ) ( -4.14681389844940e-03 , 1.22066593920410e-02 , 1.69127991486588e-02 , 1.89860855706422e-02 , -1.07863857447177e-02 , 4.91617372007565e-03 , 1.23071555309342e-02 , 1.77101930919321e-02 , -1.62795237560133e-02 , -1.20742429299629e-02 , -4.82436126980393e-03 , 5.06384588223362e-03 , -1.32128196421779e-02 , -9.08495906809948e-03 , -6.62146792223792e-03 , -1.16545021409847e-03 ) 3.81959230272477e-01 - 32 ( 3.08512587407585e+00 , 4.49707969992627e+00 , 5.15042982483635e+00 , 6.17125913901907e+00 , 2.50979233827432e+00 , 3.81229855394099e+00 , 4.50268874982513e+00 , 5.33177568452012e+00 , 1.33980944632461e+00 , 2.37745103512446e+00 , 3.02491187404977e+00 , 3.81067490080305e+00 , 2.22992148435915e+00 , 2.67904816565005e+00 , 2.88404450587321e+00 , 3.32662115516356e+00 ) ( -4.19334740738677e-03 , 1.22501856597967e-02 , 1.68820961190666e-02 , 1.89829372788785e-02 , -1.07921188400013e-02 , 5.01864637029710e-03 , 1.23000120215299e-02 , 1.77265599742085e-02 , -1.62748657233307e-02 , -1.20225135633812e-02 , -4.94989687037609e-03 , 4.99914062134037e-03 , -1.32246045788317e-02 , -9.03332860324969e-03 , -6.67616648316557e-03 , -1.09835120335049e-03 ) 3.81860258406506e-01 - 33 ( 3.08045463612035e+00 , 4.50288519574339e+00 , 5.14520389945312e+00 , 6.17009473437244e+00 , 2.50787564665153e+00 , 3.82219055462722e+00 , 4.50226213985759e+00 , 5.33778558315697e+00 , 1.34086920751867e+00 , 2.38582693260688e+00 , 3.01621801871649e+00 , 3.80779720585457e+00 , 2.22768857418667e+00 , 2.68577746739276e+00 , 2.87938997999308e+00 , 3.33213575320596e+00 ) ( -4.26045165351063e-03 , 1.22908700845057e-02 , 1.68471856050619e-02 , 1.89834261058958e-02 , -1.08150192814251e-02 , 5.12591079306563e-03 , 1.22853421660068e-02 , 1.77447558708082e-02 , -1.62727379942027e-02 , -1.19520165190434e-02 , -5.06601412276133e-03 , 4.95319659434038e-03 , -1.32435252222438e-02 , -8.96495734999776e-03 , -6.73869467996829e-03 , -1.03675678531612e-03 ) 3.81801393250440e-01 - 34 ( 3.07497912028674e+00 , 4.50829914380588e+00 , 5.13922512638278e+00 , 6.16896017294668e+00 , 2.50485309322197e+00 , 3.83220702719942e+00 , 4.50102851686806e+00 , 5.34369562943610e+00 , 1.34176277954839e+00 , 2.39661859710098e+00 , 3.00923587723178e+00 , 3.80745750891794e+00 , 2.22552073001822e+00 , 2.69443239824280e+00 , 2.87483587690196e+00 , 3.33768680861078e+00 ) ( -4.34421640334799e-03 , 1.23259510194731e-02 , 1.68090579813687e-02 , 1.89878261610829e-02 , -1.08552901312531e-02 , 5.22942992226076e-03 , 1.22614658996729e-02 , 1.77642609680764e-02 , -1.62733896680575e-02 , -1.18660435429885e-02 , -5.16722789914439e-03 , 4.93281774262076e-03 , -1.32680512200940e-02 , -8.88197829739069e-03 , -6.80664460048118e-03 , -9.80979854271153e-04 ) 3.81791215770808e-01 - 35 ( 3.06898072833861e+00 , 4.51288823770881e+00 , 5.13261897921919e+00 , 6.16794500499526e+00 , 2.50074653237299e+00 , 3.84158061480535e+00 , 4.49879685463616e+00 , 5.34919353390091e+00 , 1.34229502305346e+00 , 2.40928100895182e+00 , 3.00430451680425e+00 , 3.80996140411077e+00 , 2.22360417042348e+00 , 2.70468750491233e+00 , 2.87057086954244e+00 , 3.34320509110129e+00 ) ( -4.44031491071235e-03 , 1.23527234681521e-02 , 1.67689785292895e-02 , 1.89962130882339e-02 , -1.09121854118585e-02 , 5.32120212173631e-03 , 1.22276539257989e-02 , 1.77845576873594e-02 , -1.62769366926278e-02 , -1.17686217470126e-02 , -5.24875745576491e-03 , 4.94273803932348e-03 , -1.32965365848290e-02 , -8.78720894171396e-03 , -6.87713385744937e-03 , -9.30987598810157e-04 ) 3.81835385504166e-01 - 36 ( 3.06273532842122e+00 , 4.51625453668437e+00 , 5.12558687876965e+00 , 6.16711285462378e+00 , 2.49564989962145e+00 , 3.84963128763360e+00 , 4.49551609079525e+00 , 5.35403199606795e+00 , 1.34235952057393e+00 , 2.42319130947787e+00 , 3.00166756440291e+00 , 3.81540250051618e+00 , 2.22209336160822e+00 , 2.71615108200234e+00 , 2.86679976404971e+00 , 3.34863558090078e+00 ) ( -4.54435368066141e-03 , 1.23686804950677e-02 , 1.67284311224198e-02 , 1.90084516119658e-02 , -1.09840196310911e-02 , 5.39437685684171e-03 , 1.21842739531386e-02 , 1.78051583090107e-02 , -1.62833596534709e-02 , -1.16643470067951e-02 , -5.30682059345081e-03 , 4.98516473295461e-03 , -1.33273660427321e-02 , -8.68399148739366e-03 , -6.94692018851069e-03 , -8.86427786439946e-04 ) 3.81936327036083e-01 - 37 ( 3.05649192132167e+00 , 4.51806131059166e+00 , 5.11839243202510e+00 , 6.16649586507377e+00 , 2.48972865327600e+00 , 3.85581806466917e+00 , 4.49128596625538e+00 , 5.35804830483488e+00 , 1.34195825281763e+00 , 2.43768478118170e+00 , 3.00145507450914e+00 , 3.82364960560225e+00 , 2.22109872744306e+00 , 2.72838935969239e+00 , 2.86373525953246e+00 , 3.35394019899047e+00 ) ( -4.65218982014911e-03 , 1.23716418558672e-02 , 1.66890397155335e-02 , 1.90241913089743e-02 , -1.10682357362770e-02 , 5.44373642248271e-03 , 1.21328465988092e-02 , 1.78256268057558e-02 , -1.62925100639911e-02 , -1.15581857866223e-02 , -5.33886828047797e-03 , 5.05955490104775e-03 , -1.33590658100595e-02 , -8.57601333848149e-03 , -7.01254065783080e-03 , -8.46660146239399e-04 ) 3.82093031722223e-01 - 38 ( 3.05045519889590e+00 , 4.51805473611829e+00 , 5.11134114887472e+00 , 6.16609340466301e+00 , 2.48321341701307e+00 , 3.85977678463866e+00 , 4.48635217324219e+00 , 5.36117618444632e+00 , 1.34120085885188e+00 , 2.45209075172033e+00 , 3.00367159434843e+00 , 3.83435311397414e+00 , 2.22068007522442e+00 , 2.74095124971729e+00 , 2.86158715760799e+00 , 3.35910007198241e+00 ) ( -4.76019163320950e-03 , 1.23598714041820e-02 , 1.66524680402616e-02 , 1.90428744709146e-02 , -1.11615338118528e-02 , 5.46602270063782e-03 , 1.20759997181952e-02 , 1.78455990056507e-02 , -1.63041248954833e-02 , -1.14552422088381e-02 , -5.34375549496949e-03 , 5.16264172534908e-03 , -1.33903719338111e-02 , -8.46711508398639e-03 , -7.07047588479804e-03 , -8.10789012685766e-04 ) 3.82300990443223e-01 - 39 ( 3.04477330521684e+00 , 4.51608052262827e+00 , 5.10475536253321e+00 , 6.16587487663191e+00 , 2.47638766200614e+00 , 3.86134206537838e+00 , 4.48108638301749e+00 , 5.36344937417303e+00 , 1.34028312443992e+00 , 2.46576763054109e+00 , 3.00819152091531e+00 , 3.84697007374176e+00 , 2.22084607834437e+00 , 2.75339260865446e+00 , 2.86054956607522e+00 , 3.36411702305049e+00 ) ( -4.86543044142400e-03 , 1.23321843370416e-02 , 1.66202988292410e-02 , 1.90637594104161e-02 , -1.12600574805245e-02 , 5.46010858659612e-03 , 1.20173150916460e-02 , 1.78648032651105e-02 , -1.63178447979581e-02 , -1.13604904210382e-02 , -5.32184447669693e-03 , 5.28870221435157e-03 , -1.34202591847899e-02 , -8.36109247803980e-03 , -7.11733590781375e-03 , -7.77701446405796e-04 ) 3.82552280895823e-01 - 40 ( 3.03953158571266e+00 , 4.51209497787138e+00 , 5.09894673253801e+00 , 6.16578599788259e+00 , 2.46957015768712e+00 , 3.86055335003907e+00 , 4.47595360314062e+00 , 5.36499714872809e+00 , 1.33944926913138e+00 , 2.47813660022930e+00 , 3.01476283614106e+00 , 3.86080601681174e+00 , 2.22155937137345e+00 , 2.76529935955117e+00 , 2.86078736612033e+00 , 3.36901381742548e+00 ) ( -4.96580059531963e-03 , 1.22880424119538e-02 , 1.65938976533907e-02 , 1.90859603276296e-02 , -1.13596279919568e-02 , 5.42702340653616e-03 , 1.19610688381882e-02 , 1.78830800540778e-02 , -1.63332290150278e-02 , -1.12784800774510e-02 , -5.27503313674526e-03 , 5.43003604266082e-03 , -1.34479399632883e-02 , -8.26149951627528e-03 , -7.15005910784782e-03 , -7.46119889758067e-04 ) 3.82835834419373e-01 + 20 ( 3.04650863884945e+00 , 4.49435411437724e+00 , 5.18841527762764e+00 , 6.16645837340779e+00 , 2.49717925480425e+00 , 3.86424836018692e+00 , 4.55750848697779e+00 , 5.34080670765490e+00 , 1.36568581546352e+00 , 2.47047097097987e+00 , 3.12336009885461e+00 , 3.85074280281206e+00 , 2.22178524357949e+00 , 2.73185149414085e+00 , 2.91864419906098e+00 , 3.29101397431997e+00 ) ( -5.02542974750439e-03 , 1.19730728164444e-02 , 1.69673824742426e-02 , 1.90642123537368e-02 , -1.12042672914772e-02 , 5.29965572263668e-03 , 1.25370495916030e-02 , 1.76884949726336e-02 , -1.63470133927038e-02 , -1.14570941759426e-02 , -4.05868153495143e-03 , 5.13846947912402e-03 , -1.35305636185385e-02 , -8.76608365877139e-03 , -6.59544443572543e-03 , -1.91369494935530e-03 ) 3.82208090906906e-01 + 21 ( 3.05358451430521e+00 , 4.49021607894136e+00 , 5.18408103579128e+00 , 6.16725452682985e+00 , 2.49739586887847e+00 , 3.85055803176977e+00 , 4.54707448765203e+00 , 5.33385181877346e+00 , 1.36217943428986e+00 , 2.45839729727885e+00 , 3.12037538162696e+00 , 3.85284349947326e+00 , 2.22398282791541e+00 , 2.72481510484303e+00 , 2.91680739868595e+00 , 3.29080759705819e+00 ) ( -4.89897222229807e-03 , 1.19791313915530e-02 , 1.69742633770421e-02 , 1.90673755260435e-02 , -1.11771991089292e-02 , 5.18394936500707e-03 , 1.24881958008396e-02 , 1.76843138062651e-02 , -1.63494863600467e-02 , -1.15455916046476e-02 , -4.05710100264393e-03 , 5.21127646149069e-03 , -1.34967807334349e-02 , -8.81361359484131e-03 , -6.58240414833905e-03 , -1.87397588842609e-03 ) 3.82415073616570e-01 + 22 ( 3.06080810208345e+00 , 4.48595132812722e+00 , 5.18009807804700e+00 , 6.16843183990917e+00 , 2.49798391786306e+00 , 3.83656952252473e+00 , 4.53705219502262e+00 , 5.32739339769826e+00 , 1.35810535030362e+00 , 2.44491630862121e+00 , 3.11639519256500e+00 , 3.85445062174997e+00 , 2.22645629766064e+00 , 2.71687952037979e+00 , 2.91504287466697e+00 , 3.29119674274122e+00 ) ( -4.76696535200487e-03 , 1.19835479453930e-02 , 1.69807629789190e-02 , 1.90668703403292e-02 , -1.11425894926847e-02 , 5.06534159173061e-03 , 1.24420691523186e-02 , 1.76797272289167e-02 , -1.63491285179391e-02 , -1.16425743073302e-02 , -4.06508397889694e-03 , 5.27951326763638e-03 , -1.34568327363580e-02 , -8.86739837135399e-03 , -6.56503633790696e-03 , -1.82377839347999e-03 ) 3.82568429497945e-01 + 23 ( 3.06790414004814e+00 , 4.48200450135334e+00 , 5.17656382793119e+00 , 6.16980237078029e+00 , 2.49899682565506e+00 , 3.82315020180593e+00 , 4.52789434465689e+00 , 5.32174323381354e+00 , 1.35381897115236e+00 , 2.43073302861496e+00 , 3.11128737638165e+00 , 3.85508563485620e+00 , 2.22898609562760e+00 , 2.70844682598514e+00 , 2.91326470539741e+00 , 3.29220745957774e+00 ) ( -4.63463283228587e-03 , 1.19886381037132e-02 , 1.69863384514790e-02 , 1.90629238539922e-02 , -1.11010960454939e-02 , 4.95233310232833e-03 , 1.24010752251076e-02 , 1.76752321475924e-02 , -1.63460880163246e-02 , -1.17423776630453e-02 , -4.08607045606707e-03 , 5.33543540685033e-03 , -1.34132176179305e-02 , -8.92431330478125e-03 , -6.54597178922480e-03 , -1.76461825305729e-03 ) 3.82664136113375e-01 + 24 ( 3.07456896251547e+00 , 4.47877932788847e+00 , 5.17350292421948e+00 , 6.17118403235812e+00 , 2.50042929771976e+00 , 3.81112677848175e+00 , 4.51996576479011e+00 , 5.31719422129534e+00 , 1.34964937406132e+00 , 2.41659320693017e+00 , 3.10495847674859e+00 , 3.85436854050369e+00 , 2.23134970982392e+00 , 2.69995765863871e+00 , 2.91137078684994e+00 , 3.29385683019661e+00 ) ( -4.50759627415720e-03 , 1.19965650781519e-02 , 1.69902999513099e-02 , 1.90559636458943e-02 , -1.10540221239449e-02 , 4.85322332287748e-03 , 1.23670789588916e-02 , 1.76714640580619e-02 , -1.63406409705032e-02 , -1.18392197113602e-02 , -4.12294937333665e-03 , 5.37265037507770e-03 , -1.33686231655847e-02 , -8.98085589562544e-03 , -6.52804679567177e-03 , -1.69807765323451e-03 ) 3.82701469800512e-01 + 25 ( 3.08049503112063e+00 , 4.47660862669065e+00 , 5.17086621218778e+00 , 6.17241473807144e+00 , 2.50221287184003e+00 , 3.80122270064462e+00 , 4.51351282067087e+00 , 5.31399204919024e+00 , 1.34587887725366e+00 , 2.40324136997555e+00 , 3.09737705599232e+00 , 3.85206778284383e+00 , 2.23334232009805e+00 , 2.69187293445037e+00 , 2.90925556205525e+00 , 3.29614768324761e+00 ) ( -4.39147560687099e-03 , 1.20091384967429e-02 , 1.69918666392056e-02 , 1.90465983705643e-02 , -1.10033293342962e-02 , 4.77538069742523e-03 , 1.23411865313985e-02 , 1.76691155082667e-02 , -1.63331907110018e-02 , -1.19276016500482e-02 , -4.17768182170728e-03 , 5.38679797880718e-03 , -1.33257388623057e-02 , -9.03332249848839e-03 , -6.51408373611267e-03 , -1.62579454590789e-03 ) 3.82683339776474e-01 + 26 ( 3.08539660358762e+00 , 4.47573108499616e+00 , 5.16853739700106e+00 , 6.17336434836052e+00 , 2.50421915077741e+00 , 3.79400439259247e+00 , 4.50864423698743e+00 , 5.31230947973394e+00 , 1.34272952084209e+00 , 2.39138079579576e+00 , 3.08859350101493e+00 , 3.84813653919452e+00 , 2.23479506256020e+00 , 2.68465243778064e+00 , 2.90682401269869e+00 , 3.29906482208583e+00 ) ( -4.29148411013601e-03 , 1.20276418302263e-02 , 1.69902333323270e-02 , 1.90355816605932e-02 , -1.09515770435773e-02 , 4.72457054302800e-03 , 1.23236006618263e-02 , 1.76688416325359e-02 , -1.63242548543774e-02 , -1.20026405094288e-02 , -4.25099682919303e-03 , 5.37602868959405e-03 , -1.32870692584683e-02 , -9.07802146377075e-03 , -6.50666849324502e-03 , -1.54945341877789e-03 ) 3.82616280373843e-01 + 27 ( 3.08903403490314e+00 , 4.47627640362272e+00 , 5.16634667961830e+00 , 6.17394349940788e+00 , 2.50627068489644e+00 , 3.78984102102476e+00 , 4.50532543312949e+00 , 5.31222723709983e+00 , 1.34035363316288e+00 , 2.38163676682551e+00 , 3.07875275681351e+00 , 3.84272979910075e+00 , 2.23558983263006e+00 , 2.67873088548860e+00 , 2.90400432155214e+00 , 3.30257333764965e+00 ) ( -4.21205604684754e-03 , 1.20527080314771e-02 , 1.69846407373501e-02 , 1.90237651417156e-02 , -1.09017840031264e-02 , 4.70442294145814e-03 , 1.23135748673525e-02 , 1.76711728196835e-02 , -1.63144400065064e-02 , -1.20603163377734e-02 , -4.34220656291962e-03 , 5.34122227195625e-03 , -1.32547619866681e-02 , -9.11150666826031e-03 , -6.50795643781969e-03 , -1.47076879862291e-03 ) 3.82510078836494e-01 + 28 ( 3.09123423008446e+00 , 4.47825901549156e+00 , 5.16409003548264e+00 , 6.17410853479198e+00 , 2.50815760716265e+00 , 3.78888026455344e+00 , 4.50338660037037e+00 , 5.31372412214171e+00 , 1.33882620808478e+00 , 2.37452389490195e+00 , 3.06809741626824e+00 , 3.83619894809814e+00 , 2.23566954486208e+00 , 2.67449273808684e+00 , 2.90075730651259e+00 , 3.30661925613651e+00 ) ( -4.15653936805056e-03 , 1.20842556462065e-02 , 1.69744443920294e-02 , 1.90120465097577e-02 , -1.08572245295259e-02 , 4.71610016367071e-03 , 1.23094771128419e-02 , 1.76764515717399e-02 , -1.63044061220960e-02 , -1.20976332878248e-02 , -4.44916678119855e-03 , 5.28592246238156e-03 , -1.32304641411155e-02 , -9.13080846091652e-03 , -6.51952626171290e-03 , -1.39145151742301e-03 ) 3.82377079846062e-01 + 29 ( 3.09190509514426e+00 , 4.48157956515127e+00 , 5.16155211481890e+00 , 6.17386201170314e+00 , 2.50965699808364e+00 , 3.79104075110282e+00 , 4.50254293510334e+00 , 5.31667718843253e+00 , 1.33813889024149e+00 , 2.37041835828804e+00 , 3.05696001593096e+00 , 3.82906376058536e+00 , 2.23504287460586e+00 , 2.67224775251169e+00 , 2.89708163035411e+00 , 3.31113228120092e+00 ) ( -4.12697759527618e-03 , 1.21214889699991e-02 , 1.69591787212609e-02 , 1.90013176216806e-02 , -1.08211849977542e-02 , 4.75819485630298e-03 , 1.23089551811130e-02 , 1.76848031256508e-02 , -1.62948248972696e-02 , -1.21127058757935e-02 , -4.56838460793265e-03 , 5.21600003506868e-03 , -1.32152197152968e-02 , -9.13363622096200e-03 , -6.54228804860898e-03 , -1.31315220707965e-03 ) 3.82231264774811e-01 + 30 ( 3.09104253787141e+00 , 4.48603307941766e+00 , 5.15853060586121e+00 , 6.17324867964149e+00 , 2.51055204409471e+00 , 3.79602095804537e+00 , 4.50242469654790e+00 , 5.32087138951799e+00 , 1.33819822708635e+00 , 2.36953676692819e+00 , 3.04574554895833e+00 , 3.82196513077521e+00 , 2.23378273934522e+00 , 2.67220981841834e+00 , 2.89301507521361e+00 , 3.31603006984730e+00 ) ( -4.12399774225813e-03 , 1.21629569276891e-02 , 1.69386135412590e-02 , 1.89924164868352e-02 , -1.07967128751336e-02 , 4.82686270700478e-03 , 1.23091825418685e-02 , 1.76961399114859e-02 , -1.62863384430780e-02 , -1.21047856613801e-02 , -4.69525042041774e-03 , 5.13908728081744e-03 , -1.32094206833609e-02 , -9.11853167669410e-03 , -6.57644051145824e-03 , -1.23738605942613e-03 ) 3.82087235527624e-01 + 31 ( 3.08872930139670e+00 , 4.49132289037063e+00 , 5.15485959514491e+00 , 6.17234728900319e+00 , 2.51064913021942e+00 , 3.80332415613268e+00 , 4.50261440870123e+00 , 5.32601736328046e+00 , 1.33883231980242e+00 , 2.37192384301024e+00 , 3.03490626643892e+00 , 3.81560419596028e+00 , 2.23201834747819e+00 , 2.67448174853771e+00 , 2.88863286904395e+00 , 3.32122334496031e+00 ) ( -4.14681388778250e-03 , 1.22066593960987e-02 , 1.69127991492826e-02 , 1.89860855651968e-02 , -1.07863857398542e-02 , 4.91617372307837e-03 , 1.23071555307691e-02 , 1.77101930888175e-02 , -1.62795237532260e-02 , -1.20742429271807e-02 , -4.82436126902551e-03 , 5.06384588244620e-03 , -1.32128196431162e-02 , -9.08495907119860e-03 , -6.62146793089459e-03 , -1.16545022393692e-03 ) 3.81959230186222e-01 + 32 ( 3.08512587519288e+00 , 4.49707970117971e+00 , 5.15042982627826e+00 , 6.17125914040548e+00 , 2.50979233884791e+00 , 3.81229855468180e+00 , 4.50268875061413e+00 , 5.33177568529891e+00 , 1.33980944637834e+00 , 2.37745103542636e+00 , 3.02491187433124e+00 , 3.81067490125072e+00 , 2.22992148412604e+00 , 2.67904816544973e+00 , 2.88404450529218e+00 , 3.32662115462332e+00 ) ( -4.19334739610082e-03 , 1.22501856640234e-02 , 1.68820961198294e-02 , 1.89829372733566e-02 , -1.07921188347344e-02 , 5.01864637358304e-03 , 1.23000120215964e-02 , 1.77265599709417e-02 , -1.62748657204962e-02 , -1.20225135605685e-02 , -4.94989686942951e-03 , 4.99914062111286e-03 , -1.32246045798754e-02 , -9.03332860650218e-03 , -6.67616649208281e-03 , -1.09835121417817e-03 ) 3.81860258318432e-01 + 33 ( 3.08045463729672e+00 , 4.50288519704754e+00 , 5.14520390095076e+00 , 6.17009473576804e+00 , 2.50787564727135e+00 , 3.82219055541500e+00 , 4.50226214069664e+00 , 5.33778558393846e+00 , 1.34086920757905e+00 , 2.38582693292515e+00 , 3.01621801902235e+00 , 3.80779720627924e+00 , 2.22768857394173e+00 , 2.68577746719359e+00 , 2.87938997939690e+00 , 3.33213575260088e+00 ) ( -4.26045164162495e-03 , 1.22908700889301e-02 , 1.68471856059909e-02 , 1.89834261003156e-02 , -1.08150192757933e-02 , 5.12591079664833e-03 , 1.22853421663085e-02 , 1.77447558673838e-02 , -1.62727379913271e-02 , -1.19520165161674e-02 , -5.06601412162525e-03 , 4.95319659363923e-03 , -1.32435252234106e-02 , -8.96495735337770e-03 , -6.73869468915883e-03 , -1.03675679717580e-03 ) 3.81801393160747e-01 + 34 ( 3.07497912152090e+00 , 4.50829914516339e+00 , 5.13922512793544e+00 , 6.16896017434785e+00 , 2.50485309388411e+00 , 3.83220702803533e+00 , 4.50102851775461e+00 , 5.34369563021521e+00 , 1.34176277961509e+00 , 2.39661859744123e+00 , 3.00923587756392e+00 , 3.80745750931824e+00 , 2.22552072975963e+00 , 2.69443239804884e+00 , 2.87483587628920e+00 , 3.33768680793807e+00 ) ( -4.34421639088351e-03 , 1.23259510241342e-02 , 1.68090579824887e-02 , 1.89878261554619e-02 , -1.08552901253035e-02 , 5.22942992615502e-03 , 1.22614659002049e-02 , 1.77642609644918e-02 , -1.62733896651479e-02 , -1.18660435400099e-02 , -5.16722789780436e-03 , 4.93281774142251e-03 , -1.32680512214032e-02 , -8.88197830087080e-03 , -6.80664460996510e-03 , -9.80979867201091e-04 ) 3.81791215679719e-01 + 35 ( 3.06898072962898e+00 , 4.51288823912276e+00 , 5.13261898082506e+00 , 6.16794500639919e+00 , 2.50074653307297e+00 , 3.84158061569010e+00 , 4.49879685556613e+00 , 5.34919353467269e+00 , 1.34229502312659e+00 , 2.40928100931996e+00 , 3.00430451716382e+00 , 3.80996140448631e+00 , 2.22360417014956e+00 , 2.70468750472754e+00 , 2.87057086891121e+00 , 3.34320509035869e+00 ) ( -4.44031489768969e-03 , 1.23527234730989e-02 , 1.67689785306207e-02 , 1.89962130825891e-02 , -1.09121854056437e-02 , 5.32120212595859e-03 , 1.22276539265459e-02 , 1.77845576836149e-02 , -1.62769366896918e-02 , -1.17686217438871e-02 , -5.24875745421665e-03 , 4.94273803761624e-03 , -1.32965365863000e-02 , -8.78720894526610e-03 , -6.87713386725385e-03 , -9.30987612841641e-04 ) 3.81835385411921e-01 + 36 ( 3.06273532976632e+00 , 4.51625453815810e+00 , 5.12558688042565e+00 , 6.16711285602853e+00 , 2.49564990035453e+00 , 3.84963128856745e+00 , 4.49551609176305e+00 , 5.35403199682776e+00 , 1.34235952065396e+00 , 2.42319130987960e+00 , 3.00166756478992e+00 , 3.81540250086734e+00 , 2.22209336131761e+00 , 2.71615108183038e+00 , 2.86679976339768e+00 , 3.34863558008665e+00 ) ( -4.54435366709869e-03 , 1.23686805003577e-02 , 1.67284311239753e-02 , 1.90084516063127e-02 , -1.09840196246657e-02 , 5.39437686141032e-03 , 1.21842739540751e-02 , 1.78051583051095e-02 , -1.62833596505170e-02 , -1.16643470034764e-02 , -5.30682059170320e-03 , 4.98516473073789e-03 , -1.33273660443829e-02 , -8.68399149098933e-03 , -6.94692019866868e-03 , -8.86427801594670e-04 ) 3.81936326942932e-01 + 37 ( 3.05649192272016e+00 , 4.51806131212852e+00 , 5.11839243372688e+00 , 6.16649586647833e+00 , 2.48972865403734e+00 , 3.85581806565182e+00 , 4.49128596725413e+00 , 5.35804830557854e+00 , 1.34195825290523e+00 , 2.43768478162201e+00 , 3.00145507492219e+00 , 3.82364960592987e+00 , 2.22109872713473e+00 , 2.72838935953640e+00 , 2.86373525885699e+00 , 3.35394019810392e+00 ) ( -4.65218980605975e-03 , 1.23716418615644e-02 , 1.66890397173181e-02 , 1.90241913033266e-02 , -1.10682357296936e-02 , 5.44373642741758e-03 , 1.21328465998996e-02 , 1.78256268017041e-02 , -1.62925100610275e-02 , -1.15581857830655e-02 , -5.33886827855517e-03 , 5.05955489833097e-03 , -1.33590658119049e-02 , -8.57601334209215e-03 , -7.01254066837880e-03 , -8.46660162526817e-04 ) 3.82093031628418e-01 + 38 ( 3.05045520034663e+00 , 4.51805473772131e+00 , 5.11134115061683e+00 , 6.16609340606711e+00 , 2.48321341779800e+00 , 3.85977678566920e+00 , 4.48635217426398e+00 , 5.36117618517027e+00 , 1.34120085894772e+00 , 2.45209075220292e+00 , 3.00367159478445e+00 , 3.83435311427914e+00 , 2.22068007489778e+00 , 2.74095124957973e+00 , 2.86158715690625e+00 , 3.35910007102331e+00 ) ( -4.76019161860031e-03 , 1.23598714103535e-02 , 1.66524680422709e-02 , 1.90428744652835e-02 , -1.11615338051583e-02 , 5.46602270595950e-03 , 1.20759997193952e-02 , 1.78455990014566e-02 , -1.63041248925182e-02 , -1.14552422050043e-02 , -5.34375549291192e-03 , 5.16264172214884e-03 , -1.33903719358613e-02 , -8.46711508758403e-03 , -7.07047589577285e-03 , -8.10789030101033e-04 ) 3.82300990349005e-01 + 39 ( 3.04477330671893e+00 , 4.51608052429989e+00 , 5.10475536430945e+00 , 6.16587487803593e+00 , 2.47638766281039e+00 , 3.86134206645524e+00 , 4.48108638405379e+00 , 5.36344937487428e+00 , 1.34028312454434e+00 , 2.46576763106795e+00 , 3.00819152136954e+00 , 3.84697007402470e+00 , 2.22084607799930e+00 , 2.75339260853697e+00 , 2.86054956534452e+00 , 3.36411702201955e+00 ) ( -4.86543042629372e-03 , 1.23321843437552e-02 , 1.66202988314624e-02 , 1.90637594048100e-02 , -1.12600574737574e-02 , 5.46010859232420e-03 , 1.20173150929056e-02 , 1.78648032607835e-02 , -1.63178447949989e-02 , -1.13604904168987e-02 , -5.32184447456055e-03 , 5.28870221068816e-03 , -1.34202591870486e-02 , -8.36109248159763e-03 , -7.11733591924846e-03 , -7.77701464928409e-04 ) 3.82552280801419e-01 + 40 ( 3.03953158726547e+00 , 4.51209497961311e+00 , 5.09894673434180e+00 , 6.16578599928733e+00 , 2.46957015850689e+00 , 3.86055335115988e+00 , 4.47595360418285e+00 , 5.36499714940424e+00 , 1.33944926924420e+00 , 2.47813660080028e+00 , 3.01476283660714e+00 , 3.86080601707240e+00 , 2.22155937101033e+00 , 2.76529935945446e+00 , 2.86078736535835e+00 , 3.36901381632414e+00 ) ( -4.96580057965820e-03 , 1.22880424192736e-02 , 1.65938976558053e-02 , 1.90859603220539e-02 , -1.13596279851453e-02 , 5.42702341268680e-03 , 1.19610688394556e-02 , 1.78830800496280e-02 , -1.63332290120811e-02 , -1.12784800729915e-02 , -5.27503313459921e-03 , 5.43003603855418e-03 , -1.34479399657521e-02 , -8.26149951976874e-03 , -7.15005911976767e-03 , -7.46119909351650e-04 ) 3.82835834324984e-01 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat index 83bec1298..ead9fed19 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat @@ -1,10 +1,10 @@ # one p(one ) - 2.00000000000000 0.09106555930578 - 4.00000000000000 0.19841141658836 - 6.00000000000000 0.14791554501384 - 8.00000000000000 0.04585062002305 - 10.00000000000000 0.00473153262406 - 12.00000000000000 0.00011711012676 + 2.00000000000000 0.09106555928620 + 4.00000000000000 0.19841141655022 + 6.00000000000000 0.14791554502557 + 8.00000000000000 0.04585062006277 + 10.00000000000000 0.00473153263289 + 12.00000000000000 0.00011711012711 14.00000000000000 0.00000057531671 16.00000000000000 0.00000000051315 18.00000000000000 0.00000000000008 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt b/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt index 157cac038..655c0f78c 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2019-04-11". +colvars: Using NAMD interface, version "2019-02-12". diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out index 3c82fd483..43bcebeb7 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -113,7 +109,6 @@ colvars: # centers = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 colvars: # targetCenters = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -124,28 +119,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - distancePairs colvar component: -colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped index f4aa065ec..416f80c08 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.04629582292620e+00 , 4.49408974875934e+00 , 5.18802765002996e+00 , 6.16600456423064e+00 , 2.49712681741192e+00 , 3.86413458721172e+00 , 4.55726429580482e+00 , 5.34046966370213e+00 , 1.36572415582545e+00 , 2.47043282429680e+00 , 3.12318599145701e+00 , 3.85046871322657e+00 , 2.22191835525029e+00 , 2.73196623733898e+00 , 2.91861957044130e+00 , 3.29084860719824e+00 ) + x ( 3.04629582333038e+00 , 4.49408974940565e+00 , 5.18802765078345e+00 , 6.16600456517094e+00 , 2.49712681746392e+00 , 3.86413458751360e+00 , 4.55726429607857e+00 , 5.34046966422931e+00 , 1.36572415578523e+00 , 2.47043282453162e+00 , 3.12318599155152e+00 , 3.85046871369096e+00 , 2.22191835508463e+00 , 2.73196623727117e+00 , 2.91861957005182e+00 , 3.29084860717030e+00 ) } restraint { diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj index 6323d1e0e..a7fca080e 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 ( 2.95543971137580e+00 , 4.40149446295507e+00 , 5.19438956774262e+00 , 6.22241603343745e+00 , 2.46985074910253e+00 , 3.82984200895935e+00 , 4.58947829164686e+00 , 5.41000980054028e+00 , 1.34023744154865e+00 , 2.42537620134385e+00 , 3.12639105039661e+00 , 3.90388793384236e+00 , 2.19602098164167e+00 , 2.66815420835178e+00 , 2.96116058328487e+00 , 3.36815290626777e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 1 ( 2.95875682371162e+00 , 4.40108078803336e+00 , 5.19334659297185e+00 , 6.22376901215503e+00 , 2.46917670614475e+00 , 3.82473558076916e+00 , 4.58659203732382e+00 , 5.40932438791137e+00 , 1.33333853625533e+00 , 2.41676042305281e+00 , 3.12170808828270e+00 , 3.90418242702239e+00 , 2.19936646916507e+00 , 2.66448925154634e+00 , 2.96000447713555e+00 , 3.36551061362995e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 2 ( 2.96294067406152e+00 , 4.40226515811672e+00 , 5.19285541585537e+00 , 6.22442847367682e+00 , 2.46935508867047e+00 , 3.82150643041244e+00 , 4.58422435395019e+00 , 5.40817951631011e+00 , 1.32707961473676e+00 , 2.41052202222919e+00 , 3.11822168290825e+00 , 3.90473111479922e+00 , 2.20349997298880e+00 , 2.66304540103662e+00 , 2.95871452980397e+00 , 3.36219422430421e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 3 ( 2.96775064184085e+00 , 4.40516130339314e+00 , 5.19307524760769e+00 , 6.22425430968166e+00 , 2.47031615575903e+00 , 3.82048584858974e+00 , 4.58270515959952e+00 , 5.40667289707967e+00 , 1.32192370925505e+00 , 2.40699266423868e+00 , 3.11597471298471e+00 , 3.90507282356790e+00 , 2.20807442665232e+00 , 2.66384581355879e+00 , 2.95730110419459e+00 , 3.35823523823449e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 4 ( 2.97293010489448e+00 , 4.40978768834604e+00 , 5.19406903504745e+00 , 6.22314788319532e+00 , 2.47196007303898e+00 , 3.82187612852118e+00 , 4.58226353677337e+00 , 5.40491259095799e+00 , 1.31825265737252e+00 , 2.40633740937283e+00 , 3.11490651576023e+00 , 3.90476431055031e+00 , 2.21272370240332e+00 , 2.66680267302744e+00 , 2.95575856583674e+00 , 3.35370432605342e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 5 ( 2.97823333783396e+00 , 4.41606221701169e+00 , 5.19580203466429e+00 , 6.22106315761185e+00 , 2.47416553030952e+00 , 3.82572100741359e+00 , 4.58300378562911e+00 , 5.40299835185958e+00 , 1.31633344994455e+00 , 2.40854582463045e+00 , 3.11487200509147e+00 , 3.90343726008758e+00 , 2.21709388501265e+00 , 2.67171937535336e+00 , 2.95407275180430e+00 , 3.34870361989151e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 6 ( 2.98344814005663e+00 , 4.42380327992932e+00 , 5.19814908068667e+00 , 6.21801314892945e+00 , 2.47679801685308e+00 , 3.83188876567920e+00 , 4.58489251310382e+00 , 5.40100490574002e+00 , 1.31630005545644e+00 , 2.41343716539880e+00 , 3.11566727602137e+00 , 3.90084606609035e+00 , 2.22087489889406e+00 , 2.67830168769063e+00 , 2.95222915709120e+00 , 3.34335752624336e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 7 ( 2.98841232072106e+00 , 4.43273687420576e+00 , 5.20090974393552e+00 , 6.21407143143529e+00 , 2.47971573107076e+00 , 3.84006896947409e+00 , 4.58775771852739e+00 , 5.39896919259108e+00 , 1.31814854765021e+00 , 2.42067606922623e+00 , 3.11705824332351e+00 , 3.89690002579640e+00 , 2.22382854110827e+00 , 2.68617638143507e+00 , 2.95021953237683e+00 , 3.33780297990201e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 8 ( 2.99302343348491e+00 , 4.44250962507488e+00 , 5.20382996321501e+00 , 6.20936877696684e+00 , 2.48277289804373e+00 , 3.84978342367452e+00 , 4.59130044220219e+00 , 5.39688319365273e+00 , 1.32174181286983e+00 , 2.42979485530452e+00 , 3.11880839065580e+00 , 3.89167562003146e+00 , 2.22580927853021e+00 , 2.69491484666178e+00 , 2.94804551645326e+00 , 3.33217989341490e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 9 ( 2.99724215287480e+00 , 4.45270758684489e+00 , 5.20662810056762e+00 , 6.20408528366133e+00 , 2.48582223189515e+00 , 3.86041172947622e+00 , 4.59511907155332e+00 , 5.39469356916339e+00 , 1.32682097127323e+00 , 2.44021975211449e+00 , 3.12070201379211e+00 , 3.88540749218761e+00 , 2.22677520661342e+00 , 2.70405886580578e+00 , 2.94571912737640e+00 , 3.32662241625028e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 10 ( 3.00109029638000e+00 , 4.46288053082589e+00 , 5.20902297728982e+00 , 6.19843864668001e+00 , 2.48871914760541e+00 , 3.87123105738516e+00 , 4.59874530584125e+00 , 5.39230853993896e+00 , 1.33302269909977e+00 , 2.45130012836348e+00 , 3.12256033873081e+00 , 3.87845986428877e+00 , 2.22678798494783e+00 , 2.71314602617717e+00 , 2.94326100435679e+00 , 3.32125154363674e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 11 ( 3.00464453575679e+00 , 4.47257069541065e+00 , 5.21076119622350e+00 , 6.19266941327513e+00 , 2.49132961383712e+00 , 3.88146798326700e+00 , 4.60168898224382e+00 , 5.38961117952632e+00 , 1.33990328897282e+00 , 2.46234094530972e+00 , 3.12424927278714e+00 , 3.87128278198068e+00 , 2.22600197555205e+00 , 2.72173288755659e+00 , 2.94069782604129e+00 , 3.31616954660697e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 12 ( 3.00802660451617e+00 , 4.48134406045834e+00 , 5.21164113869909e+00 , 6.18702434784747e+00 , 2.49354148219010e+00 , 3.89035788109011e+00 , 4.60348694962692e+00 , 5.38647692453335e+00 , 1.34697040081713e+00 , 2.47263868596420e+00 , 3.12567895936259e+00 , 3.86435935191978e+00 , 2.22464401794964e+00 , 2.72941476968443e+00 , 2.93806020626834e+00 , 3.31145665756156e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 13 ( 3.01139044147949e+00 , 4.48882134486514e+00 , 5.21153128214444e+00 , 6.18173913317131e+00 , 2.49527712737531e+00 , 3.89720566621980e+00 , 4.60374994479784e+00 , 5.38279228286598e+00 , 1.35372197423762e+00 , 2.48152014321118e+00 , 3.12679646629567e+00 , 3.85815073741861e+00 , 2.22298622225849e+00 , 2.73584170513545e+00 , 2.93538174082140e+00 , 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6.18173913371892e+00 , 2.49527712738787e+00 , 3.89720566631697e+00 , 4.60374994484304e+00 , 5.38279228320668e+00 , 1.35372197426113e+00 , 2.48152014333316e+00 , 3.12679646629641e+00 , 3.85815073776481e+00 , 2.22298622217618e+00 , 2.73584170506168e+00 , 2.93538174058148e+00 , 3.30717032254531e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 14 ( 3.01490659498393e+00 , 4.49470568819819e+00 , 5.21038109514539e+00 , 6.17702179178737e+00 , 2.49650403390072e+00 , 3.90144127859289e+00 , 4.60220148662660e+00 , 5.37847180935563e+00 , 1.35968942213934e+00 , 2.48838225386361e+00 , 3.12757367670257e+00 , 3.85304523490686e+00 , 2.22131487194857e+00 , 2.74073061696419e+00 , 2.93269901676913e+00 , 3.30334710226797e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 15 ( 3.01874444119857e+00 , 4.49880441908766e+00 , 5.20822364477587e+00 , 6.17303832367595e+00 , 2.49724029422419e+00 , 3.90266451985451e+00 , 4.59870430385402e+00 , 5.37347142047251e+00 , 1.36448009941900e+00 , 2.49273019193462e+00 , 3.12799274187020e+00 , 3.84931652446014e+00 , 2.21989896798406e+00 , 2.74387407746985e+00 , 2.93005166803435e+00 , 3.30000695737880e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 16 ( 3.02305313447408e+00 , 4.50104303470608e+00 , 5.20516981193190e+00 , 6.16990179071024e+00 , 2.49755349805131e+00 , 3.90067603040690e+00 , 4.59327213529618e+00 , 5.36779747466957e+00 , 1.36781305325599e+00 , 2.49421050420414e+00 , 3.12803142014580e+00 , 3.84709461387514e+00 , 2.21896204065284e+00 , 2.74514610274893e+00 , 2.92748124535385e+00 , 3.29715922041988e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 17 ( 3.02794278893498e+00 , 4.50147045589817e+00 , 5.20139488515695e+00 , 6.16766577694110e+00 , 2.49755330822387e+00 , 3.89549330657652e+00 , 4.58606702348901e+00 , 5.36151205347158e+00 , 1.36954253121641e+00 , 2.49263619481708e+00 , 3.12765036949056e+00 , 3.84635143644652e+00 , 2.21866044064897e+00 , 2.74450537655344e+00 , 2.92502790904681e+00 , 3.29480918130467e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 18 ( 3.03346785795678e+00 , 4.50025537469709e+00 , 5.19711906941881e+00 , 6.16632276542483e+00 , 2.49737930806754e+00 , 3.88735195260522e+00 , 4.57738383543644e+00 , 5.35473517728416e+00 , 1.36966557262771e+00 , 2.48800127032887e+00 , 3.12678413131530e+00 , 3.84690184564267e+00 , 2.21907037548788e+00 , 2.74199613753820e+00 , 2.92272466370839e+00 , 3.29296402717016e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 19 ( 3.03961480062799e+00 , 4.49767398572291e+00 , 5.19258399657282e+00 , 6.16580745526214e+00 , 2.49718604910831e+00 , 3.87669270182968e+00 , 4.56762447403876e+00 , 5.34764418843780e+00 , 1.36831274917687e+00 , 2.48048318980352e+00 , 3.12533717889256e+00 , 3.84841979399148e+00 , 2.22018461761734e+00 , 2.73774680015523e+00 , 2.92058985495922e+00 , 3.29163694657683e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 20 ( 3.04629582333038e+00 , 4.49408974940565e+00 , 5.18802765078345e+00 , 6.16600456517094e+00 , 2.49712681746392e+00 , 3.86413458751360e+00 , 4.55726429607857e+00 , 5.34046966422931e+00 , 1.36572415578523e+00 , 2.47043282453162e+00 , 3.12318599155152e+00 , 3.85046871369096e+00 , 2.22191835508463e+00 , 2.73196623727117e+00 , 2.91861957005182e+00 , 3.29084860717030e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out index ffd401600..a84b20ece 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -113,7 +109,6 @@ colvars: # centers = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 colvars: # targetCenters = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -124,33 +119,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - distancePairs colvar component: -colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 3.0463 , 4.49409 , 5.18803 , 6.166 , 2.49713 , 3.86413 , 4.55726 , 5.34047 , 1.36572 , 2.47043 , 3.12319 , 3.85047 , 2.22192 , 2.73197 , 2.91862 , 3.29085 ) colvars: Restarting linear bias "linear1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped index aebc65c59..0d4ecbc07 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.03877998802839e+00 , 4.51126454702547e+00 , 5.09780825674884e+00 , 6.16443491397830e+00 , 2.46931564760306e+00 , 3.86026518189025e+00 , 4.47534635751221e+00 , 5.36404748288555e+00 , 1.33947834845631e+00 , 2.47810087575991e+00 , 3.01439850051918e+00 , 3.86006418847475e+00 , 2.22172886244241e+00 , 2.76552022649790e+00 , 2.86065452181562e+00 , 3.36835466836590e+00 ) + x ( 3.03877998958173e+00 , 4.51126454876777e+00 , 5.09780825855294e+00 , 6.16443491538328e+00 , 2.46931564842291e+00 , 3.86026518301130e+00 , 4.47534635855439e+00 , 5.36404748356174e+00 , 1.33947834856915e+00 , 2.47810087633114e+00 , 3.01439850098518e+00 , 3.86006418873543e+00 , 2.22172886207939e+00 , 2.76552022640159e+00 , 2.86065452105383e+00 , 3.36835466726488e+00 ) } restraint { diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj index fd76bbf8c..305b720d8 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( 3.04629582292620e+00 , 4.49408974875934e+00 , 5.18802765002996e+00 , 6.16600456423064e+00 , 2.49712681741192e+00 , 3.86413458721172e+00 , 4.55726429580482e+00 , 5.34046966370213e+00 , 1.36572415582545e+00 , 2.47043282429680e+00 , 3.12318599145701e+00 , 3.85046871322657e+00 , 2.22191835525029e+00 , 2.73196623733898e+00 , 2.91861957044130e+00 , 3.29084860719824e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 21 ( 3.05334985718046e+00 , 4.48992628670576e+00 , 5.18366022382011e+00 , 6.16676026418638e+00 , 2.49733708339840e+00 , 3.85043471960129e+00 , 4.54681310121844e+00 , 5.33348650495467e+00 , 1.36221538959227e+00 , 2.45835277038889e+00 , 3.12018761704542e+00 , 3.85254424598379e+00 , 2.22412250678503e+00 , 2.72493758209268e+00 , 2.91678212339134e+00 , 3.29062579006844e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 22 ( 3.06055105810745e+00 , 4.48563517046779e+00 , 5.17964329258940e+00 , 6.16789612191897e+00 , 2.49791842471156e+00 , 3.83643598957093e+00 , 4.53677312706362e+00 , 5.32699885023723e+00 , 1.35813975612152e+00 , 2.44486600970885e+00 , 3.11619451803498e+00 , 3.85412638365591e+00 , 2.22660216073093e+00 , 2.71700934103147e+00 , 2.91501666461826e+00 , 3.29099758720831e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 23 ( 3.06762420481496e+00 , 4.48166116738223e+00 , 5.17607431570745e+00 , 6.16922431262149e+00 , 2.49892421159898e+00 , 3.82300581028315e+00 , 4.52759703894498e+00 , 5.32131852844794e+00 , 1.35385283880720e+00 , 2.43067780472622e+00 , 3.11107462093897e+00 , 3.85473675493696e+00 , 2.22913771659230e+00 , 2.70858357698744e+00 , 2.91323709555557e+00 , 3.29199001472266e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 24 ( 3.07426564475834e+00 , 4.47840815394115e+00 , 5.17297796752752e+00 , 6.17056286761805e+00 , 2.50034908316076e+00 , 3.81097097826291e+00 , 4.51964961664415e+00 , 5.31673850301500e+00 , 1.34968380481030e+00 , 2.41653410780135e+00 , 3.10473449529925e+00 , 3.85399547441392e+00 , 2.23150661412188e+00 , 2.70010092754582e+00 , 2.91134113983847e+00 , 3.29362013061070e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 25 ( 3.08016782736078e+00 , 4.47620910758893e+00 , 5.17030513268353e+00 , 6.17174981694759e+00 , 2.50212450409709e+00 , 3.80105506960300e+00 , 4.51317720954952e+00 , 5.31350456313651e+00 , 1.34591496239228e+00 , 2.40317959728505e+00 , 3.09714267643763e+00 , 3.85167104521135e+00 , 2.23350398143146e+00 , 2.69202233139669e+00 , 2.90922309147424e+00 , 3.29589074948067e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 26 ( 3.08504497817861e+00 , 4.47530287579147e+00 , 5.16793956182435e+00 , 6.17265513248033e+00 , 2.50412200519066e+00 , 3.79382467008278e+00 , 4.50828856695274e+00 , 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2.67466266635271e+00 , 2.88856492597046e+00 , 3.32082524099768e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 32 ( 3.08461411209008e+00 , 4.49647886548388e+00 , 5.14960177880497e+00 , 6.17027762501345e+00 , 2.50962807724970e+00 , 3.81205156200233e+00 , 4.50220742027401e+00 , 5.33105788157162e+00 , 1.33986789059222e+00 , 2.37740208979268e+00 , 3.02461835085086e+00 , 3.81012227725223e+00 , 2.23009844786444e+00 , 2.67923396931848e+00 , 2.88396845386184e+00 , 3.32619656829677e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , 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3.07440861054706e+00 , 4.50764161683040e+00 , 5.13831857795142e+00 , 6.16788658960396e+00 , 2.50466286051555e+00 , 3.83194370488657e+00 , 4.50050842111493e+00 , 5.34291473689179e+00 , 1.34182117058319e+00 , 2.39657731516989e+00 , 3.00892592911754e+00 , 3.80686001012132e+00 , 2.22569657326002e+00 , 2.69462787697380e+00 , 2.87474349206004e+00 , 3.33720713207171e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 35 ( 3.06838011632929e+00 , 4.51220236587325e+00 , 5.13167323139895e+00 , 6.16682524357341e+00 , 2.50054351798461e+00 , 3.84131072727126e+00 , 4.49825899074484e+00 , 5.34838227990807e+00 , 1.34235119120459e+00 , 2.40924279160001e+00 , 3.00398601362680e+00 , 3.80934088142898e+00 , 2.22377893299271e+00 , 2.70488772630918e+00 , 2.87047066085061e+00 , 3.34269688882959e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 36 ( 3.06210432358020e+00 , 4.51554021422804e+00 , 5.12460207064167e+00 , 6.16594684234922e+00 , 2.49543460206265e+00 , 3.84935590564575e+00 , 4.49496173687219e+00 , 5.35319126959797e+00 , 1.34241205413193e+00 , 2.42315536076406e+00 , 3.00134026497410e+00 , 3.81475851270793e+00 , 2.22226687720115e+00 , 2.71635592284770e+00 , 2.86669215418132e+00 , 3.34809824847139e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 37 ( 3.05583041579255e+00 , 4.51731835619197e+00 , 5.11736877060765e+00 , 6.16528355530079e+00 , 2.48950184007420e+00 , 3.85553820919296e+00 , 4.49071647008138e+00 , 5.35717902530618e+00 , 1.34200592550321e+00 , 2.43765019178148e+00 , 3.00111875581802e+00 , 3.82298171446182e+00 , 2.22127096949007e+00 , 2.72859863684456e+00 , 2.86362073623295e+00 , 3.35337316792672e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 38 ( 3.04976328673567e+00 , 4.51728290748607e+00 , 5.11027889780887e+00 , 6.16483478581600e+00 , 2.48297610118552e+00 , 3.85949338940809e+00 , 4.48576887839106e+00 , 5.36027926465160e+00 , 1.34124273659856e+00 , 2.45205659120844e+00 , 3.00332606707948e+00 , 3.83366091194011e+00 , 2.22085114879278e+00 , 2.74116471578633e+00 , 2.86146619671611e+00 , 3.35850281090275e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 39 ( 3.04405129241968e+00 , 4.51527953922953e+00 , 5.10365482996787e+00 , 6.16456998222725e+00 , 2.47614106272950e+00 , 3.86105594621195e+00 , 4.48049055445589e+00 , 5.36252568437131e+00 , 1.34031865526981e+00 , 2.46573303996854e+00 , 3.00783663914838e+00 , 3.84625320482145e+00 , 2.22101620382144e+00 , 2.75360995497976e+00 , 2.86042255254939e+00 , 3.36348904078277e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 40 ( 3.03877998958173e+00 , 4.51126454876777e+00 , 5.09780825855294e+00 , 6.16443491538328e+00 , 2.46931564842291e+00 , 3.86026518301130e+00 , 4.47534635855439e+00 , 5.36404748356174e+00 , 1.33947834856915e+00 , 2.47810087633114e+00 , 3.01439850098518e+00 , 3.86006418873543e+00 , 2.22172886207939e+00 , 2.76552022640159e+00 , 2.86065452105383e+00 , 3.36835466726488e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt b/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt index 157cac038..afda7aab6 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-09-12. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out index 8f7a57a73..aecf18686 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -152,7 +148,6 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -163,28 +158,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped index 13ed1c8c9..572603c28 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -1.02062769534156e+00 , -6.08213499811239e-03 , 3.05064351584125e+00 ) + x ( -1.02062769591997e+00 , -6.08213500496868e-03 , 3.05064351583999e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj index 193c60552..8bd23f911 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -1.08926570435186e+00 , 2.48645332384574e-02 , 3.01469929653834e+00 ) ( 4.35706281740742e-03 , -9.94581329538296e-05 , -1.20587971861533e-02 ) - 1 ( -1.08757103024838e+00 , 2.23275217750993e-02 , 3.01408140364127e+00 ) ( 4.35028412099354e-03 , -8.93100871003973e-05 , -1.20563256145651e-02 ) - 2 ( -1.08562847072074e+00 , 2.01398180220937e-02 , 3.01423212069547e+00 ) ( 4.34251388288294e-03 , -8.05592720883750e-05 , -1.20569284827819e-02 ) - 3 ( -1.08340349189933e+00 , 1.83171614296354e-02 , 3.01517854062312e+00 ) ( 4.33361396759732e-03 , -7.32686457185414e-05 , -1.20607141624925e-02 ) - 4 ( -1.08086495647312e+00 , 1.68568842988528e-02 , 3.01690562336607e+00 ) ( 4.32345982589247e-03 , -6.74275371954112e-05 , -1.20676224934643e-02 ) - 5 ( -1.07799014209397e+00 , 1.57362299347954e-02 , 3.01935667906812e+00 ) ( 4.31196056837589e-03 , -6.29449197391816e-05 , -1.20774267162725e-02 ) - 6 ( -1.07476840344796e+00 , 1.49116811703516e-02 , 3.02243644259714e+00 ) ( 4.29907361379183e-03 , -5.96467246814063e-05 , -1.20897457703886e-02 ) - 7 ( -1.07120346036405e+00 , 1.43200030870987e-02 , 3.02601615447875e+00 ) ( 4.28481384145619e-03 , -5.72800123483947e-05 , -1.21040646179150e-02 ) - 8 ( -1.06731460018291e+00 , 1.38814843649557e-02 , 3.02994023634960e+00 ) ( 4.26925840073163e-03 , -5.55259374598229e-05 , -1.21197609453984e-02 ) - 9 ( -1.06313721621703e+00 , 1.35053849628509e-02 , 3.03403440483742e+00 ) ( 4.25254886486811e-03 , -5.40215398514037e-05 , -1.21361376193497e-02 ) - 10 ( -1.05872297659907e+00 , 1.30969846845709e-02 , 3.03811518636264e+00 ) ( 4.23489190639626e-03 , -5.23879387382835e-05 , -1.21524607454506e-02 ) - 11 ( -1.05413959104298e+00 , 1.25651406036256e-02 , 3.04200058103587e+00 ) ( 4.21655836417193e-03 , -5.02605624145023e-05 , -1.21680023241435e-02 ) - 12 ( -1.04946980433283e+00 , 1.18290706904701e-02 , 3.04552119753946e+00 ) ( 4.19787921733132e-03 , -4.73162827618805e-05 , -1.21820847901579e-02 ) - 13 ( -1.04480903884802e+00 , 1.08232102376193e-02 , 3.04853081094912e+00 ) ( 4.17923615539206e-03 , -4.32928409504774e-05 , -1.21941232437965e-02 ) - 14 ( -1.04026127373743e+00 , 9.49942103360235e-03 , 3.05091517276253e+00 ) ( 4.16104509494973e-03 , -3.79976841344094e-05 , -1.22036606910501e-02 ) - 15 ( -1.03593320366363e+00 , 7.82645303080387e-03 , 3.05259815153299e+00 ) ( 4.14373281465451e-03 , -3.13058121232155e-05 , -1.22103926061320e-02 ) - 16 ( -1.03192718274189e+00 , 5.78719768553504e-03 , 3.05354476802529e+00 ) ( 4.12770873096756e-03 , -2.31487907421402e-05 , -1.22141790721012e-02 ) - 17 ( -1.02833380767736e+00 , 3.37481068352563e-03 , 3.05376123022586e+00 ) ( 4.11333523070946e-03 , -1.34992427341025e-05 , -1.22150449209035e-02 ) - 18 ( -1.02522512504349e+00 , 5.89042613610813e-04 , 3.05329243257632e+00 ) ( 4.10090050017395e-03 , -2.35617045444325e-06 , -1.22131697303053e-02 ) - 19 ( -1.02264934622731e+00 , -2.56602061946254e-03 , 3.05221745998716e+00 ) ( 4.09059738490925e-03 , 1.02640824778502e-05 , -1.22088698399486e-02 ) - 20 ( -1.02062769534156e+00 , -6.08213499811239e-03 , 3.05064351584125e+00 ) ( 4.08251078136622e-03 , 2.43285399924496e-05 , -1.22025740633650e-02 ) + 0 ( -1.08926570435185e+00 , 2.48645332384094e-02 , 3.01469929653834e+00 ) ( 4.35706281740739e-03 , -9.94581329536377e-05 , -1.20587971861534e-02 ) + 1 ( -1.08757103024997e+00 , 2.23275217747934e-02 , 3.01408140364135e+00 ) ( 4.35028412099990e-03 , -8.93100870991734e-05 , -1.20563256145654e-02 ) + 2 ( -1.08562847089983e+00 , 2.01398180516252e-02 , 3.01423212068838e+00 ) ( 4.34251388359932e-03 , -8.05592722065010e-05 , -1.20569284827535e-02 ) + 3 ( -1.08340349194734e+00 , 1.83171614284610e-02 , 3.01517854061388e+00 ) ( 4.33361396778937e-03 , -7.32686457138438e-05 , -1.20607141624555e-02 ) + 4 ( -1.08086495662244e+00 , 1.68568843161550e-02 , 3.01690562336324e+00 ) ( 4.32345982648975e-03 , -6.74275372646198e-05 , -1.20676224934530e-02 ) + 5 ( -1.07799014212969e+00 , 1.57362299159951e-02 , 3.01935667906087e+00 ) ( 4.31196056851875e-03 , -6.29449196639804e-05 , -1.20774267162435e-02 ) + 6 ( -1.07476840349588e+00 , 1.49116811517320e-02 , 3.02243644260053e+00 ) ( 4.29907361398352e-03 , -5.96467246069281e-05 , -1.20897457704021e-02 ) + 7 ( -1.07120346043007e+00 , 1.43200030669788e-02 , 3.02601615449288e+00 ) ( 4.28481384172026e-03 , -5.72800122679151e-05 , -1.21040646179715e-02 ) + 8 ( -1.06731460026733e+00 , 1.38814843394630e-02 , 3.02994023637554e+00 ) ( 4.26925840106931e-03 , -5.55259373578521e-05 , -1.21197609455021e-02 ) + 9 ( -1.06313721632696e+00 , 1.35053849341971e-02 , 3.03403440487335e+00 ) ( 4.25254886530783e-03 , -5.40215397367883e-05 , -1.21361376194934e-02 ) + 10 ( -1.05872297673822e+00 , 1.30969846539595e-02 , 3.03811518640717e+00 ) ( 4.23489190695288e-03 , -5.23879386158379e-05 , -1.21524607456287e-02 ) + 11 ( -1.05413959121528e+00 , 1.25651405718566e-02 , 3.04200058108683e+00 ) ( 4.21655836486113e-03 , -5.02605622874266e-05 , -1.21680023243473e-02 ) + 12 ( -1.04946980454194e+00 , 1.18290706584114e-02 , 3.04552119759417e+00 ) ( 4.19787921816777e-03 , -4.73162826336457e-05 , -1.21820847903767e-02 ) + 13 ( -1.04480903909869e+00 , 1.08232101954363e-02 , 3.04853081100414e+00 ) ( 4.17923615639474e-03 , -4.32928407817452e-05 , -1.21941232440166e-02 ) + 14 ( -1.04026127402952e+00 , 9.49942100347867e-03 , 3.05091517281576e+00 ) ( 4.16104509611809e-03 , -3.79976840139147e-05 , -1.22036606912630e-02 ) + 15 ( -1.03593320400088e+00 , 7.82645299533791e-03 , 3.05259815158109e+00 ) ( 4.14373281600352e-03 , -3.13058119813516e-05 , -1.22103926063244e-02 ) + 16 ( -1.03192718312749e+00 , 5.78719766133096e-03 , 3.05354476806524e+00 ) ( 4.12770873250994e-03 , -2.31487906453238e-05 , -1.22141790722609e-02 ) + 17 ( -1.02833380809396e+00 , 3.37481068267376e-03 , 3.05376123026148e+00 ) ( 4.11333523237583e-03 , -1.34992427306950e-05 , -1.22150449210459e-02 ) + 18 ( -1.02522512552484e+00 , 5.89042585372512e-04 , 3.05329243259600e+00 ) ( 4.10090050209936e-03 , -2.35617034149005e-06 , -1.22131697303840e-02 ) + 19 ( -1.02264934677565e+00 , -2.56602063071965e-03 , 3.05221745999499e+00 ) ( 4.09059738710258e-03 , 1.02640825228786e-05 , -1.22088698399800e-02 ) + 20 ( -1.02062769591997e+00 , -6.08213500496868e-03 , 3.05064351583999e+00 ) ( 4.08251078367986e-03 , 2.43285400198747e-05 , -1.22025740633599e-02 ) diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out index cfa942a30..39d87c2b9 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -152,7 +148,6 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -163,33 +158,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -1.02063 , -0.00608213 , 3.05064 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped index fa080941c..57ad6cdde 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -1.00146957910752e+00 , -7.86134846594192e-02 , 3.05294498810129e+00 ) + x ( -1.00146958058144e+00 , -7.86134845943720e-02 , 3.05294498811922e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj index a8901e5cb..411da6154 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -1.02062769534156e+00 , -6.08213499811239e-03 , 3.05064351584125e+00 ) ( 4.08251078136622e-03 , 2.43285399924496e-05 , -1.22025740633650e-02 ) - 21 ( -1.01915362990077e+00 , -9.94509781004160e-03 , 3.04869855746548e+00 ) ( 4.07661451960309e-03 , 3.97803912401664e-05 , -1.21947942298619e-02 ) - 22 ( -1.01819426467457e+00 , -1.41317848486685e-02 , 3.04652291624334e+00 ) ( 4.07277705869829e-03 , 5.65271393946740e-05 , -1.21860916649734e-02 ) - 23 ( -1.01769353572269e+00 , -1.86072293092575e-02 , 3.04426035191247e+00 ) ( 4.07077414289074e-03 , 7.44289172370300e-05 , -1.21770414076499e-02 ) - 24 ( -1.01757652300947e+00 , -2.33228912331954e-02 , 3.04204924926634e+00 ) ( 4.07030609203789e-03 , 9.32915649327817e-05 , -1.21681969970653e-02 ) - 25 ( -1.01775441423944e+00 , -2.82168582658865e-02 , 3.04001482319277e+00 ) ( 4.07101765695776e-03 , 1.12867433063546e-04 , -1.21600592927711e-02 ) - 26 ( -1.01812972547680e+00 , -3.32161441751850e-02 , 3.03826306323336e+00 ) ( 4.07251890190722e-03 , 1.32864576700740e-04 , -1.21530522529335e-02 ) - 27 ( -1.01860146079953e+00 , -3.82407265723690e-02 , 3.03687681895852e+00 ) ( 4.07440584319812e-03 , 1.52962906289476e-04 , -1.21475072758341e-02 ) - 28 ( -1.01906990926088e+00 , -4.32085185509670e-02 , 3.03591402640151e+00 ) ( 4.07627963704352e-03 , 1.72834074203868e-04 , -1.21436561056061e-02 ) - 29 ( -1.01944079088857e+00 , -4.80403043559997e-02 , 3.03540770557330e+00 ) ( 4.07776316355427e-03 , 1.92161217423999e-04 , -1.21416308222932e-02 ) - 30 ( -1.01962854699229e+00 , -5.26637607211525e-02 , 3.03536739031026e+00 ) ( 4.07851418796916e-03 , 2.10655042884610e-04 , -1.21414695612410e-02 ) - 31 ( -1.01955869904214e+00 , -5.70160615819230e-02 , 3.03578166763320e+00 ) ( 4.07823479616858e-03 , 2.28064246327692e-04 , -1.21431266705328e-02 ) - 32 ( -1.01916934949446e+00 , -6.10450112992021e-02 , 3.03662168653196e+00 ) ( 4.07667739797783e-03 , 2.44180045196809e-04 , -1.21464867461279e-02 ) - 33 ( -1.01841199592886e+00 , -6.47090594473295e-02 , 3.03784542784121e+00 ) ( 4.07364798371542e-03 , 2.58836237789318e-04 , -1.21513817113648e-02 ) - 34 ( -1.01725180900141e+00 , -6.79766894059315e-02 , 3.03940247260780e+00 ) ( 4.06900723600566e-03 , 2.71906757623726e-04 , -1.21576098904312e-02 ) - 35 ( -1.01566747325464e+00 , -7.08256323783010e-02 , 3.04123879381492e+00 ) ( 4.06266989301856e-03 , 2.83302529513204e-04 , -1.21649551752597e-02 ) - 36 ( -1.01365053401866e+00 , -7.32422529508256e-02 , 3.04330111209864e+00 ) ( 4.05460213607464e-03 , 2.92969011803303e-04 , -1.21732044483946e-02 ) - 37 ( -1.01120429036970e+00 , -7.52213164514461e-02 , 3.04554044991178e+00 ) ( 4.04481716147881e-03 , 3.00885265805785e-04 , -1.21821617996471e-02 ) - 38 ( -1.00834237984516e+00 , -7.67661955129212e-02 , 3.04791477756569e+00 ) ( 4.03336951938062e-03 , 3.07064782051685e-04 , -1.21916591102628e-02 ) - 39 ( -1.00508734834212e+00 , -7.78894402311651e-02 , 3.05039080321297e+00 ) ( 4.02034939336848e-03 , 3.11557760924660e-04 , -1.22015632128519e-02 ) - 40 ( -1.00146957910752e+00 , -7.86134846594192e-02 , 3.05294498810129e+00 ) ( 4.00587831643010e-03 , 3.14453938637677e-04 , -1.22117799524052e-02 ) + 20 ( -1.02062769591997e+00 , -6.08213500496868e-03 , 3.05064351583999e+00 ) ( 4.08251078367986e-03 , 2.43285400198747e-05 , -1.22025740633599e-02 ) + 21 ( -1.01915363052765e+00 , -9.94509780830111e-03 , 3.04869855745494e+00 ) ( 4.07661452211062e-03 , 3.97803912332044e-05 , -1.21947942298198e-02 ) + 22 ( -1.01819426535002e+00 , -1.41317848404291e-02 , 3.04652291622540e+00 ) ( 4.07277706140009e-03 , 5.65271393617164e-05 , -1.21860916649016e-02 ) + 23 ( -1.01769353644663e+00 , -1.86072292938941e-02 , 3.04426035188961e+00 ) ( 4.07077414578651e-03 , 7.44289171755765e-05 , -1.21770414075584e-02 ) + 24 ( -1.01757652378195e+00 , -2.33228912103368e-02 , 3.04204924924129e+00 ) ( 4.07030609512782e-03 , 9.32915648413473e-05 , -1.21681969969652e-02 ) + 25 ( -1.01775441505923e+00 , -2.82168582418595e-02 , 3.04001482316877e+00 ) ( 4.07101766023693e-03 , 1.12867432967438e-04 , -1.21600592926751e-02 ) + 26 ( -1.01812972634717e+00 , -3.32161441348876e-02 , 3.03826306321224e+00 ) ( 4.07251890538870e-03 , 1.32864576539550e-04 , -1.21530522528490e-02 ) + 27 ( -1.01860146171764e+00 , -3.82407265273962e-02 , 3.03687681894353e+00 ) ( 4.07440584687057e-03 , 1.52962906109585e-04 , -1.21475072757741e-02 ) + 28 ( -1.01906991022665e+00 , -4.32085185057993e-02 , 3.03591402639455e+00 ) ( 4.07627964090659e-03 , 1.72834074023197e-04 , -1.21436561055782e-02 ) + 29 ( -1.01944079190354e+00 , -4.80403042958217e-02 , 3.03540770557534e+00 ) ( 4.07776316761414e-03 , 1.92161217183287e-04 , -1.21416308223013e-02 ) + 30 ( -1.01962854805362e+00 , -5.26637606618744e-02 , 3.03536739032252e+00 ) ( 4.07851419221450e-03 , 2.10655042647498e-04 , -1.21414695612901e-02 ) + 31 ( -1.01955870015183e+00 , -5.70160615084173e-02 , 3.03578166765498e+00 ) ( 4.07823480060733e-03 , 2.28064246033669e-04 , -1.21431266706199e-02 ) + 32 ( -1.01916935065016e+00 , -6.10450112208311e-02 , 3.03662168656281e+00 ) ( 4.07667740260063e-03 , 2.44180044883324e-04 , -1.21464867462512e-02 ) + 33 ( -1.01841199712945e+00 , -6.47090593651689e-02 , 3.03784542787964e+00 ) ( 4.07364798851779e-03 , 2.58836237460676e-04 , -1.21513817115186e-02 ) + 34 ( -1.01725181024562e+00 , -6.79766893212266e-02 , 3.03940247265176e+00 ) ( 4.06900724098247e-03 , 2.71906757284906e-04 , -1.21576098906070e-02 ) + 35 ( -1.01566747454107e+00 , -7.08256322924462e-02 , 3.04123879386186e+00 ) ( 4.06266989816427e-03 , 2.83302529169785e-04 , -1.21649551754474e-02 ) + 36 ( -1.01365053534415e+00 , -7.32422528716987e-02 , 3.04330111214608e+00 ) ( 4.05460214137660e-03 , 2.92969011486795e-04 , -1.21732044485843e-02 ) + 37 ( -1.01120429173592e+00 , -7.52213163683270e-02 , 3.04554044995591e+00 ) ( 4.04481716694370e-03 , 3.00885265473308e-04 , -1.21821617998237e-02 ) + 38 ( -1.00834238124957e+00 , -7.67661954318190e-02 , 3.04791477760370e+00 ) ( 4.03336952499827e-03 , 3.07064781727276e-04 , -1.21916591104148e-02 ) + 39 ( -1.00508734978189e+00 , -7.78894401522693e-02 , 3.05039080324243e+00 ) ( 4.02034939912757e-03 , 3.11557760609077e-04 , -1.22015632129697e-02 ) + 40 ( -1.00146958058144e+00 , -7.86134845943720e-02 , 3.05294498811922e+00 ) ( 4.00587832232574e-03 , 3.14453938377488e-04 , -1.22117799524769e-02 ) diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out index d5a9ba71d..049f980a2 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -117,7 +113,6 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,28 +123,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped index 9da6963c4..4798692a9 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -1.00012595304074e+00 , 6.81665091817865e-01 , 2.98047387612439e+00 ) + x ( -1.00012595362068e+00 , 6.81665091863780e-01 , 2.98047387611607e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj index 0460e926b..2c4dc1d5b 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -1.06103618343284e+00 , 6.89338769329275e-01 , 2.94525790836472e+00 ) ( 4.24414473373135e-03 , -2.75735507731710e-03 , -1.17810316334589e-02 ) - 1 ( -1.05984233192313e+00 , 6.87788139043843e-01 , 2.94477124393299e+00 ) ( 4.23936932769251e-03 , -2.75115255617537e-03 , -1.17790849757320e-02 ) - 2 ( -1.05834139767053e+00 , 6.86747097207406e-01 , 2.94497571748830e+00 ) ( 4.23336559068213e-03 , -2.74698838882962e-03 , -1.17799028699532e-02 ) - 3 ( -1.05650257668221e+00 , 6.86210421251529e-01 , 2.94589847749821e+00 ) ( 4.22601030672886e-03 , -2.74484168500611e-03 , -1.17835939099928e-02 ) - 4 ( -1.05430079770892e+00 , 6.86147780863856e-01 , 2.94752842221134e+00 ) ( 4.21720319083568e-03 , -2.74459112345542e-03 , -1.17901136888454e-02 ) - 5 ( -1.05172167277253e+00 , 6.86504075704956e-01 , 2.94981674140592e+00 ) ( 4.20688669109011e-03 , -2.74601630281983e-03 , -1.17992669656237e-02 ) - 6 ( -1.04876508122907e+00 , 6.87201123721589e-01 , 2.95267979110080e+00 ) ( 4.19506032491627e-03 , -2.74880449488636e-03 , -1.18107191644032e-02 ) - 7 ( -1.04544721826884e+00 , 6.88141185039855e-01 , 2.95600363775429e+00 ) ( 4.18178887307535e-03 , -2.75256474015942e-03 , -1.18240145510172e-02 ) - 8 ( -1.04180123376858e+00 , 6.89212570640885e-01 , 2.95964984567615e+00 ) ( 4.16720493507430e-03 , -2.75685028256354e-03 , -1.18385993827046e-02 ) - 9 ( -1.03787678373610e+00 , 6.90297113537972e-01 , 2.96346243142858e+00 ) ( 4.15150713494440e-03 , -2.76118845415189e-03 , -1.18538497257143e-02 ) - 10 ( -1.03373882399961e+00 , 6.91278691950712e-01 , 2.96727611987909e+00 ) ( 4.13495529599842e-03 , -2.76511476780285e-03 , -1.18691044795164e-02 ) - 11 ( -1.02946582281404e+00 , 6.92051560786413e-01 , 2.97092585771778e+00 ) ( 4.11786329125617e-03 , -2.76820624314565e-03 , -1.18837034308711e-02 ) - 12 ( -1.02514737799452e+00 , 6.92527153631102e-01 , 2.97425707642372e+00 ) ( 4.10058951197807e-03 , -2.77010861452441e-03 , -1.18970283056949e-02 ) - 13 ( -1.02088104335244e+00 , 6.92638311699283e-01 , 2.97713574419012e+00 ) ( 4.08352417340977e-03 , -2.77055324679713e-03 , -1.19085429767605e-02 ) - 14 ( -1.01676819341134e+00 , 6.92340498830537e-01 , 2.97945703485996e+00 ) ( 4.06707277364537e-03 , -2.76936199532215e-03 , -1.19178281394398e-02 ) - 15 ( -1.01290896014230e+00 , 6.91610275878003e-01 , 2.98115162233085e+00 ) ( 4.05163584056920e-03 , -2.76644110351201e-03 , -1.19246064893234e-02 ) - 16 ( -1.00939651098372e+00 , 6.90441852787200e-01 , 2.98218905906499e+00 ) ( 4.03758604393490e-03 , -2.76176741114880e-03 , -1.19287562362600e-02 ) - 17 ( -1.00631118523086e+00 , 6.88842837382683e-01 , 2.98257821430650e+00 ) ( 4.02524474092344e-03 , -2.75537134953073e-03 , -1.19303128572260e-02 ) - 18 ( -1.00371516461503e+00 , 6.86830298535374e-01 , 2.98236510041194e+00 ) ( 4.01486065846013e-03 , -2.74732119414150e-03 , -1.19294604016477e-02 ) - 19 ( -1.00164834841389e+00 , 6.84427986279444e-01 , 2.98162851652728e+00 ) ( 4.00659339365556e-03 , -2.73771194511777e-03 , -1.19265140661091e-02 ) - 20 ( -1.00012595304074e+00 , 6.81665091817865e-01 , 2.98047387612439e+00 ) ( 4.00050381216295e-03 , -2.72666036727146e-03 , -1.19218955044975e-02 ) + 0 ( -1.06103618343284e+00 , 6.89338769329276e-01 , 2.94525790836472e+00 ) ( 4.24414473373135e-03 , -2.75735507731710e-03 , -1.17810316334589e-02 ) + 1 ( -1.05984233192469e+00 , 6.87788139043584e-01 , 2.94477124393315e+00 ) ( 4.23936932769878e-03 , -2.75115255617434e-03 , -1.17790849757326e-02 ) + 2 ( -1.05834139784456e+00 , 6.86747097242960e-01 , 2.94497571747643e+00 ) ( 4.23336559137826e-03 , -2.74698838897184e-03 , -1.17799028699057e-02 ) + 3 ( -1.05650257672870e+00 , 6.86210421249889e-01 , 2.94589847749012e+00 ) ( 4.22601030691479e-03 , -2.74484168499956e-03 , -1.17835939099605e-02 ) + 4 ( -1.05430079785211e+00 , 6.86147780883707e-01 , 2.94752842220746e+00 ) ( 4.21720319140842e-03 , -2.74459112353483e-03 , -1.17901136888298e-02 ) + 5 ( -1.05172167280505e+00 , 6.86504075687213e-01 , 2.94981674140398e+00 ) ( 4.20688669122020e-03 , -2.74601630274885e-03 , -1.17992669656159e-02 ) + 6 ( -1.04876508127498e+00 , 6.87201123703198e-01 , 2.95267979110959e+00 ) ( 4.19506032509991e-03 , -2.74880449481279e-03 , -1.18107191644384e-02 ) + 7 ( -1.04544721833213e+00 , 6.88141185021492e-01 , 2.95600363777447e+00 ) ( 4.18178887332851e-03 , -2.75256474008597e-03 , -1.18240145510979e-02 ) + 8 ( -1.04180123385309e+00 , 6.89212570623204e-01 , 2.95964984570740e+00 ) ( 4.16720493541237e-03 , -2.75685028249282e-03 , -1.18385993828296e-02 ) + 9 ( -1.03787678384604e+00 , 6.90297113521857e-01 , 2.96346243146993e+00 ) ( 4.15150713538415e-03 , -2.76118845408743e-03 , -1.18538497258797e-02 ) + 10 ( -1.03373882413909e+00 , 6.91278691937061e-01 , 2.96727611992879e+00 ) ( 4.13495529655637e-03 , -2.76511476774824e-03 , -1.18691044797152e-02 ) + 11 ( -1.02946582298704e+00 , 6.92051560776091e-01 , 2.97092585777341e+00 ) ( 4.11786329194816e-03 , -2.76820624310436e-03 , -1.18837034310937e-02 ) + 12 ( -1.02514737820470e+00 , 6.92527153624911e-01 , 2.97425707648239e+00 ) ( 4.10058951281881e-03 , -2.77010861449964e-03 , -1.18970283059295e-02 ) + 13 ( -1.02088104360310e+00 , 6.92638311697926e-01 , 2.97713574424865e+00 ) ( 4.08352417441239e-03 , -2.77055324679170e-03 , -1.19085429769946e-02 ) + 14 ( -1.01676819370524e+00 , 6.92340498834602e-01 , 2.97945703491512e+00 ) ( 4.06707277482098e-03 , -2.76936199533841e-03 , -1.19178281396605e-02 ) + 15 ( -1.01290896048165e+00 , 6.91610275887974e-01 , 2.98115162237959e+00 ) ( 4.05163584192661e-03 , -2.76644110355190e-03 , -1.19246064895184e-02 ) + 16 ( -1.00939651136992e+00 , 6.90441852803797e-01 , 2.98218905910471e+00 ) ( 4.03758604547969e-03 , -2.76176741121519e-03 , -1.19287562364189e-02 ) + 17 ( -1.00631118564907e+00 , 6.88842837429205e-01 , 2.98257821433475e+00 ) ( 4.02524474259627e-03 , -2.75537134971682e-03 , -1.19303128573390e-02 ) + 18 ( -1.00371516509773e+00 , 6.86830298565906e-01 , 2.98236510042806e+00 ) ( 4.01486066039091e-03 , -2.74732119426362e-03 , -1.19294604017122e-02 ) + 19 ( -1.00164834896320e+00 , 6.84427986320491e-01 , 2.98162851652942e+00 ) ( 4.00659339585280e-03 , -2.73771194528196e-03 , -1.19265140661177e-02 ) + 20 ( -1.00012595362068e+00 , 6.81665091863780e-01 , 2.98047387611607e+00 ) ( 4.00050381448271e-03 , -2.72666036745512e-03 , -1.19218955044643e-02 ) diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out index 0678a53ba..33501e601 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -117,7 +113,6 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,33 +123,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -1.00013 , 0.681665 , 2.98047 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped index 91a4697ed..a98e88769 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -9.91441714242838e-01 , 6.28848618783027e-01 , 2.99185347905522e+00 ) + x ( -9.91441715714853e-01 , 6.28848618963486e-01 , 2.99185347903944e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj index 620786d60..03b7dd3c1 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -1.00012595304074e+00 , 6.81665091817865e-01 , 2.98047387612439e+00 ) ( 4.00050381216295e-03 , -2.72666036727146e-03 , -1.19218955044975e-02 ) - 21 ( -9.99138074265429e-01 , 6.78576393035151e-01 , 2.97902552992938e+00 ) ( 3.99655229706172e-03 , -2.71430557214061e-03 , -1.19161021197175e-02 ) - 22 ( -9.98651127330001e-01 , 6.75203199213713e-01 , 2.97741796071850e+00 ) ( 3.99460450932001e-03 , -2.70081279685485e-03 , -1.19096718428740e-02 ) - 23 ( -9.98610824984928e-01 , 6.71594275046680e-01 , 2.97578645097527e+00 ) ( 3.99444329993971e-03 , -2.68637710018672e-03 , -1.19031458039011e-02 ) - 24 ( -9.98946203875902e-01 , 6.67806005224566e-01 , 2.97425809128013e+00 ) ( 3.99578481550361e-03 , -2.67122402089826e-03 , -1.18970323651205e-02 ) - 25 ( -9.99574198422540e-01 , 6.63901368074702e-01 , 2.97294412314502e+00 ) ( 3.99829679369016e-03 , -2.65560547229881e-03 , -1.18917764925801e-02 ) - 26 ( -1.00040433097533e+00 , 6.59947725499445e-01 , 2.97193439794950e+00 ) ( 4.00161732390132e-03 , -2.63979090199778e-03 , -1.18877375917980e-02 ) - 27 ( -1.00134314895068e+00 , 6.56013782494476e-01 , 2.97129431693768e+00 ) ( 4.00537259580271e-03 , -2.62405512997790e-03 , -1.18851772677507e-02 ) - 28 ( -1.00229811929707e+00 , 6.52166332519549e-01 , 2.97106411686442e+00 ) ( 4.00919247718828e-03 , -2.60866533007820e-03 , -1.18842564674577e-02 ) - 29 ( -1.00318079719258e+00 , 6.48467421337220e-01 , 2.97125993942505e+00 ) ( 4.01272318877031e-03 , -2.59386968534888e-03 , -1.18850397577002e-02 ) - 30 ( -1.00390921995519e+00 , 6.44972467377165e-01 , 2.97187614716835e+00 ) ( 4.01563687982076e-03 , -2.57988986950866e-03 , -1.18875045886734e-02 ) - 31 ( -1.00440958895174e+00 , 6.41729568214161e-01 , 2.97288843458850e+00 ) ( 4.01763835580695e-03 , -2.56691827285664e-03 , -1.18915537383540e-02 ) - 32 ( -1.00461737929322e+00 , 6.38779886442533e-01 , 2.97425757145681e+00 ) ( 4.01846951717287e-03 , -2.55511954577013e-03 , -1.18970302858273e-02 ) - 33 ( -1.00447804965225e+00 , 6.36158624483086e-01 , 2.97593366047442e+00 ) ( 4.01791219860901e-03 , -2.54463449793234e-03 , -1.19037346418977e-02 ) - 34 ( -1.00394748506057e+00 , 6.33895972784570e-01 , 2.97786077690709e+00 ) ( 4.01578994024229e-03 , -2.53558389113828e-03 , -1.19114431076284e-02 ) - 35 ( -1.00299228402442e+00 , 6.32017486363480e-01 , 2.97998162117694e+00 ) ( 4.01196913609766e-03 , -2.52806994545392e-03 , -1.19199264847078e-02 ) - 36 ( -1.00158988930755e+00 , 6.30543620030167e-01 , 2.98224176225043e+00 ) ( 4.00635955723021e-03 , -2.52217448012067e-03 , -1.19289670490017e-02 ) - 37 ( -9.99728646517214e-01 , 6.29488492386688e-01 , 2.98459308225513e+00 ) ( 3.99891458606886e-03 , -2.51795396954675e-03 , -1.19383723290205e-02 ) - 38 ( -9.97407894168705e-01 , 6.28858255557523e-01 , 2.98699626416501e+00 ) ( 3.98963157667482e-03 , -2.51543302223009e-03 , -1.19479850566600e-02 ) - 39 ( -9.94638187594213e-01 , 6.28649565173414e-01 , 2.98942235139329e+00 ) ( 3.97855275037685e-03 , -2.51459826069366e-03 , -1.19576894055732e-02 ) - 40 ( -9.91441714242838e-01 , 6.28848618783027e-01 , 2.99185347905522e+00 ) ( 3.96576685697135e-03 , -2.51539447513211e-03 , -1.19674139162209e-02 ) + 20 ( -1.00012595362068e+00 , 6.81665091863780e-01 , 2.98047387611607e+00 ) ( 4.00050381448271e-03 , -2.72666036745512e-03 , -1.19218955044643e-02 ) + 21 ( -9.99138074893485e-01 , 6.78576393089195e-01 , 2.97902552991010e+00 ) ( 3.99655229957394e-03 , -2.71430557235678e-03 , -1.19161021196404e-02 ) + 22 ( -9.98651128006031e-01 , 6.75203199276404e-01 , 2.97741796069013e+00 ) ( 3.99460451202413e-03 , -2.70081279710561e-03 , -1.19096718427605e-02 ) + 23 ( -9.98610825708839e-01 , 6.71594275118549e-01 , 2.97578645094022e+00 ) ( 3.99444330283536e-03 , -2.68637710047419e-03 , -1.19031458037609e-02 ) + 24 ( -9.98946204647680e-01 , 6.67806005306121e-01 , 2.97425809124110e+00 ) ( 3.99578481859072e-03 , -2.67122402122448e-03 , -1.18970323649644e-02 ) + 25 ( -9.99574199242226e-01 , 6.63901368166392e-01 , 2.97294412310483e+00 ) ( 3.99829679696891e-03 , -2.65560547266557e-03 , -1.18917764924193e-02 ) + 26 ( -1.00040433184298e+00 , 6.59947725601624e-01 , 2.97193439791086e+00 ) ( 4.00161732737193e-03 , -2.63979090240649e-03 , -1.18877375916435e-02 ) + 27 ( -1.00134314986632e+00 , 6.56013782607379e-01 , 2.97129431690302e+00 ) ( 4.00537259946528e-03 , -2.62405513042951e-03 , -1.18851772676121e-02 ) + 28 ( -1.00229812026062e+00 , 6.52166332643251e-01 , 2.97106411683570e+00 ) ( 4.00919248104249e-03 , -2.60866533057301e-03 , -1.18842564673428e-02 ) + 29 ( -1.00318079820382e+00 , 6.48467421471618e-01 , 2.97125993940365e+00 ) ( 4.01272319281527e-03 , -2.59386968588647e-03 , -1.18850397576146e-02 ) + 30 ( -1.00390922101371e+00 , 6.44972467521952e-01 , 2.97187614715496e+00 ) ( 4.01563688405484e-03 , -2.57988987008781e-03 , -1.18875045886199e-02 ) + 31 ( -1.00440959005691e+00 , 6.41729568368808e-01 , 2.97288843458314e+00 ) ( 4.01763836022764e-03 , -2.56691827347523e-03 , -1.18915537383326e-02 ) + 32 ( -1.00461738044422e+00 , 6.38779886606265e-01 , 2.97425757145878e+00 ) ( 4.01846952177690e-03 , -2.55511954642506e-03 , -1.18970302858351e-02 ) + 33 ( -1.00447805084808e+00 , 6.36158624654867e-01 , 2.97593366048238e+00 ) ( 4.01791220339232e-03 , -2.54463449861947e-03 , -1.19037346419295e-02 ) + 34 ( -1.00394748630005e+00 , 6.33895972963095e-01 , 2.97786077691918e+00 ) ( 4.01578994520019e-03 , -2.53558389185238e-03 , -1.19114431076767e-02 ) + 35 ( -1.00299228530624e+00 , 6.32017486547197e-01 , 2.97998162119086e+00 ) ( 4.01196914122495e-03 , -2.52806994618879e-03 , -1.19199264847635e-02 ) + 36 ( -1.00158989063031e+00 , 6.30543620217316e-01 , 2.98224176226361e+00 ) ( 4.00635956252122e-03 , -2.52217448086926e-03 , -1.19289670490544e-02 ) + 37 ( -9.99728647879413e-01 , 6.29488492575348e-01 , 2.98459308226489e+00 ) ( 3.99891459151765e-03 , -2.51795397030139e-03 , -1.19383723290595e-02 ) + 38 ( -9.97407895568871e-01 , 6.28858255745633e-01 , 2.98699626416867e+00 ) ( 3.98963158227548e-03 , -2.51543302298253e-03 , -1.19479850566747e-02 ) + 39 ( -9.94638189030939e-01 , 6.28649565358814e-01 , 2.98942235138835e+00 ) ( 3.97855275612376e-03 , -2.51459826143525e-03 , -1.19576894055534e-02 ) + 40 ( -9.91441715714853e-01 , 6.28848618963486e-01 , 2.99185347903944e+00 ) ( 3.96576686285941e-03 , -2.51539447585394e-03 , -1.19674139161578e-02 ) diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out index c28a9ea83..402d5433b 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: Reading legacy options lowerWall and lowerWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). colvars: # lowerWall = 0.1 colvars: Reading legacy options upperWall and upperWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). @@ -117,7 +113,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -131,7 +126,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -147,27 +141,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped index c116ac47b..e53a1f4de 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491521323e+00 + x 3.21685491539556e+00 } restraint { diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj index d5d525eb6..222aa6880 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095402e+00 -1.20174855638161e-02 - 2 3.20383991841948e+00 -1.20153596736779e-02 - 3 3.20396638982490e+00 -1.20158655592996e-02 - 4 3.20472672277551e+00 -1.20189068911021e-02 - 5 3.20606083670179e+00 -1.20242433468072e-02 - 6 3.20787669543948e+00 -1.20315067817579e-02 - 7 3.21005568755800e+00 -1.20402227502320e-02 - 8 3.21245908142754e+00 -1.20498363257101e-02 - 9 3.21493559049101e+00 -1.20597423619640e-02 - 10 3.21733015640955e+00 -1.20693206256382e-02 - 11 3.21949374123820e+00 -1.20779749649528e-02 - 12 3.22129339461899e+00 -1.20851735784760e-02 - 13 3.22262143319445e+00 -1.20904857327778e-02 - 14 3.22340249773966e+00 -1.20936099909586e-02 - 15 3.22359762729192e+00 -1.20943905091677e-02 - 16 3.22320508654863e+00 -1.20928203461945e-02 - 17 3.22225829334495e+00 -1.20890331733798e-02 - 18 3.22082156074746e+00 -1.20832862429898e-02 - 19 3.21898439787187e+00 -1.20759375914875e-02 - 20 3.21685491521323e+00 -1.20674196608529e-02 +# step one fa_one + 0 3.20554673468334e+00 -1.20221869387334e-02 + 1 3.20437139095464e+00 -1.20174855638185e-02 + 2 3.20383991847368e+00 -1.20153596738947e-02 + 3 3.20396638983244e+00 -1.20158655593298e-02 + 4 3.20472672282330e+00 -1.20189068912932e-02 + 5 3.20606083670688e+00 -1.20242433468275e-02 + 6 3.20787669545864e+00 -1.20315067818346e-02 + 7 3.21005568759325e+00 -1.20402227503730e-02 + 8 3.21245908147994e+00 -1.20498363259198e-02 + 9 3.21493559056115e+00 -1.20597423622446e-02 + 10 3.21733015649727e+00 -1.20693206259891e-02 + 11 3.21949374134263e+00 -1.20779749653705e-02 + 12 3.22129339473872e+00 -1.20851735789549e-02 + 13 3.22262143332763e+00 -1.20904857333105e-02 + 14 3.22340249788422e+00 -1.20936099915369e-02 + 15 3.22359762744577e+00 -1.20943905097831e-02 + 16 3.22320508670988e+00 -1.20928203468395e-02 + 17 3.22225829351165e+00 -1.20890331740466e-02 + 18 3.22082156091933e+00 -1.20832862436773e-02 + 19 3.21898439805351e+00 -1.20759375922140e-02 + 20 3.21685491539556e+00 -1.20674196615823e-02 diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out index 2607e31b0..2340e1d34 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: Reading legacy options lowerWall and lowerWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). colvars: # lowerWall = 0.1 colvars: Reading legacy options upperWall and upperWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). @@ -117,7 +113,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -131,7 +126,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -147,32 +141,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "onew" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped index 1b9898933..c542b2a71 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397364200070e+00 + x 3.21397364247543e+00 } restraint { diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj index 8b5e494a7..1b5a859eb 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 3.21685491521323e+00 -1.20674196608529e-02 - 21 3.21455264073267e+00 -1.20582105629307e-02 - 22 3.21220094103318e+00 -1.20488037641327e-02 - 23 3.20991934284523e+00 -1.20396773713809e-02 - 24 3.20781628562398e+00 -1.20312651424959e-02 - 25 3.20598302292944e+00 -1.20239320917178e-02 - 26 3.20448930614687e+00 -1.20179572245875e-02 - 27 3.20338117886792e+00 -1.20135247154717e-02 - 28 3.20268080933861e+00 -1.20107232373544e-02 - 29 3.20238791142161e+00 -1.20095516456865e-02 - 30 3.20248233467135e+00 -1.20099293386854e-02 - 31 3.20292744714189e+00 -1.20117097885676e-02 - 32 3.20367415705454e+00 -1.20146966282182e-02 - 33 3.20466539988114e+00 -1.20186615995246e-02 - 34 3.20584087581816e+00 -1.20233635032726e-02 - 35 3.20714161837695e+00 -1.20285664735078e-02 - 36 3.20851394921166e+00 -1.20340557968466e-02 - 37 3.20991249801338e+00 -1.20396499920535e-02 - 38 3.21130224431234e+00 -1.20452089772494e-02 - 39 3.21265973069097e+00 -1.20506389227639e-02 - 40 3.21397364200070e+00 -1.20558945680028e-02 +# step one fa_one + 20 3.21685491539556e+00 -1.20674196615823e-02 + 21 3.21455264092142e+00 -1.20582105636857e-02 + 22 3.21220094123025e+00 -1.20488037649210e-02 + 23 3.20991934305299e+00 -1.20396773722120e-02 + 24 3.20781628584511e+00 -1.20312651433804e-02 + 25 3.20598302316673e+00 -1.20239320926669e-02 + 26 3.20448930640296e+00 -1.20179572256119e-02 + 27 3.20338117914512e+00 -1.20135247165805e-02 + 28 3.20268080963872e+00 -1.20107232385549e-02 + 29 3.20238791174576e+00 -1.20095516469830e-02 + 30 3.20248233501992e+00 -1.20099293400797e-02 + 31 3.20292744751448e+00 -1.20117097900579e-02 + 32 3.20367415744996e+00 -1.20146966297998e-02 + 33 3.20466540029747e+00 -1.20186616011899e-02 + 34 3.20584087625286e+00 -1.20233635050114e-02 + 35 3.20714161882697e+00 -1.20285664753079e-02 + 36 3.20851394967362e+00 -1.20340557986945e-02 + 37 3.20991249848372e+00 -1.20396499939349e-02 + 38 3.21130224478748e+00 -1.20452089791499e-02 + 39 3.21265973116748e+00 -1.20506389246699e-02 + 40 3.21397364247543e+00 -1.20558945699017e-02 diff --git a/namd/tests/library/000_distancewalls-compatible/namd-version.txt b/namd/tests/library/000_distancewalls-compatible/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancewalls-compatible/namd-version.txt +++ b/namd/tests/library/000_distancewalls-compatible/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out index 5da428bfa..104a466ca 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -132,27 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped index a0bbaca3d..ed4ff587f 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491521323e+00 + x 3.21685491541898e+00 } restraint { diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj index d5d525eb6..222aa6880 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095402e+00 -1.20174855638161e-02 - 2 3.20383991841948e+00 -1.20153596736779e-02 - 3 3.20396638982490e+00 -1.20158655592996e-02 - 4 3.20472672277551e+00 -1.20189068911021e-02 - 5 3.20606083670179e+00 -1.20242433468072e-02 - 6 3.20787669543948e+00 -1.20315067817579e-02 - 7 3.21005568755800e+00 -1.20402227502320e-02 - 8 3.21245908142754e+00 -1.20498363257101e-02 - 9 3.21493559049101e+00 -1.20597423619640e-02 - 10 3.21733015640955e+00 -1.20693206256382e-02 - 11 3.21949374123820e+00 -1.20779749649528e-02 - 12 3.22129339461899e+00 -1.20851735784760e-02 - 13 3.22262143319445e+00 -1.20904857327778e-02 - 14 3.22340249773966e+00 -1.20936099909586e-02 - 15 3.22359762729192e+00 -1.20943905091677e-02 - 16 3.22320508654863e+00 -1.20928203461945e-02 - 17 3.22225829334495e+00 -1.20890331733798e-02 - 18 3.22082156074746e+00 -1.20832862429898e-02 - 19 3.21898439787187e+00 -1.20759375914875e-02 - 20 3.21685491521323e+00 -1.20674196608529e-02 +# step one fa_one + 0 3.20554673468334e+00 -1.20221869387334e-02 + 1 3.20437139095464e+00 -1.20174855638185e-02 + 2 3.20383991847368e+00 -1.20153596738947e-02 + 3 3.20396638983244e+00 -1.20158655593298e-02 + 4 3.20472672282330e+00 -1.20189068912932e-02 + 5 3.20606083670688e+00 -1.20242433468275e-02 + 6 3.20787669545864e+00 -1.20315067818346e-02 + 7 3.21005568759325e+00 -1.20402227503730e-02 + 8 3.21245908147994e+00 -1.20498363259198e-02 + 9 3.21493559056115e+00 -1.20597423622446e-02 + 10 3.21733015649727e+00 -1.20693206259891e-02 + 11 3.21949374134263e+00 -1.20779749653705e-02 + 12 3.22129339473872e+00 -1.20851735789549e-02 + 13 3.22262143332763e+00 -1.20904857333105e-02 + 14 3.22340249788422e+00 -1.20936099915369e-02 + 15 3.22359762744577e+00 -1.20943905097831e-02 + 16 3.22320508670988e+00 -1.20928203468395e-02 + 17 3.22225829351165e+00 -1.20890331740466e-02 + 18 3.22082156091933e+00 -1.20832862436773e-02 + 19 3.21898439805351e+00 -1.20759375922140e-02 + 20 3.21685491539556e+00 -1.20674196615823e-02 diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out index abfe2c323..442f83cc6 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -132,32 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped index 24da413b3..6869425e6 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21397364200070e+00 + x 3.21397364247543e+00 } diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj index 8b5e494a7..744ca6324 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 3.21685491521323e+00 -1.20674196608529e-02 - 21 3.21455264073267e+00 -1.20582105629307e-02 - 22 3.21220094103318e+00 -1.20488037641327e-02 - 23 3.20991934284523e+00 -1.20396773713809e-02 - 24 3.20781628562398e+00 -1.20312651424959e-02 - 25 3.20598302292944e+00 -1.20239320917178e-02 - 26 3.20448930614687e+00 -1.20179572245875e-02 - 27 3.20338117886792e+00 -1.20135247154717e-02 - 28 3.20268080933861e+00 -1.20107232373544e-02 - 29 3.20238791142161e+00 -1.20095516456865e-02 - 30 3.20248233467135e+00 -1.20099293386854e-02 - 31 3.20292744714189e+00 -1.20117097885676e-02 - 32 3.20367415705454e+00 -1.20146966282182e-02 - 33 3.20466539988114e+00 -1.20186615995246e-02 - 34 3.20584087581816e+00 -1.20233635032726e-02 - 35 3.20714161837695e+00 -1.20285664735078e-02 - 36 3.20851394921166e+00 -1.20340557968466e-02 - 37 3.20991249801338e+00 -1.20396499920535e-02 - 38 3.21130224431234e+00 -1.20452089772494e-02 - 39 3.21265973069097e+00 -1.20506389227639e-02 - 40 3.21397364200070e+00 -1.20558945680028e-02 +# step one fa_one + 20 3.21685491539556e+00 -1.20674196615823e-02 + 21 3.21455264092142e+00 -1.20582105636857e-02 + 22 3.21220094123025e+00 -1.20488037649210e-02 + 23 3.20991934305299e+00 -1.20396773722120e-02 + 24 3.20781628584511e+00 -1.20312651433804e-02 + 25 3.20598302316673e+00 -1.20239320926669e-02 + 26 3.20448930640296e+00 -1.20179572256119e-02 + 27 3.20338117914513e+00 -1.20135247165805e-02 + 28 3.20268080963872e+00 -1.20107232385549e-02 + 29 3.20238791174576e+00 -1.20095516469830e-02 + 30 3.20248233501992e+00 -1.20099293400797e-02 + 31 3.20292744751448e+00 -1.20117097900579e-02 + 32 3.20367415744996e+00 -1.20146966297998e-02 + 33 3.20466540029747e+00 -1.20186616011899e-02 + 34 3.20584087625286e+00 -1.20233635050114e-02 + 35 3.20714161882697e+00 -1.20285664753079e-02 + 36 3.20851394967362e+00 -1.20340557986945e-02 + 37 3.20991249848372e+00 -1.20396499939349e-02 + 38 3.21130224478748e+00 -1.20452089791499e-02 + 39 3.21265973116748e+00 -1.20506389246699e-02 + 40 3.21397364247543e+00 -1.20558945699017e-02 diff --git a/namd/tests/library/000_distancewalls/namd-version.txt b/namd/tests/library/000_distancewalls/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancewalls/namd-version.txt +++ b/namd/tests/library/000_distancewalls/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out index 77591e0dc..6050e7b8b 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -93,7 +89,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,28 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceXY colvar component (derived from distanceZ): -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped index c8670d81f..e4b21622a 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.10714243532007e+00 + x 6.10714243551413e+00 } restraint { diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj index 53d38880d..f720fa8df 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 6.28105056411478e+00 -2.47242022564591e-02 - 1 6.27348215345428e+00 -2.46939286138171e-02 - 2 6.26560937402036e+00 -2.46624374960814e-02 - 3 6.25746867772245e+00 -2.46298747108898e-02 - 4 6.24910164328359e+00 -2.45964065731343e-02 - 5 6.24055013191846e+00 -2.45622005276738e-02 - 6 6.23185200432364e+00 -2.45274080172946e-02 - 7 6.22303839583394e+00 -2.44921535833358e-02 - 8 6.21413319108828e+00 -2.44565327643531e-02 - 9 6.20515473551492e+00 -2.44206189420597e-02 - 10 6.19611912777932e+00 -2.43844765111173e-02 - 11 6.18704379217786e+00 -2.43481751687115e-02 - 12 6.17794986550634e+00 -2.43117994620254e-02 - 13 6.16886233368985e+00 -2.42754493347594e-02 - 14 6.15980779734801e+00 -2.42392311893920e-02 - 15 6.15081082211236e+00 -2.42032432884494e-02 - 16 6.14189045972150e+00 -2.41675618388860e-02 - 17 6.13305851983281e+00 -2.41322340793312e-02 - 18 6.12432058994875e+00 -2.40972823597950e-02 - 19 6.11567981072365e+00 -2.40627192428946e-02 - 20 6.10714243532007e+00 -2.40285697412803e-02 + 1 6.27348215345519e+00 -2.46939286138208e-02 + 2 6.26560937402416e+00 -2.46624374960966e-02 + 3 6.25746867772978e+00 -2.46298747109191e-02 + 4 6.24910164339331e+00 -2.45964065735732e-02 + 5 6.24055013199026e+00 -2.45622005279610e-02 + 6 6.23185200440414e+00 -2.45274080176166e-02 + 7 6.22303839597047e+00 -2.44921535838819e-02 + 8 6.21413319113433e+00 -2.44565327645373e-02 + 9 6.20515473557225e+00 -2.44206189422890e-02 + 10 6.19611912784920e+00 -2.43844765113968e-02 + 11 6.18704379226119e+00 -2.43481751690448e-02 + 12 6.17794986560366e+00 -2.43117994624146e-02 + 13 6.16886233380139e+00 -2.42754493352055e-02 + 14 6.15980779747392e+00 -2.42392311898957e-02 + 15 6.15081082225229e+00 -2.42032432890092e-02 + 16 6.14189045993828e+00 -2.41675618397531e-02 + 17 6.13305851999790e+00 -2.41322340799916e-02 + 18 6.12432059012462e+00 -2.40972823604985e-02 + 19 6.11567981090937e+00 -2.40627192436375e-02 + 20 6.10714243551413e+00 -2.40285697420565e-02 diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out index 075f0e20f..41e804f09 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -93,7 +89,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,33 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceXY colvar component (derived from distanceZ): -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 6.10714 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 4c3a90cc1..7dee8d34e 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.98331278916950e+00 + x 5.98331278931269e+00 } restraint { diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 911bdd5e5..32bba6125 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 6.10714243532007e+00 -2.40285697412803e-02 - 21 6.09872341342112e+00 -2.39948936536845e-02 - 22 6.09045001143359e+00 -2.39618000457344e-02 - 23 6.08236193472670e+00 -2.39294477389068e-02 - 24 6.07450749039471e+00 -2.38980299615788e-02 - 25 6.06693661268103e+00 -2.38677464507241e-02 - 26 6.05969250620041e+00 -2.38387700248016e-02 - 27 6.05280395335489e+00 -2.38112158134196e-02 - 28 6.04628004883300e+00 -2.37851201953320e-02 - 29 6.04010849181403e+00 -2.37604339672561e-02 - 30 6.03425782309445e+00 -2.37370312923778e-02 - 31 6.02868299608911e+00 -2.37147319843564e-02 - 32 6.02333268352863e+00 -2.36933307341145e-02 - 33 6.01815611215759e+00 -2.36726244486304e-02 - 34 6.01310736859049e+00 -2.36524294743619e-02 - 35 6.00814619516367e+00 -2.36325847806547e-02 - 36 6.00323573477869e+00 -2.36129429391148e-02 - 37 5.99833888974827e+00 -2.35933555589931e-02 - 38 5.99341543880525e+00 -2.35736617552210e-02 - 39 5.98842160564732e+00 -2.35536864225893e-02 - 40 5.98331278916950e+00 -2.35332511566780e-02 + 20 6.10714243551413e+00 -2.40285697420565e-02 + 21 6.09872341362206e+00 -2.39948936544883e-02 + 22 6.09045001163983e+00 -2.39618000465593e-02 + 23 6.08236193493661e+00 -2.39294477397464e-02 + 24 6.07450749060677e+00 -2.38980299624271e-02 + 25 6.06693661289397e+00 -2.38677464515759e-02 + 26 6.05969250641318e+00 -2.38387700256527e-02 + 27 6.05280395356655e+00 -2.38112158142662e-02 + 28 6.04628004904281e+00 -2.37851201961713e-02 + 29 6.04010849202162e+00 -2.37604339680865e-02 + 30 6.03425782329929e+00 -2.37370312931972e-02 + 31 6.02868299629071e+00 -2.37147319851628e-02 + 32 6.02333268372630e+00 -2.36933307349052e-02 + 33 6.01815611235053e+00 -2.36726244494021e-02 + 34 6.01310736877805e+00 -2.36524294751122e-02 + 35 6.00814619534536e+00 -2.36325847813815e-02 + 36 6.00323573491681e+00 -2.36129429396672e-02 + 37 5.99833888991827e+00 -2.35933555596731e-02 + 38 5.99341543896732e+00 -2.35736617558693e-02 + 39 5.98842160580047e+00 -2.35536864232019e-02 + 40 5.98331278931269e+00 -2.35332511572508e-02 diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 2c3cfb574..47628ecd0 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -128,7 +124,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -156,7 +152,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -167,27 +162,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 72f369787..176efa019 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -8.59990180563031e-01 + x -8.59990198173114e-01 } restraint { diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 4c2bf9e40..70fa4a67c 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 -8.26433309912956e-01 3.70573323965182e-03 - 1 -8.30798422481479e-01 3.72319368992592e-03 - 2 -8.34843463278505e-01 3.73937385311402e-03 - 3 -8.38485394485613e-01 3.75394157794245e-03 - 4 -8.41661116098088e-01 3.76664446439235e-03 - 5 -8.44330033670842e-01 3.77732013468337e-03 - 6 -8.46475937017231e-01 3.78590374806892e-03 - 7 -8.48108706693449e-01 3.79243482677379e-03 - 8 -8.49265839004939e-01 3.79706335601975e-03 - 9 -8.50013078434704e-01 3.80005231373882e-03 - 10 -8.50442876788669e-01 3.80177150715468e-03 - 11 -8.50669506981126e-01 3.80267802792450e-03 - 12 -8.50820419731476e-01 3.80328167892590e-03 - 13 -8.51024556129912e-01 3.80409822451965e-03 - 14 -8.51399343953497e-01 3.80559737581399e-03 - 15 -8.52038548534679e-01 3.80815419413872e-03 - 16 -8.53002864518614e-01 3.81201145807446e-03 - 17 -8.54314489576230e-01 3.81725795830492e-03 - 18 -8.55956217377252e-01 3.82382486950901e-03 - 19 -8.57875090444802e-01 3.83150036177921e-03 - 20 -8.59990180563031e-01 3.83996072225212e-03 + 0 -8.26433309912938e-01 3.70573323965175e-03 + 1 -8.30798422653703e-01 3.72319369061481e-03 + 2 -8.34843463959367e-01 3.73937385583747e-03 + 3 -8.38485395966467e-01 3.75394158386587e-03 + 4 -8.41661118716793e-01 3.76664447486717e-03 + 5 -8.44330037532375e-01 3.77732015012950e-03 + 6 -8.46475942328684e-01 3.78590376931474e-03 + 7 -8.48108713604438e-01 3.79243485441775e-03 + 8 -8.49265847455379e-01 3.79706338982152e-03 + 9 -8.50013088506371e-01 3.80005235402549e-03 + 10 -8.50442888427590e-01 3.80177155371036e-03 + 11 -8.50669520082139e-01 3.80267808032856e-03 + 12 -8.50820434143500e-01 3.80328173657400e-03 + 13 -8.51024571667568e-01 3.80409828667027e-03 + 14 -8.51399360397394e-01 3.80559744158957e-03 + 15 -8.52038565660105e-01 3.80815426264042e-03 + 16 -8.53002882142410e-01 3.81201152856964e-03 + 17 -8.54314507410905e-01 3.81725802964362e-03 + 18 -8.55956235278788e-01 3.82382494111515e-03 + 19 -8.57875108259331e-01 3.83150043303732e-03 + 20 -8.59990198173114e-01 3.83996079269246e-03 diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index c538704bb..f5cc9bea4 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -128,7 +124,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -156,7 +152,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -167,32 +162,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -0.85999 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index e14a8519c..45102536d 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -8.73679341988515e-01 + x -8.73679344015558e-01 } restraint { diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 196573273..3deea24fd 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -8.59990180563031e-01 3.83996072225212e-03 - 21 -8.62203454907955e-01 3.84881381963182e-03 - 22 -8.64411966660376e-01 3.85764786664150e-03 - 23 -8.66519183472681e-01 3.86607673389073e-03 - 24 -8.68443525944736e-01 3.87377410377894e-03 - 25 -8.70123145503911e-01 3.88049258201564e-03 - 26 -8.71517297801704e-01 3.88606919120682e-03 - 27 -8.72605590311192e-01 3.89042236124477e-03 - 28 -8.73386584894720e-01 3.89354633957888e-03 - 29 -8.73876656083864e-01 3.89550662433546e-03 - 30 -8.74108973746083e-01 3.89643589498433e-03 - 31 -8.74131737353112e-01 3.89652694941245e-03 - 32 -8.74004671163881e-01 3.89601868465552e-03 - 33 -8.73793440724393e-01 3.89517376289757e-03 - 34 -8.73562583048199e-01 3.89425033219280e-03 - 35 -8.73368244828915e-01 3.89347297931566e-03 - 36 -8.73251943874718e-01 3.89300777549887e-03 - 37 -8.73236008871937e-01 3.89294403548775e-03 - 38 -8.73320778720346e-01 3.89328311488138e-03 - 39 -8.73483517910175e-01 3.89393407164070e-03 - 40 -8.73679341988515e-01 3.89471736795406e-03 + 20 -8.59990198173114e-01 3.83996079269246e-03 + 21 -8.62203472237901e-01 3.84881388895160e-03 + 22 -8.64411983661211e-01 3.85764793464484e-03 + 23 -8.66519200121738e-01 3.86607680048695e-03 + 24 -8.68443542236674e-01 3.87377416894670e-03 + 25 -8.70123161439966e-01 3.88049264575987e-03 + 26 -8.71517313394698e-01 3.88606925357879e-03 + 27 -8.72605605560332e-01 3.89042242224133e-03 + 28 -8.73386599791250e-01 3.89354639916500e-03 + 29 -8.73876670619764e-01 3.89550668247906e-03 + 30 -8.74108987877203e-01 3.89643595150881e-03 + 31 -8.74131751029475e-01 3.89652700411790e-03 + 32 -8.74004684295612e-01 3.89601873718245e-03 + 33 -8.73793453194366e-01 3.89517381277746e-03 + 34 -8.73562594705087e-01 3.89425037882035e-03 + 35 -8.73368255487214e-01 3.89347302194886e-03 + 36 -8.73251953225498e-01 3.89300781290199e-03 + 37 -8.73236016855329e-01 3.89294406742132e-03 + 38 -8.73320784989416e-01 3.89328313995766e-03 + 39 -8.73483522192930e-01 3.89393408877172e-03 + 40 -8.73679344015558e-01 3.89471737606223e-03 diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out index 2e51c81a1..f979e078c 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -93,7 +89,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,27 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 743d82299..315e08bfa 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.36084906819583e+00 + x -1.36084906835146e+00 } restraint { diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj index 04f28cf76..5a45e7f71 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 -1.30811322832419e+00 5.63245291329675e-03 - 1 -1.31312967389517e+00 5.65251869558068e-03 - 2 -1.31783653970327e+00 5.67134615881307e-03 - 3 -1.32215424605829e+00 5.68861698423318e-03 - 4 -1.32602357036953e+00 5.70409428147812e-03 - 5 -1.32940837597080e+00 5.71763350388318e-03 - 6 -1.33229787218032e+00 5.72919148872128e-03 - 7 -1.33470872947835e+00 5.73883491791339e-03 - 8 -1.33668672329647e+00 5.74674689318588e-03 - 9 -1.33830687027260e+00 5.75322748109041e-03 - 10 -1.33967061044650e+00 5.75868244178601e-03 - 11 -1.34089899817730e+00 5.76359599270922e-03 - 12 -1.34212195003997e+00 5.76848780015989e-03 - 13 -1.34346488791768e+00 5.77385955167074e-03 - 14 -1.34503502472400e+00 5.78014009889602e-03 - 15 -1.34690966827500e+00 5.78763867309998e-03 - 16 -1.34912827121975e+00 5.79651308487899e-03 - 17 -1.35168908892136e+00 5.80675635568542e-03 - 18 -1.35455056705533e+00 5.81820226822131e-03 - 19 -1.35763717560197e+00 5.83054870240789e-03 - 20 -1.36084906819583e+00 5.84339627278333e-03 + 1 -1.31312967389554e+00 5.65251869558218e-03 + 2 -1.31783653970528e+00 5.67134615882111e-03 + 3 -1.32215424606121e+00 5.68861698424484e-03 + 4 -1.32602357044897e+00 5.70409428179589e-03 + 5 -1.32940837601300e+00 5.71763350405199e-03 + 6 -1.33229787222417e+00 5.72919148889668e-03 + 7 -1.33470872956429e+00 5.73883491825714e-03 + 8 -1.33668672330288e+00 5.74674689321152e-03 + 9 -1.33830687028298e+00 5.75322748113191e-03 + 10 -1.33967061046305e+00 5.75868244185221e-03 + 11 -1.34089899820229e+00 5.76359599280915e-03 + 12 -1.34212195007558e+00 5.76848780030233e-03 + 13 -1.34346488796592e+00 5.77385955186369e-03 + 14 -1.34503502478640e+00 5.78014009914560e-03 + 15 -1.34690966835284e+00 5.78763867341137e-03 + 16 -1.34912827135129e+00 5.79651308540518e-03 + 17 -1.35168908903116e+00 5.80675635612465e-03 + 18 -1.35455056718115e+00 5.81820226872460e-03 + 19 -1.35763717574320e+00 5.83054870297280e-03 + 20 -1.36084906835146e+00 5.84339627340585e-03 diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out index a23ca29bd..485b39b01 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -93,7 +89,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,32 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.36085 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 136c16382..412aeb991 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.39034316039439e+00 + x -1.39034316080283e+00 } restraint { diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj index a4c9b3a4c..befbe002b 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -1.36084906819583e+00 5.84339627278333e-03 - 21 -1.36407445392026e+00 5.85629781568104e-03 - 22 -1.36720290808304e+00 5.86881163233218e-03 - 23 -1.37013738742009e+00 5.88054954968036e-03 - 24 -1.37280289903525e+00 5.89121159614099e-03 - 25 -1.37515071153241e+00 5.90060284612964e-03 - 26 -1.37715842575073e+00 5.90863370300290e-03 - 27 -1.37882731750845e+00 5.91530927003381e-03 - 28 -1.38017874358088e+00 5.92071497432353e-03 - 29 -1.38125089771898e+00 5.92500359087591e-03 - 30 -1.38209611844487e+00 5.92838447377948e-03 - 31 -1.38277799970331e+00 5.93111199881324e-03 - 32 -1.38336718471100e+00 5.93346873884401e-03 - 33 -1.38393522958249e+00 5.93574091832994e-03 - 34 -1.38454693837034e+00 5.93818775348136e-03 - 35 -1.38525254040143e+00 5.94101016160571e-03 - 36 -1.38608129795618e+00 5.94432519182472e-03 - 37 -1.38703765719641e+00 5.94815062878565e-03 - 38 -1.38810029482091e+00 5.95240117928366e-03 - 39 -1.38922386299017e+00 5.95689545196067e-03 - 40 -1.39034316039439e+00 5.96137264157755e-03 + 20 -1.36084906835146e+00 5.84339627340585e-03 + 21 -1.36407445408937e+00 5.85629781635750e-03 + 22 -1.36720290826447e+00 5.86881163305788e-03 + 23 -1.37013738761253e+00 5.88054955045011e-03 + 24 -1.37280289923745e+00 5.89121159694979e-03 + 25 -1.37515071174335e+00 5.90060284697339e-03 + 26 -1.37715842596968e+00 5.90863370387872e-03 + 27 -1.37882731773524e+00 5.91530927094096e-03 + 28 -1.38017874381549e+00 5.92071497526196e-03 + 29 -1.38125089796176e+00 5.92500359184703e-03 + 30 -1.38209611869660e+00 5.92838447478640e-03 + 31 -1.38277799996508e+00 5.93111199986032e-03 + 32 -1.38336718498411e+00 5.93346873993646e-03 + 33 -1.38393522986837e+00 5.93574091947349e-03 + 34 -1.38454693867054e+00 5.93818775468217e-03 + 35 -1.38525254071746e+00 5.94101016286982e-03 + 36 -1.38608129820739e+00 5.94432519282957e-03 + 37 -1.38703765754614e+00 5.94815063018456e-03 + 38 -1.38810029519008e+00 5.95240118076033e-03 + 39 -1.38922386337907e+00 5.95689545351630e-03 + 40 -1.39034316080283e+00 5.96137264321130e-03 diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index c0a1e5523..6a560e3a5 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -122,25 +118,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "ref" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "ref2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -158,7 +154,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -186,7 +182,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -197,27 +192,16 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index d5eed6ce9..2e49c4c9e 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.08397176151429e+00 + x -1.08397176799240e+00 } restraint { diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index f93b97049..65f7e07c6 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 -9.80249904624397e-01 4.32099961849759e-03 - 1 -9.84212417024538e-01 4.33684966809815e-03 - 2 -9.88661109713663e-01 4.35464443885465e-03 - 3 -9.93533514317858e-01 4.37413405727143e-03 - 4 -9.98748276916619e-01 4.39499310766648e-03 - 5 -1.00421405294110e+00 4.41685621176441e-03 - 6 -1.00983863113832e+00 4.43935452455326e-03 - 7 -1.01553670456534e+00 4.46214681826137e-03 - 8 -1.02123525373971e+00 4.48494101495885e-03 - 9 -1.02687633616795e+00 4.50750534467179e-03 - 10 -1.03241787163978e+00 4.52967148655913e-03 - 11 -1.03783351061600e+00 4.55133404246400e-03 - 12 -1.04311256849593e+00 4.57245027398371e-03 - 13 -1.04826043601893e+00 4.59304174407571e-03 - 14 -1.05329903171149e+00 4.61319612684598e-03 - 15 -1.05826630299168e+00 4.63306521196671e-03 - 16 -1.06321375752698e+00 4.65285503010794e-03 - 17 -1.06820149508569e+00 4.67280598034278e-03 - 18 -1.07329085286143e+00 4.69316341144574e-03 - 19 -1.07853543510507e+00 4.71414174042029e-03 - 20 -1.08397176151429e+00 4.73588704605716e-03 + 1 -9.84212417045979e-01 4.33684966818392e-03 + 2 -9.88661109800629e-01 4.35464443920252e-03 + 3 -9.93533514516252e-01 4.37413405806501e-03 + 4 -9.98748277164812e-01 4.39499310865925e-03 + 5 -1.00421405344078e+00 4.41685621376314e-03 + 6 -1.00983863188372e+00 4.43935452753490e-03 + 7 -1.01553670554762e+00 4.46214682219049e-03 + 8 -1.02123525515648e+00 4.48494102062594e-03 + 9 -1.02687633794460e+00 4.50750535177839e-03 + 10 -1.03241787380232e+00 4.52967149520928e-03 + 11 -1.03783351318359e+00 4.55133405273438e-03 + 12 -1.04311257148085e+00 4.57245028592339e-03 + 13 -1.04826043942746e+00 4.59304175770984e-03 + 14 -1.05329903554539e+00 4.61319614218156e-03 + 15 -1.05826630725091e+00 4.63306522900363e-03 + 16 -1.06321376214922e+00 4.65285504859689e-03 + 17 -1.06820150020073e+00 4.67280600080292e-03 + 18 -1.07329085842513e+00 4.69316343370051e-03 + 19 -1.07853544110981e+00 4.71414176443922e-03 + 20 -1.08397176799240e+00 4.73588707196959e-03 diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index 061d003d9..ba5525f63 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -122,25 +118,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "ref" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "ref2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -158,7 +154,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -186,7 +182,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -197,32 +192,21 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.08397 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index fe4b2733e..d4af65402 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.16407036445456e+00 + x -1.16407038814966e+00 } restraint { diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index e130970be..6b3544c2b 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -1.08397176151429e+00 4.73588704605716e-03 - 21 -1.08961113878614e+00 4.75844455514457e-03 - 22 -1.09543448080392e+00 4.78173792321566e-03 - 23 -1.10139152374815e+00 4.80556609499262e-03 - 24 -1.10740502102334e+00 4.82962008409337e-03 - 25 -1.11337932023318e+00 4.85351728093272e-03 - 26 -1.11921161432554e+00 4.87684645730215e-03 - 27 -1.12480356375684e+00 4.89921425502736e-03 - 28 -1.13007105240499e+00 4.92028420961995e-03 - 29 -1.13495045141868e+00 4.93980180567474e-03 - 30 -1.13940077305703e+00 4.95760309222813e-03 - 31 -1.14340231104241e+00 4.97360924416963e-03 - 32 -1.14695342368223e+00 4.98781369472891e-03 - 33 -1.15006758434473e+00 5.00027033737893e-03 - 34 -1.15277234867027e+00 5.01108939468107e-03 - 35 -1.15511060843172e+00 5.02044243372689e-03 - 36 -1.15714306128669e+00 5.02857224514677e-03 - 37 -1.15894998077622e+00 5.03579992310487e-03 - 38 -1.16063037878806e+00 5.04252151515225e-03 - 39 -1.16229745749708e+00 5.04918982998831e-03 - 40 -1.16407036445456e+00 5.05628145781825e-03 + 20 -1.08397176799240e+00 4.73588707196959e-03 + 21 -1.08961114576828e+00 4.75844458307313e-03 + 22 -1.09543448832272e+00 4.78173795329088e-03 + 23 -1.10139153184823e+00 4.80556612739293e-03 + 24 -1.10740502975272e+00 4.82962011901087e-03 + 25 -1.11337932964347e+00 4.85351731857390e-03 + 26 -1.11921162447008e+00 4.87684649788032e-03 + 27 -1.12480357468871e+00 4.89921429875483e-03 + 28 -1.13007106417501e+00 4.92028425670005e-03 + 29 -1.13495046407338e+00 4.93980185629353e-03 + 30 -1.13940078663755e+00 4.95760314655019e-03 + 31 -1.14340232558319e+00 4.97360930233275e-03 + 32 -1.14695343921062e+00 4.98781375684249e-03 + 33 -1.15006760088067e+00 5.00027040352269e-03 + 34 -1.15277236622642e+00 5.01108946490570e-03 + 35 -1.15511062701432e+00 5.02044250805728e-03 + 36 -1.15714308092986e+00 5.02857232371945e-03 + 37 -1.15895000141084e+00 5.03580000564338e-03 + 38 -1.16063040046971e+00 5.04252160187884e-03 + 39 -1.16229748017487e+00 5.04918992069947e-03 + 40 -1.16407038814966e+00 5.05628155259863e-03 diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out index 39a4e5160..d0a584bcb 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,123 +1,104 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). colvars: # smp = on [default] +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 +colvars: # colvarsTrajAppend = off [default] colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] +colvars: # scriptingAfterBiases = on [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" colvars: Initializing a new "eigenvector" component. -colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. +colvars: Atom group "atoms" defined, 10 atoms initialized: total mass = 120.11, total charge = 0.53. colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_refpos2.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( -0.0422 , 0.1463 , 0.0241 ) colvars: # differenceVector = on -colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = x_vec - x_ref. -colvars: # normalizeVector = off [default] -colvars: Normalizing the vector so that the norm of the projection |v â‹… (x_vec - x_ref)| = 1. +colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = v - x0. +colvars: "differenceVector" is on: normalizing the vector. colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerWallConstant = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] +colvars: # timeStepFactor = 1 [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = on colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] -colvars: # outputFreq = 10 [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] +colvars: # forceConstant = 0.001 colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] +colvars: # targetForceConstant = 0 [default] colvars: # outputCenters = off [default] -colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] -colvars: # targetForceConstant = -1 [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -126,32 +107,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - eigenvector colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group one:0/0. 10 atoms: total mass = 120.11. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Writing to colvar trajectory file "test.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Writing the state file "test.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.tmp.colvars.state". -colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Writing the state file "test.tmp.colvars.state". colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 394993cd3..76e206e36 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -3.60947829036805e-02 + x -3.60947829208825e-02 } restraint { diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj index 9598d462c..4a835eab3 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 -3.63490056109624e-02 5.45396022443850e-04 - 1 -3.61854039791530e-02 5.44741615916612e-04 - 2 -3.60399977705685e-02 5.44159991082274e-04 - 3 -3.59299659182762e-02 5.43719863673105e-04 - 4 -3.58694335566139e-02 5.43477734226456e-04 - 5 -3.58677543994292e-02 5.43471017597717e-04 - 6 -3.59283042400466e-02 5.43713216960186e-04 - 7 -3.60479478822797e-02 5.44191791529119e-04 - 8 -3.62172258806581e-02 5.44868903522632e-04 - 9 -3.64212097862254e-02 5.45684839144902e-04 - 10 -3.66409048748858e-02 5.46563619499543e-04 - 11 -3.68550253056277e-02 5.47420101222511e-04 - 12 -3.70419376830354e-02 5.48167750732142e-04 - 13 -3.71815653192522e-02 5.48726261277009e-04 - 14 -3.72570812792000e-02 5.49028325116800e-04 - 15 -3.72562760818578e-02 5.49025104327431e-04 - 16 -3.71725450680349e-02 5.48690180272139e-04 - 17 -3.70054820445949e-02 5.48021928178380e-04 - 18 -3.67610840776074e-02 5.47044336310430e-04 - 19 -3.64515682403436e-02 5.45806272961374e-04 - 20 -3.60947829036805e-02 5.44379131614722e-04 + 0 -3.63490056109622e-02 5.45396022443849e-04 + 1 -3.61854039791939e-02 5.44741615916776e-04 + 2 -3.60399977707408e-02 5.44159991082963e-04 + 3 -3.59299659186929e-02 5.43719863674771e-04 + 4 -3.58694335574107e-02 5.43477734229643e-04 + 5 -3.58677544007612e-02 5.43471017603045e-04 + 6 -3.59283042420775e-02 5.43713216968310e-04 + 7 -3.60479478851721e-02 5.44191791540688e-04 + 8 -3.62172258845634e-02 5.44868903538253e-04 + 9 -3.64212097912740e-02 5.45684839165096e-04 + 10 -3.66409048811813e-02 5.46563619524725e-04 + 11 -3.68550253132438e-02 5.47420101252975e-04 + 12 -3.70419376920114e-02 5.48167750768046e-04 + 13 -3.71815653295922e-02 5.48726261318369e-04 + 14 -3.72570812908718e-02 5.49028325163487e-04 + 15 -3.72562760947929e-02 5.49025104379172e-04 + 16 -3.71725450821299e-02 5.48690180328520e-04 + 17 -3.70054820597152e-02 5.48021928238861e-04 + 18 -3.67610840935948e-02 5.47044336374379e-04 + 19 -3.64515682570253e-02 5.45806273028101e-04 + 20 -3.60947829208825e-02 5.44379131683530e-04 diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out index dbec86827..2ea9819fd 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,123 +1,104 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). colvars: # smp = on [default] +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 +colvars: # colvarsTrajAppend = off [default] colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] +colvars: # scriptingAfterBiases = on [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" colvars: Initializing a new "eigenvector" component. -colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. +colvars: Atom group "atoms" defined, 10 atoms initialized: total mass = 120.11, total charge = 0.53. colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_refpos2.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( -0.0422 , 0.1463 , 0.0241 ) colvars: # differenceVector = on -colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = x_vec - x_ref. -colvars: # normalizeVector = off [default] -colvars: Normalizing the vector so that the norm of the projection |v â‹… (x_vec - x_ref)| = 1. +colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = v - x0. +colvars: "differenceVector" is on: normalizing the vector. colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerWallConstant = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] +colvars: # timeStepFactor = 1 [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = on colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] -colvars: # outputFreq = 10 [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] +colvars: # forceConstant = 0.001 colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] +colvars: # targetForceConstant = 0 [default] colvars: # outputCenters = off [default] -colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] -colvars: # targetForceConstant = -1 [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -126,37 +107,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - eigenvector colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -0.0360948 -colvars: Restarting harmonic bias "harmonic1" from step number 20. +colvars: Restarting restraint bias "harmonic1". colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group one:0/0. 10 atoms: total mass = 120.11. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Writing to colvar trajectory file "test.restart.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Writing the state file "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "test.restart.tmp.colvars.state". -colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "test.restart.tmp.colvars.state". +colvars: Writing the state file "test.restart.tmp.colvars.state". colvars: Saving collective variables state to "test.restart.colvars.state". diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 4076dc85b..1fe5f317a 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -3.91331067677280e-02 + x -3.91331067913926e-02 } restraint { diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 4d83b139d..4abf779ac 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -3.60947829036805e-02 5.44379131614722e-04 - 21 -3.57131824132596e-02 5.42852729653038e-04 - 22 -3.53323468161238e-02 5.41329387264495e-04 - 23 -3.49790898711468e-02 5.39916359484587e-04 - 24 -3.46792960881774e-02 5.38717184352710e-04 - 25 -3.44557301955042e-02 5.37822920782017e-04 - 26 -3.43261260186189e-02 5.37304504074476e-04 - 27 -3.43018371648415e-02 5.37207348659366e-04 - 28 -3.43872193023786e-02 5.37548877209514e-04 - 29 -3.45797526537476e-02 5.38319010614990e-04 - 30 -3.48707654110141e-02 5.39483061644056e-04 - 31 -3.52465332512768e-02 5.40986133005107e-04 - 32 -3.56895209286986e-02 5.42758083714794e-04 - 33 -3.61795835030006e-02 5.44718334012002e-04 - 34 -3.66950290848698e-02 5.46780116339479e-04 - 35 -3.72135323147184e-02 5.48854129258874e-04 - 36 -3.77129610291621e-02 5.50851844116648e-04 - 37 -3.81722113079504e-02 5.52688845231802e-04 - 38 -3.85721257419771e-02 5.54288502967908e-04 - 39 -3.88965020615558e-02 5.55586008246223e-04 - 40 -3.91331067677280e-02 5.56532427070912e-04 + 20 -3.60947829208825e-02 5.44379131683530e-04 + 21 -3.57131824308181e-02 5.42852729723272e-04 + 22 -3.53323468338979e-02 5.41329387335592e-04 + 23 -3.49790898890280e-02 5.39916359556112e-04 + 24 -3.46792961060943e-02 5.38717184424377e-04 + 25 -3.44557302134239e-02 5.37822920853696e-04 + 26 -3.43261260365440e-02 5.37304504146176e-04 + 27 -3.43018371828071e-02 5.37207348731229e-04 + 28 -3.43872193204467e-02 5.37548877281787e-04 + 29 -3.45797526720018e-02 5.38319010688007e-04 + 30 -3.48707654295545e-02 5.39483061718218e-04 + 31 -3.52465332702127e-02 5.40986133080851e-04 + 32 -3.56895209481391e-02 5.42758083792556e-04 + 33 -3.61795835230441e-02 5.44718334092176e-04 + 34 -3.66950291055903e-02 5.46780116422361e-04 + 35 -3.72135323361536e-02 5.48854129344615e-04 + 36 -3.77129610513006e-02 5.50851844205202e-04 + 37 -3.81722113307229e-02 5.52688845322892e-04 + 38 -3.85721257652529e-02 5.54288503061011e-04 + 39 -3.88965020851454e-02 5.55586008340582e-04 + 40 -3.91331067913926e-02 5.56532427165571e-04 diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt index 157cac038..fc4f9e327 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. +colvars: Using NAMD interface, version 2016-11-23. diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out index 49596f239..4e6b96f89 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -115,7 +116,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -140,12 +140,10 @@ colvars: colvars: - NAMD engine: colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 496bf49f0..b33e34fce 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.24500295778074e-01 + x 4.24500295670889e-01 } restraint { diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj index 70125860e..7342a9653 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 3.02535061282782e-01 -8.10140245131129e-04 - 1 3.02349470333834e-01 -8.09397881335335e-04 - 2 3.02228609121183e-01 -8.08914436484731e-04 - 3 3.02455495419550e-01 -8.09821981678201e-04 - 4 3.03339070528187e-01 -8.13356282112746e-04 - 5 3.05186413718739e-01 -8.20745654874956e-04 - 6 3.08272259775151e-01 -8.33089039100606e-04 - 7 3.12808407688626e-01 -8.51233630754504e-04 - 8 3.18915879048982e-01 -8.75663516195929e-04 - 9 3.26602899382103e-01 -9.06411597528411e-04 - 10 3.35751830583773e-01 -9.43007322335093e-04 - 11 3.46117928882162e-01 -9.84471715528649e-04 - 12 3.57341831565545e-01 -1.02936732626218e-03 - 13 3.68975854299315e-01 -1.07590341719726e-03 - 14 3.80521732691115e-01 -1.12208693076446e-03 - 15 3.91475201717795e-01 -1.16590080687118e-03 - 16 4.01371580289910e-01 -1.20548632115964e-03 - 17 4.09826708750263e-01 -1.23930683500105e-03 - 18 4.16568902011881e-01 -1.26627560804752e-03 - 19 4.21459383117517e-01 -1.28583753247007e-03 - 20 4.24500295778074e-01 -1.29800118311230e-03 + 0 3.02535061282783e-01 -8.10140245131131e-04 + 1 3.02349470333696e-01 -8.09397881334783e-04 + 2 3.02228609120613e-01 -8.08914436482450e-04 + 3 3.02455495418290e-01 -8.09821981673159e-04 + 4 3.03339070526050e-01 -8.13356282104201e-04 + 5 3.05186413715613e-01 -8.20745654862452e-04 + 6 3.08272259770955e-01 -8.33089039083821e-04 + 7 3.12808407683237e-01 -8.51233630732947e-04 + 8 3.18915879042108e-01 -8.75663516168431e-04 + 9 3.26602899373167e-01 -9.06411597492667e-04 + 10 3.35751830571806e-01 -9.43007322287224e-04 + 11 3.46117928865759e-01 -9.84471715463035e-04 + 12 3.57341831542918e-01 -1.02936732617167e-03 + 13 3.68975854268464e-01 -1.07590341707386e-03 + 14 3.80521732650089e-01 -1.12208693060036e-03 + 15 3.91475201665008e-01 -1.16590080666003e-03 + 16 4.01371580224434e-01 -1.20548632089774e-03 + 17 4.09826708672045e-01 -1.23930683468818e-03 + 18 4.16568901921835e-01 -1.26627560768734e-03 + 19 4.21459383017533e-01 -1.28583753207013e-03 + 20 4.24500295670889e-01 -1.29800118268356e-03 diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out index 61612ef51..db684e80d 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -115,7 +116,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -140,7 +140,6 @@ colvars: colvars: - NAMD engine: colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.4245 @@ -150,7 +149,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index f4f671fdc..d9441d73e 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.37434841876234e-01 + x 4.37434841805229e-01 } restraint { diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 2f8530fb3..6dd2653f7 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 4.24500295778074e-01 -1.29800118311230e-03 - 21 4.25830516124699e-01 -1.30332206449880e-03 - 22 4.25710168991809e-01 -1.30284067596723e-03 - 23 4.24495296936454e-01 -1.29798118774582e-03 - 24 4.22604814614221e-01 -1.29041925845688e-03 - 25 4.20482665167116e-01 -1.28193066066846e-03 - 26 4.18558612471422e-01 -1.27423444988569e-03 - 27 4.17211123890820e-01 -1.26884449556328e-03 - 28 4.16735269467297e-01 -1.26694107786919e-03 - 29 4.17317729261698e-01 -1.26927091704679e-03 - 30 4.19020232680582e-01 -1.27608093072233e-03 - 31 4.21772286278215e-01 -1.28708914511286e-03 - 32 4.25373865453946e-01 -1.30149546181578e-03 - 33 4.29508654225993e-01 -1.31803461690397e-03 - 34 4.33768111234715e-01 -1.33507244493886e-03 - 35 4.37685869084879e-01 -1.35074347633952e-03 - 36 4.40780679735902e-01 -1.36312271894361e-03 - 37 4.42604459084554e-01 -1.37041783633822e-03 - 38 4.42790500312300e-01 -1.37116200124920e-03 - 39 4.41096173922242e-01 -1.36438469568897e-03 - 40 4.37434841876234e-01 -1.34973936750494e-03 + 20 4.24500295670889e-01 -1.29800118268356e-03 + 21 4.25830516013726e-01 -1.30332206405490e-03 + 22 4.25710168880892e-01 -1.30284067552357e-03 + 23 4.24495296829610e-01 -1.29798118731844e-03 + 24 4.22604814515337e-01 -1.29041925806135e-03 + 25 4.20482665079664e-01 -1.28193066031866e-03 + 26 4.18558612398180e-01 -1.27423444959272e-03 + 27 4.17211123833643e-01 -1.26884449533457e-03 + 28 4.16735269426941e-01 -1.26694107770777e-03 + 29 4.17317729237757e-01 -1.26927091695103e-03 + 30 4.19020232671458e-01 -1.27608093068583e-03 + 31 4.21772286281203e-01 -1.28708914512481e-03 + 32 4.25373865465361e-01 -1.30149546186144e-03 + 33 4.29508654241388e-01 -1.31803461696555e-03 + 34 4.33768111249166e-01 -1.33507244499666e-03 + 35 4.37685869093343e-01 -1.35074347637337e-03 + 36 4.40780679733648e-01 -1.36312271893459e-03 + 37 4.42604459067608e-01 -1.37041783627043e-03 + 38 4.42790500277900e-01 -1.37116200111160e-03 + 39 4.41096173869207e-01 -1.36438469547683e-03 + 40 4.37434841805229e-01 -1.34973936722092e-03 diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt index 157cac038..017b69b3a 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2022-04-14. +colvars: Using NAMD interface, version "2022-04-06". diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out index 479a448a6..99840490b 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,20 +70,19 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_random.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( 2.23122 , -1.11745 , -1.91143 ) colvars: # differenceVector = off [default] colvars: Centering the provided vector to zero. -colvars: # normalizeVector = off [default] -colvars: The norm of the vector is |v| = 23.5625. +colvars: The norm of the vector is |v| = 0.00180118. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,7 +110,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -126,26 +120,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - eigenvector colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 98d60150c..81e913df1 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.96593083265021e+00 + x 9.96593083012934e+00 } restraint { diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj index 4010095ee..57c3f5382 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 7.12848384426395e+00 -2.81139353770558e-02 - 1 7.12389036856740e+00 -2.80955614742696e-02 - 2 7.12039004727828e+00 -2.80815601891131e-02 - 3 7.12467766714325e+00 -2.80987106685730e-02 - 4 7.14407407731135e+00 -2.81762963092454e-02 - 5 7.18586833886829e+00 -2.83434733554732e-02 - 6 7.25659559563629e+00 -2.86263823825451e-02 - 7 7.36131202502140e+00 -2.90452481000856e-02 - 8 7.50293456624851e+00 -2.96117382649940e-02 - 9 7.68171812033882e+00 -3.03268724813553e-02 - 10 7.89494414916322e+00 -3.11797765966529e-02 - 11 8.13688859836978e+00 -3.21475543934791e-02 - 12 8.39911418370808e+00 -3.31964567348323e-02 - 13 8.67108915525047e+00 -3.42843566210019e-02 - 14 8.94107690223794e+00 -3.53643076089518e-02 - 15 9.19718784397990e+00 -3.63887513759196e-02 - 16 9.42845597136909e+00 -3.73138238854764e-02 - 17 9.62580650887713e+00 -3.81032260355085e-02 - 18 9.78281209829472e+00 -3.87312483931789e-02 - 19 9.89617742737599e+00 -3.91847097095039e-02 - 20 9.96593083265021e+00 -3.94637233306008e-02 + 0 7.12848384426398e+00 -2.81139353770559e-02 + 1 7.12389036856418e+00 -2.80955614742567e-02 + 2 7.12039004726484e+00 -2.80815601890594e-02 + 3 7.12467766711354e+00 -2.80987106684541e-02 + 4 7.14407407726102e+00 -2.81762963090441e-02 + 5 7.18586833879461e+00 -2.83434733551784e-02 + 6 7.25659559553746e+00 -2.86263823821498e-02 + 7 7.36131202489437e+00 -2.90452480995775e-02 + 8 7.50293456608652e+00 -2.96117382643461e-02 + 9 7.68171812012824e+00 -3.03268724805129e-02 + 10 7.89494414888129e+00 -3.11797765955252e-02 + 11 8.13688859798339e+00 -3.21475543919336e-02 + 12 8.39911418317517e+00 -3.31964567327007e-02 + 13 8.67108915452401e+00 -3.42843566180960e-02 + 14 8.94107690127196e+00 -3.53643076050878e-02 + 15 9.19718784273722e+00 -3.63887513709489e-02 + 16 9.42845596982786e+00 -3.73138238793115e-02 + 17 9.62580650703617e+00 -3.81032260281447e-02 + 18 9.78281209617585e+00 -3.87312483847034e-02 + 19 9.89617742502377e+00 -3.91847097000951e-02 + 20 9.96593083012934e+00 -3.94637233205174e-02 diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out index ea096f39d..f758c6696 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,20 +70,19 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_random.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( 2.23122 , -1.11745 , -1.91143 ) colvars: # differenceVector = off [default] colvars: Centering the provided vector to zero. -colvars: # normalizeVector = off [default] -colvars: The norm of the vector is |v| = 23.5625. +colvars: The norm of the vector is |v| = 0.00180118. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,7 +110,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -126,31 +120,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - eigenvector colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 9.96593 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index d228f8399..5b5148d25 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.02340499670145e+01 + x 1.02340499653749e+01 } restraint { diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 977dc1547..eb7bf1ecb 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.96593083265021e+00 -3.94637233306008e-02 - 21 9.99532793321660e+00 -3.95813117328664e-02 - 22 9.99048850273347e+00 -3.95619540109339e-02 - 23 9.95980058803785e+00 -3.94392023521514e-02 - 24 9.91314195361405e+00 -3.92525678144562e-02 - 25 9.86098750735006e+00 -3.90439500294002e-02 - 26 9.81348370507768e+00 -3.88539348203107e-02 - 27 9.77957161075872e+00 -3.87182864430349e-02 - 28 9.76622794926487e+00 -3.86649117970595e-02 - 29 9.77787383954832e+00 -3.87114953581933e-02 - 30 9.81598266583797e+00 -3.88639306633519e-02 - 31 9.87890737157304e+00 -3.91156294862921e-02 - 32 9.96194305255191e+00 -3.94477722102076e-02 - 33 1.00576385222471e+01 -3.98305540889885e-02 - 34 1.01563633552530e+01 -4.02254534210120e-02 - 35 1.02471188262364e+01 -4.05884753049457e-02 - 36 1.03185507061932e+01 -4.08742028247726e-02 - 37 1.03600827317051e+01 -4.10403309268204e-02 - 38 1.03630544983541e+01 -4.10522179934165e-02 - 39 1.03217296680099e+01 -4.08869186720396e-02 - 40 1.02340499670145e+01 -4.05361998680579e-02 + 20 9.96593083012934e+00 -3.94637233205174e-02 + 21 9.99532793060757e+00 -3.95813117224303e-02 + 22 9.99048850012704e+00 -3.95619540005082e-02 + 23 9.95980058552870e+00 -3.94392023421148e-02 + 24 9.91314195129389e+00 -3.92525678051756e-02 + 25 9.86098750530072e+00 -3.90439500212029e-02 + 26 9.81348370336466e+00 -3.88539348134586e-02 + 27 9.77957160942564e+00 -3.87182864377026e-02 + 28 9.76622794832969e+00 -3.86649117933188e-02 + 29 9.77787383900133e+00 -3.87114953560053e-02 + 30 9.81598266564158e+00 -3.88639306625663e-02 + 31 9.87890737166341e+00 -3.91156294866536e-02 + 32 9.96194305284228e+00 -3.94477722113691e-02 + 33 1.00576385226328e+01 -3.98305540905312e-02 + 34 1.01563633556180e+01 -4.02254534224719e-02 + 35 1.02471188264620e+01 -4.05884753058479e-02 + 36 1.03185507061678e+01 -4.08742028246714e-02 + 37 1.03600827313353e+01 -4.10403309253412e-02 + 38 1.03630544975746e+01 -4.10522179902983e-02 + 39 1.03217296667927e+01 -4.08869186671706e-02 + 40 1.02340499653749e+01 -4.05361998614995e-02 diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt b/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt index 157cac038..fc4f9e327 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. +colvars: Using NAMD interface, version 2016-11-23. diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out index ac4d45dde..cabed47f2 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "eulerTheta" @@ -59,9 +55,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -74,15 +69,15 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -105,9 +100,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -119,15 +113,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -150,9 +144,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -164,15 +157,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -198,7 +191,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPsi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -215,7 +207,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPhi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -232,7 +223,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerTheta" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -244,30 +234,17 @@ colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - eulerPhi colvar component (derived from orientation): -colvars: - eulerPsi colvar component (derived from orientation): -colvars: - eulerTheta colvar component (derived from orientation): -colvars: Fu2017 https://doi.org/10.1021/acs.jctc.7b00791 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped index 9750dbd1a..9fed64568 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name eulerTheta - x 7.42926968363036e-01 + x 7.42926968363034e-01 } colvar { @@ -15,7 +15,7 @@ colvar { colvar { name eulerPsi - x -4.93710444441009e+00 + x -4.93710444441010e+00 } restraint { diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj index 1109293ce..d0984ff5d 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step eulerTheta fa_eulerTheta eulerPhi fa_eulerPhi eulerPsi fa_eulerPsi E_harmonic1 E_harmonic2 E_harmonic3 - 0 1.12335897633008e+00 -1.12335897633008e-01 -9.19929987926339e+00 9.19929987926340e-01 -5.23950348243898e+00 5.23950348243898e-01 1.37261983712451e+00 4.23135591343078e+00 6.30967694850688e-02 - 1 1.10359290098423e+00 -1.10359290098423e-01 -9.22565834570168e+00 9.22565834570168e-01 -5.25149538780149e+00 5.25149538780149e-01 1.37891019040501e+00 4.25563859558075e+00 6.08958645551400e-02 - 2 1.08440461653865e+00 -1.08440461653865e-01 -9.25678498979173e+00 9.25678498979173e-01 -5.25779637281106e+00 5.25779637281106e-01 1.38222113489726e+00 4.28440341736168e+00 5.87966686185170e-02 - 3 1.06529304335568e+00 -1.06529304335568e-01 -9.29208424764168e+00 9.29208424764168e-01 -5.25763403749821e+00 5.25763403749821e-01 1.38213578361299e+00 4.31714148326353e+00 5.67424634111001e-02 - 4 1.04571544240957e+00 -1.04571544240957e-01 -9.33104631969662e+00 9.33104631969662e-01 -5.25046695843815e+00 5.25046695843815e-01 1.37837016408254e+00 4.35342127101619e+00 5.46760393246926e-02 + 0 1.12335897633009e+00 -1.12335897633009e-01 -9.19929987926340e+00 9.19929987926340e-01 -5.23950348243898e+00 5.23950348243898e-01 1.37261983712451e+00 4.23135591343078e+00 6.30967694850690e-02 + 1 1.10359290098423e+00 -1.10359290098423e-01 -9.22565834570168e+00 9.22565834570168e-01 -5.25149538780149e+00 5.25149538780149e-01 1.37891019040502e+00 4.25563859558075e+00 6.08958645551397e-02 + 2 1.08440461653865e+00 -1.08440461653865e-01 -9.25678498979173e+00 9.25678498979173e-01 -5.25779637281105e+00 5.25779637281106e-01 1.38222113489725e+00 4.28440341736168e+00 5.87966686185170e-02 + 3 1.06529304335568e+00 -1.06529304335568e-01 -9.29208424764168e+00 9.29208424764168e-01 -5.25763403749821e+00 5.25763403749821e-01 1.38213578361299e+00 4.31714148326353e+00 5.67424634110999e-02 + 4 1.04571544240957e+00 -1.04571544240957e-01 -9.33104631969663e+00 9.33104631969663e-01 -5.25046695843814e+00 5.25046695843814e-01 1.37837016408253e+00 4.35342127101620e+00 5.46760393246926e-02 5 1.02517685434404e+00 -1.02517685434404e-01 -9.37327661318995e+00 9.37327661318995e-01 -5.23607026451037e+00 5.23607026451037e-01 1.37082159074448e+00 4.39291572336868e+00 5.25493791341371e-02 6 1.00330582597764e+00 -1.00330582597764e-01 -9.41848339102013e+00 9.41848339102013e-01 -5.21460973558002e+00 5.21460973558002e-01 1.35960773472030e+00 4.43539146934610e+00 5.03311290220341e-02 - 7 9.79907540363570e-01 -9.79907540363570e-02 -9.46643852313838e+00 9.46643852313838e-01 -5.18668671653799e+00 5.18668671653799e-01 1.34508595477558e+00 4.48067291561792e+00 4.80109393830691e-02 - 8 9.54992420449578e-01 -9.54992420449578e-02 -9.51692832794413e+00 9.51692832794413e-01 -5.15334195139500e+00 5.15334195139500e-01 1.32784666340038e+00 4.52859623996127e+00 4.56005261558072e-02 - 9 9.28783692054886e-01 -9.28783692054886e-02 -9.56970831738818e+00 9.56970831738818e-01 -5.11601429466745e+00 5.11601429466745e-01 1.30868011316208e+00 4.57896586399443e+00 4.31319573313553e-02 - 10 9.01709043906521e-01 -9.01709043906521e-02 -9.62447028619222e+00 9.62447028619222e-01 -5.07645787560575e+00 5.07645787560575e-01 1.28852122813998e+00 4.63152141448985e+00 4.06539599931406e-02 - 11 8.74379467191584e-01 -8.74379467191584e-02 -9.68082504780323e+00 9.68082504780323e-01 -5.03662790099944e+00 5.03662790099944e-01 1.26838103065630e+00 4.68591868030872e+00 3.82269726323119e-02 + 7 9.79907540363569e-01 -9.79907540363569e-02 -9.46643852313838e+00 9.46643852313838e-01 -5.18668671653799e+00 5.18668671653799e-01 1.34508595477558e+00 4.48067291561792e+00 4.80109393830689e-02 + 8 9.54992420449583e-01 -9.54992420449583e-02 -9.51692832794413e+00 9.51692832794413e-01 -5.15334195139500e+00 5.15334195139500e-01 1.32784666340038e+00 4.52859623996127e+00 4.56005261558077e-02 + 9 9.28783692054884e-01 -9.28783692054884e-02 -9.56970831738819e+00 9.56970831738819e-01 -5.11601429466744e+00 5.11601429466744e-01 1.30868011316208e+00 4.57896586399444e+00 4.31319573313551e-02 + 10 9.01709043906520e-01 -9.01709043906520e-02 -9.62447028619222e+00 9.62447028619222e-01 -5.07645787560575e+00 5.07645787560575e-01 1.28852122813998e+00 4.63152141448985e+00 4.06539599931406e-02 + 11 8.74379467191583e-01 -8.74379467191583e-02 -9.68082504780323e+00 9.68082504780323e-01 -5.03662790099944e+00 5.03662790099944e-01 1.26838103065630e+00 4.68591868030872e+00 3.82269726323119e-02 12 8.47554676237916e-01 -8.47554676237916e-02 -9.73829978053727e+00 9.73829978053727e-01 -4.99855008771719e+00 4.99855008771719e-01 1.24927514897088e+00 4.74172413078062e+00 3.59174464606379e-02 - 13 8.22093180764617e-01 -8.22093180764617e-02 -9.79634420282249e+00 9.79634420282249e-01 -4.96419034641283e+00 4.96419034641283e-01 1.23215928977092e+00 4.79841798700869e+00 3.37918598929842e-02 + 13 8.22093180764618e-01 -8.22093180764618e-02 -9.79634420282249e+00 9.79634420282249e-01 -4.96419034641283e+00 4.96419034641283e-01 1.23215928977092e+00 4.79841798700869e+00 3.37918598929844e-02 14 7.98887326318826e-01 -7.98887326318826e-02 -9.85433604587600e+00 9.85433604587600e-01 -4.93533870265480e+00 4.93533870265480e-01 1.21787840549612e+00 4.85539694525255e+00 3.19110480076421e-02 - 15 7.78788129749853e-01 -7.78788129749853e-02 -9.91157703203216e+00 9.91157703203216e-01 -4.91351570715390e+00 4.91351570715390e-01 1.20713183022241e+00 4.91196796309537e+00 3.03255475519637e-02 - 16 7.62528356252244e-01 -7.62528356252244e-02 -9.96727776858339e+00 9.96727776858339e-01 -4.89990324848287e+00 4.89990324848287e-01 1.20045259222465e+00 4.96733130580484e+00 2.90724747044375e-02 - 17 7.50652833132862e-01 -7.50652833132862e-02 -1.00205407738012e+01 1.00205407738012e+00 -4.89529691190416e+00 4.89529691190416e-01 1.19819659278492e+00 5.02056186997061e+00 2.81739837945196e-02 + 15 7.78788129749855e-01 -7.78788129749855e-02 -9.91157703203216e+00 9.91157703203216e-01 -4.91351570715390e+00 4.91351570715390e-01 1.20713183022241e+00 4.91196796309537e+00 3.03255475519638e-02 + 16 7.62528356252240e-01 -7.62528356252240e-02 -9.96727776858340e+00 9.96727776858340e-01 -4.89990324848287e+00 4.89990324848287e-01 1.20045259222465e+00 4.96733130580484e+00 2.90724747044372e-02 + 17 7.50652833132860e-01 -7.50652833132860e-02 -1.00205407738012e+01 1.00205407738012e+00 -4.89529691190416e+00 4.89529691190416e-01 1.19819659278492e+00 5.02056186997061e+00 2.81739837945194e-02 18 7.43463015261251e-01 -7.43463015261251e-02 -1.00703584090617e+01 1.00703584090617e+00 -4.90007484689111e+00 4.90007484689111e-01 1.20053667525675e+00 5.07060592434798e+00 2.76368627530676e-02 - 19 7.40979904753968e-01 -7.40979904753968e-02 -1.01156425246949e+01 1.01156425246949e+00 -4.91417861741104e+00 4.91417861741104e-01 1.20745757419099e+00 5.11631118437074e+00 2.74525609624600e-02 - 20 7.42926968363036e-01 -7.42926968363036e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441009e+00 4.93710444441009e-01 1.21875001475069e+00 5.15650108652104e+00 2.75970240160545e-02 + 19 7.40979904753968e-01 -7.40979904753968e-02 -1.01156425246949e+01 1.01156425246949e+00 -4.91417861741104e+00 4.91417861741104e-01 1.20745757419099e+00 5.11631118437075e+00 2.74525609624599e-02 + 20 7.42926968363034e-01 -7.42926968363034e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441010e+00 4.93710444441010e-01 1.21875001475070e+00 5.15650108652104e+00 2.75970240160544e-02 diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out index 7ec5027d5..17479fe12 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "eulerTheta" @@ -59,9 +55,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -74,15 +69,15 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -105,9 +100,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -119,15 +113,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -150,9 +144,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -164,15 +157,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -198,7 +191,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPsi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -215,7 +207,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPhi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -232,7 +223,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerTheta" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -244,25 +234,9 @@ colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - eulerPhi colvar component (derived from orientation): -colvars: - eulerPsi colvar component (derived from orientation): -colvars: - eulerTheta colvar component (derived from orientation): -colvars: Fu2017 https://doi.org/10.1021/acs.jctc.7b00791 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "eulerTheta" from value: 0.742927 @@ -272,11 +246,14 @@ colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: Restarting harmonic bias "harmonic2" from step number 20. colvars: Restarting harmonic bias "harmonic3" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped index 2c39b1548..0abbdad76 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name eulerTheta - x 4.92888911241030e-01 + x 4.92888911241022e-01 } colvar { @@ -15,7 +15,7 @@ colvar { colvar { name eulerPsi - x -5.16556439137703e+00 + x -5.16556439137704e+00 } restraint { diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj index 3f2d8e1ad..b66de304b 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step eulerTheta fa_eulerTheta eulerPhi fa_eulerPhi eulerPsi fa_eulerPsi E_harmonic1 E_harmonic2 E_harmonic3 - 20 7.42926968363036e-01 -7.42926968363036e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441009e+00 4.93710444441009e-01 1.21875001475069e+00 5.15650108652104e+00 2.75970240160545e-02 - 21 7.48733320101761e-01 -7.48733320101761e-02 -1.01883183460673e+01 1.01883183460673e+00 -4.96790750263877e+00 4.96790750263877e-01 1.23400524773873e+00 5.19009153604058e+00 2.80300792315303e-02 - 22 7.57557122198821e-01 -7.57557122198821e-02 -1.02139454102856e+01 1.02139454102856e+00 -5.00522572559092e+00 5.00522572559092e-01 1.25261422820586e+00 5.21623404221472e+00 2.86946396697080e-02 - 23 7.68329051637894e-01 -7.68329051637894e-02 -1.02317713436666e+01 1.02317713436666e+00 -5.04733083960333e+00 5.04733083960333e-01 1.27377743022054e+00 5.23445724145382e+00 2.95164765795393e-02 - 24 7.79814875676107e-01 -7.79814875676107e-02 -1.02418490445600e+01 1.02418490445600e+00 -5.09221216535160e+00 5.09221216535160e-01 1.29653123684774e+00 5.24477359257776e+00 3.04055620162871e-02 - 25 7.90694011146757e-01 -7.90694011146757e-02 -1.02447281510328e+01 1.02447281510328e+00 -5.13769297452897e+00 5.13769297452897e-01 1.31979445502622e+00 5.24772274442816e+00 3.12598509631674e-02 - 26 7.99647836011620e-01 -7.99647836011620e-02 -1.02414229458545e+01 1.02414229458545e+00 -5.18157169207901e+00 5.18157169207901e-01 1.34243426000773e+00 5.24433719779371e+00 3.19718330819034e-02 - 27 8.05448995815155e-01 -8.05448995815155e-02 -1.02333134884667e+01 1.02333134884667e+00 -5.22177344695617e+00 5.22177344695617e-01 1.36334589656683e+00 5.23603524766171e+00 3.24374042429820e-02 - 28 8.07042333855102e-01 -8.07042333855102e-02 -1.02219996119654e+01 1.02219996119654e+00 -5.25649361343075e+00 5.25649361343075e-01 1.38153625540191e+00 5.22446380335108e+00 3.25658664317145e-02 - 29 8.03610000016903e-01 -8.03610000016903e-02 -1.02091368712812e+01 1.02091368712812e+00 -5.28431542925356e+00 5.28431542925356e-01 1.39619947779236e+00 5.21132378282767e+00 3.22894516063584e-02 - 30 7.94616975119391e-01 -7.94616975119391e-02 -1.01962849681356e+01 1.01962849681356e+00 -5.30428814909504e+00 5.30428814909504e-01 1.40677363843150e+00 5.19821135757143e+00 3.15708068573945e-02 - 31 7.79837159581488e-01 -7.79837159581488e-02 -1.01847936556627e+01 1.01847936556627e+00 -5.31595928178051e+00 5.31595928178051e-01 1.41297115427742e+00 5.18650109042138e+00 3.04072997732061e-02 - 32 7.59362971789403e-01 -7.59362971789403e-02 -1.01757407630825e+01 1.01757407630825e+00 -5.31936241154539e+00 5.31936241154539e-01 1.41478082326810e+00 5.17728500387294e+00 2.88316061462417e-02 - 33 7.33602066496011e-01 -7.33602066496011e-02 -1.01699237742566e+01 1.01699237742566e+00 -5.31496943853745e+00 5.31496943853745e-01 1.41244500662936e+00 5.17136747870943e+00 2.69085995983609e-02 - 34 7.03263342872247e-01 -7.03263342872247e-02 -1.01678925721792e+01 1.01678925721792e+00 -5.30362109991434e+00 5.30362109991434e-01 1.40641983857283e+00 5.16930196796881e+00 2.47289664713924e-02 - 35 6.69331542581692e-01 -6.69331542581692e-02 -1.01700001127699e+01 1.01700001127699e+00 -5.28645108127907e+00 5.28645108127907e-01 1.39732825173783e+00 5.17144511468704e+00 2.24002356947393e-02 - 36 6.33027051643078e-01 -6.33027051643078e-02 -1.01764433502072e+01 1.01764433502072e+00 -5.26481622337318e+00 5.26481622337318e-01 1.38591449329467e+00 5.17799996299881e+00 2.00361624055964e-02 - 37 5.95746809302786e-01 -5.95746809302786e-02 -1.01872719611055e+01 1.01872719611055e+00 -5.24023891452942e+00 5.24023891452942e-01 1.37300519406742e+00 5.18902550047631e+00 1.77457130397225e-02 - 38 5.58984709726032e-01 -5.58984709726032e-02 -1.02023564051939e+01 1.02023564051939e+00 -5.21435969588687e+00 5.21435969588687e-01 1.35947735190447e+00 5.20440381093002e+00 1.56231952853748e-02 - 39 5.24235101803498e-01 -5.24235101803498e-02 -1.02213251856666e+01 1.02213251856666e+00 -5.18889149341549e+00 5.18889149341549e-01 1.34622974652198e+00 5.22377442755710e+00 1.37411220981462e-02 - 40 4.92888911241030e-01 -4.92888911241030e-02 -1.02434969074251e+01 1.02434969074251e+00 -5.16556439137703e+00 5.16556439137703e-01 1.33415277407312e+00 5.24646144462135e+00 1.21469739412184e-02 + 20 7.42926968363034e-01 -7.42926968363034e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441010e+00 4.93710444441010e-01 1.21875001475070e+00 5.15650108652104e+00 2.75970240160544e-02 + 21 7.48733320101764e-01 -7.48733320101764e-02 -1.01883183460673e+01 1.01883183460673e+00 -4.96790750263877e+00 4.96790750263877e-01 1.23400524773873e+00 5.19009153604059e+00 2.80300792315305e-02 + 22 7.57557122198820e-01 -7.57557122198820e-02 -1.02139454102856e+01 1.02139454102856e+00 -5.00522572559092e+00 5.00522572559092e-01 1.25261422820586e+00 5.21623404221472e+00 2.86946396697079e-02 + 23 7.68329051637896e-01 -7.68329051637896e-02 -1.02317713436666e+01 1.02317713436666e+00 -5.04733083960333e+00 5.04733083960333e-01 1.27377743022054e+00 5.23445724145384e+00 2.95164765795395e-02 + 24 7.79814875676108e-01 -7.79814875676108e-02 -1.02418490445600e+01 1.02418490445600e+00 -5.09221216535160e+00 5.09221216535160e-01 1.29653123684774e+00 5.24477359257777e+00 3.04055620162872e-02 + 25 7.90694011146758e-01 -7.90694011146758e-02 -1.02447281510328e+01 1.02447281510328e+00 -5.13769297452897e+00 5.13769297452897e-01 1.31979445502622e+00 5.24772274442817e+00 3.12598509631674e-02 + 26 7.99647836011618e-01 -7.99647836011618e-02 -1.02414229458545e+01 1.02414229458545e+00 -5.18157169207901e+00 5.18157169207901e-01 1.34243426000773e+00 5.24433719779373e+00 3.19718330819032e-02 + 27 8.05448995815154e-01 -8.05448995815154e-02 -1.02333134884667e+01 1.02333134884667e+00 -5.22177344695617e+00 5.22177344695617e-01 1.36334589656682e+00 5.23603524766172e+00 3.24374042429820e-02 + 28 8.07042333855100e-01 -8.07042333855101e-02 -1.02219996119655e+01 1.02219996119655e+00 -5.25649361343075e+00 5.25649361343075e-01 1.38153625540191e+00 5.22446380335109e+00 3.25658664317144e-02 + 29 8.03610000016902e-01 -8.03610000016902e-02 -1.02091368712812e+01 1.02091368712812e+00 -5.28431542925356e+00 5.28431542925356e-01 1.39619947779236e+00 5.21132378282767e+00 3.22894516063583e-02 + 30 7.94616975119385e-01 -7.94616975119385e-02 -1.01962849681356e+01 1.01962849681356e+00 -5.30428814909504e+00 5.30428814909504e-01 1.40677363843151e+00 5.19821135757144e+00 3.15708068573941e-02 + 31 7.79837159581490e-01 -7.79837159581490e-02 -1.01847936556627e+01 1.01847936556627e+00 -5.31595928178051e+00 5.31595928178051e-01 1.41297115427742e+00 5.18650109042140e+00 3.04072997732063e-02 + 32 7.59362971789398e-01 -7.59362971789398e-02 -1.01757407630825e+01 1.01757407630825e+00 -5.31936241154539e+00 5.31936241154539e-01 1.41478082326810e+00 5.17728500387295e+00 2.88316061462413e-02 + 33 7.33602066496012e-01 -7.33602066496012e-02 -1.01699237742566e+01 1.01699237742566e+00 -5.31496943853745e+00 5.31496943853745e-01 1.41244500662935e+00 5.17136747870945e+00 2.69085995983609e-02 + 34 7.03263342872243e-01 -7.03263342872243e-02 -1.01678925721792e+01 1.01678925721792e+00 -5.30362109991434e+00 5.30362109991434e-01 1.40641983857283e+00 5.16930196796882e+00 2.47289664713921e-02 + 35 6.69331542581688e-01 -6.69331542581688e-02 -1.01700001127700e+01 1.01700001127700e+00 -5.28645108127908e+00 5.28645108127908e-01 1.39732825173784e+00 5.17144511468705e+00 2.24002356947391e-02 + 36 6.33027051643073e-01 -6.33027051643073e-02 -1.01764433502072e+01 1.01764433502072e+00 -5.26481622337318e+00 5.26481622337318e-01 1.38591449329467e+00 5.17799996299882e+00 2.00361624055961e-02 + 37 5.95746809302784e-01 -5.95746809302784e-02 -1.01872719611055e+01 1.01872719611055e+00 -5.24023891452942e+00 5.24023891452942e-01 1.37300519406743e+00 5.18902550047632e+00 1.77457130397224e-02 + 38 5.58984709726027e-01 -5.58984709726027e-02 -1.02023564051939e+01 1.02023564051939e+00 -5.21435969588688e+00 5.21435969588688e-01 1.35947735190448e+00 5.20440381093004e+00 1.56231952853745e-02 + 39 5.24235101803488e-01 -5.24235101803488e-02 -1.02213251856666e+01 1.02213251856666e+00 -5.18889149341550e+00 5.18889149341550e-01 1.34622974652199e+00 5.22377442755711e+00 1.37411220981457e-02 + 40 4.92888911241022e-01 -4.92888911241022e-02 -1.02434969074251e+01 1.02434969074251e+00 -5.16556439137704e+00 5.16556439137704e-01 1.33415277407312e+00 5.24646144462136e+00 1.21469739412180e-02 diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt index 157cac038..3226d7191 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.15alpha1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-11-09". +colvars: Using NAMD interface, version "2020-10-26". diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out index 346415abf..92061cd24 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,28 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - groupCoord colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped index f285fde00..bb2a2b55a 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.19072319981190e-06 + x 3.19072319783456e-06 } restraint { diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj index 3bfd80daf..194c5d94f 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.17405979638661e-06 3.99987303760814e-04 - 1 3.18134448326459e-06 3.99987274622067e-04 - 2 3.18580682150308e-06 3.99987256772714e-04 - 3 3.18739100900219e-06 3.99987250435964e-04 - 4 3.18623907585806e-06 3.99987255043697e-04 - 5 3.18267103066260e-06 3.99987269315877e-04 - 6 3.17715514861791e-06 3.99987291379406e-04 - 7 3.17027321053934e-06 3.99987318907158e-04 - 8 3.16268340733906e-06 3.99987349266371e-04 - 9 3.15508117715307e-06 3.99987379675291e-04 - 10 3.14815708828368e-06 3.99987407371647e-04 - 11 3.14255208141271e-06 3.99987429791674e-04 - 12 3.13881288855239e-06 3.99987444748446e-04 - 13 3.13735264456987e-06 3.99987450589422e-04 - 14 3.13842207883868e-06 3.99987446311685e-04 - 15 3.14209486005973e-06 3.99987431620560e-04 - 16 3.14826794572284e-06 3.99987406928217e-04 - 17 3.15667508008936e-06 3.99987373299680e-04 - 18 3.16691009231148e-06 3.99987332359631e-04 - 19 3.17845677325003e-06 3.99987286172907e-04 - 20 3.19072319981190e-06 3.99987237107201e-04 + 1 3.18134448325853e-06 3.99987274622067e-04 + 2 3.18580682147849e-06 3.99987256772714e-04 + 3 3.18739100894646e-06 3.99987250435964e-04 + 4 3.18623907575867e-06 3.99987255043697e-04 + 5 3.18267103050743e-06 3.99987269315878e-04 + 6 3.17715514839544e-06 3.99987291379406e-04 + 7 3.17027321023885e-06 3.99987318907159e-04 + 8 3.16268340695069e-06 3.99987349266372e-04 + 9 3.15508117666781e-06 3.99987379675293e-04 + 10 3.14815708769336e-06 3.99987407371649e-04 + 11 3.14255208070990e-06 3.99987429791677e-04 + 12 3.13881288773027e-06 3.99987444748449e-04 + 13 3.13735264362211e-06 3.99987450589426e-04 + 14 3.13842207775938e-06 3.99987446311689e-04 + 15 3.14209485884323e-06 3.99987431620565e-04 + 16 3.14826794436374e-06 3.99987406928223e-04 + 17 3.15667507858251e-06 3.99987373299686e-04 + 18 3.16691009065201e-06 3.99987332359637e-04 + 19 3.17845677143355e-06 3.99987286172914e-04 + 20 3.19072319783456e-06 3.99987237107209e-04 diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out index da182042c..d73e8c3c6 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,33 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - groupCoord colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.19072e-06 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 6e6309f87..2617a40e7 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.18473698183816e-06 + x 3.18473697725417e-06 } restraint { diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj index d3a79e359..e995df08f 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.19072319981190e-06 3.99987237107201e-04 - 21 3.20307950136251e-06 3.99987187681995e-04 - 22 3.21489838209560e-06 3.99987140406472e-04 - 23 3.22559675174575e-06 3.99987097612993e-04 - 24 3.23467513046995e-06 3.99987061299478e-04 - 25 3.24175015008330e-06 3.99987032999400e-04 - 26 3.24657591479334e-06 3.99987013696341e-04 - 27 3.24905200103034e-06 3.99987003791996e-04 - 28 3.24921865907333e-06 3.99987003125364e-04 - 29 3.24724234522045e-06 3.99987011030619e-04 - 30 3.24339473356695e-06 3.99987026421066e-04 - 31 3.23802801454050e-06 3.99987047887942e-04 - 32 3.23154776620721e-06 3.99987073808935e-04 - 33 3.22438446230774e-06 3.99987102462151e-04 - 34 3.21696475248629e-06 3.99987132140990e-04 - 35 3.20968467122739e-06 3.99987161261315e-04 - 36 3.20288713565953e-06 3.99987188451457e-04 - 37 3.19684522920946e-06 3.99987212619083e-04 - 38 3.19175121091107e-06 3.99987232995156e-04 - 39 3.18771015284195e-06 3.99987249159389e-04 - 40 3.18473698183816e-06 3.99987261052073e-04 + 20 3.19072319783456e-06 3.99987237107209e-04 + 21 3.20307949922131e-06 3.99987187682003e-04 + 22 3.21489837978856e-06 3.99987140406481e-04 + 23 3.22559674927215e-06 3.99987097613003e-04 + 24 3.23467512783040e-06 3.99987061299489e-04 + 25 3.24175014727985e-06 3.99987032999411e-04 + 26 3.24657591182937e-06 3.99987013696353e-04 + 27 3.24905199791042e-06 3.99987003792008e-04 + 28 3.24921865580300e-06 3.99987003125377e-04 + 29 3.24724234180586e-06 3.99987011030633e-04 + 30 3.24339473001463e-06 3.99987026421080e-04 + 31 3.23802801085701e-06 3.99987047887957e-04 + 32 3.23154776239895e-06 3.99987073808950e-04 + 33 3.22438445838087e-06 3.99987102462166e-04 + 34 3.21696474844672e-06 3.99987132141006e-04 + 35 3.20968466708086e-06 3.99987161261332e-04 + 36 3.20288713141188e-06 3.99987188451474e-04 + 37 3.19684522486685e-06 3.99987212619101e-04 + 38 3.19175120648019e-06 3.99987232995174e-04 + 39 3.18771014833031e-06 3.99987249159407e-04 + 40 3.18473697725417e-06 3.99987261052091e-04 diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out index 346415abf..92061cd24 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,28 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - groupCoord colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped index a61c41a68..79a79deb8 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 7.87058667467717e-01 + x 7.87058667403396e-01 } restraint { diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj index 5a74dc300..9c2fb8adc 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 7.90587472610727e-01 -2.76234989044291e-03 - 1 7.90951498267255e-01 -2.76380599306902e-03 - 2 7.91115918558132e-01 -2.76446367423253e-03 - 3 7.91076626157176e-01 -2.76430650462870e-03 - 4 7.90841020777686e-01 -2.76336408311074e-03 - 5 7.90427382732787e-01 -2.76170953093115e-03 - 6 7.89863736340070e-01 -2.75945494536028e-03 - 7 7.89186342108997e-01 -2.75674536843599e-03 - 8 7.88437860267658e-01 -2.75375144107063e-03 - 9 7.87665135265936e-01 -2.75066054106374e-03 - 10 7.86916534938388e-01 -2.74766613975355e-03 - 11 7.86238889949708e-01 -2.74495555979883e-03 - 12 7.85674262880010e-01 -2.74269705152004e-03 - 13 7.85256932814059e-01 -2.74102773125624e-03 - 14 7.85011021491553e-01 -2.74004408596621e-03 - 15 7.84949075541991e-01 -2.73979630216797e-03 - 16 7.85071723408572e-01 -2.74028689363429e-03 - 17 7.85368315181469e-01 -2.74147326072588e-03 - 18 7.85818317068877e-01 -2.74327326827551e-03 - 19 7.86393206518082e-01 -2.74557282607233e-03 - 20 7.87058667467717e-01 -2.74823466987087e-03 + 1 7.90951498267062e-01 -2.76380599306825e-03 + 2 7.91115918557351e-01 -2.76446367422940e-03 + 3 7.91076626155406e-01 -2.76430650462163e-03 + 4 7.90841020774526e-01 -2.76336408309811e-03 + 5 7.90427382727841e-01 -2.76170953091136e-03 + 6 7.89863736332951e-01 -2.75945494533180e-03 + 7 7.89186342099336e-01 -2.75674536839735e-03 + 8 7.88437860255107e-01 -2.75375144102043e-03 + 9 7.87665135250171e-01 -2.75066054100068e-03 + 10 7.86916534919116e-01 -2.74766613967646e-03 + 11 7.86238889926666e-01 -2.74495555970666e-03 + 12 7.85674262852968e-01 -2.74269705141187e-03 + 13 7.85256932782819e-01 -2.74102773113128e-03 + 14 7.85011021455946e-01 -2.74004408582379e-03 + 15 7.84949075501872e-01 -2.73979630200749e-03 + 16 7.85071723363813e-01 -2.74028689345525e-03 + 17 7.85368315131961e-01 -2.74147326052785e-03 + 18 7.85818317014519e-01 -2.74327326805808e-03 + 19 7.86393206458784e-01 -2.74557282583514e-03 + 20 7.87058667403396e-01 -2.74823466961359e-03 diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out index 1fe205c90..0cd0f727b 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,33 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - groupCoord colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.787059 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index e43a36e68..5187120c9 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 7.87942474885153e-01 + x 7.87942474735044e-01 } restraint { diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj index ec60b338f..93a7f33a7 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 7.87058667467717e-01 -2.74823466987087e-03 - 21 7.87776958977482e-01 -2.75110783590993e-03 - 22 7.88509370083721e-01 -2.75403748033489e-03 - 23 7.89218651458299e-01 -2.75687460583319e-03 - 24 7.89871253752910e-01 -2.75948501501164e-03 - 25 7.90439158435954e-01 -2.76175663374382e-03 - 26 7.90901124501041e-01 -2.76360449800416e-03 - 27 7.91243274323407e-01 -2.76497309729363e-03 - 28 7.91459063648406e-01 -2.76583625459362e-03 - 29 7.91548789417463e-01 -2.76619515766985e-03 - 30 7.91518769927385e-01 -2.76607507970954e-03 - 31 7.91380310221072e-01 -2.76552124088429e-03 - 32 7.91148491294645e-01 -2.76459396517858e-03 - 33 7.90840825111090e-01 -2.76336330044436e-03 - 34 7.90475830319600e-01 -2.76190332127840e-03 - 35 7.90071649332906e-01 -2.76028659733162e-03 - 36 7.89644839916602e-01 -2.75857935966641e-03 - 37 7.89209440664736e-01 -2.75683776265894e-03 - 38 7.88776327332720e-01 -2.75510530933088e-03 - 39 7.88352818509478e-01 -2.75341127403791e-03 - 40 7.87942474885153e-01 -2.75176989954061e-03 + 20 7.87058667403396e-01 -2.74823466961359e-03 + 21 7.87776958908072e-01 -2.75110783563229e-03 + 22 7.88509370009168e-01 -2.75403748003667e-03 + 23 7.89218651378568e-01 -2.75687460551427e-03 + 24 7.89871253667991e-01 -2.75948501467196e-03 + 25 7.90439158345860e-01 -2.76175663338344e-03 + 26 7.90901124405813e-01 -2.76360449762325e-03 + 27 7.91243274223110e-01 -2.76497309689244e-03 + 28 7.91459063543128e-01 -2.76583625417251e-03 + 29 7.91548789307309e-01 -2.76619515722924e-03 + 30 7.91518769812477e-01 -2.76607507924991e-03 + 31 7.91380310101543e-01 -2.76552124040617e-03 + 32 7.91148491170643e-01 -2.76459396468257e-03 + 33 7.90840824982783e-01 -2.76336329993113e-03 + 34 7.90475830187182e-01 -2.76190332074873e-03 + 35 7.90071649196610e-01 -2.76028659678644e-03 + 36 7.89644839776708e-01 -2.75857935910683e-03 + 37 7.89209440521591e-01 -2.75683776208636e-03 + 38 7.88776327186739e-01 -2.75510530874696e-03 + 39 7.88352818361151e-01 -2.75341127344460e-03 + 40 7.87942474735044e-01 -2.75176989894018e-03 diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt b/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out index 74de50e14..722ed98b3 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -102,7 +98,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -113,26 +108,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 36d404925..390d537cf 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.00485448890467e+00 + x 5.00485448897596e+00 } restraint { diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj index 023e68dee..cbea421ce 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 5.03768855197227e+00 -1.97507542078891e-02 - 1 5.03744876419417e+00 -1.97497950567767e-02 - 2 5.03694642879576e+00 -1.97477857151830e-02 - 3 5.03620505705731e+00 -1.97448202282292e-02 - 4 5.03525398207188e+00 -1.97410159282875e-02 - 5 5.03412335571070e+00 -1.97364934228428e-02 - 6 5.03284080256979e+00 -1.97313632102792e-02 - 7 5.03142972215272e+00 -1.97257188886109e-02 - 8 5.02990878553163e+00 -1.97196351421265e-02 - 9 5.02829203784451e+00 -1.97131681513781e-02 - 10 5.02658916662064e+00 -1.97063566664825e-02 - 11 5.02480574439595e+00 -1.96992229775838e-02 - 12 5.02294349117820e+00 -1.96917739647128e-02 - 13 5.02100072378728e+00 -1.96840028951491e-02 - 14 5.01897316903736e+00 -1.96758926761494e-02 - 15 5.01685523476086e+00 -1.96674209390434e-02 - 16 5.01464172185107e+00 -1.96585668874043e-02 - 17 5.01232984699556e+00 -1.96493193879822e-02 - 18 5.00992134539975e+00 -1.96396853815990e-02 - 19 5.00742432915842e+00 -1.96296973166337e-02 - 20 5.00485448890467e+00 -1.96194179556187e-02 + 0 5.03768855197214e+00 -1.97507542078886e-02 + 1 5.03744876419419e+00 -1.97497950567768e-02 + 2 5.03694642879595e+00 -1.97477857151838e-02 + 3 5.03620505705716e+00 -1.97448202282286e-02 + 4 5.03525398207157e+00 -1.97410159282863e-02 + 5 5.03412335568541e+00 -1.97364934227416e-02 + 6 5.03284080257023e+00 -1.97313632102809e-02 + 7 5.03142972215521e+00 -1.97257188886209e-02 + 8 5.02990878553720e+00 -1.97196351421488e-02 + 9 5.02829203785433e+00 -1.97131681514173e-02 + 10 5.02658916663561e+00 -1.97063566665424e-02 + 11 5.02480574441698e+00 -1.96992229776679e-02 + 12 5.02294349120610e+00 -1.96917739648244e-02 + 13 5.02100072380662e+00 -1.96840028952265e-02 + 14 5.01897316908046e+00 -1.96758926763219e-02 + 15 5.01685523480251e+00 -1.96674209392100e-02 + 16 5.01464172191010e+00 -1.96585668876404e-02 + 17 5.01232984706209e+00 -1.96493193882483e-02 + 18 5.00992134545152e+00 -1.96396853818061e-02 + 19 5.00742432922767e+00 -1.96296973169107e-02 + 20 5.00485448897596e+00 -1.96194179559038e-02 diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out index 42156fb61..c40533751 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -102,7 +98,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -113,31 +108,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 5.00485 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index ab515bb61..9d22ab655 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.96897275206382e+00 + x 4.96897275199397e+00 } restraint { diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj index a61b26a78..12760b2af 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.00485448890467e+00 -1.96194179556187e-02 - 21 5.00223519406431e+00 -1.96089407762573e-02 - 22 4.99959613490376e+00 -1.95983845396151e-02 - 23 4.99697045871106e+00 -1.95878818348442e-02 - 24 4.99439079635605e+00 -1.95775631854242e-02 - 25 4.99188501582648e+00 -1.95675400633059e-02 - 26 4.98947279561833e+00 -1.95578911824733e-02 - 27 4.98716399834632e+00 -1.95486559933853e-02 - 28 4.98495936495158e+00 -1.95398374598063e-02 - 29 4.98285340667393e+00 -1.95314136266957e-02 - 30 4.98083878791299e+00 -1.95233551516520e-02 - 31 4.97891115941913e+00 -1.95156446376765e-02 - 32 4.97707338948989e+00 -1.95082935579595e-02 - 33 4.97533838450258e+00 -1.95013535380103e-02 - 34 4.97373007483673e+00 -1.94949202993469e-02 - 35 4.97228253708149e+00 -1.94891301483260e-02 - 36 4.97103753059614e+00 -1.94841501223846e-02 - 37 4.97004091948501e+00 -1.94801636779400e-02 - 38 4.96933848311783e+00 -1.94773539324713e-02 - 39 4.96897154887735e+00 -1.94758861955094e-02 - 40 4.96897275206382e+00 -1.94758910082553e-02 + 20 5.00485448897596e+00 -1.96194179559038e-02 + 21 5.00223519413610e+00 -1.96089407765444e-02 + 22 4.99959613497035e+00 -1.95983845398814e-02 + 23 4.99697045876934e+00 -1.95878818350774e-02 + 24 4.99439079640308e+00 -1.95775631856123e-02 + 25 4.99188501584048e+00 -1.95675400633619e-02 + 26 4.98947279563574e+00 -1.95578911825430e-02 + 27 4.98716399834319e+00 -1.95486559933728e-02 + 28 4.98495936493070e+00 -1.95398374597228e-02 + 29 4.98285340663966e+00 -1.95314136265587e-02 + 30 4.98083878784580e+00 -1.95233551513832e-02 + 31 4.97891115935444e+00 -1.95156446374178e-02 + 32 4.97707338941302e+00 -1.95082935576521e-02 + 33 4.97533838441641e+00 -1.95013535376657e-02 + 34 4.97373007474449e+00 -1.94949202989780e-02 + 35 4.97228253698659e+00 -1.94891301479464e-02 + 36 4.97103753049164e+00 -1.94841501219666e-02 + 37 4.97004091939466e+00 -1.94801636775786e-02 + 38 4.96933848303369e+00 -1.94773539321348e-02 + 39 4.96897154880133e+00 -1.94758861952053e-02 + 40 4.96897275199397e+00 -1.94758910079759e-02 diff --git a/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt b/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out index 62fe7a40c..2331c1a41 100644 --- a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -94,7 +90,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -105,26 +100,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - hBond colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out index 293e9d354..07423f3dd 100644 --- a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -94,7 +90,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -105,31 +100,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - hBond colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.999923 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt b/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out index 9b7934c0b..1c304f72b 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -102,7 +98,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -113,27 +108,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: - inertia colvar component (derived from gyration): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped index b526c1a3b..d529f420f 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.47943794570369e+02 + x 2.47943794577146e+02 } restraint { diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj index 54b38db6c..9c2662344 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 2.53783059466725e+02 -1.01473223786690e+00 + 0 2.53783059466712e+02 -1.01473223786685e+00 1 2.53741340236853e+02 -1.01456536094741e+00 - 2 2.53638721286741e+02 -1.01415488514697e+00 - 3 2.53479585453035e+02 -1.01351834181214e+00 - 4 2.53270136271682e+02 -1.01268054508673e+00 - 5 2.53017700005431e+02 -1.01167080002172e+00 - 6 2.52730128240016e+02 -1.01052051296007e+00 - 7 2.52415319838942e+02 -1.00926127935577e+00 - 8 2.52080840138270e+02 -1.00792336055308e+00 - 9 2.51733604628119e+02 -1.00653441851248e+00 - 10 2.51379609094601e+02 -1.00511843637841e+00 - 11 2.51023709838303e+02 -1.00369483935321e+00 - 12 2.50669473380297e+02 -1.00227789352119e+00 - 13 2.50319117864268e+02 -1.00087647145707e+00 - 14 2.49973559958431e+02 -9.99494239833723e-01 - 15 2.49632568521358e+02 -9.98130274085430e-01 - 16 2.49295012996826e+02 -9.96780051987302e-01 - 17 2.48959183654063e+02 -9.95436734616253e-01 - 18 2.48623152206619e+02 -9.94092608826476e-01 - 19 2.48285132610319e+02 -9.92740530441276e-01 - 20 2.47943794570369e+02 -9.91375178281476e-01 + 2 2.53638721286758e+02 -1.01415488514703e+00 + 3 2.53479585453019e+02 -1.01351834181208e+00 + 4 2.53270136271656e+02 -1.01268054508662e+00 + 5 2.53017700001829e+02 -1.01167080000732e+00 + 6 2.52730128240095e+02 -1.01052051296038e+00 + 7 2.52415319839252e+02 -1.00926127935701e+00 + 8 2.52080840138888e+02 -1.00792336055555e+00 + 9 2.51733604629136e+02 -1.00653441851654e+00 + 10 2.51379609096128e+02 -1.00511843638451e+00 + 11 2.51023709840432e+02 -1.00369483936173e+00 + 12 2.50669473383116e+02 -1.00227789353246e+00 + 13 2.50319117866126e+02 -1.00087647146451e+00 + 14 2.49973559962786e+02 -9.99494239851145e-01 + 15 2.49632568526903e+02 -9.98130274107611e-01 + 16 2.49295013002611e+02 -9.96780052010444e-01 + 17 2.48959183660263e+02 -9.95436734641053e-01 + 18 2.48623152213820e+02 -9.94092608855281e-01 + 19 2.48285132616888e+02 -9.92740530467554e-01 + 20 2.47943794577146e+02 -9.91375178308586e-01 diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out index c94891992..33f101cd0 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -102,7 +98,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -113,32 +108,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: - inertia colvar component (derived from gyration): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 247.944 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 9096628e7..1d4d73e13 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.41656580638813e+02 + x 2.41656580632151e+02 } restraint { diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 270b72c1a..72dbacfd9 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.47943794570369e+02 -9.91375178281476e-01 - 21 2.47598477040393e+02 -9.89993908161571e-01 - 22 2.47249255867815e+02 -9.88597023471262e-01 - 23 2.46896846069752e+02 -9.87187384279007e-01 - 24 2.46542363780136e+02 -9.85769455120543e-01 - 25 2.46187019170014e+02 -9.84348076680055e-01 - 26 2.45831840553059e+02 -9.82927362212236e-01 - 27 2.45477524529067e+02 -9.81510098116269e-01 - 28 2.45124466798686e+02 -9.80097867194745e-01 - 29 2.44772967366842e+02 -9.78691869467368e-01 - 30 2.44423548281158e+02 -9.77294193124631e-01 - 31 2.44077290782282e+02 -9.75909163129130e-01 - 32 2.43736099728340e+02 -9.74544398913360e-01 - 33 2.43402829973457e+02 -9.73211319893828e-01 - 34 2.43081248681633e+02 -9.71924994726533e-01 - 35 2.42775844782379e+02 -9.70703379129517e-01 - 36 2.42491523393473e+02 -9.69566093573892e-01 - 37 2.42233234222450e+02 -9.68532936889801e-01 - 38 2.42005579220911e+02 -9.67622316883644e-01 - 39 2.41812431256466e+02 -9.66849725025865e-01 - 40 2.41656580638813e+02 -9.66226322555252e-01 + 20 2.47943794577146e+02 -9.91375178308586e-01 + 21 2.47598477046097e+02 -9.89993908184388e-01 + 22 2.47249255874236e+02 -9.88597023496945e-01 + 23 2.46896846075395e+02 -9.87187384301580e-01 + 24 2.46542363784743e+02 -9.85769455138973e-01 + 25 2.46187019172168e+02 -9.84348076688674e-01 + 26 2.45831840554944e+02 -9.82927362219775e-01 + 27 2.45477524529089e+02 -9.81510098116355e-01 + 28 2.45124466797313e+02 -9.80097867189253e-01 + 29 2.44772967363848e+02 -9.78691869455392e-01 + 30 2.44423548274181e+02 -9.77294193096724e-01 + 31 2.44077290776696e+02 -9.75909163106782e-01 + 32 2.43736099721675e+02 -9.74544398886700e-01 + 33 2.43402829965980e+02 -9.73211319863919e-01 + 34 2.43081248673642e+02 -9.71924994694569e-01 + 35 2.42775844774184e+02 -9.70703379096737e-01 + 36 2.42491523384140e+02 -9.69566093536562e-01 + 37 2.42233234214778e+02 -9.68532936859112e-01 + 38 2.42005579213859e+02 -9.67622316855437e-01 + 39 2.41812431250163e+02 -9.66849725000653e-01 + 40 2.41656580632151e+02 -9.66226322528602e-01 diff --git a/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt b/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out index 71d0dcbba..bb024e575 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -76,7 +72,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -104,7 +100,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -115,28 +110,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: - inertia colvar component (derived from gyration): -colvars: - inertiaZ colvar component (derived from inertia): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 179a7851f..3f0ca8ee3 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.75096078961602e+01 + x 2.75096079010709e+01 } restraint { diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj index bdcc58815..208c352c5 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 2.74164641878496e+01 -1.09265856751398e-01 - 1 2.74002934369676e+01 -1.09201173747870e-01 - 2 2.73891905422880e+01 -1.09156762169152e-01 - 3 2.73840806710794e+01 -1.09136322684318e-01 - 4 2.73853106962415e+01 -1.09141242784966e-01 - 5 2.73926707772583e+01 -1.09170683109033e-01 - 6 2.74054700019287e+01 -1.09221880007715e-01 - 7 2.74226468646496e+01 -1.09290587458598e-01 - 8 2.74428938157855e+01 -1.09371575263142e-01 - 9 2.74647792825400e+01 -1.09459117130160e-01 - 10 2.74868564347115e+01 -1.09547425738846e-01 - 11 2.75077518051641e+01 -1.09631007220656e-01 - 12 2.75262294370741e+01 -1.09704917748296e-01 - 13 2.75412308249068e+01 -1.09764923299627e-01 - 14 2.75518987119582e+01 -1.09807594847833e-01 - 15 2.75575987144433e+01 -1.09830394857773e-01 - 16 2.75579511788616e+01 -1.09831804715446e-01 - 17 2.75528755131993e+01 -1.09811502052797e-01 - 18 2.75426367029528e+01 -1.09770546811811e-01 - 19 2.75278759428108e+01 -1.09711503771243e-01 - 20 2.75096078961602e+01 -1.09638431584641e-01 + 0 2.74164641878528e+01 -1.09265856751411e-01 + 1 2.74002934369697e+01 -1.09201173747879e-01 + 2 2.73891905423028e+01 -1.09156762169211e-01 + 3 2.73840806711159e+01 -1.09136322684464e-01 + 4 2.73853106963141e+01 -1.09141242785257e-01 + 5 2.73926707769495e+01 -1.09170683107798e-01 + 6 2.74054700020936e+01 -1.09221880008374e-01 + 7 2.74226468649512e+01 -1.09290587459805e-01 + 8 2.74428938162688e+01 -1.09371575265075e-01 + 9 2.74647792832602e+01 -1.09459117133041e-01 + 10 2.74868564357227e+01 -1.09547425742891e-01 + 11 2.75077518065206e+01 -1.09631007226083e-01 + 12 2.75262294388280e+01 -1.09704917755312e-01 + 13 2.75412308252314e+01 -1.09764923300926e-01 + 14 2.75518987145933e+01 -1.09807594858373e-01 + 15 2.75575987160543e+01 -1.09830394864217e-01 + 16 2.75579511825093e+01 -1.09831804730037e-01 + 17 2.75528755165223e+01 -1.09811502066089e-01 + 18 2.75426367051080e+01 -1.09770546820432e-01 + 19 2.75278759473936e+01 -1.09711503789574e-01 + 20 2.75096079010709e+01 -1.09638431604284e-01 diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out index 938486ff2..297ae52c8 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -76,7 +72,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -104,7 +100,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -115,33 +110,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: - inertia colvar component (derived from gyration): -colvars: - inertiaZ colvar component (derived from inertia): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 27.5096 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index f8c9a41c7..8f94c73f0 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.83560354842176e+01 + x 2.83560354929576e+01 } restraint { diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 060386c56..88f514f27 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.75096078961602e+01 -1.09638431584641e-01 - 21 2.74891754878350e+01 -1.09556701951340e-01 - 22 2.74681653014033e+01 -1.09472661205613e-01 - 23 2.74482979809375e+01 -1.09393191923750e-01 - 24 2.74313142837939e+01 -1.09325257135176e-01 - 25 2.74188770303968e+01 -1.09275508121587e-01 - 26 2.74125030723945e+01 -1.09250012289578e-01 - 27 2.74135300949930e+01 -1.09254120379972e-01 - 28 2.74231135180919e+01 -1.09292454072368e-01 - 29 2.74422414944483e+01 -1.09368965977793e-01 - 30 2.74717522224079e+01 -1.09487008889632e-01 - 31 2.75123380776605e+01 -1.09649352310642e-01 - 32 2.75645249027809e+01 -1.09858099611124e-01 - 33 2.76286215047991e+01 -1.10114486019196e-01 - 34 2.77046429906839e+01 -1.10418571962736e-01 - 35 2.77922201138172e+01 -1.10768880455269e-01 - 36 2.78905144303044e+01 -1.11162057721218e-01 - 37 2.79981624989707e+01 -1.11592649995883e-01 - 38 2.81132700839839e+01 -1.12053080335936e-01 - 39 2.82334689354104e+01 -1.12533875741642e-01 - 40 2.83560354842176e+01 -1.13024141936871e-01 + 20 2.75096079010709e+01 -1.09638431604284e-01 + 21 2.74891754936655e+01 -1.09556701974662e-01 + 22 2.74681653074554e+01 -1.09472661229822e-01 + 23 2.74482979871198e+01 -1.09393191948479e-01 + 24 2.74313142900221e+01 -1.09325257160089e-01 + 25 2.74188770369929e+01 -1.09275508147972e-01 + 26 2.74125030784876e+01 -1.09250012313950e-01 + 27 2.74135301010474e+01 -1.09254120404190e-01 + 28 2.74231135227322e+01 -1.09292454090929e-01 + 29 2.74422414999913e+01 -1.09368965999965e-01 + 30 2.74717522279309e+01 -1.09487008911723e-01 + 31 2.75123380832048e+01 -1.09649352332819e-01 + 32 2.75645249083534e+01 -1.09858099633413e-01 + 33 2.76286215104829e+01 -1.10114486041931e-01 + 34 2.77046429965729e+01 -1.10418571986291e-01 + 35 2.77922201200098e+01 -1.10768880480039e-01 + 36 2.78905144368573e+01 -1.11162057747429e-01 + 37 2.79981625060488e+01 -1.11592650024195e-01 + 38 2.81132700916190e+01 -1.12053080366476e-01 + 39 2.82334689436511e+01 -1.12533875774604e-01 + 40 2.83560354929576e+01 -1.13024141971830e-01 diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt b/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out index 6906658ec..7a60e0951 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -124,7 +120,6 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -135,27 +130,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped index fc86e531f..1fc7844e2 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99760693961232e-01 , 1.39216433781234e-02 , 1.19362778059823e-02 , -1.19276119968650e-02 ) + x ( 9.99760693961651e-01 , 1.39216433541339e-02 , 1.19362778078050e-02 , -1.19276119878887e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj index 6b248bf72..0b4deda96 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ) ( 3.40696724956404e-06 , -8.24547608834386e-05 , -5.71707735043921e-05 , 5.95895265542447e-05 ) - 1 ( 9.99574091957316e-01 , 2.05772012681827e-02 , 1.42218162872608e-02 , -1.50317469765464e-02 ) ( 3.40702245731717e-06 , -8.22854314314116e-05 , -5.68711105890293e-05 , 6.01099133459647e-05 ) - 2 ( 9.99576136464269e-01 , 2.04824081529267e-02 , 1.41395609289210e-02 , -1.51026879779696e-02 ) ( 3.39066871847757e-06 , -8.19064783448245e-05 , -5.65422596983307e-05 , 6.03936791309106e-05 ) - 3 ( 9.99580389456459e-01 , 2.03360832362100e-02 , 1.40447201598598e-02 , -1.51074342068980e-02 ) ( 3.35664956461634e-06 , -8.13215747866998e-05 , -5.61631631603791e-05 , 6.04128300627651e-05 ) - 4 ( 9.99586941288893e-01 , 2.01392187843744e-02 , 1.39321349532439e-02 , -1.50417514643494e-02 ) ( 3.30424218006268e-06 , -8.05346892421722e-05 , -5.57131918051387e-05 , 6.01504354667054e-05 ) - 5 ( 9.99595790783329e-01 , 1.98928875288094e-02 , 1.37976726200861e-02 , -1.49047745466495e-02 ) ( 3.23345586896751e-06 , -7.95501051453821e-05 , -5.51758162860883e-05 , 5.96030305121391e-05 ) - 6 ( 9.99606822686916e-01 , 1.95985462816866e-02 , 1.36390185716578e-02 , -1.46994623648640e-02 ) ( 3.14521237059840e-06 , -7.83736341592375e-05 , -5.45417724591643e-05 , 5.87824356543135e-05 ) - 7 ( 9.99619795207092e-01 , 1.92585009913588e-02 , 1.34562172678871e-02 , -1.44327885918466e-02 ) ( 3.04144558769446e-06 , -7.70144759396220e-05 , -5.38112245330522e-05 , 5.77165195903442e-05 ) - 8 ( 9.99634343041458e-01 , 1.88763707874475e-02 , 1.32519032638778e-02 , -1.41155905952574e-02 ) ( 2.92507738195028e-06 , -7.54870750602017e-05 , -5.29946899027906e-05 , 5.64485969671590e-05 ) - 9 ( 9.99649997284953e-01 , 1.84574075512748e-02 , 1.30312276083930e-02 , -1.37620544141233e-02 ) ( 2.79985837307062e-06 , -7.38124013486557e-05 , -5.21127465828725e-05 , 5.50353716238521e-05 ) - 10 ( 9.99666219499820e-01 , 1.80085725925678e-02 , 1.28015269417140e-02 , -1.33888689618389e-02 ) ( 2.67009544562864e-06 , -7.20182596706942e-05 , -5.11947122255672e-05 , 5.35435574715432e-05 ) - 11 ( 9.99682444082188e-01 , 1.75383327410858e-02 , 1.25717990443000e-02 , -1.30141364413955e-02 ) ( 2.54031287827201e-06 , -7.01384778123604e-05 , -5.02765491650432e-05 , 5.20455241394477e-05 ) - 12 ( 9.99698121444835e-01 , 1.70562079173577e-02 , 1.23520473368371e-02 , -1.26561715276433e-02 ) ( 2.41490692643697e-06 , -6.82111000167390e-05 , -4.93982449315156e-05 , 5.06144968497088e-05 ) - 13 ( 9.99712754470273e-01 , 1.65721860651408e-02 , 1.21525545409691e-02 , -1.23323402730933e-02 ) ( 2.29785421817066e-06 , -6.62760490695734e-05 , -4.86009086497119e-05 , 4.93199138526125e-05 ) - 14 ( 9.99725922506310e-01 , 1.60961851478372e-02 , 1.19831437077868e-02 , -1.20580661581261e-02 ) ( 2.19251978606965e-06 , -6.43729753517290e-05 , -4.79238159509638e-05 , 4.82234509889984e-05 ) - 15 ( 9.99737290704466e-01 , 1.56377365616588e-02 , 1.18524811131054e-02 , -1.18460736780739e-02 ) ( 2.10158233787459e-06 , -6.25399902397942e-05 , -4.74016204460428e-05 , 4.73759951950515e-05 ) - 16 ( 9.99746606872211e-01 , 1.52059608592562e-02 , 1.17674662824491e-02 , -1.17058762653601e-02 ) ( 2.02705940720648e-06 , -6.08135677599179e-05 , -4.70619130717184e-05 , 4.68155946238250e-05 ) - 17 ( 9.99753691558999e-01 , 1.48097478384659e-02 , 1.17327398910912e-02 , -1.16434701770315e-02 ) ( 1.97038663356000e-06 , -5.92292632592778e-05 , -4.69232526672145e-05 , 4.65662324496665e-05 ) - 18 ( 9.99758428359742e-01 , 1.44579282356846e-02 , 1.17503257360525e-02 , -1.16611783232732e-02 ) ( 1.93249530916090e-06 , -5.78223985998645e-05 , -4.69937329410254e-05 , 4.66372007220352e-05 ) - 19 ( 9.99760760149601e-01 , 1.41591986489713e-02 , 1.18194125264703e-02 , -1.17575952575529e-02 ) ( 1.91384248526716e-06 , -5.66277607619860e-05 , -4.72701090993454e-05 , 4.70228794642514e-05 ) - 20 ( 9.99760693961232e-01 , 1.39216433781234e-02 , 1.19362778059823e-02 , -1.19276119968650e-02 ) ( 1.91437194998574e-06 , -5.56776887857508e-05 , -4.77374935480734e-05 , 4.77028358420824e-05 ) + 0 ( 9.99574098859266e-01 , 2.06195455609807e-02 , 1.42967532305094e-02 , -1.49016132553015e-02 ) ( 3.40696724955871e-06 , -8.24547608833287e-05 , -5.71707735043578e-05 , 5.95895265542064e-05 ) + 1 ( 9.99574091957315e-01 , 2.05772012682538e-02 , 1.42218162872588e-02 , -1.50317469765650e-02 ) ( 3.40702245733137e-06 , -8.22854314316960e-05 , -5.68711105890215e-05 , 6.01099133460393e-05 ) + 2 ( 9.99576136464277e-01 , 2.04824081529012e-02 , 1.41395609284123e-02 , -1.51026879779233e-02 ) ( 3.39066871841008e-06 , -8.19064783447229e-05 , -5.65422596962969e-05 , 6.03936791307258e-05 ) + 3 ( 9.99580389456449e-01 , 2.03360832367537e-02 , 1.40447201596166e-02 , -1.51074342070060e-02 ) ( 3.35664956469004e-06 , -8.13215747888733e-05 , -5.61631631594061e-05 , 6.04128300631967e-05 ) + 4 ( 9.99586941288897e-01 , 2.01392187847421e-02 , 1.39321349524241e-02 , -1.50417514643484e-02 ) ( 3.30424218003071e-06 , -8.05346892436429e-05 , -5.57131918018609e-05 , 6.01504354667014e-05 ) + 5 ( 9.99595790783300e-01 , 1.98928875282193e-02 , 1.37976726208478e-02 , -1.49047745486655e-02 ) ( 3.23345586919841e-06 , -7.95501051430208e-05 , -5.51758162891334e-05 , 5.96030305201998e-05 ) + 6 ( 9.99606822686883e-01 , 1.95985462834746e-02 , 1.36390185710864e-02 , -1.46994623652575e-02 ) ( 3.14521237086393e-06 , -7.83736341663858e-05 , -5.45417724568780e-05 , 5.87824356558856e-05 ) + 7 ( 9.99619795207068e-01 , 1.92585009929308e-02 , 1.34562172673074e-02 , -1.44327885919656e-02 ) ( 3.04144558788717e-06 , -7.70144759459075e-05 , -5.38112245307334e-05 , 5.77165195908192e-05 ) + 8 ( 9.99634343041421e-01 , 1.88763707892861e-02 , 1.32519032639492e-02 , -1.41155905953322e-02 ) ( 2.92507738224423e-06 , -7.54870750675527e-05 , -5.29946899030751e-05 , 5.64485969674567e-05 ) + 9 ( 9.99649997284929e-01 , 1.84574075526462e-02 , 1.30312276086889e-02 , -1.37620544137684e-02 ) ( 2.79985837326511e-06 , -7.38124013541386e-05 , -5.21127465840553e-05 , 5.50353716224322e-05 ) + 10 ( 9.99666219499819e-01 , 1.80085725929327e-02 , 1.28015269423414e-02 , -1.33888689608095e-02 ) ( 2.67009544563575e-06 , -7.20182596721535e-05 , -5.11947122280763e-05 , 5.35435574674263e-05 ) + 11 ( 9.99682444082219e-01 , 1.75383327400058e-02 , 1.25717990452909e-02 , -1.30141364395225e-02 ) ( 2.54031287802513e-06 , -7.01384778080426e-05 , -5.02765491690069e-05 , 5.20455241319585e-05 ) + 12 ( 9.99698121444904e-01 , 1.70562079144180e-02 , 1.23520473382012e-02 , -1.26561715247952e-02 ) ( 2.41490692588102e-06 , -6.82111000049856e-05 , -4.93982449369732e-05 , 5.06144968383214e-05 ) + 13 ( 9.99712754470511e-01 , 1.65721860535352e-02 , 1.21525545431810e-02 , -1.23323402672332e-02 ) ( 2.29785421626925e-06 , -6.62760490231703e-05 , -4.86009086585655e-05 , 4.93199138291843e-05 ) + 14 ( 9.99725922506467e-01 , 1.60961851402786e-02 , 1.19831437097085e-02 , -1.20580661532487e-02 ) ( 2.19251978481122e-06 , -6.43729753215068e-05 , -4.79238159586543e-05 , 4.82234509694974e-05 ) + 15 ( 9.99737290704757e-01 , 1.56377365465832e-02 , 1.18524811149563e-02 , -1.18460736715164e-02 ) ( 2.10158233554066e-06 , -6.25399901795148e-05 , -4.74016204534546e-05 , 4.73759951688351e-05 ) + 16 ( 9.99746606872466e-01 , 1.52059608462364e-02 , 1.17674662844455e-02 , -1.17058762584516e-02 ) ( 2.02705940516384e-06 , -6.08135677078579e-05 , -4.70619130797105e-05 , 4.68155945962039e-05 ) + 17 ( 9.99753691559363e-01 , 1.48097478197070e-02 , 1.17327398928793e-02 , -1.16434701678110e-02 ) ( 1.97038663064612e-06 , -5.92292631842689e-05 , -4.69232526743774e-05 , 4.65662324128018e-05 ) + 18 ( 9.99758428360226e-01 , 1.44579282082185e-02 , 1.17503257388760e-02 , -1.16611783129527e-02 ) ( 1.93249530528609e-06 , -5.78223984900366e-05 , -4.69937329523329e-05 , 4.66372006807749e-05 ) + 19 ( 9.99760760149993e-01 , 1.41591986268333e-02 , 1.18194125288315e-02 , -1.17575952484608e-02 ) ( 1.91384248212681e-06 , -5.66277606734629e-05 , -4.72701091088012e-05 , 4.70228794279011e-05 ) + 20 ( 9.99760693961651e-01 , 1.39216433541339e-02 , 1.19362778078050e-02 , -1.19276119878887e-02 ) ( 1.91437194663135e-06 , -5.56776886898237e-05 , -4.77374935553765e-05 , 4.77028358061962e-05 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out index 69fbc3cc3..d4c3e96c6 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -124,7 +120,6 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -135,32 +130,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.999761 , 0.0139216 , 0.0119363 , -0.0119276 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped index ad9c0da83..a1d021f26 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99742652479780e-01 , 1.40902379967357e-02 , 1.15309598522144e-02 , -1.35325892118309e-02 ) + x ( 9.99742652480851e-01 , 1.40902379472968e-02 , 1.15309598520170e-02 , -1.35325891843641e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj index 326f48b81..7507a9c22 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( 9.99760693961232e-01 , 1.39216433781234e-02 , 1.19362778059823e-02 , -1.19276119968650e-02 ) ( 1.91437194998574e-06 , -5.56776887857508e-05 , -4.77374935480734e-05 , 4.77028358420824e-05 ) - 21 ( 9.99758313633365e-01 , 1.37518501939863e-02 , 1.20943629910000e-02 , -1.21625376074929e-02 ) ( 1.93341304624615e-06 , -5.49985371073767e-05 , -4.83696566183854e-05 , 4.86423111428367e-05 ) - 22 ( 9.99753796261908e-01 , 1.36537811906101e-02 , 1.22845204605505e-02 , -1.24503685149034e-02 ) ( 1.96954907904872e-06 , -5.46061598016831e-05 , -4.91300159268110e-05 , 4.97932992497502e-05 ) - 23 ( 9.99747426627959e-01 , 1.36276729311783e-02 , 1.24954569253732e-02 , -1.27762685273114e-02 ) ( 2.02050191429012e-06 , -5.45015123963486e-05 , -4.99734110112214e-05 , 5.10964682698865e-05 ) - 24 ( 9.99739603282054e-01 , 1.36692734966396e-02 , 1.27143797755336e-02 , -1.31233051644571e-02 ) ( 2.08308333026075e-06 , -5.46676014211123e-05 , -5.08486896583343e-05 , 5.24841072376327e-05 ) - 25 ( 9.99730831051212e-01 , 1.37696613473913e-02 , 1.29278128060350e-02 , -1.34734378717380e-02 ) ( 2.15325498254029e-06 , -5.50687609506525e-05 , -5.17019710993255e-05 , 5.38840796896415e-05 ) - 26 ( 9.99721697040658e-01 , 1.39157628774382e-02 , 1.31225011979706e-02 , -1.38086919002263e-02 ) ( 2.22632039893925e-06 , -5.56527231861050e-05 , -5.24802652295864e-05 , 5.52245187456788e-05 ) - 27 ( 9.99712830629082e-01 , 1.40915177790539e-02 , 1.32862957768867e-02 , -1.41123969189936e-02 ) ( 2.29724500602795e-06 , -5.63552791136652e-05 , -5.31350077850472e-05 , 5.64387796831146e-05 ) - 28 ( 9.99704851767406e-01 , 1.42794879664030e-02 , 1.34089105192784e-02 , -1.43703408036104e-02 ) ( 2.36106970392215e-06 , -5.71067120286679e-05 , -5.36250874992332e-05 , 5.74700518643537e-05 ) - 29 ( 9.99698315096535e-01 , 1.44626114353530e-02 , 1.34824838999583e-02 , -1.45716948741664e-02 ) ( 2.41335786868624e-06 , -5.78388096174942e-05 , -5.39190880531035e-05 , 5.82750556079333e-05 ) - 30 ( 9.99693659068928e-01 , 1.46257879779070e-02 , 1.35019242353861e-02 , -1.47096018078657e-02 ) ( 2.45060231455666e-06 , -5.84912028734389e-05 , -5.39966660823142e-05 , 5.88263897186958e-05 ) - 31 ( 9.99691168692138e-01 , 1.47570433407831e-02 , 1.34650605673288e-02 , -1.47813752642869e-02 ) ( 2.47052328600467e-06 , -5.90160190716963e-05 , -5.38491520890833e-05 , 5.91133267252955e-05 ) - 32 ( 9.99690957800930e-01 , 1.48481228383961e-02 , 1.33726419051513e-02 , -1.47883260618358e-02 ) ( 2.47221024191153e-06 , -5.93802536948794e-05 , -5.34795460369745e-05 , 5.91411158724805e-05 ) - 33 ( 9.99692972559779e-01 , 1.48944891632750e-02 , 1.32282283630868e-02 , -1.47352903443807e-02 ) ( 2.45609382625367e-06 , -5.95657608180521e-05 , -5.29020819770730e-05 , 5.89290958968973e-05 ) - 34 ( 9.99697013269497e-01 , 1.48948261575969e-02 , 1.30380054972646e-02 , -1.46299769799956e-02 ) ( 2.42377143532588e-06 , -5.95672690438967e-05 , -5.21414867843392e-05 , 5.85080863417083e-05 ) - 35 ( 9.99702767875048e-01 , 1.48502581713688e-02 , 1.28105336093448e-02 , -1.44822637683003e-02 ) ( 2.37773919669474e-06 , -5.93892610389970e-05 , -5.12319796595224e-05 , 5.79175751320903e-05 ) - 36 ( 9.99709848841837e-01 , 1.47635626794789e-02 , 1.25564244174860e-02 , -1.43035503105882e-02 ) ( 2.32109700852655e-06 , -5.90428266173175e-05 , -5.02159814612746e-05 , 5.72031331010642e-05 ) - 37 ( 9.99717826025458e-01 , 1.46386367865957e-02 , 1.22879235275554e-02 , -1.41062247019792e-02 ) ( 2.25728562747236e-06 , -5.85435311676375e-05 , -4.91424471081696e-05 , 5.64142834839795e-05 ) - 38 ( 9.99726251232708e-01 , 1.44803731708344e-02 , 1.20183761975352e-02 , -1.39032378460851e-02 ) ( 2.18989021501695e-06 , -5.79109211903237e-05 , -4.80647306944381e-05 , 5.56028012328199e-05 ) - 39 ( 9.99734674139844e-01 , 1.42949333703084e-02 , 1.17615680015969e-02 , -1.37077248507170e-02 ) ( 2.12251301251851e-06 , -5.71696185014405e-05 , -4.70379496155383e-05 , 5.48211999270969e-05 ) - 40 ( 9.99742652479780e-01 , 1.40902379967357e-02 , 1.15309598522144e-02 , -1.35325892118309e-02 ) ( 2.05869185355315e-06 , -5.63512816728506e-05 , -4.61159255607322e-05 , 5.41210692548650e-05 ) + 20 ( 9.99760693961651e-01 , 1.39216433541339e-02 , 1.19362778078050e-02 , -1.19276119878887e-02 ) ( 1.91437194663135e-06 , -5.56776886898237e-05 , -4.77374935553765e-05 , 4.77028358061962e-05 ) + 21 ( 9.99758313633772e-01 , 1.37518501706272e-02 , 1.20943629928691e-02 , -1.21625375985983e-02 ) ( 1.93341304299124e-06 , -5.49985370139702e-05 , -4.83696566258740e-05 , 4.86423111072771e-05 ) + 22 ( 9.99753796262334e-01 , 1.36537811661746e-02 , 1.22845204621472e-02 , -1.24503685059100e-02 ) ( 1.96954907564106e-06 , -5.46061597039727e-05 , -4.91300159332110e-05 , 4.97932992137969e-05 ) + 23 ( 9.99747426628399e-01 , 1.36276729060903e-02 , 1.24954569267165e-02 , -1.27762685182456e-02 ) ( 2.02050191076346e-06 , -5.45015122960296e-05 , -4.99734110166082e-05 , 5.10964682336444e-05 ) + 24 ( 9.99739603282506e-01 , 1.36692734713397e-02 , 1.27143797766633e-02 , -1.31233051552796e-02 ) ( 2.08308332664440e-06 , -5.46676013199467e-05 , -5.08486896628677e-05 , 5.24841072009449e-05 ) + 25 ( 9.99730831051754e-01 , 1.37696613185747e-02 , 1.29278128058886e-02 , -1.34734378611172e-02 ) ( 2.15325497820459e-06 , -5.50687608354267e-05 , -5.17019710987588e-05 , 5.38840796471852e-05 ) + 26 ( 9.99721697041131e-01 , 1.39157628525684e-02 , 1.31225011988153e-02 , -1.38086918902498e-02 ) ( 2.22632039515597e-06 , -5.56527230866618e-05 , -5.24802652329812e-05 , 5.52245187057974e-05 ) + 27 ( 9.99712830629568e-01 , 1.40915177545030e-02 , 1.32862957776279e-02 , -1.41123969084309e-02 ) ( 2.29724500214521e-06 , -5.63552790154987e-05 , -5.31350077880288e-05 , 5.64387796408899e-05 ) + 28 ( 9.99704851767985e-01 , 1.42794879373133e-02 , 1.34089105192648e-02 , -1.43703407922426e-02 ) ( 2.36106969928898e-06 , -5.71067119123539e-05 , -5.36250874991995e-05 , 5.74700518189137e-05 ) + 29 ( 9.99698315097026e-01 , 1.44626114126131e-02 , 1.34824839010541e-02 , -1.45716948620744e-02 ) ( 2.41335786476355e-06 , -5.78388095265717e-05 , -5.39190880575035e-05 , 5.82750555595938e-05 ) + 30 ( 9.99693659069529e-01 , 1.46257879511962e-02 , 1.35019242354909e-02 , -1.47096017934521e-02 ) ( 2.45060230974677e-06 , -5.84912027666410e-05 , -5.39966660827548e-05 , 5.88263896610770e-05 ) + 31 ( 9.99691168692650e-01 , 1.47570433195187e-02 , 1.34650605688713e-02 , -1.47813752494873e-02 ) ( 2.47052328190881e-06 , -5.90160189866762e-05 , -5.38491520952702e-05 , 5.91133266661292e-05 ) + 32 ( 9.99690957801472e-01 , 1.48481228167761e-02 , 1.33726419068354e-02 , -1.47883260454137e-02 ) ( 2.47221023758033e-06 , -5.93802536084388e-05 , -5.34795460437290e-05 , 5.91411158068268e-05 ) + 33 ( 9.99692972560360e-01 , 1.48944891406353e-02 , 1.32282283648437e-02 , -1.47352903262270e-02 ) ( 2.45609382160275e-06 , -5.95657607275349e-05 , -5.29020819841198e-05 , 5.89290958243205e-05 ) + 34 ( 9.99697013270129e-01 , 1.48948261332085e-02 , 1.30380054990091e-02 , -1.46299769600688e-02 ) ( 2.42377143026910e-06 , -5.95672689463881e-05 , -5.21414867913377e-05 , 5.85080862620418e-05 ) + 35 ( 9.99702767875741e-01 , 1.48502581444742e-02 , 1.28105336109831e-02 , -1.44822637466295e-02 ) ( 2.37773919115572e-06 , -5.93892609314672e-05 , -5.12319796660980e-05 , 5.79175750454513e-05 ) + 36 ( 9.99709848842744e-01 , 1.47635626439325e-02 , 1.25564244173485e-02 , -1.43035502840116e-02 ) ( 2.32109700127172e-06 , -5.90428264751950e-05 , -5.02159814607548e-05 , 5.72031329948130e-05 ) + 37 ( 9.99717826026293e-01 , 1.46386367524169e-02 , 1.22879235287665e-02 , -1.41062246772189e-02 ) ( 2.25728562079388e-06 , -5.85435310309807e-05 , -4.91424471130407e-05 , 5.64142833849880e-05 ) + 38 ( 9.99726251233621e-01 , 1.44803731319332e-02 , 1.20183761983179e-02 , -1.39032378202861e-02 ) ( 2.18989020771502e-06 , -5.79109210347829e-05 , -4.80647306975977e-05 , 5.56028011296765e-05 ) + 39 ( 9.99734674140845e-01 , 1.42949333257481e-02 , 1.17615680020998e-02 , -1.37077248236990e-02 ) ( 2.12251300450785e-06 , -5.71696183232687e-05 , -4.70379496175808e-05 , 5.48211998190806e-05 ) + 40 ( 9.99742652480851e-01 , 1.40902379472968e-02 , 1.15309598520170e-02 , -1.35325891843641e-02 ) ( 2.05869184498829e-06 , -5.63512814751691e-05 , -4.61159255599756e-05 , 5.41210691450550e-05 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out index ec40acc6d..9a2c9b63c 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -127,7 +123,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -138,27 +133,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped index 279228b77..01d155e7c 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99760693817830e-01 , 1.39216455125237e-02 , 1.19362887805905e-02 , -1.19276105428297e-02 ) + x ( 9.99760693818246e-01 , 1.39216454886428e-02 , 1.19362887828950e-02 , -1.19276105335207e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.27813232055650e-03 + accumulatedWork 2.27813232055700e-03 } } diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj index b339c9cfb..7b97e03f8 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ) ( 3.40696724956404e-06 , -8.24547608834386e-05 , -5.71707735043921e-05 , 5.95895265542447e-05 ) 1.70372550452894e-06 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 - 1 ( 9.99574091957316e-01 , 2.05772012681827e-02 , 1.42218162872608e-02 , -1.50317469765464e-02 ) ( -2.89857105413568e-06 , -8.20357344749931e-05 , 3.85760678003605e-04 , 5.99275084882400e-05 ) 1.98926088015520e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.24615390673096e-05 - 2 ( 9.99576136464117e-01 , 2.04824081526900e-02 , 1.41395609423227e-02 , -1.51026879758038e-02 ) ( -1.05168657309248e-05 , -8.04517476314451e-05 , 9.23378079065106e-04 , 5.93210345447713e-05 ) 1.07841143774898e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.63130419745432e-04 - 3 ( 9.99580389455824e-01 , 2.03360832354197e-02 , 1.40447202158084e-02 , -1.51074341979379e-02 ) ( -1.95312689952873e-05 , -7.71426868980550e-05 , 1.56340858862322e-03 , 5.73083839534375e-05 ) 3.06732891307828e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.94155785846739e-04 - 4 ( 9.99586941287241e-01 , 2.01392187829879e-02 , 1.39321350986197e-02 , -1.50417514413077e-02 ) ( -2.97615745192475e-05 , -7.14911802640544e-05 , 2.29629026903105e-03 , 5.33959422838193e-05 ) 6.60224608309061e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.47035553394974e-04 - 5 ( 9.99595790779906e-01 , 1.98928875276492e-02 , 1.37976729205755e-02 , -1.49047744995720e-02 ) ( -4.06413192373749e-05 , -6.31016250631435e-05 , 3.08637898561543e-03 , 4.72789830443403e-05 ) 1.19170050962515e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.18350423122506e-03 - 6 ( 9.99606822680751e-01 , 1.95985462832515e-02 , 1.36390191111118e-02 , -1.46994622814130e-02 ) ( -5.12953295469620e-05 , -5.21496651296818e-05 , 3.87653754434035e-03 , 3.91137191750376e-05 ) 1.87930300176431e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.61639198938578e-03 - 7 ( 9.99619795197032e-01 , 1.92585010007719e-02 , 1.34562181453815e-02 , -1.44327884579218e-02 ) ( -6.08644895994507e-05 , -3.94609367964904e-05 , 4.60962560797712e-03 , 2.95729845802817e-05 ) 2.65684805734531e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.95913218474063e-03 - 8 ( 9.99634343026221e-01 , 1.88763708133848e-02 , 1.32519045886273e-02 , -1.41155903958815e-02 ) ( -6.88272478670076e-05 , -2.61706583210457e-05 , 5.24998743936081e-03 , 1.95701968827877e-05 ) 3.44602164993228e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.17342875845415e-03 - 9 ( 9.99649997263207e-01 , 1.84574076067301e-02 , 1.30312294934032e-02 , -1.37620541344282e-02 ) ( -7.50701457814478e-05 , -1.32797169768971e-05 , 5.78803752266657e-03 , 9.90150880448157e-06 ) 4.18841103516792e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.26930643841353e-03 - 10 ( 9.99666219470249e-01 , 1.80085726953522e-02 , 1.28015294972442e-02 , -1.33888685880002e-02 ) ( -7.97587545516019e-05 , -1.43682091227853e-06 , 6.23146712392729e-03 , 1.06823603982523e-06 ) 4.85469339763710e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 11 ( 9.99682444043555e-01 , 1.75383329140093e-02 , 1.25718023719501e-02 , -1.30141359614126e-02 ) ( -7.83400542234201e-05 , -1.37439039732904e-06 , 6.23240419814605e-03 , 1.01985197695800e-06 ) 4.85612527277641e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 12 ( 9.99698121396159e-01 , 1.70562081867899e-02 , 1.23520515136698e-02 , -1.26561709329443e-02 ) ( -7.69825486892822e-05 , -1.31342687266466e-06 , 6.23330027301218e-03 , 9.74598505501407e-07 ) 4.85749516015860e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 13 ( 9.99712754410809e-01 , 1.65721864606089e-02 , 1.21525596183800e-02 , -1.23323395586735e-02 ) ( -7.57498609725947e-05 , -1.25570151512460e-06 , 6.23411347952713e-03 , 9.34441421212952e-07 ) 4.85873892087829e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 14 ( 9.99725922435513e-01 , 1.60961857012553e-02 , 1.19831497116778e-02 , -1.20580653224807e-02 ) ( -7.47028381344618e-05 , -1.20276040466548e-06 , 6.23480386682432e-03 , 9.01018650997467e-07 ) 4.85979525378250e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 15 ( 9.99737290621952e-01 , 1.56377373062154e-02 , 1.18524880452973e-02 , -1.18460727229225e-02 ) ( -7.38952136243442e-05 , -1.15585759347365e-06 , 6.23533622413239e-03 , 8.75598102302748e-07 ) 4.86061005415662e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 16 ( 9.99746606777718e-01 , 1.52059618280014e-02 , 1.17674741231820e-02 , -1.17058751951783e-02 ) ( -7.33697991663691e-05 , -1.11594113737261e-06 , 6.23568254122528e-03 , 8.59075396019594e-07 ) 4.86114023321333e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 17 ( 9.99753691452358e-01 , 1.48097490626708e-02 , 1.17327486023943e-02 , -1.16434689984246e-02 ) ( -7.31554048026095e-05 , -1.08368010737810e-06 , 6.23582398802628e-03 , 8.51992540931742e-07 ) 4.86135680289371e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 18 ( 9.99758428240858e-01 , 1.44579297430799e-02 , 1.17503352657271e-02 , -1.16611770442436e-02 ) ( -7.32645959690450e-05 , -1.05951032894958e-06 , 6.23575235353917e-03 , 8.54557861715953e-07 ) 4.86124712106538e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 19 ( 9.99760760018442e-01 , 1.41592004620220e-02 , 1.18194228124135e-02 , -1.17575938867382e-02 ) ( -7.36923301249498e-05 , -1.04367416334025e-06 , 6.23547092568478e-03 , 8.66651827943935e-07 ) 4.86081625811507e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 20 ( 9.99760693817830e-01 , 1.39216455125237e-02 , 1.19362887805905e-02 , -1.19276105428297e-02 ) ( -7.44154910767136e-05 , -1.03623406462822e-06 , 6.23499480535782e-03 , 8.87811454686164e-07 ) 4.86008746876767e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 1 ( 9.99574091957314e-01 , 2.05772012682737e-02 , 1.42218162872633e-02 , -1.50317469765766e-02 ) ( -2.89857105411844e-06 , -8.20357344753561e-05 , 3.85760678003595e-04 , 5.99275084883605e-05 ) 1.98926088015600e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.24615390673084e-05 + 2 ( 9.99576136464107e-01 , 2.04824081530443e-02 , 1.41395609423345e-02 , -1.51026879759213e-02 ) ( -1.05168657308638e-05 , -8.04517476328365e-05 , 9.23378079065062e-04 , 5.93210345452325e-05 ) 1.07841143774923e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.63130419745423e-04 + 3 ( 9.99580389455804e-01 , 2.03360832361746e-02 , 1.40447202158361e-02 , -1.51074341981852e-02 ) ( -1.95312689951841e-05 , -7.71426869009185e-05 , 1.56340858862312e-03 , 5.73083839543752e-05 ) 3.06732891307857e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.94155785846709e-04 + 4 ( 9.99586941287210e-01 , 2.01392187842197e-02 , 1.39321350986691e-02 , -1.50417514416994e-02 ) ( -2.97615745191412e-05 , -7.14911802684271e-05 , 2.29629026903087e-03 , 5.33959422852095e-05 ) 6.60224608309056e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.47035553394905e-04 + 5 ( 9.99595790779864e-01 , 1.98928875293495e-02 , 1.37976729206519e-02 , -1.49047745000832e-02 ) ( -4.06413192373453e-05 , -6.31016250685387e-05 , 3.08637898561516e-03 , 4.72789830459629e-05 ) 1.19170050962504e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.18350423122495e-03 + 6 ( 9.99606822680701e-01 , 1.95985462853154e-02 , 1.36390191112217e-02 , -1.46994622819746e-02 ) ( -5.12953295471253e-05 , -5.21496651351779e-05 , 3.87653754433995e-03 , 3.91137191765353e-05 ) 1.87930300176401e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.61639198938565e-03 + 7 ( 9.99619795196980e-01 , 1.92585010029931e-02 , 1.34562181455343e-02 , -1.44327884584219e-02 ) ( -6.08644895999444e-05 , -3.94609368010510e-05 , 4.60962560797654e-03 , 2.95729845813135e-05 ) 2.65684805734470e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.95913218474054e-03 + 8 ( 9.99634343026175e-01 , 1.88763708154653e-02 , 1.32519045888371e-02 , -1.41155903961733e-02 ) ( -6.88272478679810e-05 , -2.61706583239472e-05 , 5.24998743935999e-03 , 1.95701968832050e-05 ) 3.44602164993124e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.17342875845418e-03 + 9 ( 9.99649997263176e-01 , 1.84574076082982e-02 , 1.30312294936897e-02 , -1.37620541343428e-02 ) ( -7.50701457830531e-05 , -1.32797169780534e-05 , 5.78803752266541e-03 , 9.90150880444109e-06 ) 4.18841103516628e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.26930643841376e-03 + 10 ( 9.99666219470242e-01 , 1.80085726959886e-02 , 1.28015294976327e-02 , -1.33888685873615e-02 ) ( -7.97587545540024e-05 , -1.43682091237256e-06 , 6.23146712392570e-03 , 1.06823603980643e-06 ) 4.85469339763468e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 11 ( 9.99682444043579e-01 , 1.75383329132778e-02 , 1.25718023724709e-02 , -1.30141359600538e-02 ) ( -7.83400542266416e-05 , -1.37439039732819e-06 , 6.23240419814393e-03 , 1.01985197689343e-06 ) 4.85612527277317e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 12 ( 9.99698121396221e-01 , 1.70562081842655e-02 , 1.23520515143566e-02 , -1.26561709307220e-02 ) ( -7.69825486935338e-05 , -1.31342687254272e-06 , 6.23330027300938e-03 , 9.74598505384046e-07 ) 4.85749516015432e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 13 ( 9.99712754410915e-01 , 1.65721864559041e-02 , 1.21525596192655e-02 , -1.23323395554808e-02 ) ( -7.57498609780799e-05 , -1.25570151485890e-06 , 6.23411347952353e-03 , 9.34441421038598e-07 ) 4.85873892087277e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 14 ( 9.99725922435667e-01 , 1.60961856940404e-02 , 1.19831497127895e-02 , -1.20580653182552e-02 ) ( -7.47028381413507e-05 , -1.20276040423710e-06 , 6.23480386681979e-03 , 9.01018650764673e-07 ) 4.85979525377557e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 15 ( 9.99737290622154e-01 , 1.56377372962370e-02 , 1.18524880466519e-02 , -1.18460727176508e-02 ) ( -7.38952136327416e-05 , -1.15585759286722e-06 , 6.23533622412687e-03 , 8.75598102012420e-07 ) 4.86061005414818e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 16 ( 9.99746606777969e-01 , 1.52059618150989e-02 , 1.17674741247817e-02 , -1.17058751888952e-02 ) ( -7.33697991762876e-05 , -1.11594113657630e-06 , 6.23568254121877e-03 , 8.59075395674407e-07 ) 4.86114023320336e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 17 ( 9.99753691452656e-01 , 1.48097490467918e-02 , 1.17327486042245e-02 , -1.16434689912063e-02 ) ( -7.31554048139585e-05 , -1.08368010638398e-06 , 6.23582398801883e-03 , 8.51992540535477e-07 ) 4.86135680288230e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 18 ( 9.99758428241199e-01 , 1.44579297242938e-02 , 1.17503352677578e-02 , -1.16611770361988e-02 ) ( -7.32645959816383e-05 , -1.05951032775465e-06 , 6.23575235353089e-03 , 8.54557861273005e-07 ) 4.86124712105271e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 19 ( 9.99760760018823e-01 , 1.41592004405267e-02 , 1.18194228146038e-02 , -1.17575938779946e-02 ) ( -7.36923301385327e-05 , -1.04367416194781e-06 , 6.23547092567585e-03 , 8.66651827458857e-07 ) 4.86081625810141e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 20 ( 9.99760693818246e-01 , 1.39216454886428e-02 , 1.19362887828950e-02 , -1.19276105335207e-02 ) ( -7.44154910910036e-05 , -1.03623406304924e-06 , 6.23499480534843e-03 , 8.87811454163381e-07 ) 4.86008746875330e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out index 124c00f20..f89ad9c5b 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -127,7 +123,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -138,32 +133,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.999761 , 0.0139216 , 0.0119363 , -0.0119276 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped index 938849f24..cc10dd18f 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99742652208198e-01 , 1.40902436380753e-02 , 1.15309792258764e-02 , -1.35325868934950e-02 ) + x ( 9.99742652209286e-01 , 1.40902435879328e-02 , 1.15309792246189e-02 , -1.35325868663831e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.27813232055650e-03 + accumulatedWork 2.27813232055700e-03 } } diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj index f4c99c252..789205d92 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( 9.99760693817830e-01 , 1.39216455125237e-02 , 1.19362887805905e-02 , -1.19276105428297e-02 ) ( -7.44154910767136e-05 , -1.03623406462822e-06 , 6.23499480535782e-03 , 8.87811454686164e-07 ) 4.86008746876767e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 21 ( 9.99758313477823e-01 , 1.37518526575684e-02 , 1.20943745854034e-02 , -1.21625360781649e-02 ) ( -7.53933764513610e-05 , -1.03704924514109e-06 , 6.23435061795974e-03 , 9.17196335136740e-07 ) 4.85910171319849e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 22 ( 9.99753796094403e-01 , 1.36537839828244e-02 , 1.22845326084587e-02 , -1.24503669172219e-02 ) ( -7.65692635123717e-05 , -1.04571764348986e-06 , 6.23357553387972e-03 , 9.53550193092197e-07 ) 4.85791609893525e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 23 ( 9.99747426448760e-01 , 1.36276760432249e-02 , 1.24954695663346e-02 , -1.27762668671144e-02 ) ( -7.78731950221508e-05 , -1.06149878072943e-06 , 6.23271549316725e-03 , 9.95180077564155e-07 ) 4.85660109630414e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 24 ( 9.99739603091531e-01 , 1.36692769122303e-02 , 1.27143928574664e-02 , -1.31233034465857e-02 ) ( -7.92260158415096e-05 , -1.08324442268912e-06 , 6.23182259924548e-03 , 1.03997785377014e-06 ) 4.85523649062815e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 25 ( 9.99730830849845e-01 , 1.37696650440250e-02 , 1.29278262869396e-02 , -1.34734361002817e-02 ) ( -8.05444416081335e-05 , -1.10936858990258e-06 , 6.23095181082655e-03 , 1.08550257104459e-06 ) 4.85390628561639e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 26 ( 9.99721696829043e-01 , 1.39157668280219e-02 , 1.31225150468116e-02 , -1.38086900788067e-02 ) ( -8.17466563396149e-05 , -1.13788408534165e-06 , 6.23015725332975e-03 , 1.12912848240953e-06 ) 4.85269306084392e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 27 ( 9.99712830407931e-01 , 1.40915219536903e-02 , 1.32863099736998e-02 , -1.41123950509825e-02 ) ( -8.27577572384685e-05 , -1.16651774138799e-06 , 6.22948859731456e-03 , 1.16824564830883e-06 ) 4.85167246950209e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 28 ( 9.99704851537533e-01 , 1.42794923342033e-02 , 1.34089250546046e-02 , -1.43703388922140e-02 ) ( -8.35143962951262e-05 , -1.19289526289459e-06 , 6.22898794028392e-03 , 1.20048449829351e-06 ) 4.85090853484415e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 29 ( 9.99698314858842e-01 , 1.44626159661916e-02 , 1.34824987737283e-02 , -1.45716929223678e-02 ) ( -8.39681998992706e-05 , -1.21476630545989e-06 , 6.22868748240922e-03 , 1.22392806508725e-06 ) 4.85045017322160e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 30 ( 9.99693658824374e-01 , 1.46257926440631e-02 , 1.35019394553724e-02 , -1.47095998182711e-02 ) ( -8.40878559098745e-05 , -1.23022841404033e-06 , 6.22860808562373e-03 , 1.23727773912788e-06 ) 4.85032906201587e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 31 ( 9.99691168441709e-01 , 1.47570481184252e-02 , 1.34650761472677e-02 , -1.47813732389598e-02 ) ( -8.38600119204497e-05 , -1.23790853634409e-06 , 6.22875863536561e-03 , 1.23994907142371e-06 ) 4.85055871364153e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 32 ( 9.99690957545599e-01 , 1.48481277088428e-02 , 1.33726578626311e-02 , -1.47883240021993e-02 ) ( -8.32892561524428e-05 , -1.23707181983747e-06 , 6.22913603471590e-03 , 1.23208927377770e-06 ) 4.85113448594715e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 33 ( 9.99692972300467e-01 , 1.48944941139382e-02 , 1.32282447172976e-02 , -1.47352882512418e-02 ) ( -8.23974522780850e-05 , -1.22764528906839e-06 , 6.22972565465496e-03 , 1.21452310271978e-06 ) 4.85203425682343e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 34 ( 9.99697013007040e-01 , 1.48948311824960e-02 , 1.30380222667125e-02 , -1.46299748536945e-02 ) ( -8.12226196239937e-05 , -1.21016387141186e-06 , 6.23050211131550e-03 , 1.18864502663254e-06 ) 4.85321956880239e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 35 ( 9.99702767610164e-01 , 1.48502632711203e-02 , 1.28105508096523e-02 , -1.44822616089398e-02 ) ( -7.98174260852071e-05 , -1.18566220820019e-06 , 6.23143031865720e-03 , 1.15628052954330e-06 ) 4.85463717257082e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 36 ( 9.99709848575105e-01 , 1.47635678606929e-02 , 1.25564420594164e-02 , -1.43035481182791e-02 ) ( -7.82472390280891e-05 , -1.15554370595586e-06 , 6.23246684237661e-03 , 1.11953798410207e-06 ) 4.85622102004825e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 37 ( 9.99717825757301e-01 , 1.46386420606817e-02 , 1.22879416154002e-02 , -1.41062224770323e-02 ) ( -7.65875917958683e-05 , -1.12145478824491e-06 , 6.23356163672657e-03 , 1.08066654511663e-06 ) 4.85789484544842e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 38 ( 9.99726250963382e-01 , 1.44803785522926e-02 , 1.20183947280021e-02 , -1.39032355891063e-02 ) ( -7.49209174022956e-05 , -1.08518031253540e-06 , 6.23466024929070e-03 , 1.04192839208965e-06 ) 4.85957547889764e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 39 ( 9.99734673869434e-01 , 1.42949388746288e-02 , 1.17615869633091e-02 , -1.37077225625754e-02 ) ( -7.33324894813423e-05 , -1.04856166546951e-06 , 6.23570652180672e-03 , 1.00548820292743e-06 ) 4.86117694882555e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 40 ( 9.99742652208198e-01 , 1.40902436380753e-02 , 1.15309792258764e-02 , -1.35325868934950e-02 ) ( -7.19056858067241e-05 , -1.01342943580709e-06 , 6.23664570366618e-03 , 9.73320423177462e-07 ) 4.86261525438764e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 20 ( 9.99760693818246e-01 , 1.39216454886428e-02 , 1.19362887828950e-02 , -1.19276105335207e-02 ) ( -7.44154910910036e-05 , -1.03623406304924e-06 , 6.23499480534843e-03 , 8.87811454163381e-07 ) 4.86008746875330e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 21 ( 9.99758313478268e-01 , 1.37518526317376e-02 , 1.20943745877787e-02 , -1.21625360684149e-02 ) ( -7.53933764660893e-05 , -1.03704924339528e-06 , 6.23435061795005e-03 , 9.17196334580247e-07 ) 4.85910171318368e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 22 ( 9.99753796094871e-01 , 1.36537839555646e-02 , 1.22845326108695e-02 , -1.24503669071325e-02 ) ( -7.65692635273181e-05 , -1.04571764160572e-06 , 6.23357553386989e-03 , 9.53550192505157e-07 ) 4.85791609892022e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 23 ( 9.99747426449245e-01 , 1.36276760151045e-02 , 1.24954695687563e-02 , -1.27762668567522e-02 ) ( -7.78731950371622e-05 , -1.06149877874316e-06 , 6.23271549315738e-03 , 9.95180076948371e-07 ) 4.85660109628904e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 24 ( 9.99739603092028e-01 , 1.36692768838184e-02 , 1.27143928598848e-02 , -1.31233034359725e-02 ) ( -7.92260158564982e-05 , -1.08324442064198e-06 , 6.23182259923561e-03 , 1.03997785312531e-06 ) 4.85523649061308e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 25 ( 9.99730830850349e-01 , 1.37696650158448e-02 , 1.29278262893479e-02 , -1.34734360893895e-02 ) ( -8.05444416230567e-05 , -1.10936858783720e-06 , 6.23095181081672e-03 , 1.08550257036763e-06 ) 4.85390628560139e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 26 ( 9.99721696829550e-01 , 1.39157668005032e-02 , 1.31225150492047e-02 , -1.38086900675579e-02 ) ( -8.17466563544410e-05 , -1.13788408329726e-06 , 6.23015725331999e-03 , 1.12912848169394e-06 ) 4.85269306082901e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 27 ( 9.99712830408440e-01 , 1.40915219271310e-02 , 1.32863099760682e-02 , -1.41123950392548e-02 ) ( -8.27577572531398e-05 , -1.16651773939557e-06 , 6.22948859730489e-03 , 1.16824564754451e-06 ) 4.85167246948734e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 28 ( 9.99704851538043e-01 , 1.42794923087412e-02 , 1.34089250569295e-02 , -1.43703388798510e-02 ) ( -8.35143963095269e-05 , -1.19289526097260e-06 , 6.22898794027442e-03 , 1.20048449746711e-06 ) 4.85090853482966e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 29 ( 9.99698314859356e-01 , 1.44626159417893e-02 , 1.34824987759774e-02 , -1.45716929091923e-02 ) ( -8.39681999132023e-05 , -1.21476630361119e-06 , 6.22868748240004e-03 , 1.22392806418303e-06 ) 4.85045017320758e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 30 ( 9.99693658824898e-01 , 1.46257926205038e-02 , 1.35019394575005e-02 , -1.47095998041003e-02 ) ( -8.40878559230599e-05 , -1.23022841225092e-06 , 6.22860808561504e-03 , 1.23727773812928e-06 ) 4.85032906200261e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 31 ( 9.99691168442251e-01 , 1.47570480953222e-02 , 1.34650761492187e-02 , -1.47813732236213e-02 ) ( -8.38600119325431e-05 , -1.23790853458392e-06 , 6.22875863535765e-03 , 1.23994907031517e-06 ) 4.85055871362938e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 32 ( 9.99690957546167e-01 , 1.48481276856586e-02 , 1.33726578643432e-02 , -1.47883239855450e-02 ) ( -8.32892561630635e-05 , -1.23707181806292e-06 , 6.22913603470891e-03 , 1.23208927254656e-06 ) 4.85113448593648e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 33 ( 9.99692972301071e-01 , 1.48944940900112e-02 , 1.32282447187099e-02 , -1.47352882331596e-02 ) ( -8.23974522868586e-05 , -1.22764528722624e-06 , 6.22972565464919e-03 , 1.21452310135798e-06 ) 4.85203425681462e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 34 ( 9.99697013007692e-01 , 1.48948311570748e-02 , 1.30380222677718e-02 , -1.46299748341174e-02 ) ( -8.12226196305917e-05 , -1.21016386944397e-06 , 6.23050211131118e-03 , 1.18864502513774e-06 ) 4.85321956879579e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 35 ( 9.99702767610873e-01 , 1.48502632434009e-02 , 1.28105508103196e-02 , -1.44822615878513e-02 ) ( -7.98174260893882e-05 , -1.18566220604831e-06 , 6.23143031865448e-03 , 1.15628052791932e-06 ) 4.85463717256666e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 36 ( 9.99709848575880e-01 , 1.47635678298615e-02 , 1.25564420596702e-02 , -1.43035480957163e-02 ) ( -7.82472390297188e-05 , -1.15554370356586e-06 , 6.23246684237558e-03 , 1.11953798235853e-06 ) 4.85622102004666e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 37 ( 9.99717825758149e-01 , 1.46386420259571e-02 , 1.22879416152389e-02 , -1.41062224530848e-02 ) ( -7.65875917949357e-05 , -1.12145478557008e-06 , 6.23356163672723e-03 , 1.08066654326796e-06 ) 4.85789484544943e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 38 ( 9.99726250964308e-01 , 1.44803785129685e-02 , 1.20183947274420e-02 , -1.39032355639129e-02 ) ( -7.49209173989000e-05 , -1.08518030953821e-06 , 6.23466024929299e-03 , 1.04192839015343e-06 ) 4.85957547890113e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 39 ( 9.99734673870441e-01 , 1.42949388301149e-02 , 1.17615869623806e-02 , -1.37077225363170e-02 ) ( -7.33324894756701e-05 , -1.04856166212217e-06 , 6.23570652181050e-03 , 1.00548820092254e-06 ) 4.86117694883134e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 40 ( 9.99742652209286e-01 , 1.40902435879328e-02 , 1.15309792246189e-02 , -1.35325868663831e-02 ) ( -7.19056857990176e-05 , -1.01342943209091e-06 , 6.23664570367131e-03 , 9.73320421122090e-07 ) 4.86261525439548e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out index ab5aa163d..116aff668 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -106,7 +102,6 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -117,26 +112,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped index 869052fe0..1f5d27b1f 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.95047582249982e-01 , -8.94218407198434e-02 , 1.03501830123263e-02 , -4.21534953752505e-02 ) + x ( 9.95047582247901e-01 , -8.94218407474711e-02 , 1.03501830154734e-02 , -4.21534953649891e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj index 479a43598..883efbc35 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( 9.95725692918276e-01 , -7.96585470771598e-02 , 1.34264420545571e-02 , -4.47726589977838e-02 ) ( 3.41700762028735e-05 , 3.17725061894150e-04 , -5.35525350301741e-05 , 1.78579654954758e-04 ) - 1 ( 9.95703202497434e-01 , -7.99005029585730e-02 , 1.32741369737813e-02 , -4.48869630396400e-02 ) ( 3.43497422149501e-05 , 3.18685319686495e-04 , -5.29442547720273e-05 , 1.79032867583579e-04 ) - 2 ( 9.95678521556875e-01 , -8.01968009437818e-02 , 1.31263198798365e-02 , -4.49494666832817e-02 ) ( 3.45469057626449e-05 , 3.19861820323622e-04 , -5.23538161311184e-05 , 1.79279199004076e-04 ) - 3 ( 9.95652403679467e-01 , -8.05419873410536e-02 , 1.29777382161078e-02 , -4.49539501406355e-02 ) ( 3.47555464982458e-05 , 3.21232958651731e-04 , -5.17602977204288e-05 , 1.79293941998351e-04 ) - 4 ( 9.95625468036827e-01 , -8.09309980554691e-02 , 1.28228853926643e-02 , -4.48962644370436e-02 ) ( 3.49707179806798e-05 , 3.22778657195090e-04 , -5.11417606091293e-05 , 1.79060635556877e-04 ) - 5 ( 9.95598135270229e-01 , -8.13594233176651e-02 , 1.26568594199537e-02 , -4.47750063482282e-02 ) ( 3.51890598474303e-05 , 3.24481408186395e-04 , -5.04786710663926e-05 , 1.78573747440431e-04 ) - 6 ( 9.95570599010826e-01 , -8.18234325659399e-02 , 1.24760860076073e-02 , -4.45921018374740e-02 ) ( 3.54090252523799e-05 , 3.26325967036996e-04 , -4.97567836449325e-05 , 1.77840996130284e-04 ) - 7 ( 9.95542831967203e-01 , -8.23194900206118e-02 , 1.22788215872927e-02 , -4.43531489512843e-02 ) ( 3.56308321570564e-05 , 3.28298218081753e-04 , -4.89691474794440e-05 , 1.76884717864206e-04 ) - 8 ( 9.95514620285900e-01 , -8.28440052668668e-02 , 1.20654160973878e-02 , -4.40674179270895e-02 ) ( 3.58561887764231e-05 , 3.30383787230043e-04 , -4.81171552717718e-05 , 1.75741870293466e-04 ) - 9 ( 9.95485617186302e-01 , -8.33930320021245e-02 , 1.18383657119753e-02 , -4.37474717666082e-02 ) ( 3.60878650745618e-05 , 3.32566851194540e-04 , -4.72107550666910e-05 , 1.74462525031735e-04 ) - 10 ( 9.95455406148209e-01 , -8.39620802385744e-02 , 1.16022024359213e-02 , -4.34084364029869e-02 ) ( 3.63291879744745e-05 , 3.34829401794161e-04 , -4.62680115842287e-05 , 1.73106963909578e-04 ) - 11 ( 9.95423564349720e-01 , -8.45460630928600e-02 , 1.13632516811963e-02 , -4.30670089979245e-02 ) ( 3.65835345916786e-05 , 3.37151047680939e-04 , -4.53141408272277e-05 , 1.71741730755538e-04 ) - 12 ( 9.95389718654174e-01 , -8.51393630184037e-02 , 1.11292589640790e-02 , -4.27403375898543e-02 ) ( 3.68538850093158e-05 , 3.39509291391604e-04 , -4.43800222441335e-05 , 1.70435169051391e-04 ) - 13 ( 9.95353590494649e-01 , -8.57359613149864e-02 , 1.09088757881713e-02 , -4.24449202596133e-02 ) ( 3.71424637623492e-05 , 3.41880056834273e-04 , -4.35001487970268e-05 , 1.69253036043655e-04 ) - 14 ( 9.95315031423055e-01 , -8.63295419632000e-02 , 1.07110129745439e-02 , -4.21956467992482e-02 ) ( 3.74504559166966e-05 , 3.44238112758864e-04 , -4.27100481277245e-05 , 1.68254684207691e-04 ) - 15 ( 9.95274054252229e-01 , -8.69134880395287e-02 , 1.05441067567461e-02 , -4.20050513847555e-02 ) ( 3.77777583793028e-05 , 3.46557067272315e-04 , -4.20433559514056e-05 , 1.67490084069610e-04 ) - 16 ( 9.95230862600358e-01 , -8.74807544192303e-02 , 1.04153736849348e-02 , -4.18827855448026e-02 ) ( 3.81227440029491e-05 , 3.48808869035314e-04 , -4.15288452842110e-05 , 1.66997726013206e-04 ) - 17 ( 9.95185875295753e-01 , -8.80236982613176e-02 , 1.03301362013300e-02 , -4.18352774854899e-02 ) ( 3.84820667784462e-05 , 3.50963139203125e-04 , -4.11877380890261e-05 , 1.66803265549611e-04 ) - 18 ( 9.95139736354077e-01 , -8.85340180775604e-02 , 1.02912848947750e-02 , -4.18655255239391e-02 ) ( 3.88505822918751e-05 , 3.52986932995553e-04 , -4.10315624487717e-05 , 1.66918702819926e-04 ) - 19 ( 9.95093299817054e-01 , -8.90029543523046e-02 , 1.02989187503535e-02 , -4.19729799792916e-02 ) ( 3.92214689751451e-05 , 3.54845537784723e-04 , -4.10607197161619e-05 , 1.67341913103511e-04 ) - 20 ( 9.95047582249982e-01 , -8.94218407198434e-02 , 1.03501830123263e-02 , -4.21534953752505e-02 ) ( 3.95866076414231e-05 , 3.56504660172752e-04 , -4.12638394360000e-05 , 1.68056454920554e-04 ) + 0 ( 9.95725692918273e-01 , -7.96585470771966e-02 , 1.34264420545491e-02 , -4.47726589977706e-02 ) ( 3.41700762028921e-05 , 3.17725061894297e-04 , -5.35525350301423e-05 , 1.78579654954705e-04 ) + 1 ( 9.95703202497440e-01 , -7.99005029584874e-02 , 1.32741369737811e-02 , -4.48869630396686e-02 ) ( 3.43497422149066e-05 , 3.18685319686154e-04 , -5.29442547720266e-05 , 1.79032867583693e-04 ) + 2 ( 9.95678521556900e-01 , -8.01968009433796e-02 , 1.31263198798460e-02 , -4.49494666834364e-02 ) ( 3.45469057624427e-05 , 3.19861820322023e-04 , -5.23538161311571e-05 , 1.79279199004696e-04 ) + 3 ( 9.95652403679522e-01 , -8.05419873402017e-02 , 1.29777382160836e-02 , -4.49539501409555e-02 ) ( 3.47555464978077e-05 , 3.21232958648346e-04 , -5.17602977203342e-05 , 1.79293941999634e-04 ) + 4 ( 9.95625468036919e-01 , -8.09309980540691e-02 , 1.28228853926206e-02 , -4.48962644375516e-02 ) ( 3.49707179799499e-05 , 3.22778657189527e-04 , -5.11417606089582e-05 , 1.79060635558914e-04 ) + 5 ( 9.95598135270061e-01 , -8.13594233179634e-02 , 1.26568594211301e-02 , -4.47750063510777e-02 ) ( 3.51890598487685e-05 , 3.24481408187548e-04 , -5.04786710710785e-05 , 1.78573747451775e-04 ) + 6 ( 9.95570599011000e-01 , -8.18234325633647e-02 , 1.24760860073947e-02 , -4.45921018383624e-02 ) ( 3.54090252509857e-05 , 3.26325967026764e-04 , -4.97567836440902e-05 , 1.77840996133848e-04 ) + 7 ( 9.95542831967394e-01 , -8.23194900179106e-02 , 1.22788215872136e-02 , -4.43531489520439e-02 ) ( 3.56308321555336e-05 , 3.28298218071023e-04 , -4.89691474791349e-05 , 1.76884717867258e-04 ) + 8 ( 9.95514620286082e-01 , -8.28440052644148e-02 , 1.20654160975387e-02 , -4.40674179275458e-02 ) ( 3.58561887749678e-05 , 3.30383787220305e-04 , -4.81171552723796e-05 , 1.75741870295307e-04 ) + 9 ( 9.95485617186446e-01 , -8.33930320003749e-02 , 1.18383657124410e-02 , -4.37474717665303e-02 ) ( 3.60878650734080e-05 , 3.32566851187595e-04 , -4.72107550685531e-05 , 1.74462525031441e-04 ) + 10 ( 9.95455406148282e-01 , -8.39620802380189e-02 , 1.16022024367708e-02 , -4.34084364021512e-02 ) ( 3.63291879738892e-05 , 3.34829401791962e-04 , -4.62680115876186e-05 , 1.73106963906254e-04 ) + 11 ( 9.95423564349686e-01 , -8.45460630939964e-02 , 1.13632516824820e-02 , -4.30670089961288e-02 ) ( 3.65835345919473e-05 , 3.37151047685463e-04 , -4.53141408323535e-05 , 1.71741730748373e-04 ) + 12 ( 9.95389718653998e-01 , -8.51393630217013e-02 , 1.11292589658322e-02 , -4.27403375869374e-02 ) ( 3.68538850107258e-05 , 3.39509291404714e-04 , -4.43800222511196e-05 , 1.70435169039739e-04 ) + 13 ( 9.95353590493668e-01 , -8.57359613292896e-02 , 1.09088757916328e-02 , -4.24449202528342e-02 ) ( 3.71424637701849e-05 , 3.41880056891084e-04 , -4.35001488108009e-05 , 1.69253036016511e-04 ) + 14 ( 9.95315031422500e-01 , -8.63295419718748e-02 , 1.07110129770663e-02 , -4.21956467939341e-02 ) ( 3.74504559211243e-05 , 3.44238112793326e-04 , -4.27100481377666e-05 , 1.68254684186438e-04 ) + 15 ( 9.95274054250948e-01 , -8.69134880574461e-02 , 1.05441067595788e-02 , -4.20050513773208e-02 ) ( 3.77777583895344e-05 , 3.46557067343460e-04 , -4.20433559626645e-05 , 1.67490084039822e-04 ) + 16 ( 9.95230862599338e-01 , -8.74807544340958e-02 , 1.04153736880360e-02 , -4.18827855372420e-02 ) ( 3.81227440111029e-05 , 3.48808869094348e-04 , -4.15288452965480e-05 , 1.66997725982946e-04 ) + 17 ( 9.95185875294234e-01 , -8.80236982832042e-02 , 1.03301362042927e-02 , -4.18352774748477e-02 ) ( 3.84820667905813e-05 , 3.50963139290033e-04 , -4.11877381007968e-05 , 1.66803265507009e-04 ) + 18 ( 9.95139736351655e-01 , -8.85340181100190e-02 , 1.02912848994442e-02 , -4.18655255117140e-02 ) ( 3.88505823112175e-05 , 3.52986933124393e-04 , -4.10315624673211e-05 , 1.66918702770913e-04 ) + 19 ( 9.95093299815157e-01 , -8.90029543780060e-02 , 1.02989187541513e-02 , -4.19729799688224e-02 ) ( 3.92214689902938e-05 , 3.54845537886740e-04 , -4.10607197312513e-05 , 1.67341913061558e-04 ) + 20 ( 9.95047582247901e-01 , -8.94218407474711e-02 , 1.03501830154734e-02 , -4.21534953649891e-02 ) ( 3.95866076580436e-05 , 3.56504660282400e-04 , -4.12638394484893e-05 , 1.68056454879410e-04 ) diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out index 90fb86396..5914612e6 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -106,7 +102,6 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -117,31 +112,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.995048 , -0.0894218 , 0.0103502 , -0.0421535 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped index dfd0bab71..ed7e25462 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.94724148740762e-01 , -9.22283983670171e-02 , 8.57198031977685e-03 , -4.40943488444842e-02 ) + x ( 9.94724148736992e-01 , -9.22283984220502e-02 , 8.57198032337350e-03 , -4.40943488137254e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj index 726901e4a..c0667eff6 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( 9.95047582249982e-01 , -8.94218407198434e-02 , 1.03501830123263e-02 , -4.21534953752505e-02 ) ( 3.95866076414231e-05 , 3.56504660172752e-04 , -4.12638394360000e-05 , 1.68056454920554e-04 ) - 21 ( 9.95003682841854e-01 , -8.97829884973678e-02 , 1.04393119593296e-02 , -4.23993735029785e-02 ) ( 3.99372197110201e-05 , 3.57933932791603e-04 , -4.16179506583343e-05 , 1.69031737078635e-04 ) - 22 ( 9.94962679616141e-01 , -9.00807729420692e-02 , 1.05578791054915e-02 , -4.26995515904153e-02 ) ( 4.02646961408769e-05 , 3.59111217737913e-04 , -4.20894792359408e-05 , 1.70223761050075e-04 ) - 23 ( 9.94925517924194e-01 , -9.03126986506125e-02 , 1.06952529194415e-02 , -4.30400024478075e-02 ) ( 4.05614878861151e-05 , 3.60026823408699e-04 , -4.26360632742869e-05 , 1.71576706180971e-04 ) - 24 ( 9.94892911463656e-01 , -9.04801848123271e-02 , 1.08392437997452e-02 , -4.34043968918623e-02 ) ( 4.08218962464344e-05 , 3.60686606780452e-04 , -4.32091299802860e-05 , 1.73025559869822e-04 ) - 25 ( 9.94865274497008e-01 , -9.05888500075216e-02 , 1.09769033218979e-02 , -4.37750322417940e-02 ) ( 4.10426139951310e-05 , 3.61113088545953e-04 , -4.37570789441720e-05 , 1.74499809774828e-04 ) - 26 ( 9.94842696775133e-01 , -9.06481847893688e-02 , 1.10954059422353e-02 , -4.41339691683329e-02 ) ( 4.12229254634621e-05 , 3.61344139392317e-04 , -4.42287942193370e-05 , 1.75927969701260e-04 ) - 27 ( 9.94824962048116e-01 , -9.06706488864391e-02 , 1.11829212623721e-02 , -4.44642619247934e-02 ) ( 4.13645585785194e-05 , 3.61429384974983e-04 , -4.45771195389264e-05 , 1.77242481863921e-04 ) - 28 ( 9.94811601036927e-01 , -9.06703674651151e-02 , 1.12293836982419e-02 , -4.47511323638196e-02 ) ( 4.14712617591352e-05 , 3.61425022578285e-04 , -4.47619257552785e-05 , 1.78384399194370e-04 ) - 29 ( 9.94801963555091e-01 , -9.06616843247956e-02 , 1.12270902231604e-02 , -4.49829384038806e-02 ) ( 4.15482279400340e-05 , 3.61388073059340e-04 , -4.47524941989370e-05 , 1.79307251474472e-04 ) - 30 ( 9.94795293173688e-01 , -9.06578422928237e-02 , 1.11710965045517e-02 , -4.51518207071648e-02 ) ( 4.16014983262487e-05 , 3.61371140630078e-04 , -4.45290973603736e-05 , 1.79979630419292e-04 ) - 31 ( 9.94790790369875e-01 , -9.06700109711078e-02 , 1.10594217982803e-02 , -4.52539688344244e-02 ) ( 4.16374581364648e-05 , 3.61418554057688e-04 , -4.40838177059692e-05 , 1.80386257885433e-04 ) - 32 ( 9.94787655103003e-01 , -9.07067883182348e-02 , 1.08930998886607e-02 , -4.52895151494764e-02 ) ( 4.16624966373904e-05 , 3.61564391012379e-04 , -4.34207527408272e-05 , 1.80527568750601e-04 ) - 33 ( 9.94785106318339e-01 , -9.07741836818644e-02 , 1.06761181594841e-02 , -4.52621290390331e-02 ) ( 4.16828514234531e-05 , 3.61832415325462e-04 , -4.25557737151859e-05 , 1.80418096959853e-04 ) - 34 ( 9.94782383326987e-01 , -9.08759671977928e-02 , 1.04152699871068e-02 , -4.51784302432211e-02 ) ( 4.17045974180370e-05 , 3.62237469779759e-04 , -4.15159383007289e-05 , 1.80084138464314e-04 ) - 35 ( 9.94778740636462e-01 , -9.10141757972667e-02 , 1.01199149985978e-02 , -4.50473562165450e-02 ) ( 4.17336881618950e-05 , 3.62787491302079e-04 , -4.03385356442665e-05 , 1.79561229978004e-04 ) - 36 ( 9.94773451641488e-01 , -9.11895285998344e-02 , 9.80161261516879e-03 , -4.48795964015018e-02 ) ( 4.17759263281172e-05 , 3.63485167001368e-04 , -3.90696262280471e-05 , 1.78891895192706e-04 ) - 37 ( 9.94765834654937e-01 , -9.14015536567541e-02 , 9.47358561494656e-03 , -4.46871499202457e-02 ) ( 4.18367558146745e-05 , 3.64328445106307e-04 , -3.77619042411093e-05 , 1.78123885156437e-04 ) - 38 ( 9.94755307047952e-01 , -9.16483517814180e-02 , 9.14999202764146e-03 , -4.44829895755552e-02 ) ( 4.19208293491576e-05 , 3.65309606419041e-04 , -3.64717959612317e-05 , 1.77308845149173e-04 ) - 39 ( 9.94741461700454e-01 , -9.19260830853272e-02 , 8.84503297238212e-03 , -4.42807521881895e-02 ) ( 4.20313979285352e-05 , 3.66413236480337e-04 , -3.52559039764323e-05 , 1.76501088466893e-04 ) - 40 ( 9.94724148740762e-01 , -9.22283983670171e-02 , 8.57198031977685e-03 , -4.40943488444842e-02 ) ( 4.21696580457610e-05 , 3.67613980120615e-04 , -3.41671313680286e-05 , 1.75756050918744e-04 ) + 20 ( 9.95047582247901e-01 , -8.94218407474711e-02 , 1.03501830154734e-02 , -4.21534953649891e-02 ) ( 3.95866076580436e-05 , 3.56504660282400e-04 , -4.12638394484893e-05 , 1.68056454879410e-04 ) + 21 ( 9.95003682839837e-01 , -8.97829885242213e-02 , 1.04393119624910e-02 , -4.23993734926744e-02 ) ( 3.99372197271322e-05 , 3.57933932898174e-04 , -4.16179506708815e-05 , 1.69031737037327e-04 ) + 22 ( 9.94962679614012e-01 , -9.00807729701850e-02 , 1.05578791084465e-02 , -4.26995515799716e-02 ) ( 4.02646961578782e-05 , 3.59111217849485e-04 , -4.20894792476610e-05 , 1.70223761008198e-04 ) + 23 ( 9.94925517922001e-01 , -9.03126986794675e-02 , 1.06952529221899e-02 , -4.30400024372660e-02 ) ( 4.05614879036287e-05 , 3.60026823523198e-04 , -4.26360632851805e-05 , 1.71576706138696e-04 ) + 24 ( 9.94892911461449e-01 , -9.04801848414051e-02 , 1.08392438023233e-02 , -4.34043968812029e-02 ) ( 4.08218962640658e-05 , 3.60686606895834e-04 , -4.32091299904993e-05 , 1.73025559827073e-04 ) + 25 ( 9.94865274494471e-01 , -9.05888500412821e-02 , 1.09769033233308e-02 , -4.37750322292276e-02 ) ( 4.10426140153920e-05 , 3.61113088679918e-04 , -4.37570789498096e-05 , 1.74499809724437e-04 ) + 26 ( 9.94842696773042e-01 , -9.06481848174512e-02 , 1.10954059447183e-02 , -4.41339691571599e-02 ) ( 4.12229254801604e-05 , 3.61344139503753e-04 , -4.42287942291727e-05 , 1.75927969656476e-04 ) + 27 ( 9.94824962046056e-01 , -9.06706489146701e-02 , 1.11829212647168e-02 , -4.44642619127326e-02 ) ( 4.13645585949729e-05 , 3.61429385087017e-04 , -4.45771195482112e-05 , 1.77242481815600e-04 ) + 28 ( 9.94811601034407e-01 , -9.06703674988958e-02 , 1.12293836999313e-02 , -4.47511323509693e-02 ) ( 4.14712617792593e-05 , 3.61425022712328e-04 , -4.47619257619370e-05 , 1.78384399142845e-04 ) + 29 ( 9.94801963553301e-01 , -9.06616843507634e-02 , 1.12270902259919e-02 , -4.49829383904157e-02 ) ( 4.15482279543266e-05 , 3.61388073162416e-04 , -4.47524942101701e-05 , 1.79307251420585e-04 ) + 30 ( 9.94795293171562e-01 , -9.06578423239697e-02 , 1.11710965065822e-02 , -4.51518206909619e-02 ) ( 4.16014983432260e-05 , 3.61371140753713e-04 , -4.45290973684036e-05 , 1.79979630354449e-04 ) + 31 ( 9.94790790368376e-01 , -9.06700109952209e-02 , 1.10594218017861e-02 , -4.52539688182038e-02 ) ( 4.16374581484353e-05 , 3.61418554153441e-04 , -4.40838177198993e-05 , 1.80386257820595e-04 ) + 32 ( 9.94787655101548e-01 , -9.07067883426823e-02 , 1.08930998924629e-02 , -4.52895151315648e-02 ) ( 4.16624966490124e-05 , 3.61564391109476e-04 , -4.34207527559406e-05 , 1.80527568679028e-04 ) + 33 ( 9.94785106316866e-01 , -9.07741837073836e-02 , 1.06761181635399e-02 , -4.52621290192839e-02 ) ( 4.16828514352205e-05 , 3.61832415426825e-04 , -4.25557737313109e-05 , 1.80418096880953e-04 ) + 34 ( 9.94782383325423e-01 , -9.08759672251909e-02 , 1.04152699913556e-02 , -4.51784302215533e-02 ) ( 4.17045974305217e-05 , 3.62237469888589e-04 , -4.15159383176215e-05 , 1.80084138377755e-04 ) + 35 ( 9.94778740634731e-01 , -9.10141758273820e-02 , 1.01199150029673e-02 , -4.50473561929485e-02 ) ( 4.17336881757203e-05 , 3.62787491421699e-04 , -4.03385356616366e-05 , 1.79561229883738e-04 ) + 36 ( 9.94773451639091e-01 , -9.11895286402353e-02 , 9.80161261834228e-03 , -4.48795963718487e-02 ) ( 4.17759263472595e-05 , 3.63485167161823e-04 , -3.90696262406339e-05 , 1.78891895074220e-04 ) + 37 ( 9.94765834652613e-01 , -9.14015536948658e-02 , 9.47358561936806e-03 , -4.46871498930807e-02 ) ( 4.18367558332307e-05 , 3.64328445257653e-04 , -3.77619042586746e-05 , 1.78123885047879e-04 ) + 38 ( 9.94755307045228e-01 , -9.16483518244586e-02 , 9.14999203197848e-03 , -4.44829895469045e-02 ) ( 4.19208293709127e-05 , 3.65309606589932e-04 , -3.64717959784524e-05 , 1.77308845034647e-04 ) + 39 ( 9.94741461697262e-01 , -9.19260831338689e-02 , 8.84503297656702e-03 , -4.42807521582896e-02 ) ( 4.20313979540273e-05 , 3.66413236673037e-04 , -3.52559039930375e-05 , 1.76501088347335e-04 ) + 40 ( 9.94724148736992e-01 , -9.22283984220502e-02 , 8.57198032337350e-03 , -4.40943488137254e-02 ) ( 4.21696580758678e-05 , 3.67613980339042e-04 , -3.41671313822781e-05 , 1.75756050795697e-04 ) diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt b/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out index 913368e3f..e51e7ce01 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -109,7 +105,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -120,26 +115,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped index 68355e27e..75d556e11 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.95047581774198e-01 , -8.94218449655825e-02 , 1.03501990061269e-02 , -4.21534936725870e-02 ) + x ( 9.95047581772214e-01 , -8.94218449921444e-02 , 1.03501990099413e-02 , -4.21534936621476e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.26088591477162e-03 + accumulatedWork 2.26088591477312e-03 } } diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj index 509adba31..c68dda8dd 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 0 ( 9.95725692918276e-01 , -7.96585470771598e-02 , 1.34264420545571e-02 , -4.47726589977838e-02 ) ( 3.41700762028735e-05 , 3.17725061894150e-04 , -5.35525350301741e-05 , 1.78579654954758e-04 ) 1.71094220294084e-05 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 - 1 ( 9.95703202497434e-01 , -7.99005029585730e-02 , 1.32741369737813e-02 , -4.48869630396400e-02 ) ( 2.83367138120423e-05 , 3.17696149303822e-04 , 3.90264420205889e-04 , 1.78477165769913e-04 ) 3.57367786265048e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.25751658795693e-05 - 2 ( 9.95678521556407e-01 , -8.01968009477312e-02 , 1.31263198967770e-02 , -4.49494666816481e-02 ) ( 2.10043163774406e-05 , 3.14124330884285e-04 , 9.28834252114772e-04 , 1.76063396271639e-04 ) 1.24105832996037e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.62928156880148e-04 - 3 ( 9.95652403677488e-01 , -8.05419873579345e-02 , 1.29777382869545e-02 , -4.49539501337857e-02 ) ( 1.18560940376575e-05 , 3.04619185568056e-04 , 1.56985791890468e-03 , 1.70021080023323e-04 ) 3.23286808547749e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.92924287234955e-04 - 4 ( 9.95625468031602e-01 , -8.09309981004511e-02 , 1.28228855771687e-02 , -4.48962644191386e-02 ) ( 7.70725693236790e-07 , 2.86357930588497e-04 , 2.30368856073467e-03 , 1.58856330355165e-04 ) 6.76777222122836e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.43830024565543e-04 - 5 ( 9.95598135259239e-01 , -8.13594234131779e-02 , 1.26568598023747e-02 , -4.47750063109274e-02 ) ( -1.19638357685023e-05 , 2.57128422733453e-04 , 3.09452499115324e-03 , 1.41506985517112e-04 ) 1.20779591337073e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.17743292406584e-03 - 6 ( 9.95570598990727e-01 , -8.18234327423189e-02 , 1.24760866963825e-02 , -4.45921017698568e-02 ) ( -2.55774576553760e-05 , 2.16780943542518e-04 , 3.88503951911507e-03 , 1.18141192226147e-04 ) 1.89439219877622e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.60702762768025e-03 - 7 ( 9.95542831933873e-01 , -8.23194903158855e-02 , 1.22788227118873e-02 , -4.43531488400399e-02 ) ( -3.90575682790280e-05 , 1.67766250719849e-04 , 4.61795501118427e-03 , 9.03912482932004e-05 ) 2.67041875895129e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.94669840769354e-03 - 8 ( 9.95514620234602e-01 , -8.28440057254391e-02 , 1.20654178024697e-02 , -4.40674177570056e-02 ) ( -5.15481325620161e-05 , 1.14015827333934e-04 , 5.25759497784956e-03 , 6.06487222586368e-05 ) 3.45770500468423e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.15860938064172e-03 - 9 ( 9.95485617111931e-01 , -8.33930326725034e-02 , 1.18383681499865e-02 , -4.37474715212837e-02 ) ( -6.25780827741211e-05 , 5.92548196854455e-05 , 5.79445555467542e-03 , 3.10847135979329e-05 ) 4.19801357307849e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.25291457221835e-03 - 10 ( 9.95455406045573e-01 , -8.39620811705810e-02 , 1.16022057593680e-02 , -4.34084360656384e-02 ) ( -7.20363521575908e-05 , 6.07593470320788e-06 , 6.23635565891445e-03 , 3.14126114343633e-06 ) 4.86217099062632e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 11 ( 9.95423564213814e-01 , -8.45460643347972e-02 , 1.13632560356581e-02 , -4.30670085521597e-02 ) ( -7.05611115363754e-05 , 5.99309127286019e-06 , 6.23732857268019e-03 , 3.05282706099796e-06 ) 4.86366147886625e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 12 ( 9.95389718481259e-01 , -8.51393646053625e-02 , 1.11292644683300e-02 , -4.27403370224198e-02 ) ( -6.91159591047267e-05 , 5.91174364473551e-06 , 6.23828095599262e-03 , 2.96772141696521e-06 ) 4.86512125722331e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 13 ( 9.95353590282289e-01 , -8.57359632682770e-02 , 1.09088825330022e-02 , -4.24449195605181e-02 ) ( -6.77542728844581e-05 , 5.83609473859762e-06 , 6.23917763573012e-03 , 2.88924929847956e-06 ) 4.86649632743153e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 14 ( 9.95315031170072e-01 , -8.63295442907098e-02 , 1.07110210230709e-02 , -4.21956459616350e-02 ) ( -6.65310885163908e-05 , 5.77063379223042e-06 , 6.23998242899872e-03 , 2.82053638151088e-06 ) 4.86773104444897e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 15 ( 9.95274053958565e-01 , -8.69134907370101e-02 , 1.05441161461300e-02 , -4.20050504045343e-02 ) ( -6.54985597796452e-05 , 5.71973964965100e-06 , 6.24066111879459e-03 , 2.76433440018415e-06 ) 4.86877270224177e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 16 ( 9.95230862266868e-01 , -8.74807574724623e-02 , 1.04153844293258e-02 , -4.18827844200880e-02 ) ( -6.47013396955228e-05 , 5.68724546298252e-06 , 6.24118446606660e-03 , 2.72285794673419e-06 ) 4.86957619519322e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 17 ( 9.95185874923942e-01 , -8.80237016490180e-02 , 1.03301482957764e-02 , -4.18352762159005e-02 ) ( -6.41723928153701e-05 , 5.67601661319342e-06 , 6.24153092939405e-03 , 2.69765663532097e-06 ) 4.87010824163727e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 18 ( 9.95139735945799e-01 , -8.85340217748383e-02 , 1.02912983197793e-02 , -4.18655241098357e-02 ) ( -6.39296531495683e-05 , 5.68759250541073e-06 , 6.24168882977397e-03 , 2.68952021368430e-06 ) 4.87035075381305e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 19 ( 9.95093299374205e-01 , -8.90029583343626e-02 , 1.02989334767443e-02 , -4.19729784210373e-02 ) ( -6.39737894420540e-05 , 5.72193232512286e-06 , 6.24165779846845e-03 , 2.69841077761449e-06 ) 4.87030309260599e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 20 ( 9.95047581774198e-01 , -8.94218449655825e-02 , 1.03501990061269e-02 , -4.21534936725870e-02 ) ( -6.42872031582073e-05 , 5.77729187968484e-06 , 6.24144943237969e-03 , 2.72341771508647e-06 ) 4.86998308194352e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 0 ( 9.95725692918276e-01 , -7.96585470771598e-02 , 1.34264420545571e-02 , -4.47726589977838e-02 ) ( 3.41700762028735e-05 , 3.17725061894150e-04 , -5.35525350301742e-05 , 1.78579654954758e-04 ) 1.71094220294084e-05 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 + 1 ( 9.95703202497441e-01 , -7.99005029584633e-02 , 1.32741369737848e-02 , -4.48869630396836e-02 ) ( 2.83367138119876e-05 , 3.17696149303388e-04 , 3.90264420205874e-04 , 1.78477165770087e-04 ) 3.57367786264763e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.25751658795682e-05 + 2 ( 9.95678521556434e-01 , -8.01968009473040e-02 , 1.31263198967912e-02 , -4.49494666818169e-02 ) ( 2.10043163772193e-05 , 3.14124330882618e-04 , 9.28834252114706e-04 , 1.76063396272304e-04 ) 1.24105832995919e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.62928156880146e-04 + 3 ( 9.95652403677545e-01 , -8.05419873570241e-02 , 1.29777382869849e-02 , -4.49539501341403e-02 ) ( 1.18560940371760e-05 , 3.04619185564628e-04 , 1.56985791890452e-03 , 1.70021080024672e-04 ) 3.23286808547484e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.92924287234960e-04 + 4 ( 9.95625468031697e-01 , -8.09309980989665e-02 , 1.28228855772213e-02 , -4.48962644197014e-02 ) ( 7.70725692445905e-07 , 2.86357930583270e-04 , 2.30368856073438e-03 , 1.58856330357171e-04 ) 6.76777222122379e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.43830024565586e-04 + 5 ( 9.95598135259372e-01 , -8.13594234111277e-02 , 1.26568598024581e-02 , -4.47750063116703e-02 ) ( -1.19638357695980e-05 , 2.57128422727014e-04 , 3.09452499115279e-03 , 1.41506985519482e-04 ) 1.20779591337005e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.17743292406597e-03 + 6 ( 9.95570598990892e-01 , -8.18234327398263e-02 , 1.24760866965111e-02 , -4.45921017706951e-02 ) ( -2.55774576567467e-05 , 2.16780943535973e-04 , 3.88503951911439e-03 , 1.18141192228400e-04 ) 1.89439219877529e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.60702762768054e-03 + 7 ( 9.95542831934058e-01 , -8.23194903131902e-02 , 1.22788227120833e-02 , -4.43531488408355e-02 ) ( -3.90575682806717e-05 , 1.67766250714442e-04 , 4.61795501118331e-03 , 9.03912482948679e-05 ) 2.67041875895001e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.94669840769403e-03 + 8 ( 9.95514620234786e-01 , -8.28440057228855e-02 , 1.20654178027640e-02 , -4.40674177575778e-02 ) ( -5.15481325640461e-05 , 1.14015827330549e-04 , 5.25759497784824e-03 , 6.06487222594931e-05 ) 3.45770500468243e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.15860938064247e-03 + 9 ( 9.95485617112086e-01 , -8.33930326705179e-02 , 1.18383681504187e-02 , -4.37474715214257e-02 ) ( -6.25780827768114e-05 , 5.92548196842370e-05 , 5.79445555467360e-03 , 3.10847135981400e-05 ) 4.19801357307588e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.25291457221944e-03 + 10 ( 9.95455406045667e-01 , -8.39620811696408e-02 , 1.16022057599854e-02 , -4.34084360651368e-02 ) ( -7.20363521614028e-05 , 6.07593470346080e-06 , 6.23635565891194e-03 , 3.14126114356596e-06 ) 4.86217099062247e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 11 ( 9.95423564213811e-01 , -8.45460643353971e-02 , 1.13632560365135e-02 , -4.30670085508141e-02 ) ( -7.05611115416490e-05 , 5.99309127335064e-06 , 6.23732857267671e-03 , 3.05282706113075e-06 ) 4.86366147886091e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 12 ( 9.95389718481123e-01 , -8.51393646079810e-02 , 1.11292644694778e-02 , -4.27403370200617e-02 ) ( -6.91159591117955e-05 , 5.91174364552275e-06 , 6.23828095598795e-03 , 2.96772141710540e-06 ) 4.86512125721615e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 13 ( 9.95353590281985e-01 , -8.57359632733491e-02 , 1.09088825344929e-02 , -4.24449195570245e-02 ) ( -6.77542728936322e-05 , 5.83609473973489e-06 , 6.23917763572405e-03 , 2.88924929863384e-06 ) 4.86649632742223e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 14 ( 9.95315031169567e-01 , -8.63295442986035e-02 , 1.07110210249439e-02 , -4.21956459569390e-02 ) ( -6.65310885279126e-05 , 5.77063379376035e-06 , 6.23998242899110e-03 , 2.82053638168687e-06 ) 4.86773104443728e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 15 ( 9.95274053957830e-01 , -8.69134907480067e-02 , 1.05441161484066e-02 , -4.20050503986284e-02 ) ( -6.54985597936450e-05 , 5.71973965160146e-06 , 6.24066111878534e-03 , 2.76433440038838e-06 ) 4.86877270222756e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 16 ( 9.95230862265883e-01 , -8.74807574867389e-02 , 1.04153844320038e-02 , -4.18827844130215e-02 ) ( -6.47013397119858e-05 , 5.68724546536339e-06 , 6.24118446605571e-03 , 2.72285794697030e-06 ) 4.86957619517651e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 17 ( 9.95185874922694e-01 , -8.80237016666293e-02 , 1.03301482988283e-02 , -4.18352762077715e-02 ) ( -6.41723928341247e-05 , 5.67601661599500e-06 , 6.24153092938165e-03 , 2.69765663558857e-06 ) 4.87010824161822e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 18 ( 9.95139735944289e-01 , -8.85340217957036e-02 , 1.02912983231547e-02 , -4.18655241007787e-02 ) ( -6.39296531703027e-05 , 5.68759250860446e-06 , 6.24168882976025e-03 , 2.68952021397884e-06 ) 4.87035075379198e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 19 ( 9.95093299372444e-01 , -8.90029583582581e-02 , 1.02989334803762e-02 , -4.19729784112083e-02 ) ( -6.39737894643545e-05 , 5.72193232866381e-06 , 6.24165779845369e-03 , 2.69841077792800e-06 ) 4.87030309258332e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 20 ( 9.95047581772214e-01 , -8.94218449921444e-02 , 1.03501990099413e-02 , -4.21534936621476e-02 ) ( -6.42872031816166e-05 , 5.77729188351618e-06 , 6.24144943236418e-03 , 2.72341771540914e-06 ) 4.86998308191970e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out index 023407b4d..5455bcf82 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -109,7 +105,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -120,31 +115,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.995048 , -0.0894218 , 0.0103502 , -0.0421535 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped index 0d834a02a..80ded7bf8 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.94724147282287e-01 , -9.22284123842412e-02 , 8.57202435943065e-03 , -4.40943438661931e-02 ) + x ( 9.94724147278495e-01 , -9.22284124393750e-02 , 8.57202436227895e-03 , -4.40943438358672e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.26088591477162e-03 + accumulatedWork 2.26088591477312e-03 } } diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj index a8608cd4b..545a4a767 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( 9.95047581774198e-01 , -8.94218449655825e-02 , 1.03501990061269e-02 , -4.21534936725870e-02 ) ( -6.42872031582073e-05 , 5.77729187968484e-06 , 6.24144943237969e-03 , 2.72341771508647e-06 ) 4.86998308194352e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 21 ( 9.95003682334260e-01 , -8.97829929925345e-02 , 1.04393291863312e-02 , -4.23993716546049e-02 ) ( -6.48343047311814e-05 , 5.85024762290276e-06 , 6.24108712857907e-03 , 2.76273729542017e-06 ) 4.86942673646249e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 22 ( 9.94962679077155e-01 , -9.00807776816361e-02 , 1.05578975352894e-02 , -4.26995495938328e-02 ) ( -6.55630799832673e-05 , 5.93587413507200e-06 , 6.24060508570187e-03 , 2.81368743184070e-06 ) 4.86868668807296e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 23 ( 9.94925517353414e-01 , -9.03127036401896e-02 , 1.06952725287408e-02 , -4.30400002994432e-02 ) ( -6.64079280825436e-05 , 6.02806885909569e-06 , 6.24004647490369e-03 , 2.87277509190952e-06 ) 4.86782932654013e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 24 ( 9.94892910859826e-01 , -9.04801900685380e-02 , 1.08392645748153e-02 , -4.34043945874284e-02 ) ( -6.72936746700319e-05 , 6.11999985937453e-06 , 6.23946083147816e-03 , 2.93583477853088e-06 ) 4.86693074746560e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 25 ( 9.94865273858061e-01 , -9.05888555574097e-02 , 1.09769252601266e-02 , -4.37750297767849e-02 ) ( -6.81405121220271e-05 , 6.20463008653664e-06 , 6.23890081877020e-03 , 2.99824813020128e-06 ) 4.86607175534625e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 26 ( 9.94842696098306e-01 , -9.06481906689943e-02 , 1.10954290528118e-02 , -4.41339665385350e-02 ) ( -6.88694319684040e-05 , 6.27525278601464e-06 , 6.23841864350692e-03 , 3.05523799686328e-06 ) 4.86533236044889e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 27 ( 9.94824961330116e-01 , -9.06706551388669e-02 , 1.11829455661831e-02 , -4.44642591266877e-02 ) ( -6.94075830663685e-05 , 6.32596815807546e-06 , 6.23806249527008e-03 , 3.10221081977458e-06 ) 4.86478634363342e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 28 ( 9.94811600274131e-01 , -9.06703741379878e-02 , 1.12294092270974e-02 , -4.47511293948060e-02 ) ( -6.96929861680878e-05 , 6.35204608481931e-06 , 6.23787339223321e-03 , 3.13510602516003e-06 ) 4.86449646840391e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 29 ( 9.94801962743773e-01 , -9.06616914676642e-02 , 1.12271170184627e-02 , -4.49829352623114e-02 ) ( -6.96781856436282e-05 , 6.35015048766679e-06 , 6.23788272163551e-03 , 3.15070680536035e-06 ) 4.86451076872475e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 30 ( 9.94795292310257e-01 , -9.06578499543900e-02 , 1.11711246155064e-02 , -4.51518173922375e-02 ) ( -6.93326642576498e-05 , 6.31843588504616e-06 , 6.23811060337159e-03 , 3.14687435704348e-06 ) 4.86486009296005e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 31 ( 9.94790789451105e-01 , -9.06700191965351e-02 , 1.10594512797368e-02 , -4.52539653460176e-02 ) ( -6.86440920532849e-05 , 6.25655284528142e-06 , 6.23856504120304e-03 , 3.12268408184823e-06 ) 4.86555683503798e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 32 ( 9.94787654126230e-01 , -9.07067971467051e-02 , 1.08931307986771e-02 , -4.52895114880088e-02 ) ( -6.76186432835818e-05 , 6.16560784024465e-06 , 6.23924171412794e-03 , 3.07846132699065e-06 ) 4.86659461748473e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 33 ( 9.94785105281604e-01 , -9.07741931445759e-02 , 1.06761505567364e-02 , -4.52621252053962e-02 ) ( -6.62806416135132e-05 , 6.04811203105849e-06 , 6.24012423798566e-03 , 3.01572941078122e-06 ) 4.86794866290398e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 34 ( 9.94782382229110e-01 , -9.08759773165833e-02 , 1.04153039282901e-02 , -4.51784262387849e-02 ) ( -6.46716868136083e-05 , 5.90792805430392e-06 , 6.24118479330421e-03 , 2.93708964356536e-06 ) 4.86957669766956e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 35 ( 9.94778739477024e-01 , -9.10141865840077e-02 , 1.01199505360086e-02 , -4.50473520431876e-02 ) ( -6.28492246685917e-05 , 5.75019432326694e-06 , 6.24238513756400e-03 , 2.84605112366581e-06 ) 4.87142042443290e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 36 ( 9.94773450420717e-01 , -9.11895400566741e-02 , 9.80164979465735e-03 , -4.48795920616019e-02 ) ( -6.08843396302519e-05 , 5.58118526905689e-06 , 6.24367813620281e-03 , 2.74682072022538e-06 ) 4.87340778324529e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 37 ( 9.94765833373519e-01 , -9.14015657772049e-02 , 9.47362447441949e-03 , -4.46871454165775e-02 ) ( -5.88584935456410e-05 , 5.40806518365723e-06 , 6.24500998010697e-03 , 2.64405749758712e-06 ) 4.87545627651339e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 38 ( 9.94755305706783e-01 , -9.16483645522010e-02 , 9.15003259624412e-03 , -4.44829849110689e-02 ) ( -5.68590654435119e-05 , 5.23851476636451e-06 , 6.24632316888377e-03 , 2.54259608938115e-06 ) 4.87747749878614e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 39 ( 9.94741460300375e-01 , -9.19260964888404e-02 , 8.84507527042971e-03 , -4.42807473656820e-02 ) ( -5.49738529586110e-05 , 5.08024638875575e-06 , 6.24756014036145e-03 , 2.44715173914973e-06 ) 4.87938270367466e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 40 ( 9.94724147282287e-01 , -9.22284123842412e-02 , 8.57202435943065e-03 , -4.40943438661931e-02 ) ( -5.32850484997073e-05 , 4.94046056926641e-06 , 6.24866720237444e-03 , 2.36203097903292e-06 ) 4.88108888622058e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 20 ( 9.95047581772214e-01 , -8.94218449921444e-02 , 1.03501990099413e-02 , -4.21534936621476e-02 ) ( -6.42872031816166e-05 , 5.77729188351618e-06 , 6.24144943236418e-03 , 2.72341771540914e-06 ) 4.86998308191970e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 21 ( 9.95003682332090e-01 , -8.97829930212753e-02 , 1.04393291902568e-02 , -4.23993716437056e-02 ) ( -6.48343047552602e-05 , 5.85024762696099e-06 , 6.24108712856311e-03 , 2.76273729574205e-06 ) 4.86942673643799e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 22 ( 9.94962679074848e-01 , -9.00807777119746e-02 , 1.05578975392661e-02 , -4.26995495825972e-02 ) ( -6.55630800076457e-05 , 5.93587413929206e-06 , 6.24060508568570e-03 , 2.81368743215307e-06 ) 4.86868668804814e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 23 ( 9.94925517351027e-01 , -9.03127036714925e-02 , 1.06952725327247e-02 , -4.30400002879546e-02 ) ( -6.64079281069542e-05 , 6.02806886341535e-06 , 6.24004647488748e-03 , 2.87277509220557e-06 ) 4.86782932651527e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 24 ( 9.94892910857417e-01 , -9.04801901001701e-02 , 1.08392645787803e-02 , -4.34043945757192e-02 ) ( -6.72936746943171e-05 , 6.11999986373752e-06 , 6.23946083146203e-03 , 2.93583477880549e-06 ) 4.86693074744086e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 25 ( 9.94865273855686e-01 , -9.05888555887877e-02 , 1.09769252640617e-02 , -4.37750297648312e-02 ) ( -6.81405121461231e-05 , 6.20463009089469e-06 , 6.23890081875418e-03 , 2.99824813044994e-06 ) 4.86607175532170e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 26 ( 9.94842696096015e-01 , -9.06481906996373e-02 , 1.10954290567160e-02 , -4.41339665262560e-02 ) ( -6.88694319923092e-05 , 6.27525279032860e-06 , 6.23841864349104e-03 , 3.05523799708078e-06 ) 4.86533236042453e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 27 ( 9.94824961327947e-01 , -9.06706551684395e-02 , 1.11829455700586e-02 , -4.44642591139523e-02 ) ( -6.94075830901017e-05 , 6.32596816231558e-06 , 6.23806249525430e-03 , 3.10221081995358e-06 ) 4.86478634360924e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 28 ( 9.94811600272105e-01 , -9.06703741663319e-02 , 1.12294092309447e-02 , -4.47511293814425e-02 ) ( -6.96929861916542e-05 , 6.35204608896586e-06 , 6.23787339221755e-03 , 3.13510602529034e-06 ) 4.86449646837991e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 29 ( 9.94801962741897e-01 , -9.06616914948174e-02 , 1.12271170222758e-02 , -4.49829352481218e-02 ) ( -6.96781856669942e-05 , 6.35015049171011e-06 , 6.23788272161999e-03 , 3.15070680542899e-06 ) 4.86451076870096e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 30 ( 9.94795292308519e-01 , -9.06578499805883e-02 , 1.11711246192723e-02 , -4.51518173770135e-02 ) ( -6.93326642807366e-05 , 6.31843588898705e-06 , 6.23811060335627e-03 , 3.14687435703579e-06 ) 4.86486009293656e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 31 ( 9.94790789449473e-01 , -9.06700192222035e-02 , 1.10594512834366e-02 , -4.52539653295560e-02 ) ( -6.86440920759764e-05 , 6.25655284913111e-06 , 6.23856504118798e-03 , 3.12268408174970e-06 ) 4.86555683501490e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 32 ( 9.94787654124658e-01 , -9.07067971724354e-02 , 1.08931308022897e-02 , -4.52895114701268e-02 ) ( -6.76186433057460e-05 , 6.16560784402434e-06 , 6.23924171411324e-03 , 3.07846132678909e-06 ) 4.86659461746219e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 33 ( 9.94785105280032e-01 , -9.07741931710955e-02 , 1.06761505602423e-02 , -4.52621251859446e-02 ) ( -6.62806416350276e-05 , 6.04811203479819e-06 , 6.24012423797141e-03 , 3.01572941046886e-06 ) 4.86794866288210e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 34 ( 9.94782382227464e-01 , -9.08759773447180e-02 , 1.04153039316759e-02 , -4.51784262176578e-02 ) ( -6.46716868343866e-05 , 5.90792805804091e-06 , 6.24118479329044e-03 , 2.93708964314039e-06 ) 4.86957669764842e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 35 ( 9.94778739475224e-01 , -9.10141866146385e-02 , 1.01199505392699e-02 , -4.50473520203313e-02 ) ( -6.28492246886030e-05 , 5.75019432704345e-06 , 6.24238513755075e-03 , 2.84605112313311e-06 ) 4.87142042441254e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 36 ( 9.94773450418677e-01 , -9.11895400906934e-02 , 9.80164979780012e-03 , -4.48795920370193e-02 ) ( -6.08843396495280e-05 , 5.58118527291748e-06 , 6.24367813619005e-03 , 2.74682071959611e-06 ) 4.87340778322567e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 37 ( 9.94765833371153e-01 , -9.14015658154700e-02 , 9.47362447745856e-03 , -4.46871453903308e-02 ) ( -5.88584935642695e-05 , 5.40806518764580e-06 , 6.24500998009463e-03 , 2.64405749687727e-06 ) 4.87545627649441e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 38 ( 9.94755305704011e-01 , -9.16483645954890e-02 , 9.15003259920000e-03 , -4.44829848832778e-02 ) ( -5.68590654616153e-05 , 5.23851477052131e-06 , 6.24632316887178e-03 , 2.54259608860927e-06 ) 4.87747749876768e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 39 ( 9.94741460297122e-01 , -9.19260965378052e-02 , 8.84507527332342e-03 , -4.42807473365176e-02 ) ( -5.49738529763158e-05 , 5.08024639311451e-06 , 6.24756014034971e-03 , 2.44715173833410e-06 ) 4.87938270365658e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 40 ( 9.94724147278495e-01 , -9.22284124393750e-02 , 8.57202436227895e-03 , -4.40943438358672e-02 ) ( -5.32850485171137e-05 , 4.94046057385252e-06 , 6.24866720236290e-03 , 2.36203097818903e-06 ) 4.88108888620278e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt b/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index e9a9f6185..22567fc90 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,28 +132,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 57a7f087b..174f4aa5e 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.50586699278142e+00 + x 2.50586699060249e+00 } restraint { diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 10296e333..9e8670803 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.34454807259353e+00 -1.29781922903741e-02 - 1 3.34456621005910e+00 -1.29782648402364e-02 - 2 3.33650183431222e+00 -1.29460073372489e-02 - 3 3.31967608166225e+00 -1.28787043266490e-02 - 4 3.29359679352004e+00 -1.27743871740802e-02 - 5 3.25804972932359e+00 -1.26321989172944e-02 - 6 3.21319557896124e+00 -1.24527823158450e-02 - 7 3.15964721748749e+00 -1.22385888699500e-02 - 8 3.09850657670722e+00 -1.19940263068289e-02 - 9 3.03134993698711e+00 -1.17253997479484e-02 - 10 2.96016041310420e+00 -1.14406416524168e-02 - 11 2.88721545965500e+00 -1.11488618386200e-02 - 12 2.81494477280673e+00 -1.08597790912269e-02 - 13 2.74578033381965e+00 -1.05831213352786e-02 - 14 2.68202224624271e+00 -1.03280889849708e-02 - 15 2.62573819607844e+00 -1.01029527843138e-02 - 16 2.57870029937537e+00 -9.91480119750147e-03 - 17 2.54234658740788e+00 -9.76938634963152e-03 - 18 2.51774460925550e+00 -9.67097843702200e-03 - 19 2.50553744233726e+00 -9.62214976934902e-03 - 20 2.50586699278142e+00 -9.62346797112569e-03 + 1 3.34456621006869e+00 -1.29782648402748e-02 + 2 3.33650183434893e+00 -1.29460073373957e-02 + 3 3.31967608173955e+00 -1.28787043269582e-02 + 4 3.29359679364577e+00 -1.27743871745831e-02 + 5 3.25804972949454e+00 -1.26321989179782e-02 + 6 3.21319557916635e+00 -1.24527823166654e-02 + 7 3.15964721770391e+00 -1.22385888708157e-02 + 8 3.09850657690298e+00 -1.19940263076119e-02 + 9 3.03134993712323e+00 -1.17253997484929e-02 + 10 2.96016041313917e+00 -1.14406416525567e-02 + 11 2.88721545954542e+00 -1.11488618381817e-02 + 12 2.81494477251460e+00 -1.08597790900584e-02 + 13 2.74578033330936e+00 -1.05831213332374e-02 + 14 2.68202224548980e+00 -1.03280889819592e-02 + 15 2.62573819506619e+00 -1.01029527802647e-02 + 16 2.57870029809758e+00 -9.91480119239031e-03 + 17 2.54234658587039e+00 -9.76938634348154e-03 + 18 2.51774460747483e+00 -9.67097842989931e-03 + 19 2.50553744033959e+00 -9.62214976135836e-03 + 20 2.50586699060249e+00 -9.62346796240996e-03 diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index e3acdcd80..706323615 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,33 +132,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 2.50587 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 86c2b39dd..92df7f52f 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.59806114483912e+00 + x 2.59806113934628e+00 } restraint { diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 64498a7a8..08b065f51 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.50586699278142e+00 -9.62346797112569e-03 - 21 2.51828912676855e+00 -9.67315650707419e-03 - 22 2.54171016632473e+00 -9.76684066529891e-03 - 23 2.57437672315441e+00 -9.89750689261763e-03 - 24 2.61394044202478e+00 -1.00557617680991e-02 - 25 2.65760032709751e+00 -1.02304013083901e-02 - 26 2.70230713671789e+00 -1.04092285468715e-02 - 27 2.74500166801146e+00 -1.05800066720458e-02 - 28 2.78285410384574e+00 -1.07314164153830e-02 - 29 2.81347402051205e+00 -1.08538960820482e-02 - 30 2.83506753731124e+00 -1.09402701492450e-02 - 31 2.84652760280228e+00 -1.09861104112091e-02 - 32 2.84745364262997e+00 -1.09898145705199e-02 - 33 2.83810685957546e+00 -1.09524274383019e-02 - 34 2.81931679148249e+00 -1.08772671659299e-02 - 35 2.79236160667317e+00 -1.07694464266927e-02 - 36 2.75884756305916e+00 -1.06353902522366e-02 - 37 2.72060909042328e+00 -1.04824363616931e-02 - 38 2.67964054352647e+00 -1.03185621741059e-02 - 39 2.63805615046828e+00 -1.01522246018731e-02 - 40 2.59806114483912e+00 -9.99224457935649e-03 + 20 2.50586699060249e+00 -9.62346796240996e-03 + 21 2.51828912444925e+00 -9.67315649779702e-03 + 22 2.54171016390634e+00 -9.76684065562536e-03 + 23 2.57437672068062e+00 -9.89750688272248e-03 + 24 2.61394043953042e+00 -1.00557617581217e-02 + 25 2.65760032461011e+00 -1.02304012984404e-02 + 26 2.70230713425706e+00 -1.04092285370282e-02 + 27 2.74500166558147e+00 -1.05800066623259e-02 + 28 2.78285410144146e+00 -1.07314164057658e-02 + 29 2.81347401811216e+00 -1.08538960724486e-02 + 30 2.83506753488489e+00 -1.09402701395396e-02 + 31 2.84652760030681e+00 -1.09861104012272e-02 + 32 2.84745364001396e+00 -1.09898145600559e-02 + 33 2.83810685678234e+00 -1.09524274271294e-02 + 34 2.81931678845251e+00 -1.08772671538101e-02 + 35 2.79236160334505e+00 -1.07694464133802e-02 + 36 2.75884755937459e+00 -1.06353902374984e-02 + 37 2.72060908633430e+00 -1.04824363453372e-02 + 38 2.67964053899086e+00 -1.03185621559634e-02 + 39 2.63805614546050e+00 -1.01522245818420e-02 + 40 2.59806113934628e+00 -9.99224455738511e-03 diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out index 23e52329c..9e25d6b26 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,27 +114,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 3794713ae..b775835f5 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.14042524977569e+01 + x 1.14042525000436e+01 } restraint { diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj index 208ef8be6..362277f2e 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.05987658982707e+01 -4.19950635930827e-02 - 1 1.06266098865076e+01 -4.21064395460305e-02 - 2 1.06570380232944e+01 -4.22281520931778e-02 - 3 1.06891026494686e+01 -4.23564105978743e-02 - 4 1.07220322922544e+01 -4.24881291690175e-02 - 5 1.07553082614248e+01 -4.26212330456994e-02 - 6 1.07886956710148e+01 -4.27547826840591e-02 - 7 1.08222315380552e+01 -4.28889261522210e-02 - 8 1.08561787307268e+01 -4.30247149229071e-02 - 9 1.08909573892425e+01 -4.31638295569698e-02 - 10 1.09270659265304e+01 -4.33082637061217e-02 - 11 1.09650029613683e+01 -4.34600118454733e-02 - 12 1.10051994774624e+01 -4.36207979098498e-02 - 13 1.10479655806188e+01 -4.37918623224750e-02 - 14 1.10934497458239e+01 -4.39737989832956e-02 - 15 1.11416047500329e+01 -4.41664190001316e-02 - 16 1.11921570615955e+01 -4.43686282463821e-02 - 17 1.12445838365001e+01 -4.45783353460005e-02 - 18 1.12981079838905e+01 -4.47924319355620e-02 - 19 1.13517227431649e+01 -4.50068909726597e-02 - 20 1.14042524977569e+01 -4.52170099910277e-02 + 1 1.06266098864992e+01 -4.21064395459970e-02 + 2 1.06570380232614e+01 -4.22281520930457e-02 + 3 1.06891026493980e+01 -4.23564105975918e-02 + 4 1.07220322921382e+01 -4.24881291685529e-02 + 5 1.07553082612621e+01 -4.26212330450483e-02 + 6 1.07886956708129e+01 -4.27547826832515e-02 + 7 1.08222315378305e+01 -4.28889261513219e-02 + 8 1.08561787305042e+01 -4.30247149220168e-02 + 9 1.08909573890554e+01 -4.31638295562217e-02 + 10 1.09270659264173e+01 -4.33082637056690e-02 + 11 1.09650029613711e+01 -4.34600118454845e-02 + 12 1.10051994776244e+01 -4.36207979104977e-02 + 13 1.10479655809806e+01 -4.37918623239224e-02 + 14 1.10934497464229e+01 -4.39737989856916e-02 + 15 1.11416047509002e+01 -4.41664190036009e-02 + 16 1.11921570627529e+01 -4.43686282510115e-02 + 17 1.12445838379582e+01 -4.45783353518327e-02 + 18 1.12981079856473e+01 -4.47924319425893e-02 + 19 1.13517227452027e+01 -4.50068909808106e-02 + 20 1.14042525000436e+01 -4.52170100001743e-02 diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 8a00c0457..659cdc13a 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,32 +114,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 11.4043 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index d6e8c97ef..a902f9774 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.17634448022492e+01 + x 1.17634448064811e+01 } restraint { diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 4da52b8db..9b350dcb7 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.14042524977569e+01 -4.52170099910277e-02 - 21 1.14544480755564e+01 -4.54177923022257e-02 - 22 1.15011053897376e+01 -4.56044215589506e-02 - 23 1.15431885942609e+01 -4.57727543770436e-02 - 24 1.15799356423833e+01 -4.59197425695332e-02 - 25 1.16109269835055e+01 -4.60437079340218e-02 - 26 1.16361065785131e+01 -4.61444263140523e-02 - 27 1.16557559207023e+01 -4.62230236828094e-02 - 28 1.16704320370109e+01 -4.62817281480436e-02 - 29 1.16808864175993e+01 -4.63235456703971e-02 - 30 1.16879826712242e+01 -4.63519306848966e-02 - 31 1.16926277176089e+01 -4.63705108704357e-02 - 32 1.16957259267591e+01 -4.63829037070363e-02 - 33 1.16981585973899e+01 -4.63926343895594e-02 - 34 1.17007830899012e+01 -4.64031323596047e-02 - 35 1.17044386469586e+01 -4.64177545878343e-02 - 36 1.17099416836191e+01 -4.64397667344764e-02 - 37 1.17180555417655e+01 -4.64722221670619e-02 - 38 1.17294285106548e+01 -4.65177140426191e-02 - 39 1.17445071542025e+01 -4.65780286168101e-02 - 40 1.17634448022492e+01 -4.66537792089967e-02 + 20 1.14042525000436e+01 -4.52170100001743e-02 + 21 1.14544480780461e+01 -4.54177923121844e-02 + 22 1.15011053923729e+01 -4.56044215694917e-02 + 23 1.15431885969782e+01 -4.57727543879128e-02 + 24 1.15799356451165e+01 -4.59197425804660e-02 + 25 1.16109269861924e+01 -4.60437079447695e-02 + 26 1.16361065810996e+01 -4.61444263243983e-02 + 27 1.16557559231474e+01 -4.62230236925897e-02 + 28 1.16704320392906e+01 -4.62817281571624e-02 + 29 1.16808864197082e+01 -4.63235456788327e-02 + 30 1.16879826731775e+01 -4.63519306927099e-02 + 31 1.16926277194411e+01 -4.63705108777642e-02 + 32 1.16957259285228e+01 -4.63829037140912e-02 + 33 1.16981585991540e+01 -4.63926343966159e-02 + 34 1.17007830917475e+01 -4.64031323669901e-02 + 35 1.17044386489778e+01 -4.64177545959111e-02 + 36 1.17099416859060e+01 -4.64397667436240e-02 + 37 1.17180555444153e+01 -4.64722221776613e-02 + 38 1.17294285137575e+01 -4.65177140550300e-02 + 39 1.17445071578377e+01 -4.65780286313510e-02 + 40 1.17634448064811e+01 -4.66537792259242e-02 diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index e3dd29780..3159c4a1d 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,28 +132,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationProj colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 6aab80c05..8993379a3 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.99042890071513e-01 + x 9.99042890073178e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 6408cd312..52560e9b2 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 9.98296758220625e-01 -3.59318703288250e-03 - 1 9.98296730621305e-01 -3.59318692248522e-03 - 2 9.98304905164688e-01 -3.59321962065875e-03 - 3 9.98321909943251e-01 -3.59328763977300e-03 - 4 9.98348106341271e-01 -3.59339242536509e-03 - 5 9.98383489829552e-01 -3.59353395931821e-03 - 6 9.98427599823242e-01 -3.59371039929297e-03 - 7 9.98479469810032e-01 -3.59391787924013e-03 - 8 9.98537639417837e-01 -3.59415055767135e-03 - 9 9.98600233958691e-01 -3.59440093583477e-03 - 10 9.98665100608690e-01 -3.59466040243476e-03 - 11 9.98729977781407e-01 -3.59491991112563e-03 - 12 9.98792667791781e-01 -3.59517067116713e-03 - 13 9.98851182637630e-01 -3.59540473055052e-03 - 14 9.98903839987366e-01 -3.59561535994946e-03 - 15 9.98949300566769e-01 -3.59579720226708e-03 - 16 9.98986555615076e-01 -3.59594622246030e-03 - 17 9.99014887276758e-01 -3.59605954910703e-03 - 18 9.99033829853492e-01 -3.59613531941397e-03 - 19 9.99043154766428e-01 -3.59617261906571e-03 - 20 9.99042890071513e-01 -3.59617156028605e-03 + 1 9.98296730621296e-01 -3.59318692248518e-03 + 2 9.98304905164651e-01 -3.59321962065860e-03 + 3 9.98321909943172e-01 -3.59328763977269e-03 + 4 9.98348106341147e-01 -3.59339242536459e-03 + 5 9.98383489829382e-01 -3.59353395931753e-03 + 6 9.98427599823041e-01 -3.59371039929216e-03 + 7 9.98479469809825e-01 -3.59391787923930e-03 + 8 9.98537639417652e-01 -3.59415055767061e-03 + 9 9.98600233958565e-01 -3.59440093583426e-03 + 10 9.98665100608658e-01 -3.59466040243463e-03 + 11 9.98729977781503e-01 -3.59491991112601e-03 + 12 9.98792667792032e-01 -3.59517067116813e-03 + 13 9.98851182638057e-01 -3.59540473055223e-03 + 14 9.98903839987981e-01 -3.59561535995193e-03 + 15 9.98949300567580e-01 -3.59579720227032e-03 + 16 9.98986555616080e-01 -3.59594622246432e-03 + 17 9.99014887277948e-01 -3.59605954911179e-03 + 18 9.99033829854858e-01 -3.59613531941943e-03 + 19 9.99043154767953e-01 -3.59617261907181e-03 + 20 9.99042890073178e-01 -3.59617156029271e-03 diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index 8798aa21c..deb021ce1 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,33 +132,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationProj colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.999043 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 8b0add5c8..0f04cd392 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.98970741879346e-01 + x 9.98970741883698e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 32cfd70e2..7997c7579 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.99042890071513e-01 -3.59617156028605e-03 - 21 9.99033371043944e-01 -3.59613348417578e-03 - 22 9.99015305958516e-01 -3.59606122383406e-03 - 23 9.98989833767277e-01 -3.59595933506911e-03 - 24 9.98958548398355e-01 -3.59583419359342e-03 - 25 9.98923468752275e-01 -3.59569387500910e-03 - 26 9.98886942695769e-01 -3.59554777078308e-03 - 27 9.98851487059890e-01 -3.59540594823956e-03 - 28 9.98819580887699e-01 -3.59527832355080e-03 - 29 9.98793441988564e-01 -3.59517376795426e-03 - 30 9.98774823522244e-01 -3.59509929408898e-03 - 31 9.98764865062350e-01 -3.59505946024940e-03 - 32 9.98764021743129e-01 -3.59505608697251e-03 - 33 9.98772078283373e-01 -3.59508831313349e-03 - 34 9.98788236182522e-01 -3.59515294473009e-03 - 35 9.98811247689749e-01 -3.59524499075900e-03 - 36 9.98839563234612e-01 -3.59535825293845e-03 - 37 9.98871462837275e-01 -3.59548585134910e-03 - 38 9.98905154300893e-01 -3.59562061720357e-03 - 39 9.98938836852973e-01 -3.59575534741189e-03 - 40 9.98970741879346e-01 -3.59588296751738e-03 + 20 9.99042890073178e-01 -3.59617156029271e-03 + 21 9.99033371045725e-01 -3.59613348418290e-03 + 22 9.99015305960388e-01 -3.59606122384155e-03 + 23 9.98989833769218e-01 -3.59595933507687e-03 + 24 9.98958548400342e-01 -3.59583419360137e-03 + 25 9.98923468754291e-01 -3.59569387501716e-03 + 26 9.98886942697797e-01 -3.59554777079119e-03 + 27 9.98851487061923e-01 -3.59540594824769e-03 + 28 9.98819580889739e-01 -3.59527832355896e-03 + 29 9.98793441990623e-01 -3.59517376796249e-03 + 30 9.98774823524341e-01 -3.59509929409736e-03 + 31 9.98764865064516e-01 -3.59505946025807e-03 + 32 9.98764021745399e-01 -3.59505608698159e-03 + 33 9.98772078285790e-01 -3.59508831314316e-03 + 34 9.98788236185128e-01 -3.59515294474051e-03 + 35 9.98811247692583e-01 -3.59524499077033e-03 + 36 9.98839563237711e-01 -3.59535825295084e-03 + 37 9.98871462840668e-01 -3.59548585136267e-03 + 38 9.98905154304598e-01 -3.59562061721839e-03 + 39 9.98938836857002e-01 -3.59575534742801e-03 + 40 9.98970741883698e-01 -3.59588296753479e-03 diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out index 15ba472df..0867faa1d 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,27 +114,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationProj colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped index dbd322f7c..fbbe4454a 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.80239375949467e-01 + x 9.80239375941569e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj index 2a3c28388..63a14b625 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 9.82939311075160e-01 -3.53175724430064e-03 - 1 9.82849734901045e-01 -3.53139893960418e-03 - 2 9.82751436474708e-01 -3.53100574589883e-03 - 3 9.82647417671745e-01 -3.53058967068698e-03 - 4 9.82540144796735e-01 -3.53016057918694e-03 - 5 9.82431293276323e-01 -3.52972517310529e-03 - 6 9.82321634339533e-01 -3.52928653735813e-03 - 7 9.82211059380067e-01 -3.52884423752027e-03 - 8 9.82098716903652e-01 -3.52839486761461e-03 - 9 9.81983226206096e-01 -3.52793290482439e-03 - 10 9.81862929059119e-01 -3.52745171623648e-03 - 11 9.81736142358021e-01 -3.52694456943208e-03 - 12 9.81601381064589e-01 -3.52640552425836e-03 - 13 9.81457536905773e-01 -3.52583014762309e-03 - 14 9.81304019863068e-01 -3.52521607945227e-03 - 15 9.81140882071682e-01 -3.52456352828673e-03 - 16 9.80968935309110e-01 -3.52387574123644e-03 - 17 9.80789847969960e-01 -3.52315939187984e-03 - 18 9.80606184563440e-01 -3.52242473825376e-03 - 19 9.80421345128356e-01 -3.52168538051342e-03 - 20 9.80239375949467e-01 -3.52095750379787e-03 + 1 9.82849734901072e-01 -3.53139893960429e-03 + 2 9.82751436474814e-01 -3.53100574589926e-03 + 3 9.82647417671973e-01 -3.53058967068789e-03 + 4 9.82540144797111e-01 -3.53016057918845e-03 + 5 9.82431293276853e-01 -3.52972517310741e-03 + 6 9.82321634340193e-01 -3.52928653736077e-03 + 7 9.82211059380804e-01 -3.52884423752322e-03 + 8 9.82098716904383e-01 -3.52839486761753e-03 + 9 9.81983226206714e-01 -3.52793290482686e-03 + 10 9.81862929059493e-01 -3.52745171623797e-03 + 11 9.81736142358011e-01 -3.52694456943204e-03 + 12 9.81601381064049e-01 -3.52640552425620e-03 + 13 9.81457536904562e-01 -3.52583014761825e-03 + 14 9.81304019861054e-01 -3.52521607944422e-03 + 15 9.81140882068755e-01 -3.52456352827502e-03 + 16 9.80968935305186e-01 -3.52387574122074e-03 + 17 9.80789847964994e-01 -3.52315939185998e-03 + 18 9.80606184557429e-01 -3.52242473822972e-03 + 19 9.80421345121349e-01 -3.52168538048540e-03 + 20 9.80239375941569e-01 -3.52095750376628e-03 diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out index 5af1ca243..821e0a8d3 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,32 +114,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationProj colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.980239 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 32bda65e7..39341551b 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.78952248453755e-01 + x 9.78952248438667e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj index f961e9ce6..36e1592b7 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.80239375949467e-01 -3.52095750379787e-03 - 21 9.80064651415975e-01 -3.52025860566390e-03 - 22 9.79901460938148e-01 -3.51960584375259e-03 - 23 9.79753565304145e-01 -3.51901426121658e-03 - 24 9.79623803009410e-01 -3.51849521203764e-03 - 25 9.79513820811740e-01 -3.51805528324696e-03 - 26 9.79423974214543e-01 -3.51769589685817e-03 - 27 9.79353401323632e-01 -3.51741360529453e-03 - 28 9.79300233731289e-01 -3.51720093492516e-03 - 29 9.79261883509026e-01 -3.51704753403610e-03 - 30 9.79235340258555e-01 -3.51694136103422e-03 - 31 9.79217422310898e-01 -3.51686968924359e-03 - 32 9.79204946067415e-01 -3.51681978426966e-03 - 33 9.79194803551154e-01 -3.51677921420462e-03 - 34 9.79183967865525e-01 -3.51673587146210e-03 - 35 9.79169472616686e-01 -3.51667789046674e-03 - 36 9.79148426614635e-01 -3.51659370645854e-03 - 37 9.79118117487522e-01 -3.51647246995009e-03 - 38 9.79076227155221e-01 -3.51630490862088e-03 - 39 9.79021136068235e-01 -3.51608454427294e-03 - 40 9.78952248453755e-01 -3.51580899381502e-03 + 20 9.80239375941569e-01 -3.52095750376628e-03 + 21 9.80064651407338e-01 -3.52025860562935e-03 + 22 9.79901460928968e-01 -3.51960584371587e-03 + 23 9.79753565294644e-01 -3.51901426117858e-03 + 24 9.79623802999823e-01 -3.51849521199929e-03 + 25 9.79513820802291e-01 -3.51805528320916e-03 + 26 9.79423974205426e-01 -3.51769589682171e-03 + 27 9.79353401314998e-01 -3.51741360525999e-03 + 28 9.79300233723229e-01 -3.51720093489292e-03 + 29 9.79261883501562e-01 -3.51704753400625e-03 + 30 9.79235340251636e-01 -3.51694136100655e-03 + 31 9.79217422304405e-01 -3.51686968921762e-03 + 32 9.79204946061162e-01 -3.51681978424465e-03 + 33 9.79194803544898e-01 -3.51677921417959e-03 + 34 9.79183967858975e-01 -3.51673587143590e-03 + 35 9.79169472609521e-01 -3.51667789043808e-03 + 36 9.79148426606516e-01 -3.51659370642606e-03 + 37 9.79118117478109e-01 -3.51647246991243e-03 + 38 9.79076227144190e-01 -3.51630490857676e-03 + 39 9.79021136055294e-01 -3.51608454422118e-03 + 40 9.78952248438667e-01 -3.51580899375467e-03 diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 188d105ae..e3e2b88a3 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -98,7 +94,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,27 +132,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 95457b174..a5b66188c 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.51992448739790e-01 + x 6.51992447935402e-01 } restraint { diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 9ff521cd9..20f9e8ab6 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 6.42446480928994e-01 -2.16978592371598e-03 - 1 6.41362151829732e-01 -2.16544860731893e-03 - 2 6.39964191531625e-01 -2.15985676612650e-03 - 3 6.38339929638892e-01 -2.15335971855557e-03 - 4 6.36588007574356e-01 -2.14635203029742e-03 - 5 6.34817335440207e-01 -2.13926934176083e-03 - 6 6.33145320204402e-01 -2.13258128081761e-03 - 7 6.31694089901779e-01 -2.12677635960711e-03 - 8 6.30583853252009e-01 -2.12233541300803e-03 - 9 6.29923415729674e-01 -2.11969366291869e-03 - 10 6.29798996911838e-01 -2.11919598764735e-03 - 11 6.30263472118592e-01 -2.12105388847437e-03 - 12 6.31328581658953e-01 -2.12531432663581e-03 - 13 6.32962276844382e-01 -2.13184910737753e-03 - 14 6.35092221778593e-01 -2.14036888711437e-03 - 15 6.37614971049963e-01 -2.15045988419985e-03 - 16 6.40409022430485e-01 -2.16163608972194e-03 - 17 6.43349209707525e-01 -2.17339683883010e-03 - 18 6.46319867665476e-01 -2.18527947066190e-03 - 19 6.49224738102162e-01 -2.19689895240865e-03 - 20 6.51992448739790e-01 -2.20796979495916e-03 + 0 6.42446480928998e-01 -2.16978592371599e-03 + 1 6.41362151827951e-01 -2.16544860731180e-03 + 2 6.39964191522473e-01 -2.15985676608989e-03 + 3 6.38339929621363e-01 -2.15335971848545e-03 + 4 6.36588007540679e-01 -2.14635203016272e-03 + 5 6.34817335398304e-01 -2.13926934159321e-03 + 6 6.33145320132662e-01 -2.13258128053065e-03 + 7 6.31694089805813e-01 -2.12677635922325e-03 + 8 6.30583853131960e-01 -2.12233541252784e-03 + 9 6.29923415581364e-01 -2.11969366232546e-03 + 10 6.29798996732227e-01 -2.11919598692891e-03 + 11 6.30263471904012e-01 -2.12105388761605e-03 + 12 6.31328581404817e-01 -2.12531432561927e-03 + 13 6.32962276627263e-01 -2.13184910650905e-03 + 14 6.35092221427288e-01 -2.14036888570915e-03 + 15 6.37614970671458e-01 -2.15045988268583e-03 + 16 6.40409021950152e-01 -2.16163608780061e-03 + 17 6.43349209139955e-01 -2.17339683655982e-03 + 18 6.46319867119914e-01 -2.18527946847966e-03 + 19 6.49224737403552e-01 -2.19689894961421e-03 + 20 6.51992447935402e-01 -2.20796979174161e-03 diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index f1030f219..d4194b991 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -98,7 +94,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,32 +132,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.651992 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 2c5997d6d..57f5c66cf 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.75350774458524e-01 + x 6.75350774255469e-01 } restraint { diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index db5a45ae4..465a8190b 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 6.51992448739790e-01 -2.20796979495916e-03 - 21 6.54577359871602e-01 -2.21830943948641e-03 - 22 6.56956477797988e-01 -2.22782591119195e-03 - 23 6.59123837391726e-01 -2.23649534956690e-03 - 24 6.61084125660818e-01 -2.24433650264327e-03 - 25 6.62847214781938e-01 -2.25138885912775e-03 - 26 6.64424718041335e-01 -2.25769887216534e-03 - 27 6.65828841073339e-01 -2.26331536429336e-03 - 28 6.67072979054150e-01 -2.26829191621660e-03 - 29 6.68172991793991e-01 -2.27269196717596e-03 - 30 6.69147999050168e-01 -2.27659199620067e-03 - 31 6.70019872911646e-01 -2.28007949164658e-03 - 32 6.70811209861948e-01 -2.28324483944779e-03 - 33 6.71542241163152e-01 -2.28616896465261e-03 - 34 6.72227644663412e-01 -2.28891057865365e-03 - 35 6.72874369034013e-01 -2.29149747613605e-03 - 36 6.73481316803640e-01 -2.29392526721456e-03 - 37 6.74041160994404e-01 -2.29616464397762e-03 - 38 6.74543902662182e-01 -2.29817561064873e-03 - 39 6.74981259280343e-01 -2.29992503712137e-03 - 40 6.75350774458524e-01 -2.30140309783410e-03 + 20 6.51992447935402e-01 -2.20796979174161e-03 + 21 6.54577358969536e-01 -2.21830943587814e-03 + 22 6.56956476804603e-01 -2.22782590721841e-03 + 23 6.59123836309169e-01 -2.23649534523667e-03 + 24 6.61084124493515e-01 -2.24433649797406e-03 + 25 6.62847213541526e-01 -2.25138885416610e-03 + 26 6.64424716728470e-01 -2.25769886691388e-03 + 27 6.65828839710307e-01 -2.26331535884123e-03 + 28 6.67072977661715e-01 -2.26829191064686e-03 + 29 6.68172990385695e-01 -2.27269196154278e-03 + 30 6.69147997661702e-01 -2.27659199064681e-03 + 31 6.70019871557500e-01 -2.28007948623000e-03 + 32 6.70811208574338e-01 -2.28324483429735e-03 + 33 6.71542239966417e-01 -2.28616895986567e-03 + 34 6.72227643578755e-01 -2.28891057431502e-03 + 35 6.72874368078643e-01 -2.29149747231457e-03 + 36 6.73481315978386e-01 -2.29392526391354e-03 + 37 6.74041160330857e-01 -2.29616464132343e-03 + 38 6.74543902153436e-01 -2.29817560861374e-03 + 39 6.74981258926052e-01 -2.29992503570421e-03 + 40 6.75350774255469e-01 -2.30140309702188e-03 diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out index 0df5ce6ef..66f42f578 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,13 +70,13 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,26 +114,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 59c145889..5965781f5 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.34779999706673e-01 + x 6.34779999776054e-01 } restraint { diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj index 0de897eb5..4aec974c6 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 6.13624515542194e-01 -2.05449806216878e-03 - 1 6.12490538024418e-01 -2.04996215209767e-03 - 2 6.11173746800116e-01 -2.04469498720046e-03 - 3 6.09786235548945e-01 -2.03914494219578e-03 - 4 6.08443934153914e-01 -2.03377573661566e-03 - 5 6.07262363747078e-01 -2.02904945498831e-03 - 6 6.06352646519890e-01 -2.02541058607956e-03 - 7 6.05817100403337e-01 -2.02326840161335e-03 - 8 6.05743803259169e-01 -2.02297521303668e-03 - 9 6.06199958858187e-01 -2.02479983543275e-03 - 10 6.07224667100095e-01 -2.02889866840038e-03 - 11 6.08822487970901e-01 -2.03528995188360e-03 - 12 6.10959603602463e-01 -2.04383841440985e-03 - 13 6.13564160848909e-01 -2.05425664339564e-03 - 14 6.16531504942698e-01 -2.06612601977079e-03 - 15 6.19733849273886e-01 -2.07893539709555e-03 - 16 6.23032907695619e-01 -2.09213163078248e-03 - 17 6.26293468659005e-01 -2.10517387463602e-03 - 18 6.29395874658527e-01 -2.11758349863411e-03 - 19 6.32245759582595e-01 -2.12898303833038e-03 - 20 6.34779999706673e-01 -2.13911999882669e-03 + 0 6.13624515542246e-01 -2.05449806216899e-03 + 1 6.12490538024335e-01 -2.04996215209734e-03 + 2 6.11173746799938e-01 -2.04469498719975e-03 + 3 6.09786235548445e-01 -2.03914494219378e-03 + 4 6.08443934153189e-01 -2.03377573661276e-03 + 5 6.07262363750067e-01 -2.02904945500027e-03 + 6 6.06352646518334e-01 -2.02541058607334e-03 + 7 6.05817100403672e-01 -2.02326840161469e-03 + 8 6.05743803262677e-01 -2.02297521305071e-03 + 9 6.06199958866108e-01 -2.02479983546443e-03 + 10 6.07224667113594e-01 -2.02889866845438e-03 + 11 6.08822487990989e-01 -2.03528995196396e-03 + 12 6.10959603629905e-01 -2.04383841451962e-03 + 13 6.13564160971268e-01 -2.05425664388507e-03 + 14 6.16531504985440e-01 -2.06612601994176e-03 + 15 6.19733849359571e-01 -2.07893539743829e-03 + 16 6.23032907749212e-01 -2.09213163099685e-03 + 17 6.26293468706736e-01 -2.10517387482694e-03 + 18 6.29395874814933e-01 -2.11758349925973e-03 + 19 6.32245759668358e-01 -2.12898303867343e-03 + 20 6.34779999776054e-01 -2.13911999910422e-03 diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out index c6589b658..46a799d77 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,13 +70,13 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,31 +114,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.63478 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index c6c8eee84..1b15cce3c 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.57869102539559e-01 + x 6.57869102603360e-01 } restraint { diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 6131bf0e9..b53dc8777 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 6.34779999706673e-01 -2.13911999882669e-03 - 21 6.36968499670390e-01 -2.14787399868156e-03 - 22 6.38812086586848e-01 -2.15524834634739e-03 - 23 6.40337357406265e-01 -2.16134942962506e-03 - 24 6.41589727219131e-01 -2.16635890887652e-03 - 25 6.42626037705784e-01 -2.17050415082314e-03 - 26 6.43507870289948e-01 -2.17403148115979e-03 - 27 6.44296238099800e-01 -2.17718495239920e-03 - 28 6.45047779413727e-01 -2.18019111765491e-03 - 29 6.45812131910624e-01 -2.18324852764250e-03 - 30 6.46629948954352e-01 -2.18651979581741e-03 - 31 6.47531080128373e-01 -2.19012432051349e-03 - 32 6.48532731402192e-01 -2.19413092560877e-03 - 33 6.49637836090191e-01 -2.19855134436077e-03 - 34 6.50834212189133e-01 -2.20333684875653e-03 - 35 6.52095178886227e-01 -2.20838071554491e-03 - 36 6.53382073051404e-01 -2.21352829220561e-03 - 37 6.54648626678558e-01 -2.21859450671423e-03 - 38 6.55846616450873e-01 -2.22338646580349e-03 - 39 6.56931804632144e-01 -2.22772721852858e-03 - 40 6.57869102539559e-01 -2.23147641015824e-03 + 20 6.34779999776054e-01 -2.13911999910422e-03 + 21 6.36968499730488e-01 -2.14787399892195e-03 + 22 6.38812086644733e-01 -2.15524834657893e-03 + 23 6.40337357461428e-01 -2.16134942984571e-03 + 24 6.41589727271310e-01 -2.16635890908524e-03 + 25 6.42626037763938e-01 -2.17050415105575e-03 + 26 6.43507870335777e-01 -2.17403148134311e-03 + 27 6.44296238145373e-01 -2.17718495258149e-03 + 28 6.45047779464950e-01 -2.18019111785980e-03 + 29 6.45812131951865e-01 -2.18324852780746e-03 + 30 6.46629949006064e-01 -2.18651979602426e-03 + 31 6.47531080168799e-01 -2.19012432067520e-03 + 32 6.48532731443661e-01 -2.19413092577464e-03 + 33 6.49637836133461e-01 -2.19855134453384e-03 + 34 6.50834212234814e-01 -2.20333684893926e-03 + 35 6.52095178934730e-01 -2.20838071573892e-03 + 36 6.53382073098997e-01 -2.21352829239599e-03 + 37 6.54648626732206e-01 -2.21859450692882e-03 + 38 6.55846616507654e-01 -2.22338646603062e-03 + 39 6.56931804692009e-01 -2.22772721876803e-03 + 40 6.57869102603360e-01 -2.23147641041344e-03 diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt b/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out index 61f83bfee..162de8092 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -107,7 +103,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -118,26 +113,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - selfCoordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 699308a19..b757a82d5 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.50086993007309e+00 + x 5.50086992991043e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj index 3eabd5c33..4497991fb 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 5.50064408080373e+00 -2.16025763232149e-02 - 1 5.50080703004882e+00 -2.16032281201953e-02 - 2 5.50068939069810e+00 -2.16027575627924e-02 - 3 5.50034727666126e+00 -2.16013891066450e-02 - 4 5.49985543899098e+00 -2.15994217559639e-02 - 5 5.49929900080157e+00 -2.15971960032063e-02 - 6 5.49876326013045e+00 -2.15950530405218e-02 - 7 5.49832342753577e+00 -2.15932937101431e-02 - 8 5.49803620216166e+00 -2.15921448086467e-02 - 9 5.49793456348608e+00 -2.15917382539443e-02 - 10 5.49802625415031e+00 -2.15921050166012e-02 - 11 5.49829556495176e+00 -2.15931822598070e-02 - 12 5.49870744203985e+00 -2.15948297681594e-02 - 13 5.49921283628923e+00 -2.15968513451569e-02 - 14 5.49975442850415e+00 -2.15990177140166e-02 - 15 5.50027220385344e+00 -2.16010888154138e-02 - 16 5.50070878638128e+00 -2.16028351455251e-02 - 17 5.50101460472211e+00 -2.16040584188884e-02 - 18 5.50115288500804e+00 -2.16046115400322e-02 - 19 5.50110418967735e+00 -2.16044167587094e-02 - 20 5.50086993007309e+00 -2.16034797202924e-02 + 1 5.50080703004843e+00 -2.16032281201937e-02 + 2 5.50068939069653e+00 -2.16027575627861e-02 + 3 5.50034727665768e+00 -2.16013891066307e-02 + 4 5.49985543898452e+00 -2.15994217559381e-02 + 5 5.49929900079136e+00 -2.15971960031654e-02 + 6 5.49876326011562e+00 -2.15950530404625e-02 + 7 5.49832342751543e+00 -2.15932937100617e-02 + 8 5.49803620213495e+00 -2.15921448085398e-02 + 9 5.49793456345215e+00 -2.15917382538086e-02 + 10 5.49802625410834e+00 -2.15921050164334e-02 + 11 5.49829556490095e+00 -2.15931822596038e-02 + 12 5.49870744197941e+00 -2.15948297679177e-02 + 13 5.49921283621840e+00 -2.15968513448736e-02 + 14 5.49975442842220e+00 -2.15990177136888e-02 + 15 5.50027220375965e+00 -2.16010888150386e-02 + 16 5.50070878627497e+00 -2.16028351450999e-02 + 17 5.50101460460263e+00 -2.16040584184105e-02 + 18 5.50115288487476e+00 -2.16046115394991e-02 + 19 5.50110418952966e+00 -2.16044167581187e-02 + 20 5.50086992991043e+00 -2.16034797196417e-02 diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out index 2b29746be..c7aa828f5 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -107,7 +103,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -118,31 +113,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - selfCoordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 5.50087 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 4e2699486..c26ac3859 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.52672800845913e+00 + x 5.52672800804253e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj index ae8c62635..2eae1fa46 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.50086993007309e+00 -2.16034797202924e-02 - 21 5.50047411702526e+00 -2.16018964681010e-02 - 22 5.49996271480815e+00 -2.15998508592326e-02 - 23 5.49940030464023e+00 -2.15976012185609e-02 - 24 5.49886427479469e+00 -2.15954570991788e-02 - 25 5.49843732358400e+00 -2.15937492943360e-02 - 26 5.49819952711805e+00 -2.15927981084722e-02 - 27 5.49822134791709e+00 -2.15928853916683e-02 - 28 5.49855877511631e+00 -2.15942351004652e-02 - 29 5.49925111600498e+00 -2.15970044640199e-02 - 30 5.50032111814578e+00 -2.16012844725831e-02 - 31 5.50177638755253e+00 -2.16071055502101e-02 - 32 5.50361077538265e+00 -2.16144431015306e-02 - 33 5.50580475246237e+00 -2.16232190098495e-02 - 34 5.50832462466879e+00 -2.16332984986752e-02 - 35 5.51112148850244e+00 -2.16444859540097e-02 - 36 5.51413136429316e+00 -2.16565254571726e-02 - 37 5.51727794304695e+00 -2.16691117721878e-02 - 38 5.52047847373687e+00 -2.16819138949475e-02 - 39 5.52365200686973e+00 -2.16946080274789e-02 - 40 5.52672800845913e+00 -2.17069120338365e-02 + 20 5.50086992991043e+00 -2.16034797196417e-02 + 21 5.50047411684707e+00 -2.16018964673883e-02 + 22 5.49996271461392e+00 -2.15998508584557e-02 + 23 5.49940030442948e+00 -2.15976012177179e-02 + 24 5.49886427456701e+00 -2.15954570982680e-02 + 25 5.49843732333905e+00 -2.15937492933562e-02 + 26 5.49819952685563e+00 -2.15927981074225e-02 + 27 5.49822134763710e+00 -2.15928853905484e-02 + 28 5.49855877481886e+00 -2.15942350992754e-02 + 29 5.49925111569040e+00 -2.15970044627616e-02 + 30 5.50032111781463e+00 -2.16012844712585e-02 + 31 5.50177638720568e+00 -2.16071055488227e-02 + 32 5.50361077502124e+00 -2.16144431000850e-02 + 33 5.50580475208785e+00 -2.16232190083514e-02 + 34 5.50832462428283e+00 -2.16332984971313e-02 + 35 5.51112148810689e+00 -2.16444859524276e-02 + 36 5.51413136388995e+00 -2.16565254555598e-02 + 37 5.51727794263797e+00 -2.16691117705519e-02 + 38 5.52047847332390e+00 -2.16819138932956e-02 + 39 5.52365200645431e+00 -2.16946080258172e-02 + 40 5.52672800804253e+00 -2.17069120321701e-02 diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt index 157cac038..b2949c9aa 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-05-08. +colvars: Using NAMD interface, version 2018-04-29. diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out index 50bb8b9f3..541860fb0 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -106,7 +102,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -117,26 +112,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - selfCoordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped index f9e22915c..3d35609cc 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.50586098376003e+00 + x 5.50586098356346e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj index 429397ed3..85b262a41 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 5.50563763999570e+00 -2.16225505599828e-02 - 1 5.50579895884978e+00 -2.16231958353991e-02 - 2 5.50568249321270e+00 -2.16227299728508e-02 - 3 5.50534379589551e+00 -2.16213751835821e-02 - 4 5.50485687050173e+00 -2.16194274820069e-02 - 5 5.50430598899447e+00 -2.16172239559779e-02 - 6 5.50377559652656e+00 -2.16151023861063e-02 - 7 5.50334015165911e+00 -2.16133606066364e-02 - 8 5.50305578666305e+00 -2.16122231466522e-02 - 9 5.50295515134696e+00 -2.16118206053878e-02 - 10 5.50304591105647e+00 -2.16121836442259e-02 - 11 5.50331251381601e+00 -2.16132500552641e-02 - 12 5.50372025645284e+00 -2.16148810258114e-02 - 13 5.50422058047457e+00 -2.16168823218983e-02 - 14 5.50475674002052e+00 -2.16190269600821e-02 - 15 5.50526932054974e+00 -2.16210772821990e-02 - 16 5.50570152000281e+00 -2.16228060800113e-02 - 17 5.50600426285527e+00 -2.16240170514211e-02 - 18 5.50614114309177e+00 -2.16245645723671e-02 - 19 5.50609291762347e+00 -2.16243716704939e-02 - 20 5.50586098376003e+00 -2.16234439350401e-02 + 0 5.50563763999569e+00 -2.16225505599828e-02 + 1 5.50579895884940e+00 -2.16231958353976e-02 + 2 5.50568249321115e+00 -2.16227299728446e-02 + 3 5.50534379589073e+00 -2.16213751835629e-02 + 4 5.50485687049274e+00 -2.16194274819710e-02 + 5 5.50430598897902e+00 -2.16172239559161e-02 + 6 5.50377559650355e+00 -2.16151023860142e-02 + 7 5.50334015162730e+00 -2.16133606065092e-02 + 8 5.50305578662091e+00 -2.16122231464836e-02 + 9 5.50295515129356e+00 -2.16118206051742e-02 + 10 5.50304591099096e+00 -2.16121836439638e-02 + 11 5.50331251373771e+00 -2.16132500549508e-02 + 12 5.50372025636123e+00 -2.16148810254449e-02 + 13 5.50422058036933e+00 -2.16168823214773e-02 + 14 5.50475673990153e+00 -2.16190269596061e-02 + 15 5.50526932041704e+00 -2.16210772816681e-02 + 16 5.50570151985664e+00 -2.16228060794265e-02 + 17 5.50600426269577e+00 -2.16240170507831e-02 + 18 5.50614114291938e+00 -2.16245645716775e-02 + 19 5.50609291743878e+00 -2.16243716697551e-02 + 20 5.50586098356346e+00 -2.16234439342538e-02 diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out index 604f12633..6fe484f98 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -106,7 +102,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -117,31 +112,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - selfCoordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 5.50586 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 2bc07b6b9..465216db6 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.53146030766424e+00 + x 5.53146030724717e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 536d293f8..ccbfc7916 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.50586098376003e+00 -2.16234439350401e-02 - 21 5.50546911228746e+00 -2.16218764491499e-02 - 22 5.50496280789046e+00 -2.16198512315618e-02 - 23 5.50440600602358e+00 -2.16176240240943e-02 - 24 5.50387532112795e+00 -2.16155012845118e-02 - 25 5.50345262459281e+00 -2.16138104983712e-02 - 26 5.50321719184149e+00 -2.16128687673660e-02 - 27 5.50323878086140e+00 -2.16129551234456e-02 - 28 5.50357282100607e+00 -2.16142912840243e-02 - 29 5.50425822661691e+00 -2.16170329064677e-02 - 30 5.50531751791649e+00 -2.16212700716660e-02 - 31 5.50675822499661e+00 -2.16270328999864e-02 - 32 5.50857426063415e+00 -2.16342970425366e-02 - 33 5.51074629106000e+00 -2.16429851642400e-02 - 34 5.51324095917529e+00 -2.16529638367011e-02 - 35 5.51600985055786e+00 -2.16640394022315e-02 - 36 5.51898962532829e+00 -2.16759585013131e-02 - 37 5.52210473752456e+00 -2.16884189500983e-02 - 38 5.52527326352281e+00 -2.17010930540912e-02 - 39 5.52841506317671e+00 -2.17136602527069e-02 - 40 5.53146030766424e+00 -2.17258412306570e-02 + 20 5.50586098356346e+00 -2.16234439342538e-02 + 21 5.50546911207949e+00 -2.16218764483180e-02 + 22 5.50496280767144e+00 -2.16198512306858e-02 + 23 5.50440600579367e+00 -2.16176240231747e-02 + 24 5.50387532088709e+00 -2.16155012835484e-02 + 25 5.50345262434073e+00 -2.16138104973629e-02 + 26 5.50321719157780e+00 -2.16128687663112e-02 + 27 5.50323878058562e+00 -2.16129551223425e-02 + 28 5.50357282071772e+00 -2.16142912828709e-02 + 29 5.50425822631558e+00 -2.16170329052623e-02 + 30 5.50531751760189e+00 -2.16212700704076e-02 + 31 5.50675822466860e+00 -2.16270328986744e-02 + 32 5.50857426029279e+00 -2.16342970411712e-02 + 33 5.51074629070554e+00 -2.16429851628222e-02 + 34 5.51324095880821e+00 -2.16529638352328e-02 + 35 5.51600985017893e+00 -2.16640394007157e-02 + 36 5.51898962493855e+00 -2.16759584997542e-02 + 37 5.52210473712539e+00 -2.16884189485016e-02 + 38 5.52527326311583e+00 -2.17010930524633e-02 + 39 5.52841506276376e+00 -2.17136602510550e-02 + 40 5.53146030724717e+00 -2.17258412289887e-02 diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt b/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 90d795b91..97875d855 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,17 +88,17 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -128,7 +124,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -139,28 +134,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - spinAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 7b11d47e8..2c69fa7d4 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.56417643630365e+00 + x -1.56417643615813e+00 } restraint { diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 813c43c6c..7fdccd94c 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 -1.84067203510482e+00 7.76268814041928e-03 - 1 -1.84826917190189e+00 7.79307668760756e-03 - 2 -1.85122278124429e+00 7.80489112497715e-03 - 3 -1.84852747918889e+00 7.79410991675556e-03 - 4 -1.83943263506144e+00 7.75773054024574e-03 - 5 -1.82355826066059e+00 7.69423304264234e-03 - 6 -1.80098250081617e+00 7.60393000326468e-03 - 7 -1.77228476375142e+00 7.48913905500567e-03 - 8 -1.73853720797388e+00 7.35414883189552e-03 - 9 -1.70124617189668e+00 7.20498468758673e-03 - 10 -1.66225195279233e+00 7.04900781116932e-03 - 11 -1.62359992640856e+00 6.89439970563425e-03 - 12 -1.58739844252513e+00 6.74959377010052e-03 - 13 -1.55567854108748e+00 6.62271416434992e-03 - 14 -1.53026683719969e+00 6.52106734879876e-03 - 15 -1.51267765483671e+00 6.45071061934683e-03 - 16 -1.50402646523430e+00 6.41610586093720e-03 - 17 -1.50496521246286e+00 6.41986084985144e-03 - 18 -1.51564034674263e+00 6.46256138697051e-03 - 19 -1.53567491271986e+00 6.54269965087945e-03 - 20 -1.56417643630365e+00 6.65670574521461e-03 + 1 -1.84826917190272e+00 7.79307668761089e-03 + 2 -1.85122278124769e+00 7.80489112499078e-03 + 3 -1.84852747919607e+00 7.79410991678428e-03 + 4 -1.83943263507235e+00 7.75773054028941e-03 + 5 -1.82355826067355e+00 7.69423304269421e-03 + 6 -1.80098250082777e+00 7.60393000331108e-03 + 7 -1.77228476375683e+00 7.48913905502733e-03 + 8 -1.73853720796757e+00 7.35414883187027e-03 + 9 -1.70124617187310e+00 7.20498468749239e-03 + 10 -1.66225195274677e+00 7.04900781098710e-03 + 11 -1.62359992633788e+00 6.89439970535152e-03 + 12 -1.58739844242825e+00 6.74959376971300e-03 + 13 -1.55567854096568e+00 6.62271416386271e-03 + 14 -1.53026683705662e+00 6.52106734822649e-03 + 15 -1.51267765467802e+00 6.45071061871208e-03 + 16 -1.50402646506685e+00 6.41610586026742e-03 + 17 -1.50496521229370e+00 6.41986084917482e-03 + 18 -1.51564034657794e+00 6.46256138631175e-03 + 19 -1.53567491256393e+00 6.54269965025573e-03 + 20 -1.56417643615813e+00 6.65670574463252e-03 diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index b11e0344c..ddf8c7f74 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,17 +88,17 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -128,7 +124,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -139,33 +134,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - spinAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.56418 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 00ee63db3..6e327970d 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.67720949927313e+00 + x -1.67720949787628e+00 } restraint { diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 0a68c54fa..5c8d1aff8 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -1.56417643630365e+00 6.65670574521461e-03 - 21 -1.59977280229335e+00 6.79909120917339e-03 - 22 -1.64067849467003e+00 6.96271397868011e-03 - 23 -1.68479233914237e+00 7.13916935656949e-03 - 24 -1.72982439584738e+00 7.31929758338951e-03 - 25 -1.77344385042163e+00 7.49377540168654e-03 - 26 -1.81343393777301e+00 7.65373575109205e-03 - 27 -1.84783676714212e+00 7.79134706856848e-03 - 28 -1.87507204676182e+00 7.90028818704729e-03 - 29 -1.89401880707755e+00 7.97607522831020e-03 - 30 -1.90405601824540e+00 8.01622407298159e-03 - 31 -1.90506463947095e+00 8.02025855788378e-03 - 32 -1.89739864549939e+00 7.98959458199754e-03 - 33 -1.88183530385872e+00 7.92734121543490e-03 - 34 -1.85951507145392e+00 7.83806028581570e-03 - 35 -1.83187886015785e+00 7.72751544063142e-03 - 36 -1.80060563931043e+00 7.60242255724172e-03 - 37 -1.76754822452589e+00 7.47019289810355e-03 - 38 -1.73466169550726e+00 7.33864678202902e-03 - 39 -1.70391870996803e+00 7.21567483987211e-03 - 40 -1.67720949927313e+00 7.10883799709252e-03 + 20 -1.56417643615813e+00 6.65670574463252e-03 + 21 -1.59977280215672e+00 6.79909120862687e-03 + 22 -1.64067849453734e+00 6.96271397814937e-03 + 23 -1.68479233900518e+00 7.13916935602071e-03 + 24 -1.72982439569390e+00 7.31929758277560e-03 + 25 -1.77344385023716e+00 7.49377540094865e-03 + 26 -1.81343393754057e+00 7.65373575016229e-03 + 27 -1.84783676684341e+00 7.79134706737363e-03 + 28 -1.87507204637838e+00 7.90028818551353e-03 + 29 -1.89401880659213e+00 7.97607522636850e-03 + 30 -1.90405601764340e+00 8.01622407057361e-03 + 31 -1.90506463874174e+00 8.02025855496697e-03 + 32 -1.89739864463758e+00 7.98959457855033e-03 + 33 -1.88183530286499e+00 7.92734121145994e-03 + 34 -1.85951507033553e+00 7.83806028134214e-03 + 35 -1.83187885892875e+00 7.72751543571502e-03 + 36 -1.80060563799079e+00 7.60242255196314e-03 + 37 -1.76754822314118e+00 7.47019289256470e-03 + 38 -1.73466169408694e+00 7.33864677634775e-03 + 39 -1.70391870854367e+00 7.21567483417467e-03 + 40 -1.67720949787628e+00 7.10883799150512e-03 diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..832c6a06f 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-14. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out index 21561ed31..38bb57ee5 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,17 +70,17 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 3 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -110,7 +106,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.000111111 according to the specified width (3). colvars: ---------------------------------------------------------------------- @@ -121,27 +116,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - spinAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 448e93eef..79a2a90e4 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -6.52196175536141e+00 + x -6.52196175528559e+00 } restraint { diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj index b5f5b8fe8..b65c4790b 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 -6.74120349419055e+00 7.60133721576728e-04 - 1 -6.74680409124828e+00 7.60756010138697e-04 - 2 -6.74928398676149e+00 7.61031554084610e-04 - 3 -6.74760118854074e+00 7.60844576504527e-04 - 4 -6.74089237392950e+00 7.60099152658834e-04 - 5 -6.72859795234419e+00 7.58733105816021e-04 - 6 -6.71056189835939e+00 7.56729099817710e-04 - 7 -6.68709018460270e+00 7.54121131622523e-04 - 8 -6.65896053827068e+00 7.50995615363409e-04 - 9 -6.62738484679749e+00 7.47487205199721e-04 - 10 -6.59393151686784e+00 7.43770168540871e-04 - 11 -6.56041836906667e+00 7.40046485451852e-04 - 12 -6.52878782065636e+00 7.36531980072929e-04 - 13 -6.50097576076332e+00 7.33441751195925e-04 - 14 -6.47878371985369e+00 7.30975968872632e-04 - 15 -6.46376168616761e+00 7.29306854018624e-04 - 16 -6.45710716430512e+00 7.28567462700569e-04 - 17 -6.45958482192202e+00 7.28842757991336e-04 - 18 -6.47146995375796e+00 7.30163328195329e-04 - 19 -6.49251798076206e+00 7.32501997862452e-04 - 20 -6.52196175536141e+00 7.35773528373490e-04 + 0 -6.74120349418967e+00 7.60133721576629e-04 + 1 -6.74680409124886e+00 7.60756010138763e-04 + 2 -6.74928398676683e+00 7.61031554085203e-04 + 3 -6.74760118854837e+00 7.60844576505375e-04 + 4 -6.74089237394015e+00 7.60099152660017e-04 + 5 -6.72859795268796e+00 7.58733105854218e-04 + 6 -6.71056189836587e+00 7.56729099818430e-04 + 7 -6.68709018460367e+00 7.54121131622629e-04 + 8 -6.65896053826554e+00 7.50995615362838e-04 + 9 -6.62738484678158e+00 7.47487205197953e-04 + 10 -6.59393151683697e+00 7.43770168537441e-04 + 11 -6.56041836901761e+00 7.40046485446401e-04 + 12 -6.52878782058752e+00 7.36531980065280e-04 + 13 -6.50097576071506e+00 7.33441751190562e-04 + 14 -6.47878371974444e+00 7.30975968860493e-04 + 15 -6.46376168610113e+00 7.29306854011237e-04 + 16 -6.45710716417506e+00 7.28567462686117e-04 + 17 -6.45958482166641e+00 7.28842757962935e-04 + 18 -6.47146995371894e+00 7.30163328190994e-04 + 19 -6.49251798066684e+00 7.32501997851872e-04 + 20 -6.52196175528559e+00 7.35773528365066e-04 diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 58c424da8..62bc7782b 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,17 +70,17 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 3 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -110,7 +106,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.000111111 according to the specified width (3). colvars: ---------------------------------------------------------------------- @@ -121,32 +116,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - spinAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -6.52196 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 311efe354..e4d09163e 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -6.64191475499626e+00 + x -6.64191475373326e+00 } restraint { diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index e9ee60f48..59936cd90 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -6.52196175536141e+00 7.35773528373490e-04 - 21 -6.55853866136453e+00 7.39837629040503e-04 - 22 -6.60054957188598e+00 7.44505507987332e-04 - 23 -6.64595045368826e+00 7.49550050409807e-04 - 24 -6.69247420112553e+00 7.54719355680614e-04 - 25 -6.73777528462053e+00 7.59752809402281e-04 - 26 -6.77958465048355e+00 7.64398294498173e-04 - 27 -6.81585908066260e+00 7.68428786740289e-04 - 28 -6.84490920657793e+00 7.71656578508659e-04 - 29 -6.86549395871066e+00 7.73943773190073e-04 - 30 -6.87687521064447e+00 7.75208356738274e-04 - 31 -6.87883312849994e+00 7.75425903166660e-04 - 32 -6.87164844230811e+00 7.74627604700902e-04 - 33 -6.85606123102412e+00 7.72895692336013e-04 - 34 -6.83321600017101e+00 7.70357333352334e-04 - 35 -6.80460002005342e+00 7.67177780005936e-04 - 36 -6.77197706433820e+00 7.63553007148689e-04 - 37 -6.73731414663200e+00 7.59701571848000e-04 - 38 -6.70269652304925e+00 7.55855169227695e-04 - 39 -6.67022757555205e+00 7.52247508394672e-04 - 40 -6.64191475499626e+00 7.49101639444029e-04 + 20 -6.52196175528559e+00 7.35773528365066e-04 + 21 -6.55853866126809e+00 7.39837629029787e-04 + 22 -6.60054957179227e+00 7.44505507976919e-04 + 23 -6.64595045358898e+00 7.49550050398775e-04 + 24 -6.69247420100935e+00 7.54719355667705e-04 + 25 -6.73777528436304e+00 7.59752809373671e-04 + 26 -6.77958465029172e+00 7.64398294476858e-04 + 27 -6.81585908038471e+00 7.68428786709412e-04 + 28 -6.84490920631285e+00 7.71656578479206e-04 + 29 -6.86549395828653e+00 7.73943773142947e-04 + 30 -6.87687521003861e+00 7.75208356670957e-04 + 31 -6.87883312782949e+00 7.75425903092165e-04 + 32 -6.87164844151262e+00 7.74627604612513e-04 + 33 -6.85606123010451e+00 7.72895692233834e-04 + 34 -6.83321599913451e+00 7.70357333237168e-04 + 35 -6.80460001891363e+00 7.67177779879293e-04 + 36 -6.77197706280820e+00 7.63553006978689e-04 + 37 -6.73731414535818e+00 7.59701571706465e-04 + 38 -6.70269652174944e+00 7.55855169083271e-04 + 39 -6.67022757425629e+00 7.52247508250699e-04 + 40 -6.64191475373326e+00 7.49101639303696e-04 diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 0b71aa10e..69afc9ed5 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -128,7 +124,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -139,28 +134,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - tilt colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 21771cc4e..1c8f75a13 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.99415492547103e-01 + x 9.99415492548698e-01 } restraint { diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 257bb1412..a797dc77d 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 9.98812440566840e-01 -3.59524976226736e-03 - 1 9.98816680233361e-01 -3.59526672093344e-03 - 2 9.98826523073495e-01 -3.59530609229398e-03 - 3 9.98842018672579e-01 -3.59536807469031e-03 - 4 9.98863121611601e-01 -3.59545248644640e-03 - 5 9.98889669016434e-01 -3.59555867606574e-03 - 6 9.98921340687004e-01 -3.59568536274802e-03 - 7 9.98957619944279e-01 -3.59583047977712e-03 - 8 9.98997773201826e-01 -3.59599109280730e-03 - 9 9.99040860340336e-01 -3.59616344136134e-03 - 10 9.99085779266818e-01 -3.59634311706727e-03 - 11 9.99131338939409e-01 -3.59652535575764e-03 - 12 9.99176347610903e-01 -3.59670539044361e-03 - 13 9.99219697607167e-01 -3.59687879042867e-03 - 14 9.99260427488015e-01 -3.59704170995206e-03 - 15 9.99297748982546e-01 -3.59719099593018e-03 - 16 9.99331038661138e-01 -3.59732415464455e-03 - 17 9.99359807085313e-01 -3.59743922834125e-03 - 18 9.99383664673950e-01 -3.59753465869580e-03 - 19 9.99402301732208e-01 -3.59760920692883e-03 - 20 9.99415492547103e-01 -3.59766197018841e-03 + 1 9.98816680233352e-01 -3.59526672093341e-03 + 2 9.98826523073460e-01 -3.59530609229384e-03 + 3 9.98842018672504e-01 -3.59536807469002e-03 + 4 9.98863121611482e-01 -3.59545248644593e-03 + 5 9.98889669016271e-01 -3.59555867606508e-03 + 6 9.98921340686809e-01 -3.59568536274724e-03 + 7 9.98957619944074e-01 -3.59583047977630e-03 + 8 9.98997773201637e-01 -3.59599109280655e-03 + 9 9.99040860340198e-01 -3.59616344136079e-03 + 10 9.99085779266763e-01 -3.59634311706705e-03 + 11 9.99131338939470e-01 -3.59652535575788e-03 + 12 9.99176347611108e-01 -3.59670539044443e-03 + 13 9.99219697607536e-01 -3.59687879043014e-03 + 14 9.99260427488563e-01 -3.59704170995425e-03 + 15 9.99297748983282e-01 -3.59719099593313e-03 + 16 9.99331038662066e-01 -3.59732415464826e-03 + 17 9.99359807086426e-01 -3.59743922834570e-03 + 18 9.99383664675241e-01 -3.59753465870096e-03 + 19 9.99402301733660e-01 -3.59760920693464e-03 + 20 9.99415492548698e-01 -3.59766197019479e-03 diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index 35a5c40ee..0ed6ee7d8 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -128,7 +124,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -139,33 +134,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - tilt colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.999415 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 71c119b43..50c49fa3e 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.99399210038338e-01 + x 9.99399210041976e-01 } restraint { diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index c3db036ec..86fc22b8b 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.99415492547103e-01 -3.59766197018841e-03 - 21 9.99423124211601e-01 -3.59769249684640e-03 - 22 9.99425243203459e-01 -3.59770097281383e-03 - 23 9.99422108246234e-01 -3.59768843298494e-03 - 24 9.99414235597450e-01 -3.59765694238980e-03 - 25 9.99402422546063e-01 -3.59760969018425e-03 - 26 9.99387736076906e-01 -3.59755094430763e-03 - 27 9.99371458556963e-01 -3.59748583422785e-03 - 28 9.99354991188822e-01 -3.59741996475529e-03 - 29 9.99339727176955e-01 -3.59735890870782e-03 - 30 9.99326916410865e-01 -3.59730766564346e-03 - 31 9.99317547849854e-01 -3.59727019139942e-03 - 32 9.99312272722288e-01 -3.59724909088915e-03 - 33 9.99311381509340e-01 -3.59724552603736e-03 - 34 9.99314833116121e-01 -3.59725933246448e-03 - 35 9.99322320512548e-01 -3.59728928205019e-03 - 36 9.99333348005097e-01 -3.59733339202039e-03 - 37 9.99347295864453e-01 -3.59738918345781e-03 - 38 9.99363457668243e-01 -3.59745383067297e-03 - 39 9.99381050365372e-01 -3.59752420146149e-03 - 40 9.99399210038338e-01 -3.59759684015335e-03 + 20 9.99415492548698e-01 -3.59766197019479e-03 + 21 9.99423124213315e-01 -3.59769249685326e-03 + 22 9.99425243205266e-01 -3.59770097282107e-03 + 23 9.99422108248105e-01 -3.59768843299242e-03 + 24 9.99414235599357e-01 -3.59765694239743e-03 + 25 9.99402422547979e-01 -3.59760969019192e-03 + 26 9.99387736078806e-01 -3.59755094431523e-03 + 27 9.99371458558828e-01 -3.59748583423531e-03 + 28 9.99354991190644e-01 -3.59741996476258e-03 + 29 9.99339727178734e-01 -3.59735890871494e-03 + 30 9.99326916412614e-01 -3.59730766565046e-03 + 31 9.99317547851597e-01 -3.59727019140639e-03 + 32 9.99312272724061e-01 -3.59724909089624e-03 + 33 9.99311381511187e-01 -3.59724552604475e-03 + 34 9.99314833118093e-01 -3.59725933247237e-03 + 35 9.99322320514697e-01 -3.59728928205879e-03 + 36 9.99333348007473e-01 -3.59733339202989e-03 + 37 9.99347295867101e-01 -3.59738918346840e-03 + 38 9.99363457671199e-01 -3.59745383068479e-03 + 39 9.99381050368662e-01 -3.59752420147465e-03 + 40 9.99399210041976e-01 -3.59759684016791e-03 diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..832c6a06f 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-14. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out index 466786003..ffac56dd2 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -110,7 +106,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.4 according to the specified width (0.05). colvars: ---------------------------------------------------------------------- @@ -121,27 +116,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - tilt colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 22e226ed8..776f51f15 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.86667458349930e-01 + x 9.86667458341471e-01 } restraint { diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj index be7100171..036a31008 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 9.89817622562351e-01 -3.55927049024940e-01 - 1 9.89739193890686e-01 -3.55895677556274e-01 - 2 9.89645626534388e-01 -3.55858250613755e-01 - 3 9.89537793456435e-01 -3.55815117382574e-01 - 4 9.89416411924999e-01 -3.55766564770000e-01 - 5 9.89282053848009e-01 -3.55712821539204e-01 - 6 9.89135240737646e-01 -3.55654096295058e-01 - 7 9.88976581441553e-01 -3.55590632576621e-01 - 8 9.88806911283522e-01 -3.55522764513409e-01 - 9 9.88627402346676e-01 -3.55450960938670e-01 - 10 9.88439627708785e-01 -3.55375851083514e-01 - 11 9.88245572588250e-01 -3.55298229035300e-01 - 12 9.88047593326962e-01 -3.55219037330785e-01 - 13 9.87848337461123e-01 -3.55139334984449e-01 - 14 9.87650651623308e-01 -3.55060260649323e-01 - 15 9.87457507491825e-01 -3.54983002996730e-01 - 16 9.87271960375771e-01 -3.54908784150308e-01 - 17 9.87097125290053e-01 -3.54838850116021e-01 - 18 9.86936130482758e-01 -3.54774452193103e-01 - 19 9.86792003048169e-01 -3.54716801219267e-01 - 20 9.86667458349930e-01 -3.54666983339972e-01 + 0 9.89817622562340e-01 -3.55927049024936e-01 + 1 9.89739193890710e-01 -3.55895677556284e-01 + 2 9.89645626534500e-01 -3.55858250613800e-01 + 3 9.89537793456669e-01 -3.55815117382668e-01 + 4 9.89416411925387e-01 -3.55766564770155e-01 + 5 9.89282053848041e-01 -3.55712821539216e-01 + 6 9.89135240738356e-01 -3.55654096295342e-01 + 7 9.88976581442317e-01 -3.55590632576927e-01 + 8 9.88806911284239e-01 -3.55522764513695e-01 + 9 9.88627402347221e-01 -3.55450960938888e-01 + 10 9.88439627709016e-01 -3.55375851083606e-01 + 11 9.88245572588017e-01 -3.55298229035207e-01 + 12 9.88047593326122e-01 -3.55219037330449e-01 + 13 9.87848337457110e-01 -3.55139334982844e-01 + 14 9.87650651620881e-01 -3.55060260648352e-01 + 15 9.87457507486578e-01 -3.54983002994631e-01 + 16 9.87271960371439e-01 -3.54908784148575e-01 + 17 9.87097125283486e-01 -3.54838850113394e-01 + 18 9.86936130473010e-01 -3.54774452189204e-01 + 19 9.86792003040408e-01 -3.54716801216163e-01 + 20 9.86667458341471e-01 -3.54666983336588e-01 diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out index 790ae8ec1..8e045427a 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -110,7 +106,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.4 according to the specified width (0.05). colvars: ---------------------------------------------------------------------- @@ -121,32 +116,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - tilt colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.986667 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index ffcadedd3..33ffc6902 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.85614564530977e-01 + x 9.85614564513385e-01 } restraint { diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj index b5e56c253..e9303a790 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.86667458349930e-01 -3.54666983339972e-01 - 21 9.86564598798781e-01 -3.54625839519512e-01 - 22 9.86484566772892e-01 -3.54593826709157e-01 - 23 9.86427228496625e-01 -3.54570891398650e-01 - 24 9.86390977455002e-01 -3.54556390982001e-01 - 25 9.86372728522180e-01 -3.54549091408872e-01 - 26 9.86368130550494e-01 -3.54547252220198e-01 - 27 9.86371969386892e-01 -3.54548787754757e-01 - 28 9.86378686084241e-01 -3.54551474433696e-01 - 29 9.86382912477289e-01 -3.54553164990916e-01 - 30 9.86379931734801e-01 -3.54551972693920e-01 - 31 9.86365997688778e-01 -3.54546399075511e-01 - 32 9.86338483201464e-01 -3.54535393280585e-01 - 33 9.86295866427772e-01 -3.54518346571109e-01 - 34 9.86237598508030e-01 -3.54495039403212e-01 - 35 9.86163919711047e-01 -3.54465567884419e-01 - 36 9.86075697598078e-01 -3.54430279039231e-01 - 37 9.85974343825943e-01 -3.54389737530377e-01 - 38 9.85861830034088e-01 -3.54344732013635e-01 - 39 9.85740778424268e-01 -3.54296311369707e-01 - 40 9.85614564530977e-01 -3.54245825812391e-01 + 20 9.86667458341471e-01 -3.54666983336588e-01 + 21 9.86564598790534e-01 -3.54625839516214e-01 + 22 9.86484566764204e-01 -3.54593826705681e-01 + 23 9.86427228487669e-01 -3.54570891395068e-01 + 24 9.86390977445951e-01 -3.54556390978380e-01 + 25 9.86372728511522e-01 -3.54549091404609e-01 + 26 9.86368130541750e-01 -3.54547252216700e-01 + 27 9.86371969378090e-01 -3.54548787751236e-01 + 28 9.86378686073627e-01 -3.54551474429451e-01 + 29 9.86382912469260e-01 -3.54553164987704e-01 + 30 9.86379931725049e-01 -3.54551972690020e-01 + 31 9.86365997681395e-01 -3.54546399072558e-01 + 32 9.86338483193996e-01 -3.54535393277598e-01 + 33 9.86295866419978e-01 -3.54518346567991e-01 + 34 9.86237598499642e-01 -3.54495039399857e-01 + 35 9.86163919701783e-01 -3.54465567880713e-01 + 36 9.86075697585368e-01 -3.54430279034147e-01 + 37 9.85974343814067e-01 -3.54389737525627e-01 + 38 9.85861830020574e-01 -3.54344732008230e-01 + 39 9.85740778408907e-01 -3.54296311363563e-01 + 40 9.85614564513385e-01 -3.54245825805354e-01 diff --git a/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt b/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out index 9990cc125..bb4bac866 100644 --- a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out +++ b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsdA" @@ -27,14 +25,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 8 atoms requested: total mass = 43.069, total charge = -0.09. @@ -42,7 +40,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -78,14 +76,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] @@ -131,14 +129,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = off [default] +colvars: # centerReference = on +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] @@ -183,14 +181,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = on +colvars: # centerReference = off [default] +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] @@ -236,14 +234,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off -colvars: # rotateToReference = off +colvars: # centerReference = off +colvars: # rotateReference = off colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 8 atoms requested: total mass = 43.069, total charge = -0.09. @@ -288,7 +286,6 @@ colvars: # centers = { 0, 0, 0, 0, 0 } colvars: # targetCenters = { 0, 0, 0, 0, 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsdA" will be rescaled to 1 according to the specified width (1). colvars: The force constant for colvar "rmsdB" will be rescaled to 1 according to the specified width (1). @@ -303,7 +300,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 5 in total. colvars: ---------------------------------------------------------------------- @@ -317,7 +313,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -336,7 +331,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -355,7 +349,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -374,7 +367,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -393,7 +385,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -409,34 +400,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdB":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdC":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdD":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdE":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdB":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdC":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. diff --git a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj index 266bf3e21..9c94197c3 100644 --- a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj +++ b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj @@ -1,2 +1,2 @@ -# step rmsdA ft_rmsdA rmsdB ft_rmsdB rmsdC ft_rmsdC rmsdD ft_rmsdD rmsdE ft_rmsdE - 0 2.61009345658189e-01 0.00000000000000e+00 1.27145912684355e+01 0.00000000000000e+00 6.68502465870546e-01 0.00000000000000e+00 9.31703240469482e-01 0.00000000000000e+00 1.24224459145532e+00 0.00000000000000e+00 +# step rmsdA ft_rmsdA rmsdB ft_rmsdB rmsdC ft_rmsdC rmsdD ft_rmsdD rmsdE ft_rmsdE + 0 2.61009345658189e-01 0.00000000000000e+00 1.27145912684355e+01 0.00000000000000e+00 6.68502465870546e-01 0.00000000000000e+00 9.31703240469482e-01 0.00000000000000e+00 1.24224459145532e+00 0.00000000000000e+00 diff --git a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out index a4dfd6895..aae270fda 100644 --- a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out +++ b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "eigenvector_Ca" @@ -57,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,20 +70,19 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "../Common/da.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( 0.9999 , 2 , 3 ) colvars: # differenceVector = on -colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = x_vec - x_ref. -colvars: # normalizeVector = off [default] -colvars: Normalizing the vector so that the norm of the projection |v â‹… (x_vec - x_ref)| = 1. +colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = v - x0. +colvars: "differenceVector" is on: normalizing the vector. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -113,7 +110,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eigenvector_Ca" will be rescaled to 10 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -124,28 +120,13 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - eigenvector colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "eigenvector_Ca":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "eigenvector_Ca":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj index d319abefa..a10b71b97 100644 --- a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj +++ b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj @@ -1,2 +1,2 @@ # step eigenvector_Ca ft_eigenvector_Ca fa_eigenvector_Ca - 0 9.99999999999999e-01 0.00000000000000e+00 -9.99999999999999e+00 + 0 1.00000000000000e+00 0.00000000000000e+00 -1.00000000000000e+01 diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out index 5b4640743..832cffd51 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -57,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -112,7 +110,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd" will be rescaled to 10000 according to the specified width (0.01). colvars: ---------------------------------------------------------------------- @@ -123,7 +120,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -137,7 +133,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -152,30 +147,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped index e621f3ff5..20535536d 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name rmsd - x 1.39198635632537e+00 + x 1.39198635631904e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 1.00000000000000e-01 - accumulatedWork -1.79849880092255e+03 + accumulatedWork -1.79849880092103e+03 } } diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj index 88056a153..62e3fc7d4 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step rmsd ft_rmsd fa_rmsd E_harmonic1 x0_rmsd W_harmonic1 0 2.17249057079325e+00 0.00000000000000e+00 -2.17456306136404e+04 2.35985764009279e+04 0.00000000000000e+00 0.00000000000000e+00 - 1 2.16345956010640e+00 -2.17419903526924e+04 -2.15552301966651e+04 2.31869403850683e+04 1.00000000000000e-02 -2.15345956010640e+02 - 2 2.13583213462443e+00 -2.14389529078214e+04 -2.11786796675906e+04 2.23837281095469e+04 2.00000000000000e-02 -4.26929169473084e+02 - 3 2.09038365006932e+00 -2.07262996388757e+04 -2.06237403371939e+04 2.12259039273649e+04 3.00000000000000e-02 -6.32967534480016e+02 - 4 2.02806882503406e+00 -1.96255637093855e+04 -1.98999689385910e+04 1.97620882653616e+04 4.00000000000000e-02 -8.31774416983422e+02 - 5 1.95030623811202e+00 -1.81667585436761e+04 -1.90215654435014e+04 1.80558189930374e+04 5.00000000000000e-02 -1.02180504079462e+03 - 6 1.85875201230836e+00 -1.63966970219124e+04 -1.80051076432067e+04 1.61775440089168e+04 6.00000000000000e-02 -1.20168024202546e+03 - 7 1.75513110974568e+00 -1.43781737213953e+04 -1.68678624085543e+04 1.41983342851636e+04 7.00000000000000e-02 -1.37019335300003e+03 - 8 1.64142178718387e+00 -1.21888818488311e+04 -1.56296320897105e+04 1.21901899874623e+04 8.00000000000000e-02 -1.52633553171842e+03 - 9 1.51964633571603e+00 -9.89848282368767e+03 -1.43106598205174e+04 1.02194432261313e+04 9.00000000000000e-02 -1.66930016529002e+03 - 10 1.39198635632537e+00 -7.49967017329654e+03 -1.29327834268169e+04 8.34614372465450e+03 1.00000000000000e-01 -1.79849880092255e+03 + 1 2.16345956010639e+00 -2.17419903527299e+04 -2.15552301966649e+04 2.31869403850679e+04 1.00000000000000e-02 -2.15345956010639e+02 + 2 2.13583213462437e+00 -2.14389529078606e+04 -2.11786796675899e+04 2.23837281095455e+04 2.00000000000000e-02 -4.26929169473075e+02 + 3 2.09038365006916e+00 -2.07262996389219e+04 -2.06237403371923e+04 2.12259039273616e+04 3.00000000000000e-02 -6.32967534479991e+02 + 4 2.02806882503376e+00 -1.96255637094443e+04 -1.98999689385880e+04 1.97620882653556e+04 4.00000000000000e-02 -8.31774416983368e+02 + 5 1.95030623811151e+00 -1.81667585437567e+04 -1.90215654434962e+04 1.80558189930276e+04 5.00000000000000e-02 -1.02180504079452e+03 + 6 1.85875201230753e+00 -1.63966970220336e+04 -1.80051076431984e+04 1.61775440089019e+04 6.00000000000000e-02 -1.20168024202527e+03 + 7 1.75513110974436e+00 -1.43781737215985e+04 -1.68678624085410e+04 1.41983342851413e+04 7.00000000000000e-02 -1.37019335299971e+03 + 8 1.64142178718173e+00 -1.21888818492009e+04 -1.56296320896891e+04 1.21901899874289e+04 8.00000000000000e-02 -1.52633553171788e+03 + 9 1.51964633571245e+00 -9.89848282440100e+03 -1.43106598204816e+04 1.02194432260802e+04 9.00000000000000e-02 -1.66930016528913e+03 + 10 1.39198635631904e+00 -7.49967017479936e+03 -1.29327834267536e+04 8.34614372457276e+03 1.00000000000000e-01 -1.79849880092103e+03 diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out index 1539c97b7..460e18798 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -57,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -112,7 +110,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd" will be rescaled to 10000 according to the specified width (0.01). colvars: ---------------------------------------------------------------------- @@ -123,7 +120,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -137,7 +133,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -152,36 +147,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "rmsd" from value: 1.39199 colvars: Restarting harmonic bias "harmonic1" from step number 10. colvars: Restarting harmonicwalls bias "rmsdw" from step number 10. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testres.colvars.state". colvars: The final output state file will be "testres.colvars.state". +colvars: Opening trajectory file "testres.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "testres.colvars.state". colvars: The final output state file will be "testres.colvars.state". diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped index e2cb96809..0329bdfbc 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name rmsd - x 3.58513981869359e-01 + x 3.58513981358481e-01 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -2.38254491368653e+03 + accumulatedWork -2.38254491346066e+03 } } diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj index cfd59f064..afd7851c5 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj @@ -1,12 +1,12 @@ # step rmsd ft_rmsd fa_rmsd E_harmonic1 x0_rmsd W_harmonic1 - 10 1.39198635632537e+00 0.00000000000000e+00 -1.29327834268169e+04 8.34614372465450e+03 1.00000000000000e-01 -1.79849880092255e+03 - 11 1.26066443054501e+00 -5.04906136264293e+03 -1.15182509497555e+04 6.62014315860736e+03 1.10000000000000e-01 -1.91356524397705e+03 - 12 1.12800176084383e+00 -2.47793069174467e+03 -1.00902976260468e+04 5.08033774932134e+03 1.20000000000000e-01 -2.01436542006143e+03 - 13 9.96492050953577e-01 3.15682479164454e+02 -8.67388543004531e+03 3.75404237182868e+03 1.30000000000000e-01 -2.10101462515679e+03 - 14 8.68461409598148e-01 2.99293971896176e+03 -7.29229871007746e+03 2.65328012636860e+03 1.40000000000000e-01 -2.17386076611661e+03 - 15 7.47100495226679e-01 6.43619261578947e+03 -5.97747595721906e+03 1.78264500699973e+03 1.50000000000000e-01 -2.23357081563928e+03 - 16 6.35910083193821e-01 1.00836160874306e+04 -4.76445993277015e+03 1.13245203642775e+03 1.60000000000000e-01 -2.28116182395866e+03 - 17 5.38589382317609e-01 1.33134883220103e+04 -3.69027971699926e+03 6.79290663786381e+02 1.70000000000000e-01 -2.31802076219042e+03 - 18 4.58478968346367e-01 1.57771913409965e+04 -2.78837447314713e+03 3.87752679056283e+02 1.80000000000000e-01 -2.34586865902505e+03 - 19 3.98248564745421e-01 1.64627514687814e+04 -2.08546813310166e+03 2.16837323592639e+02 1.90000000000000e-01 -2.36669351549960e+03 - 20 3.58513981869359e-01 1.49916694393498e+04 -1.58772495851228e+03 1.25633412240397e+02 2.00000000000000e-01 -2.38254491368653e+03 + 10 1.39198635631904e+00 0.00000000000000e+00 -1.29327834267536e+04 8.34614372457276e+03 1.00000000000000e-01 -1.79849880092103e+03 + 11 1.26066443053330e+00 -5.04906136565955e+03 -1.15182509496383e+04 6.62014315847261e+03 1.10000000000000e-01 -1.91356524397436e+03 + 12 1.12800176082188e+00 -2.47793069731417e+03 -1.00902976258270e+04 5.08033774910002e+03 1.20000000000000e-01 -2.01436542005655e+03 + 13 9.96492050911879e-01 3.15682468320502e+02 -8.67388542962791e+03 3.75404237146737e+03 1.30000000000000e-01 -2.10101462514774e+03 + 14 8.68461409518928e-01 2.99293969889592e+03 -7.29229870928447e+03 2.65328012579152e+03 1.40000000000000e-01 -2.17386076609963e+03 + 15 7.47100495082919e-01 6.43619258679187e+03 -5.97747595578002e+03 1.78264500614134e+03 1.50000000000000e-01 -2.23357081560792e+03 + 16 6.35910082961470e-01 1.00836160673481e+04 -4.76445993044432e+03 1.13245203532197e+03 1.60000000000000e-01 -2.28116182390407e+03 + 17 5.38589381992358e-01 1.33134883328259e+04 -3.69027971374350e+03 6.79290662587542e+02 1.70000000000000e-01 -2.31802076210330e+03 + 18 4.58478967939376e-01 1.57771913740319e+04 -2.78837446907315e+03 3.87752677922900e+02 1.80000000000000e-01 -2.34586865889724e+03 + 19 3.98248564275675e-01 1.64627515062483e+04 -2.08546812839950e+03 2.16837322614399e+02 1.90000000000000e-01 -2.36669351532481e+03 + 20 3.58513981358481e-01 1.49916694678179e+04 -1.58772495339839e+03 1.25633411430584e+02 2.00000000000000e-01 -2.38254491346066e+03 diff --git a/namd/tests/library/003_10ala_SMD_restart/namd-version.txt b/namd/tests/library/003_10ala_SMD_restart/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/003_10ala_SMD_restart/namd-version.txt +++ b/namd/tests/library/003_10ala_SMD_restart/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out index 24596243b..80cd2d40b 100644 --- a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out +++ b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -27,56 +25,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.011, total charge = 0.51. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -86,10 +84,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -118,7 +116,6 @@ colvars: # targetNumStages = 36 colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 10 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -129,39 +126,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. colvars: Re-initialized atom group for variable "d":0/3. 1 atoms: total mass = 14.007, total charge = -0.47. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "previous.colvars.state". -colvars: This state file was generated with version +colvars: Restarting from file "previous.colvars.state". colvars: Restarting collective variable "d" from value: -137.21 colvars: Restarting harmonic bias "harmonic1" from step number 8000. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testr.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. diff --git a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj index 4ec655cd6..1cecbe504 100644 --- a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj +++ b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step d fa_d 8000 -1.37210258611294e+02 2.21025861129385e+01 - 8002 -1.36437406938754e+02 1.43740693875392e+01 - 8004 -1.32448586831542e+02 -2.55141316845757e+01 - 8006 -1.34451844766900e+02 -5.48155233099777e+00 - 8008 -1.37758781619839e+02 2.75878161983877e+01 - 8010 -1.35039285402134e+02 3.92854021337428e-01 - 8012 -1.32417992183404e+02 -2.58200781659573e+01 - 8014 -1.35927148506493e+02 9.27148506492500e+00 - 8016 -1.37371418693785e+02 2.37141869378459e+01 - 8018 -1.33415236151160e+02 -1.58476384884008e+01 - 8020 -1.33332063901251e+02 -1.66793609874881e+01 + 8002 -1.36437406938780e+02 1.43740693877973e+01 + 8004 -1.32448586831588e+02 -2.55141316841204e+01 + 8006 -1.34451844766881e+02 -5.48155233119189e+00 + 8008 -1.37758781619817e+02 2.75878161981655e+01 + 8010 -1.35039285402271e+02 3.92854022709912e-01 + 8012 -1.32417992183434e+02 -2.58200781656637e+01 + 8014 -1.35927148506204e+02 9.27148506203707e+00 + 8016 -1.37371418693973e+02 2.37141869397252e+01 + 8018 -1.33415236151821e+02 -1.58476384817905e+01 + 8020 -1.33332063900607e+02 -1.66793609939288e+01 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out b/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out index 477048315..f8428a56e 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out @@ -1,4 +1,4 @@ -TCL: Running Colvars version 2023-07-21 +TCL: Running Colvars version 2020-04-09 TCL: Running cv units real TCL: TCL: d = 0.00000000000000e+00 @@ -13,7 +13,7 @@ TCL: E(harmonic1) = 18000 TCL: Original numsteps 20 will be ignored. TCL: Running for 20 steps TCL: d = 1.28684277602119e+01 -TCL: E(abf1) = 32.885 +TCL: E(abf1) = 0 TCL: E(harmonic1) = 94.2708 TCL: Running cv bias harm2 getconfig TCL: @@ -27,7 +27,7 @@ TCL: TCL: Running cv bias harm2 energy TCL: 17.8166 TCL: Running cv bias harm2 update -TCL: 1.78166082981433e+01 +TCL: 17.8166 TCL: Running for 20 steps TCL: Running cv bias harm2 energy TCL: 13.4817 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out index ca61c96ea..d3135664a 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -27,28 +25,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -106,7 +104,6 @@ colvars: # centers = { 12 } colvars: # targetCenters = { 12 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 250 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -117,35 +114,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Prepared sample and gradient buffers at step 0. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). +colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. +colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". colvars: ---------------------------------------------------------------------- @@ -156,7 +135,6 @@ colvars: # colvarsTrajFrequency = 2 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -173,7 +151,6 @@ colvars: # centers = { 13 } colvars: # targetCenters = { 13 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 25 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -184,296 +161,271 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Saving collective variables state to "test.colvars.state". -colvars: Features of "colvar d" (refcount) -colvars: - ON active (3) -colvars: - awake -colvars: - ON gradient (3) -colvars: - collect_gradient -colvars: - collect_atom_ids -colvars: - velocity_from_finite_differences -colvars: - ON total_force (3) -colvars: - ON total_force_calculation (1) -colvars: - ON subtract_applied_force_from_total_force -colvars: - ON Jacobian_derivative (1) -colvars: - hide_Jacobian_force -colvars: - extended_Lagrangian -colvars: - external -colvars: - Langevin_dynamics -colvars: - output_energy -colvars: - ON output_value -colvars: - output_velocity -colvars: - ON output_applied_force -colvars: - ON output_total_force -colvars: - ON lower_boundary -colvars: - ON upper_boundary -colvars: - hard_lower_boundary -colvars: - hard_upper_boundary -colvars: - reflecting_lower_boundary -colvars: - reflecting_upper_boundary -colvars: - ON grid -colvars: - running_average -colvars: - correlation_function -colvars: - scripted -colvars: - custom_function -colvars: - periodic -colvars: - ON single_component -colvars: - ON scalar (7) -colvars: - ON linear (2) -colvars: - ON homogeneous -colvars: - multiple_timestep +colvars: Features of "colvar d" ON/OFF (refcount) +colvars: - active ON (4) +colvars: - awake ON (0) +colvars: - gradient ON (3) +colvars: - collect_gradient OFF (0) +colvars: - velocity_from_finite_differences OFF (0) +colvars: - total_force ON (3) +colvars: - total_force_calculation ON (1) +colvars: - subtract_applied_force_from_total_force ON (0) +colvars: - Jacobian_derivative ON (1) +colvars: - hide_Jacobian_force OFF (0) +colvars: - extended_Lagrangian OFF (0) +colvars: - Langevin_dynamics OFF (0) +colvars: - output_energy OFF (0) +colvars: - output_value ON (0) +colvars: - output_velocity OFF (0) +colvars: - output_applied_force ON (0) +colvars: - output_total_force ON (0) +colvars: - lower_boundary ON (1) +colvars: - upper_boundary ON (1) +colvars: - hard_lower_boundary OFF (0) +colvars: - hard_upper_boundary OFF (0) +colvars: - reflecting_lower_boundary OFF (0) +colvars: - reflecting_upper_boundary OFF (0) +colvars: - grid ON (0) +colvars: - running_average OFF (0) +colvars: - correlation_function OFF (0) +colvars: - scripted OFF (0) +colvars: - custom_function OFF (0) +colvars: - periodic OFF (0) +colvars: - single_component ON (0) +colvars: - scalar ON (6) +colvars: - linear ON (2) +colvars: - homogeneous ON (0) +colvars: - multiple_timestep OFF (0) colvars: * child 1 -colvars: Features of "cvc distance0001" (refcount) -colvars: - ON active -colvars: - scalar -colvars: - periodic -colvars: - defined_width -colvars: - ON defined_lower_boundary -colvars: - defined_upper_boundary -colvars: - ON gradient (2) -colvars: - explicit_gradient -colvars: - ON inverse_gradient (2) -colvars: - ON Jacobian_derivative (1) -colvars: - total_force_from_one_group -colvars: - debug_gradient -colvars: - ON use_minimum-image_with_PBCs -colvars: - ON function_of_centers_of_mass (1) -colvars: - ON scalable_calculation (1) -colvars: - ON scalable_calculation_of_centers_of_mass -colvars: - collect_atom_ids +colvars: Features of "cvc distance0001" ON/OFF (refcount) +colvars: - active ON (0) +colvars: - scalar OFF (0) +colvars: - periodic OFF (0) +colvars: - defined_width OFF (0) +colvars: - defined_lower_boundary ON (0) +colvars: - defined_upper_boundary OFF (0) +colvars: - gradient ON (2) +colvars: - explicit_gradient ON (0) +colvars: - inverse_gradient ON (2) +colvars: - Jacobian_derivative ON (1) +colvars: - total_force_from_one_group OFF (0) +colvars: - debug_gradient OFF (0) +colvars: - use_minimum-image_with_PBCs ON (0) +colvars: - function_of_centers_of_mass ON (1) +colvars: - scalable_calculation ON (0) +colvars: - scalable_calculation_of_centers_of_mass ON (1) colvars: * child 1 -colvars: Features of "atom group group1" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids +colvars: Features of "atom group group1" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) colvars: * child 2 -colvars: Features of "atom group group2" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids -colvars: Features of "bias harmonic1" (refcount) -colvars: - ON active -colvars: - awake -colvars: - step_zero_data -colvars: - ON apply_force -colvars: - bypass_extended_Lagrangian_coordinates -colvars: - obtain_total_force -colvars: - output_accumulated_work -colvars: - history_dependent -colvars: - time_dependent -colvars: - require_scalar_variables -colvars: - calculate_a_PMF -colvars: - calculate_TI_samples -colvars: - write_TI_samples_ -colvars: - write_TI_PMF -colvars: - scale_biasing_force +colvars: Features of "atom group group2" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) +colvars: Features of "bias harmonic1" ON/OFF (refcount) +colvars: - active ON (1) +colvars: - awake ON (0) +colvars: - step_zero_data OFF (0) +colvars: - apply_force ON (0) +colvars: - bypass_extended_Lagrangian_coordinates OFF (0) +colvars: - obtain_total_force OFF (0) +colvars: - output_accumulated_work OFF (0) +colvars: - history_dependent OFF (0) +colvars: - time_dependent OFF (0) +colvars: - require_scalar_variables OFF (0) +colvars: - calculate_a_PMF OFF (0) +colvars: - calculate_TI_samples OFF (0) +colvars: - write_TI_samples_ OFF (0) +colvars: - write_TI_PMF OFF (0) colvars: * child 1 -colvars: Features of "colvar d" (refcount) -colvars: - ON active (3) -colvars: - awake -colvars: - ON gradient (3) -colvars: - collect_gradient -colvars: - collect_atom_ids -colvars: - velocity_from_finite_differences -colvars: - ON total_force (3) -colvars: - ON total_force_calculation (1) -colvars: - ON subtract_applied_force_from_total_force -colvars: - ON Jacobian_derivative (1) -colvars: - hide_Jacobian_force -colvars: - extended_Lagrangian -colvars: - external -colvars: - Langevin_dynamics -colvars: - output_energy -colvars: - ON output_value -colvars: - output_velocity -colvars: - ON output_applied_force -colvars: - ON output_total_force -colvars: - ON lower_boundary -colvars: - ON upper_boundary -colvars: - hard_lower_boundary -colvars: - hard_upper_boundary -colvars: - reflecting_lower_boundary -colvars: - reflecting_upper_boundary -colvars: - ON grid -colvars: - running_average -colvars: - correlation_function -colvars: - scripted -colvars: - custom_function -colvars: - periodic -colvars: - ON single_component -colvars: - ON scalar (7) -colvars: - ON linear (2) -colvars: - ON homogeneous -colvars: - multiple_timestep +colvars: Features of "colvar d" ON/OFF (refcount) +colvars: - active ON (4) +colvars: - awake ON (0) +colvars: - gradient ON (3) +colvars: - collect_gradient OFF (0) +colvars: - velocity_from_finite_differences OFF (0) +colvars: - total_force ON (3) +colvars: - total_force_calculation ON (1) +colvars: - subtract_applied_force_from_total_force ON (0) +colvars: - Jacobian_derivative ON (1) +colvars: - hide_Jacobian_force OFF (0) +colvars: - extended_Lagrangian OFF (0) +colvars: - Langevin_dynamics OFF (0) +colvars: - output_energy OFF (0) +colvars: - output_value ON (0) +colvars: - output_velocity OFF (0) +colvars: - output_applied_force ON (0) +colvars: - output_total_force ON (0) +colvars: - lower_boundary ON (1) +colvars: - upper_boundary ON (1) +colvars: - hard_lower_boundary OFF (0) +colvars: - hard_upper_boundary OFF (0) +colvars: - reflecting_lower_boundary OFF (0) +colvars: - reflecting_upper_boundary OFF (0) +colvars: - grid ON (0) +colvars: - running_average OFF (0) +colvars: - correlation_function OFF (0) +colvars: - scripted OFF (0) +colvars: - custom_function OFF (0) +colvars: - periodic OFF (0) +colvars: - single_component ON (0) +colvars: - scalar ON (6) +colvars: - linear ON (2) +colvars: - homogeneous ON (0) +colvars: - multiple_timestep OFF (0) colvars: * child 1 -colvars: Features of "cvc distance0001" (refcount) -colvars: - ON active -colvars: - scalar -colvars: - periodic -colvars: - defined_width -colvars: - ON defined_lower_boundary -colvars: - defined_upper_boundary -colvars: - ON gradient (2) -colvars: - explicit_gradient -colvars: - ON inverse_gradient (2) -colvars: - ON Jacobian_derivative (1) -colvars: - total_force_from_one_group -colvars: - debug_gradient -colvars: - ON use_minimum-image_with_PBCs -colvars: - ON function_of_centers_of_mass (1) -colvars: - ON scalable_calculation (1) -colvars: - ON scalable_calculation_of_centers_of_mass -colvars: - collect_atom_ids +colvars: Features of "cvc distance0001" ON/OFF (refcount) +colvars: - active ON (0) +colvars: - scalar OFF (0) +colvars: - periodic OFF (0) +colvars: - defined_width OFF (0) +colvars: - defined_lower_boundary ON (0) +colvars: - defined_upper_boundary OFF (0) +colvars: - gradient ON (2) +colvars: - explicit_gradient ON (0) +colvars: - inverse_gradient ON (2) +colvars: - Jacobian_derivative ON (1) +colvars: - total_force_from_one_group OFF (0) +colvars: - debug_gradient OFF (0) +colvars: - use_minimum-image_with_PBCs ON (0) +colvars: - function_of_centers_of_mass ON (1) +colvars: - scalable_calculation ON (0) +colvars: - scalable_calculation_of_centers_of_mass ON (1) colvars: * child 1 -colvars: Features of "atom group group1" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids +colvars: Features of "atom group group1" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) colvars: * child 2 -colvars: Features of "atom group group2" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids +colvars: Features of "atom group group2" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) colvars: Saving collective variables state to "test.colvars.state". -colvars: Features of "bias harm2" (refcount) -colvars: - ON active -colvars: - awake -colvars: - step_zero_data -colvars: - ON apply_force -colvars: - bypass_extended_Lagrangian_coordinates -colvars: - obtain_total_force -colvars: - output_accumulated_work -colvars: - history_dependent -colvars: - time_dependent -colvars: - require_scalar_variables -colvars: - calculate_a_PMF -colvars: - calculate_TI_samples -colvars: - write_TI_samples_ -colvars: - write_TI_PMF -colvars: - scale_biasing_force +colvars: Features of "bias harm2" ON/OFF (refcount) +colvars: - active ON (1) +colvars: - awake ON (0) +colvars: - step_zero_data OFF (0) +colvars: - apply_force ON (0) +colvars: - bypass_extended_Lagrangian_coordinates OFF (0) +colvars: - obtain_total_force OFF (0) +colvars: - output_accumulated_work OFF (0) +colvars: - history_dependent OFF (0) +colvars: - time_dependent OFF (0) +colvars: - require_scalar_variables OFF (0) +colvars: - calculate_a_PMF OFF (0) +colvars: - calculate_TI_samples OFF (0) +colvars: - write_TI_samples_ OFF (0) +colvars: - write_TI_PMF OFF (0) colvars: * child 1 -colvars: Features of "colvar d" (refcount) -colvars: - ON active (2) -colvars: - awake -colvars: - ON gradient (2) -colvars: - collect_gradient -colvars: - collect_atom_ids -colvars: - velocity_from_finite_differences -colvars: - ON total_force (3) -colvars: - ON total_force_calculation (1) -colvars: - ON subtract_applied_force_from_total_force -colvars: - ON Jacobian_derivative (1) -colvars: - hide_Jacobian_force -colvars: - extended_Lagrangian -colvars: - external -colvars: - Langevin_dynamics -colvars: - output_energy -colvars: - ON output_value -colvars: - output_velocity -colvars: - ON output_applied_force -colvars: - ON output_total_force -colvars: - ON lower_boundary -colvars: - ON upper_boundary -colvars: - hard_lower_boundary -colvars: - hard_upper_boundary -colvars: - reflecting_lower_boundary -colvars: - reflecting_upper_boundary -colvars: - ON grid -colvars: - running_average -colvars: - correlation_function -colvars: - scripted -colvars: - custom_function -colvars: - periodic -colvars: - ON single_component -colvars: - ON scalar (7) -colvars: - ON linear (2) -colvars: - ON homogeneous -colvars: - multiple_timestep +colvars: Features of "colvar d" ON/OFF (refcount) +colvars: - active ON (3) +colvars: - awake ON (0) +colvars: - gradient ON (2) +colvars: - collect_gradient OFF (0) +colvars: - velocity_from_finite_differences OFF (0) +colvars: - total_force ON (3) +colvars: - total_force_calculation ON (1) +colvars: - subtract_applied_force_from_total_force ON (0) +colvars: - Jacobian_derivative ON (1) +colvars: - hide_Jacobian_force OFF (0) +colvars: - extended_Lagrangian OFF (0) +colvars: - Langevin_dynamics OFF (0) +colvars: - output_energy OFF (0) +colvars: - output_value ON (0) +colvars: - output_velocity OFF (0) +colvars: - output_applied_force ON (0) +colvars: - output_total_force ON (0) +colvars: - lower_boundary ON (1) +colvars: - upper_boundary ON (1) +colvars: - hard_lower_boundary OFF (0) +colvars: - hard_upper_boundary OFF (0) +colvars: - reflecting_lower_boundary OFF (0) +colvars: - reflecting_upper_boundary OFF (0) +colvars: - grid ON (0) +colvars: - running_average OFF (0) +colvars: - correlation_function OFF (0) +colvars: - scripted OFF (0) +colvars: - custom_function OFF (0) +colvars: - periodic OFF (0) +colvars: - single_component ON (0) +colvars: - scalar ON (6) +colvars: - linear ON (2) +colvars: - homogeneous ON (0) +colvars: - multiple_timestep OFF (0) colvars: * child 1 -colvars: Features of "cvc distance0001" (refcount) -colvars: - ON active -colvars: - scalar -colvars: - periodic -colvars: - defined_width -colvars: - ON defined_lower_boundary -colvars: - defined_upper_boundary -colvars: - ON gradient (2) -colvars: - explicit_gradient -colvars: - ON inverse_gradient (2) -colvars: - ON Jacobian_derivative (1) -colvars: - total_force_from_one_group -colvars: - debug_gradient -colvars: - ON use_minimum-image_with_PBCs -colvars: - ON function_of_centers_of_mass (1) -colvars: - ON scalable_calculation (1) -colvars: - ON scalable_calculation_of_centers_of_mass -colvars: - collect_atom_ids +colvars: Features of "cvc distance0001" ON/OFF (refcount) +colvars: - active ON (0) +colvars: - scalar OFF (0) +colvars: - periodic OFF (0) +colvars: - defined_width OFF (0) +colvars: - defined_lower_boundary ON (0) +colvars: - defined_upper_boundary OFF (0) +colvars: - gradient ON (2) +colvars: - explicit_gradient ON (0) +colvars: - inverse_gradient ON (2) +colvars: - Jacobian_derivative ON (1) +colvars: - total_force_from_one_group OFF (0) +colvars: - debug_gradient OFF (0) +colvars: - use_minimum-image_with_PBCs ON (0) +colvars: - function_of_centers_of_mass ON (1) +colvars: - scalable_calculation ON (0) +colvars: - scalable_calculation_of_centers_of_mass ON (1) colvars: * child 1 -colvars: Features of "atom group group1" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids +colvars: Features of "atom group group1" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) colvars: * child 2 -colvars: Features of "atom group group2" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids +colvars: Features of "atom group group2" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "d" from value: 11.9615 colvars: Restarting abf bias "abf1" from step number 60. colvars: ---------------------------------------------------------------------- @@ -486,7 +438,6 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -500,32 +451,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 1 atoms requested. +colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 1 atoms requested. +colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. @@ -579,7 +530,6 @@ colvars: # centers = { 12 } colvars: # targetCenters = { 12 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 250 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -590,7 +540,5 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Warning: before deleting colvar d, deleting related bias harmonic1 colvars: Warning: before deleting colvar d, deleting related bias abf1 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj index 31374c82a..f029f1ae9 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj @@ -1,38 +1,38 @@ # step d ft_d fa_d E_harmonic1 - 0 0.00000000000000e+00 0.00000000000000e+00 3.00000000000000e+03 1.80000000000000e+04 + 0 0.00000000000000e+00 0.00000000000000e+00 3.00000000000000e+03 1.80000000000000e+04 # step d ft_d fa_d E_harmonic1 - 0 1.42467449615693e+01 0.00000000000000e+00 -5.61686240392322e+02 6.30982865292123e+02 - 2 1.42282559728026e+01 5.32933601659170e+00 -5.59529927201590e+02 6.20640585041297e+02 - 4 1.41727662460742e+01 3.36254334328178e+01 -5.43191561518562e+02 5.90114145009947e+02 - 6 1.40831323320984e+01 8.13697353990825e+01 -5.89087882335502e+02 5.42430039129236e+02 - 8 1.39609835871958e+01 1.43683712679872e+02 -4.90245896798950e+02 4.80682078656413e+02 - 10 1.38136915830204e+01 2.11747525531865e+02 -6.48260269443340e+02 4.11184644789902e+02 - 12 1.36437184346286e+01 2.81640059890150e+02 -6.92569668547312e+02 3.37726286542257e+02 - 14 1.34588898265283e+01 3.45729335505761e+02 -7.10451792137843e+02 2.66044940743482e+02 - 16 1.32645132385707e+01 4.00985013285219e+02 -7.17113322927902e+02 1.99874216315080e+02 - 18 1.30658878095359e+01 4.46271310489825e+02 -7.12743262873798e+02 1.42014602814653e+02 - 20 1.28684277602119e+01 4.80580458032557e+02 -6.97687398085530e+02 9.42708468383301e+01 + 0 1.42467449615693e+01 0.00000000000000e+00 -5.61686240392322e+02 6.30982865292123e+02 + 2 1.42282559728026e+01 5.32933601891204e+00 -5.59529927203773e+02 6.20640585041317e+02 + 4 1.41727662460744e+01 3.36254334374946e+01 -5.43191561518601e+02 5.90114145010033e+02 + 6 1.40831323320990e+01 8.13697354080271e+01 -5.89087882343440e+02 5.42430039129534e+02 + 8 1.39609835871970e+01 1.43683712693643e+02 -4.90245896799256e+02 4.80682078657013e+02 + 10 1.38136915830229e+01 2.11747525548495e+02 -6.48260269460101e+02 4.11184644791030e+02 + 12 1.36437184346326e+01 2.81640059905252e+02 -6.92569668563411e+02 3.37726286543895e+02 + 14 1.34588898265340e+01 3.45729335512429e+02 -7.10451792145928e+02 2.66044940745548e+02 + 16 1.32645132385777e+01 4.00985013276056e+02 -7.17113322920477e+02 1.99874216317278e+02 + 18 1.30658878095430e+01 4.46271310459046e+02 -7.12743262844788e+02 1.42014602816538e+02 + 20 1.28684277602171e+01 4.80580457979151e+02 -6.97687398033433e+02 9.42708468394674e+01 # step d ft_d fa_d E_harmonic1 E_harm2 - 20 1.28684277602119e+01 4.91888943214004e+02 -7.00052334681550e+02 9.42708468383301e+01 2.16390678535748e-01 - 22 1.26751474320465e+01 5.03084201979406e+02 -6.63749745792196e+02 5.69780068748745e+01 1.31911488632471e+00 - 24 1.24888492973171e+01 5.15335038410192e+02 -6.24768595172394e+02 2.98717044359277e+01 3.26593801066529e+00 - 26 1.23139243019797e+01 5.23015189146873e+02 -5.84344372191302e+02 1.23185584216834e+01 5.88374829267482e+00 - 28 1.21466432034073e+01 5.30527139882848e+02 -1.53268809370116e+01 2.68802863819490e+00 9.10272277863661e+00 - 30 1.19993450538088e+01 5.38695710631225e+02 2.51801102025817e+01 5.36193141719397e-05 1.25163790167116e+01 - 32 1.18850444891885e+01 5.34994463767922e+02 5.66127654731507e+01 1.65184618324038e+00 1.55390723886105e+01 - 34 1.18115458382762e+01 5.01682268034594e+02 7.68248944740457e+01 4.43937138387764e+00 1.76552911814828e+01 - 36 1.17769967624676e+01 4.41508793838497e+02 8.63258903213991e+01 6.21630549373929e+00 1.86967114876829e+01 - 38 1.17769542143717e+01 3.61640408513788e+02 8.63375910477925e+01 6.21867781082023e+00 1.86980124217904e+01 - 40 1.18061287071667e+01 2.69866690242884e+02 7.83146055291581e+01 4.69825977310700e+00 1.78166082981433e+01 + 20 1.28684277602171e+01 4.91888943151427e+02 -7.00052334624999e+02 9.42708468394674e+01 2.16390678518517e-01 + 22 1.26751474320475e+01 5.03084201909373e+02 -6.63749745722433e+02 5.69780068750397e+01 1.31911488631676e+00 + 24 1.24888492973110e+01 5.15335038327460e+02 -6.24768595087998e+02 2.98717044351878e+01 3.26593801074265e+00 + 26 1.23139243019631e+01 5.23015189033541e+02 -5.84344372073400e+02 1.23185584203791e+01 5.88374829295988e+00 + 28 1.21466432033769e+01 5.30527139707869e+02 -1.53268809286588e+01 2.68802863708136e+00 9.10272277928461e+00 + 30 1.19993450537562e+01 5.38695710361251e+02 2.51801102170466e+01 5.36193227844337e-05 1.25163790180274e+01 + 32 1.18850444890963e+01 5.34994463383540e+02 5.66127654985307e+01 1.65184618589271e+00 1.55390723911830e+01 + 34 1.18115458381165e+01 5.01682267555293e+02 7.68248945179519e+01 4.43937139139973e+00 1.76552911862265e+01 + 36 1.17769967622096e+01 4.41508793313709e+02 8.63258903923681e+01 6.21630550812685e+00 1.86967114955734e+01 + 38 1.17769542139854e+01 3.61640408006584e+02 8.63375911540067e+01 6.21867783235716e+00 1.86980124336000e+01 + 40 1.18061287066284e+01 2.69866689808628e+02 7.83146056771794e+01 4.69825979919525e+00 1.78166083142086e+01 # step d ft_d fa_d E_harm2 - 40 1.18061287071667e+01 2.21949532598602e+02 2.98467823208325e+01 1.78166082981433e+01 - 42 1.18555777465383e+01 1.74464231066044e+02 2.86105563365434e+01 1.63712786777305e+01 - 44 1.19176677655463e+01 8.22937406521174e+01 2.70583058613429e+01 1.46430383217196e+01 - 46 1.19851813921025e+01 -6.16868558833627e+00 2.53704651974387e+01 1.28732100866889e+01 - 48 1.20415309220875e+01 -8.97664353399688e+01 -3.04621864232869e+02 1.14832871664300e+01 - 50 1.20655400395174e+01 -1.50412424652567e+02 -1.19070572819524e+02 1.09151927218147e+01 - 52 1.20686235856919e+01 -1.88148861256361e+02 -2.70255157819366e+01 1.08432753141169e+01 - 54 1.20571466482814e+01 -2.05067811724940e+02 2.93687990810595e+01 1.11121555355867e+01 - 56 1.20332538295850e+01 -2.00399870515217e+02 6.58114559546446e+01 1.16824769751521e+01 - 58 1.20000609190792e+01 -1.75170570569691e+02 8.83273233309201e+01 1.24984770694101e+01 - 60 1.19614725567188e+01 -1.36757725642476e+02 2.59631860820309e+01 1.34817406306033e+01 + 40 1.18061287066284e+01 2.21949532217238e+02 2.98467823342890e+01 1.78166083142086e+01 + 42 1.18555777458287e+01 1.74464230745251e+02 2.86105563542814e+01 1.63712786980303e+01 + 44 1.19176677646512e+01 8.22937404700844e+01 2.70583058837192e+01 1.46430383459383e+01 + 46 1.19851813910175e+01 -6.16868563783110e+00 2.53704652245623e+01 1.28732101142145e+01 + 48 1.20415309208210e+01 -8.97664352869559e+01 -3.04621864055419e+02 1.14832871967769e+01 + 50 1.20655400380907e+01 -1.50412424518311e+02 -1.19070572741895e+02 1.09151927551443e+01 + 52 1.20686235841253e+01 -1.88148861003765e+02 -2.70255157752960e+01 1.08432753505955e+01 + 54 1.20571466466005e+01 -2.05067811286631e+02 2.93687990112175e+01 1.11121555752091e+01 + 56 1.20332538278214e+01 -2.00399869950163e+02 6.58114558084562e+01 1.16824770177739e+01 + 58 1.20000609172601e+01 -1.75170570145191e+02 8.83273231404457e+01 1.24984771148846e+01 + 60 1.19614725548519e+01 -1.36757725550194e+02 2.59631861287023e+01 1.34817406790728e+01 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.grad b/namd/tests/library/005_Tcl_script/AutoDiff/test.grad index 09257e021..2a30d2884 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.grad +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.grad @@ -1,18 +1,18 @@ # 1 # 1.20000000000000e+01 2.00000000000000e-01 100 0 - 1.21000000000000e+01 6.99836010424488e+01 - 1.23000000000000e+01 -5.26375313539263e+02 - 1.25000000000000e+01 -5.16708952033009e+02 - 1.27000000000000e+01 -5.05977066295794e+02 - 1.29000000000000e+01 -4.88119448153522e+02 - 1.31000000000000e+01 -4.54995001246909e+02 - 1.33000000000000e+01 -4.12314411202659e+02 - 1.35000000000000e+01 -3.59715820938218e+02 - 1.37000000000000e+01 -2.97680997031215e+02 - 1.39000000000000e+01 -2.12126120219850e+02 - 1.41000000000000e+01 -9.78647224947473e+01 - 1.43000000000000e+01 -1.38644228493632e+01 + 1.21000000000000e+01 6.99836008077528e+01 + 1.23000000000000e+01 -5.26375313396654e+02 + 1.25000000000000e+01 -5.16708951944646e+02 + 1.27000000000000e+01 -5.05977066222890e+02 + 1.29000000000000e+01 -4.88119448094002e+02 + 1.31000000000000e+01 -4.54995001210363e+02 + 1.33000000000000e+01 -4.12314411188385e+02 + 1.35000000000000e+01 -3.59715820941386e+02 + 1.37000000000000e+01 -2.97680997044662e+02 + 1.39000000000000e+01 -2.12126120236132e+02 + 1.41000000000000e+01 -9.78647225049371e+01 + 1.43000000000000e+01 -1.38644228524206e+01 1.45000000000000e+01 0.00000000000000e+00 1.47000000000000e+01 0.00000000000000e+00 1.49000000000000e+01 0.00000000000000e+00 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf b/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf index 53f87f0d2..edf8b154a 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf @@ -1,18 +1,18 @@ # 1 # 1.19000000000000e+01 2.00000000000000e-01 101 0 - 1.20000000000000e+01 7.63151734992420e+02 - 1.22000000000000e+01 7.77148455200910e+02 - 1.24000000000000e+01 6.71873392493057e+02 - 1.26000000000000e+01 5.68531602086455e+02 - 1.28000000000000e+01 4.67336188827297e+02 - 1.30000000000000e+01 3.69712299196592e+02 - 1.32000000000000e+01 2.78713298947211e+02 - 1.34000000000000e+01 1.96250416706679e+02 - 1.36000000000000e+01 1.24307252519035e+02 - 1.38000000000000e+01 6.47710531127921e+01 - 1.40000000000000e+01 2.23458290688221e+01 - 1.42000000000000e+01 2.77288456987264e+00 + 1.20000000000000e+01 7.63151734965745e+02 + 1.22000000000000e+01 7.77148455127296e+02 + 1.24000000000000e+01 6.71873392447965e+02 + 1.26000000000000e+01 5.68531602059036e+02 + 1.28000000000000e+01 4.67336188814458e+02 + 1.30000000000000e+01 3.69712299195657e+02 + 1.32000000000000e+01 2.78713298953585e+02 + 1.34000000000000e+01 1.96250416715908e+02 + 1.36000000000000e+01 1.24307252527630e+02 + 1.38000000000000e+01 6.47710531186980e+01 + 1.40000000000000e+01 2.23458290714716e+01 + 1.42000000000000e+01 2.77288457048417e+00 1.44000000000000e+01 0.00000000000000e+00 1.46000000000000e+01 0.00000000000000e+00 1.48000000000000e+01 0.00000000000000e+00 diff --git a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out index dbb4752af..ed14c521a 100644 --- a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out +++ b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsdA" @@ -57,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -108,21 +106,21 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -161,7 +159,6 @@ colvars: # centers = { 0, 0 } colvars: # targetCenters = { 0, 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsdA" will be rescaled to 1 according to the specified width (1). colvars: The force constant for colvar "rmsdB" will be rescaled to 1 according to the specified width (1). @@ -173,7 +170,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- @@ -187,7 +183,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -206,7 +201,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -222,30 +216,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "rmsdB":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "rmsdB":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj index c60285dcf..ddcb476b2 100644 --- a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj +++ b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step rmsdA ft_rmsdA rmsdB ft_rmsdB - 0 4.84870372257743e-01 0.00000000000000e+00 4.84870372257743e-01 0.00000000000000e+00 - 1 4.84397558390959e-01 2.73671250705184e+01 4.84397558390959e-01 2.73671250705184e+01 - 2 4.83907428259633e-01 2.16076116033336e+01 4.83907428259633e-01 2.16076116033336e+01 - 3 4.83522392477099e-01 1.48700273529640e+01 4.83522392477099e-01 1.48700273529640e+01 - 4 4.83083112857061e-01 9.62041735404308e+00 4.83083112857061e-01 9.62041735404308e+00 - 5 4.82621016611279e-01 6.75848681260943e+00 4.82621016611279e-01 6.75848681260943e+00 - 6 4.82181848616836e-01 3.55598529366702e+00 4.82181848616836e-01 3.55598529366702e+00 - 7 4.81645520126582e-01 3.84568150780596e+00 4.81645520126582e-01 3.84568150780596e+00 - 8 4.81136761646141e-01 7.38903469459440e+00 4.81136761646141e-01 7.38903469459440e+00 - 9 4.80598465151405e-01 1.31715075709571e+01 4.80598465151405e-01 1.31715075709571e+01 - 10 4.80094226696681e-01 2.27871464954793e+01 4.80094226696681e-01 2.27871464954793e+01 - 11 4.79704703210026e-01 3.33000067642520e+01 4.79704703210026e-01 3.33000067642520e+01 - 12 4.79506792185437e-01 4.04751300688640e+01 4.79506792185437e-01 4.04751300688640e+01 - 13 4.79327275852122e-01 4.50913689853400e+01 4.79327275852122e-01 4.50913689853400e+01 - 14 4.79314968876482e-01 4.98879888654564e+01 4.79314968876482e-01 4.98879888654564e+01 - 15 4.79397379649694e-01 4.87227323912461e+01 4.79397379649694e-01 4.87227323912461e+01 - 16 4.79394129019021e-01 4.65370310291944e+01 4.79394129019021e-01 4.65370310291944e+01 - 17 4.79404085663536e-01 4.25674541281252e+01 4.79404085663536e-01 4.25674541281252e+01 - 18 4.79306164129660e-01 3.79497992181814e+01 4.79306164129660e-01 3.79497992181814e+01 - 19 4.79258291381186e-01 3.40970490306029e+01 4.79258291381186e-01 3.40970490306029e+01 - 20 4.79299937829629e-01 2.83439956536282e+01 4.79299937829629e-01 2.83439956536282e+01 +# step rmsdA ft_rmsdA rmsdB ft_rmsdB + 0 4.84870372257743e-01 0.00000000000000e+00 4.84870372257743e-01 0.00000000000000e+00 + 1 4.84397558390947e-01 2.73671250418532e+01 4.84397558390947e-01 2.73671250418532e+01 + 2 4.83907428259583e-01 2.16076115744649e+01 4.83907428259583e-01 2.16076115744649e+01 + 3 4.83522392476985e-01 1.48700273236137e+01 4.83522392476985e-01 1.48700273236137e+01 + 4 4.83083112856857e-01 9.62041732419351e+00 4.83083112856857e-01 9.62041732419351e+00 + 5 4.82621016610959e-01 6.75848678249268e+00 4.82621016610959e-01 6.75848678249268e+00 + 6 4.82181848616375e-01 3.55598526400234e+00 4.82181848616375e-01 3.55598526400234e+00 + 7 4.81645520125956e-01 3.84568147972637e+00 4.81645520125956e-01 3.84568147972637e+00 + 8 4.81136761645330e-01 7.38903466954419e+00 4.81136761645330e-01 7.38903466954419e+00 + 9 4.80598465150393e-01 1.31715075507452e+01 4.80598465150393e-01 1.31715075507452e+01 + 10 4.80094226695461e-01 2.27871464821819e+01 4.80094226695461e-01 2.27871464821819e+01 + 11 4.79704703208599e-01 3.33000067601667e+01 4.79704703208599e-01 3.33000067601667e+01 + 12 4.79506792183813e-01 4.04751300762086e+01 4.79506792183813e-01 4.04751300762086e+01 + 13 4.79327275850325e-01 4.50913690064303e+01 4.79327275850325e-01 4.50913690064303e+01 + 14 4.79314968874545e-01 4.98879889015527e+01 4.79314968874545e-01 4.98879889015527e+01 + 15 4.79397379647665e-01 4.87227324434123e+01 4.79397379647665e-01 4.87227324434123e+01 + 16 4.79394129016958e-01 4.65370310981482e+01 4.79394129016958e-01 4.65370310981482e+01 + 17 4.79404085661514e-01 4.25674542132686e+01 4.79404085661514e-01 4.25674542132686e+01 + 18 4.79306164127760e-01 3.79497993178883e+01 4.79306164127760e-01 3.79497993178883e+01 + 19 4.79258291379496e-01 3.40970491422707e+01 4.79258291379496e-01 3.40970491422707e+01 + 20 4.79299937828241e-01 2.83439957758912e+01 4.79299937828241e-01 2.83439957758912e+01 diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out index 4ffa0e954..0e9b1d0ff 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out @@ -4,4 +4,4 @@ TCL: Running for 20 steps TCL: Resetting colvars with scripted config TCL: Reinitializing atom data TCL: Running for 20 steps -TCL: { 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1.} {0.803041923852589 -0.044335223471426634 -0.5942710294931693 -0.803041923852589 0.044335223471426634 0.5942710294931693 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.} +TCL: { 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1.} {0.8030419238525889 -0.044335223471426655 -0.5942710294931696 -0.8030419238525889 0.044335223471426655 0.5942710294931696 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.} diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out index 7d1128cfc..4169f3a81 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "unscripted.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -27,28 +25,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,14 +85,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 104 atoms requested: total mass = 727.821, total charge = 6.70552e-08. @@ -102,7 +100,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -1.09169 , -2.08869 , -2.98243 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -134,7 +132,6 @@ colvars: # centers = { 18 } colvars: # targetCenters = { 18 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 500 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 500 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -147,7 +144,6 @@ colvars: # colvarsTrajFrequency = 2 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- @@ -161,7 +157,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -178,33 +173,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "o":0/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "o":0/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08. @@ -219,7 +196,6 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "ds" @@ -233,32 +209,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 1 atoms requested. +colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 1 atoms requested. +colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. @@ -297,17 +273,17 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] -colvars: Atom group "atoms" defined with 2 atoms requested. +colvars: Atom group "atoms" defined with 2 atoms requested: total mass = 24.022, total charge = -0.03. colvars: # useX = on [default] colvars: # useY = on [default] colvars: # useZ = on [default] @@ -321,21 +297,21 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] -colvars: Atom group "atoms" defined with 104 atoms requested. +colvars: Atom group "atoms" defined with 104 atoms requested: total mass = 727.821, total charge = 6.70552e-08. colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -1.09169 , -2.08869 , -2.98243 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: This colvar uses scripted function "vector". @@ -370,7 +346,6 @@ colvars: # colvarsTrajFrequency = 2 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- @@ -384,7 +359,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -401,26 +375,4 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - cartesian colvar component: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Scripted functions (Tcl): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped index f2e2c8800..b8c350fb2 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name ds - x 1.91635808809322e+01 + x 1.91635808809730e+01 } colvar { name vec - x ( 1.91635808809322e+01 , 9.74600371905328e-01 , 2.12939348562529e-01 , -1.24954463293996e-03 , -6.93497480454941e-02 ) + x ( 1.91635808809730e+01 , 9.74600371909626e-01 , 2.12939348547346e-01 , -1.24954463323046e-03 , -6.93497480317003e-02 ) } restraint { diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj index 219a7e69d..bc74a2043 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj @@ -1,24 +1,24 @@ -# step d fa_d o - 0 1.42467449615693e+01 1.87662751921536e+03 ( 9.99999748638998e-01 , 6.84042724576856e-04 , 5.12508171642993e-05 , -1.79390207161577e-04 ) - 2 1.45977275439174e+01 1.70113622804129e+03 ( 9.99985973761768e-01 , 5.11485913752449e-03 , -3.32731800435062e-05 , -1.37455033649980e-03 ) - 4 1.50626713340642e+01 1.46866433296788e+03 ( 9.99843158592009e-01 , 1.70395625511364e-02 , -1.43866916458119e-04 , -4.82605709994617e-03 ) - 6 1.56168085965040e+01 1.19159570174801e+03 ( 9.99321288192689e-01 , 3.53760784420164e-02 , -2.78427047982270e-04 , -1.02673520124943e-02 ) - 8 1.62291266298058e+01 8.85436685097112e+02 ( 9.98133542942750e-01 , 5.85622743078173e-02 , -4.51475701501585e-04 , -1.73114600811307e-02 ) - 10 1.68643388381556e+01 5.67830580922218e+02 ( 9.96054934943680e-01 , 8.49744253320995e-02 , -6.83720355286896e-04 , -2.55625925973094e-02 ) - 12 1.74846635628564e+01 2.57668218571810e+02 ( 9.92972839556575e-01 , 1.13139164128729e-01 , -9.51259109789660e-04 , -3.46924278382252e-02 ) - 14 1.80530624332013e+01 -2.65312166006630e+01 ( 9.88977962065000e-01 , 1.41311479847713e-01 , -1.14108783882053e-03 , -4.41854515825400e-02 ) - 16 1.85372200961635e+01 -2.68610048081769e+02 ( 9.84381327963322e-01 , 1.67770992143166e-01 , -1.20902908627445e-03 , -5.33369815525160e-02 ) - 18 1.89124918771599e+01 -4.56245938579931e+02 ( 9.79545563652526e-01 , 1.91522263376275e-01 , -1.22366955068550e-03 , -6.17107283437381e-02 ) - 20 1.91635808809322e+01 -5.81790440466119e+02 ( 9.74600371905327e-01 , 2.12939348562529e-01 , -1.24954463293998e-03 , -6.93497480454941e-02 ) -# step ds fa_ds vec fa_vec - 20 1.42467449615693e+01 0.00000000000000e+00 ( 1.42467449615693e+01 , 9.99999748638998e-01 , 6.84042724576856e-04 , 5.12508171642993e-05 , -1.79390207161577e-04 ) ( 1.87662751921535e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 22 1.45977275439174e+01 0.00000000000000e+00 ( 1.45977275439174e+01 , 9.99985973761768e-01 , 5.11485913752449e-03 , -3.32731800435062e-05 , -1.37455033649980e-03 ) ( 1.70113622804130e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 24 1.50626713340642e+01 0.00000000000000e+00 ( 1.50626713340642e+01 , 9.99843158592009e-01 , 1.70395625511364e-02 , -1.43866916458118e-04 , -4.82605709994616e-03 ) ( 1.46866433296790e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 26 1.56168085965040e+01 0.00000000000000e+00 ( 1.56168085965040e+01 , 9.99321288192689e-01 , 3.53760784420164e-02 , -2.78427047982271e-04 , -1.02673520124943e-02 ) ( 1.19159570174800e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 28 1.62291266298058e+01 0.00000000000000e+00 ( 1.62291266298058e+01 , 9.98133542942750e-01 , 5.85622743078173e-02 , -4.51475701501585e-04 , -1.73114600811307e-02 ) ( 8.85436685097099e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 30 1.68643388381556e+01 0.00000000000000e+00 ( 1.68643388381556e+01 , 9.96054934943680e-01 , 8.49744253320995e-02 , -6.83720355286896e-04 , -2.55625925973094e-02 ) ( 5.67830580922200e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 32 1.74846635628564e+01 0.00000000000000e+00 ( 1.74846635628564e+01 , 9.92972839556575e-01 , 1.13139164128729e-01 , -9.51259109789661e-04 , -3.46924278382252e-02 ) ( 2.57668218571800e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 34 1.80530624332013e+01 0.00000000000000e+00 ( 1.80530624332013e+01 , 9.88977962065000e-01 , 1.41311479847713e-01 , -1.14108783882053e-03 , -4.41854515825400e-02 ) ( -2.65312166006506e+01 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 36 1.85372200961635e+01 0.00000000000000e+00 ( 1.85372200961635e+01 , 9.84381327963322e-01 , 1.67770992143166e-01 , -1.20902908627445e-03 , -5.33369815525160e-02 ) ( -2.68610048081751e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 38 1.89124918771599e+01 0.00000000000000e+00 ( 1.89124918771599e+01 , 9.79545563652526e-01 , 1.91522263376275e-01 , -1.22366955068550e-03 , -6.17107283437381e-02 ) ( -4.56245938579951e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 40 1.91635808809322e+01 0.00000000000000e+00 ( 1.91635808809322e+01 , 9.74600371905328e-01 , 2.12939348562529e-01 , -1.24954463293996e-03 , -6.93497480454941e-02 ) ( -5.81790440466101e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) +# step d fa_d o + 0 1.42467449615693e+01 1.87662751921536e+03 ( 9.99999748638998e-01 , 6.84042724576832e-04 , 5.12508171643214e-05 , -1.79390207161565e-04 ) + 2 1.45977275439175e+01 1.70113622804125e+03 ( 9.99985973761768e-01 , 5.11485913744026e-03 , -3.32731800417789e-05 , -1.37455033645004e-03 ) + 4 1.50626713340646e+01 1.46866433296768e+03 ( 9.99843158592016e-01 , 1.70395625507908e-02 , -1.43866916456290e-04 , -4.82605709972753e-03 ) + 6 1.56168085965048e+01 1.19159570174758e+03 ( 9.99321288192724e-01 , 3.53760784411667e-02 , -2.78427047992860e-04 , -1.02673520119492e-02 ) + 8 1.62291266298068e+01 8.85436685096593e+02 ( 9.98133542942867e-01 , 5.85622743061378e-02 , -4.51475701577846e-04 , -1.73114600800356e-02 ) + 10 1.68643388381563e+01 5.67830580921871e+02 ( 9.96054934943978e-01 , 8.49744253292275e-02 , -6.83720355648298e-04 , -2.55625925952464e-02 ) + 12 1.74846635628575e+01 2.57668218571256e+02 ( 9.92972839557288e-01 , 1.13139164123728e-01 , -9.51259111211344e-04 , -3.46924278340861e-02 ) + 14 1.80530624332059e+01 -2.65312166029723e+01 ( 9.88977962066854e-01 , 1.41311479837272e-01 , -1.14108784183725e-03 , -4.41854515743639e-02 ) + 16 1.85372200961765e+01 -2.68610048088240e+02 ( 9.84381327967116e-01 , 1.67770992125046e-01 , -1.20902908935363e-03 , -5.33369815394103e-02 ) + 18 1.89124918771857e+01 -4.56245938592827e+02 ( 9.79545563657221e-01 , 1.91522263357025e-01 , -1.22366955206206e-03 , -6.17107283289307e-02 ) + 20 1.91635808809730e+01 -5.81790440486497e+02 ( 9.74600371909626e-01 , 2.12939348547346e-01 , -1.24954463323043e-03 , -6.93497480317004e-02 ) +# step ds fa_ds vec fa_vec + 20 1.42467449615693e+01 0.00000000000000e+00 ( 1.42467449615693e+01 , 9.99999748638998e-01 , 6.84042724576832e-04 , 5.12508171643214e-05 , -1.79390207161565e-04 ) ( 1.87662751921535e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 22 1.45977275439175e+01 0.00000000000000e+00 ( 1.45977275439175e+01 , 9.99985973761768e-01 , 5.11485913744027e-03 , -3.32731800417788e-05 , -1.37455033645004e-03 ) ( 1.70113622804125e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 24 1.50626713340646e+01 0.00000000000000e+00 ( 1.50626713340647e+01 , 9.99843158592016e-01 , 1.70395625507908e-02 , -1.43866916456290e-04 , -4.82605709972753e-03 ) ( 1.46866433296765e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 26 1.56168085965049e+01 0.00000000000000e+00 ( 1.56168085965048e+01 , 9.99321288192724e-01 , 3.53760784411667e-02 , -2.78427047992838e-04 , -1.02673520119492e-02 ) ( 1.19159570174760e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 28 1.62291266298068e+01 0.00000000000000e+00 ( 1.62291266298068e+01 , 9.98133542942867e-01 , 5.85622743061378e-02 , -4.51475701577845e-04 , -1.73114600800356e-02 ) ( 8.85436685096600e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 30 1.68643388381563e+01 0.00000000000000e+00 ( 1.68643388381563e+01 , 9.96054934943978e-01 , 8.49744253292276e-02 , -6.83720355648297e-04 , -2.55625925952464e-02 ) ( 5.67830580921850e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 32 1.74846635628575e+01 0.00000000000000e+00 ( 1.74846635628575e+01 , 9.92972839557288e-01 , 1.13139164123728e-01 , -9.51259111211365e-04 , -3.46924278340861e-02 ) ( 2.57668218571251e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 34 1.80530624332059e+01 0.00000000000000e+00 ( 1.80530624332059e+01 , 9.88977962066854e-01 , 1.41311479837272e-01 , -1.14108784183723e-03 , -4.41854515743639e-02 ) ( -2.65312166029492e+01 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 36 1.85372200961765e+01 0.00000000000000e+00 ( 1.85372200961765e+01 , 9.84381327967116e-01 , 1.67770992125046e-01 , -1.20902908935363e-03 , -5.33369815394102e-02 ) ( -2.68610048088250e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 38 1.89124918771856e+01 0.00000000000000e+00 ( 1.89124918771856e+01 , 9.79545563657221e-01 , 1.91522263357025e-01 , -1.22366955206212e-03 , -6.17107283289307e-02 ) ( -4.56245938592801e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 40 1.91635808809730e+01 0.00000000000000e+00 ( 1.91635808809730e+01 , 9.74600371909626e-01 , 2.12939348547346e-01 , -1.24954463323041e-03 , -6.93497480317004e-02 ) ( -5.81790440486500e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/namd/tests/library/007_scripted_cv_biases/namd-version.txt b/namd/tests/library/007_scripted_cv_biases/namd-version.txt index 157cac038..3851f0163 100644 --- a/namd/tests/library/007_scripted_cv_biases/namd-version.txt +++ b/namd/tests/library/007_scripted_cv_biases/namd-version.txt @@ -1,3 +1,5 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. +colvars: Using NAMD interface, version 2016-11-23. + +Wall-compatible restart information added later. diff --git a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out index 6a9e4c603..bc3b30e0e 100644 --- a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out +++ b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "dmat" @@ -57,27 +55,27 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1_2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 2 atoms requested: total mass = 24.022, total charge = -0.03. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_9_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 2 atoms requested: total mass = 24.022, total charge = 0.14. @@ -114,7 +112,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = on colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "dmat" will be rescaled to 25 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -125,31 +122,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - distancePairs colvar component: -colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "dmat":0/0. 2 atoms: total mass = 24.022, total charge = -0.03. colvars: Re-initialized atom group for variable "dmat":0/1. 2 atoms: total mass = 24.022, total charge = 0.14. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "dmat":0/0. 2 atoms: total mass = 24.022, total charge = -0.03. colvars: Re-initialized atom group for variable "dmat":0/1. 2 atoms: total mass = 24.022, total charge = 0.14. colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj index 82cfa8cb8..4da3a5ad0 100644 --- a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj +++ b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step dmat fa_dmat x0_dmat 0 ( 1.21777809554943e+01 , 1.42467449615693e+01 , 1.04037423074584e+01 , 1.19921066122679e+01 ) ( -4.44452388735783e+00 , -6.16862403923228e+00 , -1.00935576864602e+01 , 1.97334693301965e-01 ) ( 1.20000000000000e+01 , 1.40000000000000e+01 , 1.00000000000000e+01 , 1.20000000000000e+01 ) - 1 ( 1.21756207147491e+01 , 1.42470238788079e+01 , 1.04051155961944e+01 , 1.19946270847732e+01 ) ( -4.56551786872810e+00 , -6.40059697019808e+00 , -1.02528899048608e+01 , -4.06771193291355e-02 ) ( 1.19930000000000e+01 , 1.39910000000000e+01 , 9.99500000000000e+00 , 1.19930000000000e+01 ) - 2 ( 1.21730460027225e+01 , 1.42474017558768e+01 , 1.04061807237121e+01 , 1.19973140354256e+01 ) ( -4.67615006806166e+00 , -6.63504389691996e+00 , -1.04045180928018e+01 , -2.82850885640329e-01 ) ( 1.19860000000000e+01 , 1.39820000000000e+01 , 9.99000000000000e+00 , 1.19860000000000e+01 ) - 3 ( 1.21706185978867e+01 , 1.42476454576843e+01 , 1.04071659086200e+01 , 1.19998189022153e+01 ) ( -4.79046494716631e+00 , -6.86613644210809e+00 , -1.05541477154994e+01 , -5.20472555383211e-01 ) ( 1.19790000000000e+01 , 1.39730000000000e+01 , 9.98500000000000e+00 , 1.19790000000000e+01 ) - 4 ( 1.21683952007753e+01 , 1.42481001273688e+01 , 1.04075924776308e+01 , 1.20018588027655e+01 ) ( -4.90988001938302e+00 , -7.10250318422005e+00 , -1.06898119407688e+01 , -7.46470069137661e-01 ) ( 1.19720000000000e+01 , 1.39640000000000e+01 , 9.98000000000000e+00 , 1.19720000000000e+01 ) - 5 ( 1.21663636501510e+01 , 1.42484947491514e+01 , 1.04077166779264e+01 , 1.20033662039908e+01 ) ( -5.03409125377492e+00 , -7.33736872878623e+00 , -1.08179169481593e+01 , -9.59155099770514e-01 ) ( 1.19650000000000e+01 , 1.39550000000000e+01 , 9.97500000000000e+00 , 1.19650000000000e+01 ) - 6 ( 1.21637914428202e+01 , 1.42488413632141e+01 , 1.04074400269771e+01 , 1.20048328024046e+01 ) ( -5.14478607050619e+00 , -7.57103408035369e+00 , -1.09360006744287e+01 , -1.17082006011526e+00 ) ( 1.19580000000000e+01 , 1.39460000000000e+01 , 9.97000000000000e+00 , 1.19580000000000e+01 ) - 7 ( 1.21606504826560e+01 , 1.42491108211546e+01 , 1.04064186711875e+01 , 1.20059438853592e+01 ) ( -5.24126206639965e+00 , -7.80277052886533e+00 , -1.10354667796874e+01 , -1.37359713397900e+00 ) ( 1.19510000000000e+01 , 1.39370000000000e+01 , 9.96500000000000e+00 , 1.19510000000000e+01 ) - 8 ( 1.21578350901329e+01 , 1.42493400866675e+01 , 1.04052750916551e+01 , 1.20066641446701e+01 ) ( -5.34587725332165e+00 , -8.03350216668708e+00 , -1.11318772913779e+01 , -1.56660361675320e+00 ) ( 1.19440000000000e+01 , 1.39280000000000e+01 , 9.96000000000000e+00 , 1.19440000000000e+01 ) - 9 ( 1.21551529536114e+01 , 1.42495154307442e+01 , 1.04038460769366e+01 , 1.20069492651864e+01 ) ( -5.45382384028512e+00 , -8.26288576860619e+00 , -1.12211519234160e+01 , -1.74873162966009e+00 ) ( 1.19370000000000e+01 , 1.39190000000000e+01 , 9.95500000000000e+00 , 1.19370000000000e+01 ) - 10 ( 1.21523782650640e+01 , 1.42496785499675e+01 , 1.04020777830207e+01 , 1.20068009867444e+01 ) ( -5.55945662659898e+00 , -8.49196374918688e+00 , -1.13019445755174e+01 , -1.92002466861112e+00 ) ( 1.19300000000000e+01 , 1.39100000000000e+01 , 9.95000000000000e+00 , 1.19300000000000e+01 ) + 1 ( 1.21756207147491e+01 , 1.42470238788079e+01 , 1.04051155961944e+01 , 1.19946270847732e+01 ) ( -4.56551786872841e+00 , -6.40059697019852e+00 , -1.02528899048611e+01 , -4.06771193293132e-02 ) ( 1.19930000000000e+01 , 1.39910000000000e+01 , 9.99500000000000e+00 , 1.19930000000000e+01 ) + 2 ( 1.21730460027225e+01 , 1.42474017558769e+01 , 1.04061807237121e+01 , 1.19973140354256e+01 ) ( -4.67615006806308e+00 , -6.63504389692182e+00 , -1.04045180928033e+01 , -2.82850885641173e-01 ) ( 1.19860000000000e+01 , 1.39820000000000e+01 , 9.99000000000000e+00 , 1.19860000000000e+01 ) + 3 ( 1.21706185978868e+01 , 1.42476454576845e+01 , 1.04071659086201e+01 , 1.19998189022154e+01 ) ( -4.79046494716990e+00 , -6.86613644211285e+00 , -1.05541477155027e+01 , -5.20472555385387e-01 ) ( 1.19790000000000e+01 , 1.39730000000000e+01 , 9.98500000000000e+00 , 1.19790000000000e+01 ) + 4 ( 1.21683952007756e+01 , 1.42481001273692e+01 , 1.04075924776310e+01 , 1.20018588027657e+01 ) ( -4.90988001939003e+00 , -7.10250318422965e+00 , -1.06898119407748e+01 , -7.46470069142058e-01 ) ( 1.19720000000000e+01 , 1.39640000000000e+01 , 9.98000000000000e+00 , 1.19720000000000e+01 ) + 5 ( 1.21663636501515e+01 , 1.42484947491521e+01 , 1.04077166779268e+01 , 1.20033662039911e+01 ) ( -5.03409125378686e+00 , -7.33736872880351e+00 , -1.08179169481691e+01 , -9.59155099778552e-01 ) ( 1.19650000000000e+01 , 1.39550000000000e+01 , 9.97500000000000e+00 , 1.19650000000000e+01 ) + 6 ( 1.21637914428210e+01 , 1.42488413632153e+01 , 1.04074400269777e+01 , 1.20048328024051e+01 ) ( -5.14478607052502e+00 , -7.57103408038215e+00 , -1.09360006744432e+01 , -1.17082006012863e+00 ) ( 1.19580000000000e+01 , 1.39460000000000e+01 , 9.97000000000000e+00 , 1.19580000000000e+01 ) + 7 ( 1.21606504826571e+01 , 1.42491108211564e+01 , 1.04064186711883e+01 , 1.20059438853600e+01 ) ( -5.24126206642750e+00 , -7.80277052890939e+00 , -1.10354667797074e+01 , -1.37359713399947e+00 ) ( 1.19510000000000e+01 , 1.39370000000000e+01 , 9.96499999999999e+00 , 1.19510000000000e+01 ) + 8 ( 1.21578350901344e+01 , 1.42493400866701e+01 , 1.04052750916562e+01 , 1.20066641446713e+01 ) ( -5.34587725336086e+00 , -8.03350216675169e+00 , -1.11318772914041e+01 , -1.56660361678274e+00 ) ( 1.19440000000000e+01 , 1.39280000000000e+01 , 9.95999999999999e+00 , 1.19440000000000e+01 ) + 9 ( 1.21551529536135e+01 , 1.42495154307479e+01 , 1.04038460769379e+01 , 1.20069492651880e+01 ) ( -5.45382384033828e+00 , -8.26288576869678e+00 , -1.12211519234485e+01 , -1.74873162970037e+00 ) ( 1.19370000000000e+01 , 1.39190000000000e+01 , 9.95499999999999e+00 , 1.19370000000000e+01 ) + 10 ( 1.21523782650667e+01 , 1.42496785499723e+01 , 1.04020777830222e+01 , 1.20068009867465e+01 ) ( -5.55945662666826e+00 , -8.49196374930874e+00 , -1.13019445755558e+01 , -1.92002466866330e+00 ) ( 1.19300000000000e+01 , 1.39100000000000e+01 , 9.94999999999999e+00 , 1.19300000000000e+01 ) diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out index 157b9cded..49ea4044e 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -27,28 +25,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -109,30 +107,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped index 56cddbb67..d0176330c 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 1.42698565162752e+01 + x 1.42698565162903e+01 } metadynamics { @@ -43,9 +43,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 8.33855405317537e-07 - 3.00574542330873e-04 8.54334028864708e-03 1.91497791865179e-02 - 3.38510199591916e-03 4.71875402354643e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 8.33855405052094e-07 + 3.00574542266188e-04 8.54334028777445e-03 1.91497791869240e-02 + 3.38510199644364e-03 4.71875402495671e-05 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients grid_parameters { @@ -77,9 +77,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 2.98417493776893e-05 - 6.93917949849616e-03 8.87295997392777e-02 -4.43203926802213e-02 - -5.08263278082148e-02 -1.30782612378422e-03 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 2.98417493685997e-05 + 6.93917949716513e-03 8.87295997352626e-02 -4.43203926688531e-02 + -5.08263278137392e-02 -1.30782612413995e-03 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj index eabe053dd..ce3224f94 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step d 0 1.42467449615693e+01 1 1.42470955327846e+01 - 2 1.42476939547290e+01 - 3 1.42483110732973e+01 - 4 1.42492943585134e+01 - 5 1.42503736285743e+01 - 6 1.42515602222322e+01 - 7 1.42528228624278e+01 - 8 1.42541950327196e+01 - 9 1.42556585606043e+01 - 10 1.42572498626143e+01 - 11 1.42590470996029e+01 - 12 1.42605989324670e+01 - 13 1.42621615963588e+01 - 14 1.42637368066246e+01 - 15 1.42651402747104e+01 - 16 1.42662547203247e+01 - 17 1.42670733056670e+01 - 18 1.42680933124105e+01 - 19 1.42689260104905e+01 - 20 1.42698565162752e+01 + 2 1.42476939547291e+01 + 3 1.42483110732975e+01 + 4 1.42492943585138e+01 + 5 1.42503736285750e+01 + 6 1.42515602222333e+01 + 7 1.42528228624295e+01 + 8 1.42541950327222e+01 + 9 1.42556585606080e+01 + 10 1.42572498626192e+01 + 11 1.42590470996093e+01 + 12 1.42605989324750e+01 + 13 1.42621615963684e+01 + 14 1.42637368066359e+01 + 15 1.42651402747233e+01 + 16 1.42662547203391e+01 + 17 1.42670733056824e+01 + 18 1.42680933124264e+01 + 19 1.42689260105063e+01 + 20 1.42698565162903e+01 diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf b/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf index 7af5ed5c9..f07621e5c 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf @@ -1,79 +1,79 @@ # 1 # 0.00000000000000e+00 2.00000000000000e-01 76 0 - 1.00000000000000e-01 1.91497791865179e-02 - 3.00000000000000e-01 1.91497791865179e-02 - 5.00000000000000e-01 1.91497791865179e-02 - 7.00000000000000e-01 1.91497791865179e-02 - 9.00000000000000e-01 1.91497791865179e-02 - 1.10000000000000e+00 1.91497791865179e-02 - 1.30000000000000e+00 1.91497791865179e-02 - 1.50000000000000e+00 1.91497791865179e-02 - 1.70000000000000e+00 1.91497791865179e-02 - 1.90000000000000e+00 1.91497791865179e-02 - 2.10000000000000e+00 1.91497791865179e-02 - 2.30000000000000e+00 1.91497791865179e-02 - 2.50000000000000e+00 1.91497791865179e-02 - 2.70000000000000e+00 1.91497791865179e-02 - 2.90000000000000e+00 1.91497791865179e-02 - 3.10000000000000e+00 1.91497791865179e-02 - 3.30000000000000e+00 1.91497791865179e-02 - 3.50000000000000e+00 1.91497791865179e-02 - 3.70000000000000e+00 1.91497791865179e-02 - 3.90000000000000e+00 1.91497791865179e-02 - 4.10000000000000e+00 1.91497791865179e-02 - 4.30000000000000e+00 1.91497791865179e-02 - 4.50000000000000e+00 1.91497791865179e-02 - 4.70000000000000e+00 1.91497791865179e-02 - 4.90000000000000e+00 1.91497791865179e-02 - 5.10000000000000e+00 1.91497791865179e-02 - 5.30000000000000e+00 1.91497791865179e-02 - 5.50000000000000e+00 1.91497791865179e-02 - 5.70000000000000e+00 1.91497791865179e-02 - 5.90000000000000e+00 1.91497791865179e-02 - 6.10000000000000e+00 1.91497791865179e-02 - 6.30000000000000e+00 1.91497791865179e-02 - 6.50000000000000e+00 1.91497791865179e-02 - 6.70000000000000e+00 1.91497791865179e-02 - 6.90000000000000e+00 1.91497791865179e-02 - 7.10000000000000e+00 1.91497791865179e-02 - 7.30000000000000e+00 1.91497791865179e-02 - 7.50000000000000e+00 1.91497791865179e-02 - 7.70000000000000e+00 1.91497791865179e-02 - 7.90000000000000e+00 1.91497791865179e-02 - 8.10000000000000e+00 1.91497791865179e-02 - 8.30000000000000e+00 1.91497791865179e-02 - 8.50000000000000e+00 1.91497791865179e-02 - 8.70000000000000e+00 1.91497791865179e-02 - 8.90000000000000e+00 1.91497791865179e-02 - 9.10000000000000e+00 1.91497791865179e-02 - 9.30000000000000e+00 1.91497791865179e-02 - 9.50000000000000e+00 1.91497791865179e-02 - 9.70000000000000e+00 1.91497791865179e-02 - 9.90000000000000e+00 1.91497791865179e-02 - 1.01000000000000e+01 1.91497791865179e-02 - 1.03000000000000e+01 1.91497791865179e-02 - 1.05000000000000e+01 1.91497791865179e-02 - 1.07000000000000e+01 1.91497791865179e-02 - 1.09000000000000e+01 1.91497791865179e-02 - 1.11000000000000e+01 1.91497791865179e-02 - 1.13000000000000e+01 1.91497791865179e-02 - 1.15000000000000e+01 1.91497791865179e-02 - 1.17000000000000e+01 1.91497791865179e-02 - 1.19000000000000e+01 1.91497791865179e-02 - 1.21000000000000e+01 1.91497791865179e-02 - 1.23000000000000e+01 1.91497791865179e-02 - 1.25000000000000e+01 1.91497791865179e-02 - 1.27000000000000e+01 1.91497791865179e-02 - 1.29000000000000e+01 1.91497791865179e-02 - 1.31000000000000e+01 1.91497791865179e-02 - 1.33000000000000e+01 1.91497791865179e-02 - 1.35000000000000e+01 1.91497791865179e-02 - 1.37000000000000e+01 1.91489453311125e-02 - 1.39000000000000e+01 1.88492046441870e-02 - 1.41000000000000e+01 1.06064388978708e-02 + 1.00000000000000e-01 1.91497791869240e-02 + 3.00000000000000e-01 1.91497791869240e-02 + 5.00000000000000e-01 1.91497791869240e-02 + 7.00000000000000e-01 1.91497791869240e-02 + 9.00000000000000e-01 1.91497791869240e-02 + 1.10000000000000e+00 1.91497791869240e-02 + 1.30000000000000e+00 1.91497791869240e-02 + 1.50000000000000e+00 1.91497791869240e-02 + 1.70000000000000e+00 1.91497791869240e-02 + 1.90000000000000e+00 1.91497791869240e-02 + 2.10000000000000e+00 1.91497791869240e-02 + 2.30000000000000e+00 1.91497791869240e-02 + 2.50000000000000e+00 1.91497791869240e-02 + 2.70000000000000e+00 1.91497791869240e-02 + 2.90000000000000e+00 1.91497791869240e-02 + 3.10000000000000e+00 1.91497791869240e-02 + 3.30000000000000e+00 1.91497791869240e-02 + 3.50000000000000e+00 1.91497791869240e-02 + 3.70000000000000e+00 1.91497791869240e-02 + 3.90000000000000e+00 1.91497791869240e-02 + 4.10000000000000e+00 1.91497791869240e-02 + 4.30000000000000e+00 1.91497791869240e-02 + 4.50000000000000e+00 1.91497791869240e-02 + 4.70000000000000e+00 1.91497791869240e-02 + 4.90000000000000e+00 1.91497791869240e-02 + 5.10000000000000e+00 1.91497791869240e-02 + 5.30000000000000e+00 1.91497791869240e-02 + 5.50000000000000e+00 1.91497791869240e-02 + 5.70000000000000e+00 1.91497791869240e-02 + 5.90000000000000e+00 1.91497791869240e-02 + 6.10000000000000e+00 1.91497791869240e-02 + 6.30000000000000e+00 1.91497791869240e-02 + 6.50000000000000e+00 1.91497791869240e-02 + 6.70000000000000e+00 1.91497791869240e-02 + 6.90000000000000e+00 1.91497791869240e-02 + 7.10000000000000e+00 1.91497791869240e-02 + 7.30000000000000e+00 1.91497791869240e-02 + 7.50000000000000e+00 1.91497791869240e-02 + 7.70000000000000e+00 1.91497791869240e-02 + 7.90000000000000e+00 1.91497791869240e-02 + 8.10000000000000e+00 1.91497791869240e-02 + 8.30000000000000e+00 1.91497791869240e-02 + 8.50000000000000e+00 1.91497791869240e-02 + 8.70000000000000e+00 1.91497791869240e-02 + 8.90000000000000e+00 1.91497791869240e-02 + 9.10000000000000e+00 1.91497791869240e-02 + 9.30000000000000e+00 1.91497791869240e-02 + 9.50000000000000e+00 1.91497791869240e-02 + 9.70000000000000e+00 1.91497791869240e-02 + 9.90000000000000e+00 1.91497791869240e-02 + 1.01000000000000e+01 1.91497791869240e-02 + 1.03000000000000e+01 1.91497791869240e-02 + 1.05000000000000e+01 1.91497791869240e-02 + 1.07000000000000e+01 1.91497791869240e-02 + 1.09000000000000e+01 1.91497791869240e-02 + 1.11000000000000e+01 1.91497791869240e-02 + 1.13000000000000e+01 1.91497791869240e-02 + 1.15000000000000e+01 1.91497791869240e-02 + 1.17000000000000e+01 1.91497791869240e-02 + 1.19000000000000e+01 1.91497791869240e-02 + 1.21000000000000e+01 1.91497791869240e-02 + 1.23000000000000e+01 1.91497791869240e-02 + 1.25000000000000e+01 1.91497791869240e-02 + 1.27000000000000e+01 1.91497791869240e-02 + 1.29000000000000e+01 1.91497791869240e-02 + 1.31000000000000e+01 1.91497791869240e-02 + 1.33000000000000e+01 1.91497791869240e-02 + 1.35000000000000e+01 1.91497791869240e-02 + 1.37000000000000e+01 1.91489453315190e-02 + 1.39000000000000e+01 1.88492046446579e-02 + 1.41000000000000e+01 1.06064388991496e-02 1.43000000000000e+01 -0.00000000000000e+00 - 1.45000000000000e+01 1.57646771905987e-02 - 1.47000000000000e+01 1.91025916462824e-02 - 1.49000000000000e+01 1.91497791865179e-02 - 1.51000000000000e+01 1.91497791865179e-02 + 1.45000000000000e+01 1.57646771904804e-02 + 1.47000000000000e+01 1.91025916466745e-02 + 1.49000000000000e+01 1.91497791869240e-02 + 1.51000000000000e+01 1.91497791869240e-02 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out index 51c6085f0..791e3e5d1 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "angle" @@ -57,42 +55,42 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] @@ -128,56 +126,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_6" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_7" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -220,6 +218,11 @@ colvars: # historyFreq = 5 colvars: # shared = off [default] colvars: # maxForce = [default] colvars: # integrate = on [default] +colvars: # pABFintegrateFreq = 0 [default] +colvars: # integrateInitMaxIterations = 10000 [default] +colvars: # integrateInitTol = 1e-06 [default] +colvars: # integrateMaxIterations = 100 [default] +colvars: # integrateTol = 0.0001 [default] colvars: Finished ABF setup. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -229,29 +232,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (7 scalable groups, 7 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - angle colvar component: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - Poisson integration of 2D/3D free energy surfaces: -colvars: Henin2021 https://doi.org/10.1021/acs.jctc.1c00593 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "angle":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "angle":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "angle":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. @@ -260,11 +240,11 @@ colvars: Re-initialized atom group for variable "dihedral":0/1. 1 atoms: total m colvars: Re-initialized atom group for variable "dihedral":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "dihedral":0/3. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (7 scalable groups, 7 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "angle":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "angle":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "angle":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped index cf8ab20fa..8e53a7a8c 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name angle - x 9.71572414999404e+01 + x 9.71572414998837e+01 } colvar { name dihedral - x 4.76248133822394e+01 + x 4.76248133821808e+01 } abf { @@ -256,8 +256,8 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 3.86055080717640e-01 -1.47156688763172e+00 - 1.21510007787258e-01 -3.46687391789233e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 3.86055079861384e-01 -1.47156688632534e+00 + 1.21510007293019e-01 -3.46687391825760e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj index 7fe21a71e..dfd38fd88 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step angle ft_angle fa_angle dihedral ft_dihedral fa_dihedral 0 9.68498695196423e+01 0.00000000000000e+00 0.00000000000000e+00 4.86056572577460e+01 0.00000000000000e+00 0.00000000000000e+00 - 1 9.68581311788645e+01 -1.84451708831746e-02 1.84451708831746e-02 4.84876896364246e+01 -2.26204233738360e-02 2.26204233738360e-02 - 2 9.68825903830917e+01 -1.75928069494324e-02 2.72415743578908e-02 4.83727459141996e+01 1.09239386526311e-01 -3.19992698893197e-02 - 3 9.69105533161851e+01 -3.36465334818358e-02 3.84570855185028e-02 4.82565768693385e+01 1.87476845825581e-01 -9.44915518311800e-02 - 4 9.69406101257451e+01 -8.90986866663562e-02 6.07317571850918e-02 4.81501282214520e+01 2.91829502654487e-01 -1.67448927494802e-01 - 5 9.69674902853217e+01 -1.44712759388158e-01 8.96743090627233e-02 4.80499450162547e+01 4.19420612850755e-01 -2.51333050064953e-01 - 6 9.69953149267565e+01 -1.91014192347208e-01 0.00000000000000e+00 4.79483470270909e+01 5.72126050345682e-01 0.00000000000000e+00 - 7 9.70261917919329e+01 -3.39026775359731e-01 3.39026775359731e-01 4.78551169384050e+01 1.09938746010351e+00 -1.09938746010351e+00 - 8 9.70529963144370e+01 -4.61821781835164e-02 3.62117864451490e-01 4.77722438820884e+01 2.55842716309053e-01 -1.22730881825804e+00 - 9 9.70984141114596e+01 -2.94041075882280e-02 3.71919233647566e-01 4.76919701530931e+01 3.67640478945815e-01 -1.34985564457331e+00 - 10 9.71572414999404e+01 -5.65433882802956e-02 3.86055080717640e-01 4.76248133822394e+01 4.86844972233643e-01 -1.47156688763172e+00 + 1 9.68581311788660e+01 -1.84451705170512e-02 1.84451705170512e-02 4.84876896364254e+01 -2.26204229896581e-02 2.26204229896581e-02 + 2 9.68825903830946e+01 -1.75928069356493e-02 2.72415739848758e-02 4.83727459141994e+01 1.09239386473433e-01 -3.19992702470586e-02 + 3 9.69105533161889e+01 -3.36465334276460e-02 3.84570851274245e-02 4.82565768693354e+01 1.87476845673922e-01 -9.44915521383659e-02 + 4 9.69406101257489e+01 -8.90986865550939e-02 6.07317567661980e-02 4.81501282214438e+01 2.91829502364863e-01 -1.67448927729582e-01 + 5 9.69674902853240e+01 -1.44712759211668e-01 8.96743086085316e-02 4.80499450162389e+01 4.19420612395337e-01 -2.51333050208649e-01 + 6 9.69953149267550e+01 -1.91014192106924e-01 0.00000000000000e+00 4.79483470270649e+01 5.72126049702663e-01 0.00000000000000e+00 + 7 9.70261917919283e+01 -3.39026774573669e-01 3.39026774573669e-01 4.78551169383663e+01 1.09938745929832e+00 -1.09938745929832e+00 + 8 9.70529963144229e+01 -4.61821781161425e-02 3.62117863631741e-01 4.77722438820399e+01 2.55842715985027e-01 -1.22730881729084e+00 + 9 9.70984141114285e+01 -2.94041075150722e-02 3.71919232803431e-01 4.76919701530380e+01 3.67640478440557e-01 -1.34985564343769e+00 + 10 9.71572414998837e+01 -5.65433882318097e-02 3.86055079861384e-01 4.76248133821808e+01 4.86844971550587e-01 -1.47156688632534e+00 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad b/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad index 81d482591..02118c831 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad @@ -506,7 +506,7 @@ 9.90000000000000e+01 3.30000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 3.90000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 4.50000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 - 9.90000000000000e+01 5.10000000000000e+01 8.96743090627233e-02 -2.51333050064953e-01 + 9.90000000000000e+01 5.10000000000000e+01 8.96743086085316e-02 -2.51333050208651e-01 9.90000000000000e+01 5.70000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 6.30000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 6.90000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 @@ -1439,8 +1439,8 @@ 9.90000000000000e+01 2.70000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 3.30000000000000e+01 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1.44000000000000e+02 1.39002722559773e+00 + 1.74000000000000e+02 1.50000000000000e+02 1.38713424292960e+00 + 1.74000000000000e+02 1.56000000000000e+02 1.38487642807673e+00 + 1.74000000000000e+02 1.62000000000000e+02 1.38318705222206e+00 + 1.74000000000000e+02 1.68000000000000e+02 1.38201541431330e+00 + 1.74000000000000e+02 1.74000000000000e+02 1.38132631103237e+00 + 1.74000000000000e+02 1.80000000000000e+02 1.38109883401216e+00 - 1.80000000000000e+02 0.00000000000000e+00 1.71950717310890e+00 - 1.80000000000000e+02 6.00000000000000e+00 1.71763469317717e+00 - 1.80000000000000e+02 1.20000000000000e+01 1.71204109537989e+00 - 1.80000000000000e+02 1.80000000000000e+01 1.70280652536677e+00 - 1.80000000000000e+02 2.40000000000000e+01 1.69008997738884e+00 - 1.80000000000000e+02 3.00000000000000e+01 1.67415947094321e+00 - 1.80000000000000e+02 3.60000000000000e+01 1.65541840879782e+00 - 1.80000000000000e+02 4.20000000000000e+01 1.63441424855771e+00 - 1.80000000000000e+02 4.80000000000000e+01 1.61181912918628e+00 - 1.80000000000000e+02 5.40000000000000e+01 1.58838128135519e+00 - 1.80000000000000e+02 6.00000000000000e+01 1.56485578955593e+00 - 1.80000000000000e+02 6.60000000000000e+01 1.54193226438972e+00 - 1.80000000000000e+02 7.20000000000000e+01 1.52017776042752e+00 - 1.80000000000000e+02 7.80000000000000e+01 1.50000632550894e+00 - 1.80000000000000e+02 8.40000000000000e+01 1.48167451466162e+00 - 1.80000000000000e+02 9.00000000000000e+01 1.46529791470002e+00 - 1.80000000000000e+02 9.60000000000000e+01 1.45087911228919e+00 - 1.80000000000000e+02 1.02000000000000e+02 1.43833872103392e+00 - 1.80000000000000e+02 1.08000000000000e+02 1.42754465916118e+00 - 1.80000000000000e+02 1.14000000000000e+02 1.41833662513247e+00 - 1.80000000000000e+02 1.20000000000000e+02 1.41054452719039e+00 - 1.80000000000000e+02 1.26000000000000e+02 1.40400145437701e+00 - 1.80000000000000e+02 1.32000000000000e+02 1.39855177378947e+00 - 1.80000000000000e+02 1.38000000000000e+02 1.39405569624656e+00 - 1.80000000000000e+02 1.44000000000000e+02 1.39039153739266e+00 - 1.80000000000000e+02 1.50000000000000e+02 1.38745617519842e+00 - 1.80000000000000e+02 1.56000000000000e+02 1.38516474699527e+00 - 1.80000000000000e+02 1.62000000000000e+02 1.38344975527461e+00 - 1.80000000000000e+02 1.68000000000000e+02 1.38226031473303e+00 - 1.80000000000000e+02 1.74000000000000e+02 1.38156058635732e+00 - 1.80000000000000e+02 1.80000000000000e+02 1.38132948283151e+00 + 1.80000000000000e+02 0.00000000000000e+00 1.71950717027158e+00 + 1.80000000000000e+02 6.00000000000000e+00 1.71763469034113e+00 + 1.80000000000000e+02 1.20000000000000e+01 1.71204109254773e+00 + 1.80000000000000e+02 1.80000000000000e+01 1.70280652254112e+00 + 1.80000000000000e+02 2.40000000000000e+01 1.69008997457239e+00 + 1.80000000000000e+02 3.00000000000000e+01 1.67415946813868e+00 + 1.80000000000000e+02 3.60000000000000e+01 1.65541840600784e+00 + 1.80000000000000e+02 4.20000000000000e+01 1.63441424578470e+00 + 1.80000000000000e+02 4.80000000000000e+01 1.61181912643233e+00 + 1.80000000000000e+02 5.40000000000000e+01 1.58838127862193e+00 + 1.80000000000000e+02 6.00000000000000e+01 1.56485578684440e+00 + 1.80000000000000e+02 6.60000000000000e+01 1.54193226170038e+00 + 1.80000000000000e+02 7.20000000000000e+01 1.52017775776025e+00 + 1.80000000000000e+02 7.80000000000000e+01 1.50000632286310e+00 + 1.80000000000000e+02 8.40000000000000e+01 1.48167451203620e+00 + 1.80000000000000e+02 9.00000000000000e+01 1.46529791209370e+00 + 1.80000000000000e+02 9.60000000000000e+01 1.45087910970048e+00 + 1.80000000000000e+02 1.02000000000000e+02 1.43833871846121e+00 + 1.80000000000000e+02 1.08000000000000e+02 1.42754465660285e+00 + 1.80000000000000e+02 1.14000000000000e+02 1.41833662258694e+00 + 1.80000000000000e+02 1.20000000000000e+02 1.41054452465612e+00 + 1.80000000000000e+02 1.26000000000000e+02 1.40400145185257e+00 + 1.80000000000000e+02 1.32000000000000e+02 1.39855177127351e+00 + 1.80000000000000e+02 1.38000000000000e+02 1.39405569373783e+00 + 1.80000000000000e+02 1.44000000000000e+02 1.39039153489000e+00 + 1.80000000000000e+02 1.50000000000000e+02 1.38745617270075e+00 + 1.80000000000000e+02 1.56000000000000e+02 1.38516474450159e+00 + 1.80000000000000e+02 1.62000000000000e+02 1.38344975278396e+00 + 1.80000000000000e+02 1.68000000000000e+02 1.38226031224452e+00 + 1.80000000000000e+02 1.74000000000000e+02 1.38156058387008e+00 + 1.80000000000000e+02 1.80000000000000e+02 1.38132948034468e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state index ceba9352b..38b541ee8 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state @@ -20,9 +20,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.53403286720768e-06 8.43235276972864e-04 - 3.21927751514002e-02 9.90603521389808e-02 2.46033419259411e-02 - 4.93589875891209e-04 4.23052788302019e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.53403289508330e-06 8.43235284919676e-04 + 3.21927752810740e-02 9.90603520983741e-02 2.46033418312340e-02 + 4.93589872784461e-04 4.23052788272303e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -45,9 +45,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 2.26292238292108e-05 8.26704499874479e-03 - 1.53420242499276e-01 -2.66708902934347e-02 -1.30444282639589e-01 - -5.10069715433551e-03 -6.37695701865853e-06 0.00000000000000e+00 + 0.00000000000000e+00 2.26292242192221e-05 8.26704506678145e-03 + 1.53420242800061e-01 -2.66708910635591e-02 -1.30444282281981e-01 + -5.10069712416846e-03 -6.37695701821339e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out index f11fa72fe..c68838faf 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep1.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -145,7 +143,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -159,7 +156,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -174,33 +170,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Multiple-walker metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep1r.colvars.state". colvars: The final output state file will be "test.rep1.colvars.state". +colvars: Opening trajectory file "test.rep1.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep1r.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped index 094d10a53..b96d93fd6 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 1.41656974969458e+01 + x 1.41656974949034e+01 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.53403286720768e-06 8.43235276972864e-04 - 3.21927751514002e-02 9.90603521389808e-02 2.46033419259411e-02 - 4.93589875891209e-04 4.23052788302019e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.53403289508330e-06 8.43235284919676e-04 + 3.21927752810740e-02 9.90603520983741e-02 2.46033418312340e-02 + 4.93589872784461e-04 4.23052788272303e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -55,9 +55,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 2.26292238292108e-05 8.26704499874479e-03 - 1.53420242499276e-01 -2.66708902934347e-02 -1.30444282639589e-01 - -5.10069715433551e-03 -6.37695701865853e-06 0.00000000000000e+00 + 0.00000000000000e+00 2.26292242192221e-05 8.26704506678145e-03 + 1.53420242800061e-01 -2.66708910635591e-02 -1.30444282281981e-01 + -5.10069712416846e-03 -6.37695701821339e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj index 5731bc76e..441edf82b 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj @@ -2,101 +2,101 @@ 0 1.42467449615693e+01 0.00000000000000e+00 1 1.42470955327846e+01 0.00000000000000e+00 2 1.42476657799120e+01 0.00000000000000e+00 - 3 1.42485380098359e+01 0.00000000000000e+00 - 4 1.42499968808362e+01 0.00000000000000e+00 - 5 1.42516048130991e+01 0.00000000000000e+00 - 6 1.42535349212359e+01 0.00000000000000e+00 - 7 1.42555542781170e+01 0.00000000000000e+00 - 8 1.42579210999817e+01 0.00000000000000e+00 - 9 1.42607955979351e+01 0.00000000000000e+00 - 10 1.42638739176583e+01 -1.41180095141270e-03 - 11 1.42668375588355e+01 -1.41180095141270e-03 - 12 1.42696059392625e+01 -1.41180095141270e-03 - 13 1.42727236830683e+01 -1.41180095141270e-03 - 14 1.42758764946660e+01 -1.41180095141270e-03 - 15 1.42787429047727e+01 -1.41180095141270e-03 - 16 1.42810489912705e+01 -1.41180095141270e-03 - 17 1.42825584062025e+01 -1.41180095141270e-03 - 18 1.42834947131625e+01 -1.41180095141270e-03 - 19 1.42840554431827e+01 -1.41180095141270e-03 - 20 1.42836137141448e+01 -4.81601991180831e-03 - 21 1.42824534007361e+01 -4.81601991180831e-03 - 22 1.42809048150996e+01 -4.81601991180831e-03 - 23 1.42792649819969e+01 -4.81601991180831e-03 - 24 1.42777803318197e+01 -4.81601991180831e-03 - 25 1.42752531196685e+01 -4.81601991180831e-03 - 26 1.42721001284968e+01 -4.81601991180831e-03 - 27 1.42684964153165e+01 -4.81601991180831e-03 - 28 1.42647910498589e+01 -4.81601991180831e-03 - 29 1.42606805882796e+01 -4.81601991180831e-03 - 30 1.42569926418712e+01 -5.52810721041820e-03 - 31 1.42531586691654e+01 -5.52810721041820e-03 - 32 1.42495999936203e+01 -5.52810721041820e-03 - 33 1.42462931131815e+01 -5.52810721041820e-03 - 34 1.42426029444897e+01 -5.52810721041820e-03 - 35 1.42381298876351e+01 -5.52810721041820e-03 - 36 1.42340878762643e+01 -5.52810721041820e-03 - 37 1.42306974076639e+01 -5.52810721041820e-03 - 38 1.42272038095427e+01 -5.52810721041820e-03 - 39 1.42243354346624e+01 -5.52810721041820e-03 - 40 1.42218646488258e+01 -2.67379447755370e-03 - 41 1.42190777080442e+01 -2.67379447755370e-03 - 42 1.42160211305982e+01 -2.67379447755370e-03 - 43 1.42124278516958e+01 -2.67379447755370e-03 - 44 1.42090572663500e+01 -2.67379447755370e-03 - 45 1.42058271942412e+01 -2.67379447755370e-03 - 46 1.42033823267883e+01 -2.67379447755370e-03 - 47 1.42003268233193e+01 -2.67379447755370e-03 - 48 1.41976446234730e+01 -2.67379447755370e-03 - 49 1.41956578978518e+01 -2.67379447755370e-03 - 50 1.41941111013648e+01 2.92915634676080e-03 - 51 1.41926279967057e+01 2.92915634676080e-03 - 52 1.41926027097164e+01 2.92915634676080e-03 - 53 1.41928452089335e+01 2.92915634676080e-03 - 54 1.41932447297817e+01 2.92915634676080e-03 - 55 1.41940166346614e+01 2.92915634676080e-03 - 56 1.41951734104514e+01 2.92915634676080e-03 - 57 1.41967411071552e+01 2.92915634676080e-03 - 58 1.41989912333566e+01 2.92915634676080e-03 - 59 1.42012327627117e+01 2.92915634676080e-03 - 60 1.42036332173818e+01 7.60060814309682e-03 - 61 1.42058762807719e+01 7.60060814309682e-03 - 62 1.42077667923895e+01 7.60060814309682e-03 - 63 1.42098444758797e+01 7.60060814309682e-03 - 64 1.42116396739042e+01 7.60060814309682e-03 - 65 1.42136940032780e+01 7.60060814309682e-03 - 66 1.42154217558442e+01 7.60060814309682e-03 - 67 1.42168868960268e+01 7.60060814309682e-03 - 68 1.42178935094514e+01 7.60060814309682e-03 - 69 1.42184230283353e+01 7.60060814309682e-03 - 70 1.42187771926287e+01 1.07651861772312e-02 - 71 1.42193777496991e+01 1.07651861772312e-02 - 72 1.42195540781285e+01 1.07651861772312e-02 - 73 1.42196083093533e+01 1.07651861772312e-02 - 74 1.42197149208802e+01 1.07651861772312e-02 - 75 1.42202788377849e+01 1.07651861772312e-02 - 76 1.42213115704096e+01 1.07651861772312e-02 - 77 1.42222264813178e+01 1.07651861772312e-02 - 78 1.42228883735255e+01 1.07651861772312e-02 - 79 1.42232741606514e+01 1.07651861772312e-02 - 80 1.42237439356851e+01 1.34302335321981e-02 - 81 1.42241333540472e+01 1.34302335321981e-02 - 82 1.42242035709694e+01 1.34302335321981e-02 - 83 1.42237365433589e+01 1.34302335321981e-02 - 84 1.42227422616147e+01 1.34302335321981e-02 - 85 1.42207685331590e+01 1.34302335321981e-02 - 86 1.42180863430945e+01 1.34302335321981e-02 - 87 1.42142852910421e+01 1.34302335321981e-02 - 88 1.42099549143853e+01 1.34302335321981e-02 - 89 1.42054325313174e+01 1.34302335321981e-02 - 90 1.42007097396387e+01 1.83891578232104e-02 - 91 1.41956149703609e+01 1.83891578232104e-02 - 92 1.41905358622917e+01 1.83891578232104e-02 - 93 1.41851130578922e+01 1.83891578232104e-02 - 94 1.41798559782159e+01 1.83891578232104e-02 - 95 1.41754225278760e+01 1.83891578232104e-02 - 96 1.41724186140355e+01 1.83891578232104e-02 - 97 1.41698989982796e+01 1.83891578232104e-02 - 98 1.41682594925708e+01 1.83891578232104e-02 - 99 1.41669592373547e+01 1.83891578232104e-02 - 100 1.41656974969458e+01 2.66708902934347e-02 + 3 1.42485380098361e+01 0.00000000000000e+00 + 4 1.42499968808366e+01 0.00000000000000e+00 + 5 1.42516048130998e+01 0.00000000000000e+00 + 6 1.42535349212370e+01 0.00000000000000e+00 + 7 1.42555542781187e+01 0.00000000000000e+00 + 8 1.42579210999843e+01 0.00000000000000e+00 + 9 1.42607955979387e+01 0.00000000000000e+00 + 10 1.42638739176632e+01 -1.41180095190593e-03 + 11 1.42668375588418e+01 -1.41180095190593e-03 + 12 1.42696059392705e+01 -1.41180095190593e-03 + 13 1.42727236830780e+01 -1.41180095190593e-03 + 14 1.42758764946774e+01 -1.41180095190593e-03 + 15 1.42787429047858e+01 -1.41180095190593e-03 + 16 1.42810489912851e+01 -1.41180095190593e-03 + 17 1.42825584062184e+01 -1.41180095190593e-03 + 18 1.42834947131793e+01 -1.41180095190593e-03 + 19 1.42840554431998e+01 -1.41180095190593e-03 + 20 1.42836137141615e+01 -4.81601991397794e-03 + 21 1.42824534007517e+01 -4.81601991397794e-03 + 22 1.42809048151132e+01 -4.81601991397794e-03 + 23 1.42792649820074e+01 -4.81601991397794e-03 + 24 1.42777803318261e+01 -4.81601991397794e-03 + 25 1.42752531196695e+01 -4.81601991397794e-03 + 26 1.42721001284912e+01 -4.81601991397794e-03 + 27 1.42684964153029e+01 -4.81601991397794e-03 + 28 1.42647910498358e+01 -4.81601991397794e-03 + 29 1.42606805882456e+01 -4.81601991397794e-03 + 30 1.42569926418246e+01 -5.52810720784699e-03 + 31 1.42531586691047e+01 -5.52810720784699e-03 + 32 1.42495999935438e+01 -5.52810720784699e-03 + 33 1.42462931130875e+01 -5.52810720784699e-03 + 34 1.42426029443764e+01 -5.52810720784699e-03 + 35 1.42381298875008e+01 -5.52810720784699e-03 + 36 1.42340878761072e+01 -5.52810720784699e-03 + 37 1.42306974074822e+01 -5.52810720784699e-03 + 38 1.42272038093346e+01 -5.52810720784699e-03 + 39 1.42243354344263e+01 -5.52810720784699e-03 + 40 1.42218646485599e+01 -2.67379444822040e-03 + 41 1.42190777077468e+01 -2.67379444822040e-03 + 42 1.42160211302678e+01 -2.67379444822040e-03 + 43 1.42124278513310e+01 -2.67379444822040e-03 + 44 1.42090572659494e+01 -2.67379444822040e-03 + 45 1.42058271938036e+01 -2.67379444822040e-03 + 46 1.42033823263127e+01 -2.67379444822040e-03 + 47 1.42003268228049e+01 -2.67379444822040e-03 + 48 1.41976446229193e+01 -2.67379444822040e-03 + 49 1.41956578972582e+01 -2.67379444822040e-03 + 50 1.41941111007313e+01 2.92915643758184e-03 + 51 1.41926279960324e+01 2.92915643758184e-03 + 52 1.41926027090037e+01 2.92915643758184e-03 + 53 1.41928452081821e+01 2.92915643758184e-03 + 54 1.41932447289925e+01 2.92915643758184e-03 + 55 1.41940166338356e+01 2.92915643758184e-03 + 56 1.41951734095904e+01 2.92915643758184e-03 + 57 1.41967411062606e+01 2.92915643758184e-03 + 58 1.41989912324301e+01 2.92915643758184e-03 + 59 1.42012327617553e+01 2.92915643758184e-03 + 60 1.42036332163974e+01 7.60060833091658e-03 + 61 1.42058762797617e+01 7.60060833091658e-03 + 62 1.42077667913556e+01 7.60060833091658e-03 + 63 1.42098444748241e+01 7.60060833091658e-03 + 64 1.42116396728290e+01 7.60060833091658e-03 + 65 1.42136940021851e+01 7.60060833091658e-03 + 66 1.42154217547355e+01 7.60060833091658e-03 + 67 1.42168868949041e+01 7.60060833091658e-03 + 68 1.42178935083162e+01 7.60060833091658e-03 + 69 1.42184230271890e+01 7.60060833091658e-03 + 70 1.42187771914724e+01 1.07651864810836e-02 + 71 1.42193777485337e+01 1.07651864810836e-02 + 72 1.42195540769546e+01 1.07651864810836e-02 + 73 1.42196083081712e+01 1.07651864810836e-02 + 74 1.42197149196897e+01 1.07651864810836e-02 + 75 1.42202788365857e+01 1.07651864810836e-02 + 76 1.42213115692008e+01 1.07651864810836e-02 + 77 1.42222264800984e+01 1.07651864810836e-02 + 78 1.42228883722939e+01 1.07651864810836e-02 + 79 1.42232741594059e+01 1.07651864810836e-02 + 80 1.42237439344237e+01 1.34302339631847e-02 + 81 1.42241333527676e+01 1.34302339631847e-02 + 82 1.42242035696691e+01 1.34302339631847e-02 + 83 1.42237365420353e+01 1.34302339631847e-02 + 84 1.42227422602652e+01 1.34302339631847e-02 + 85 1.42207685317808e+01 1.34302339631847e-02 + 86 1.42180863416851e+01 1.34302339631847e-02 + 87 1.42142852895987e+01 1.34302339631847e-02 + 88 1.42099549129055e+01 1.34302339631847e-02 + 89 1.42054325297988e+01 1.34302339631847e-02 + 90 1.42007097380791e+01 1.83891584072187e-02 + 91 1.41956149687583e+01 1.83891584072187e-02 + 92 1.41905358606444e+01 1.83891584072187e-02 + 93 1.41851130561985e+01 1.83891584072187e-02 + 94 1.41798559764745e+01 1.83891584072187e-02 + 95 1.41754225260859e+01 1.83891584072187e-02 + 96 1.41724186121957e+01 1.83891584072187e-02 + 97 1.41698989963895e+01 1.83891584072187e-02 + 98 1.41682594906300e+01 1.83891584072187e-02 + 99 1.41669592353631e+01 1.83891584072187e-02 + 100 1.41656974949034e+01 2.66708910635591e-02 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf index b2d0a8859..8e7f46287 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 9.90603521389808e-02 - 7.50000000000000e-01 9.90603521389808e-02 - 1.25000000000000e+00 9.90603521389808e-02 - 1.75000000000000e+00 9.90603521389808e-02 - 2.25000000000000e+00 9.90603521389808e-02 - 2.75000000000000e+00 9.90603521389808e-02 - 3.25000000000000e+00 9.90603521389808e-02 - 3.75000000000000e+00 9.90603521389808e-02 - 4.25000000000000e+00 9.90603521389808e-02 - 4.75000000000000e+00 9.90603521389808e-02 - 5.25000000000000e+00 9.90603521389808e-02 - 5.75000000000000e+00 9.90603521389808e-02 - 6.25000000000000e+00 9.90603521389808e-02 - 6.75000000000000e+00 9.90603521389808e-02 - 7.25000000000000e+00 9.90603521389808e-02 - 7.75000000000000e+00 9.90603521389808e-02 - 8.25000000000000e+00 9.90603521389808e-02 - 8.75000000000000e+00 9.90603521389808e-02 - 9.25000000000000e+00 9.90603521389808e-02 - 9.75000000000000e+00 9.90603521389808e-02 - 1.02500000000000e+01 9.90603521389808e-02 - 1.07500000000000e+01 9.90603521389808e-02 - 1.12500000000000e+01 9.90603521389808e-02 - 1.17500000000000e+01 9.90603521389808e-02 - 1.22500000000000e+01 9.90603521389808e-02 - 1.27500000000000e+01 9.90588181061136e-02 - 1.32500000000000e+01 9.82171168620079e-02 - 1.37500000000000e+01 6.68675769875805e-02 + 2.50000000000000e-01 9.90603520983742e-02 + 7.50000000000000e-01 9.90603520983742e-02 + 1.25000000000000e+00 9.90603520983742e-02 + 1.75000000000000e+00 9.90603520983742e-02 + 2.25000000000000e+00 9.90603520983742e-02 + 2.75000000000000e+00 9.90603520983742e-02 + 3.25000000000000e+00 9.90603520983742e-02 + 3.75000000000000e+00 9.90603520983742e-02 + 4.25000000000000e+00 9.90603520983742e-02 + 4.75000000000000e+00 9.90603520983742e-02 + 5.25000000000000e+00 9.90603520983742e-02 + 5.75000000000000e+00 9.90603520983742e-02 + 6.25000000000000e+00 9.90603520983742e-02 + 6.75000000000000e+00 9.90603520983742e-02 + 7.25000000000000e+00 9.90603520983742e-02 + 7.75000000000000e+00 9.90603520983742e-02 + 8.25000000000000e+00 9.90603520983742e-02 + 8.75000000000000e+00 9.90603520983742e-02 + 9.25000000000000e+00 9.90603520983742e-02 + 9.75000000000000e+00 9.90603520983742e-02 + 1.02500000000000e+01 9.90603520983742e-02 + 1.07500000000000e+01 9.90603520983742e-02 + 1.12500000000000e+01 9.90603520983742e-02 + 1.17500000000000e+01 9.90603520983742e-02 + 1.22500000000000e+01 9.90603520983742e-02 + 1.27500000000000e+01 9.90588180654791e-02 + 1.32500000000000e+01 9.82171168134545e-02 + 1.37500000000000e+01 6.68675768173003e-02 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 7.44570102130396e-02 - 1.52500000000000e+01 9.85667622630896e-02 - 1.57500000000000e+01 9.90599290861925e-02 - 1.62500000000000e+01 9.90603521389808e-02 - 1.67500000000000e+01 9.90603521389808e-02 - 1.72500000000000e+01 9.90603521389808e-02 - 1.77500000000000e+01 9.90603521389808e-02 - 1.82500000000000e+01 9.90603521389808e-02 - 1.87500000000000e+01 9.90603521389808e-02 - 1.92500000000000e+01 9.90603521389808e-02 - 1.97500000000000e+01 9.90603521389808e-02 - 2.02500000000000e+01 9.90603521389808e-02 - 2.07500000000000e+01 9.90603521389808e-02 - 2.12500000000000e+01 9.90603521389808e-02 - 2.17500000000000e+01 9.90603521389808e-02 - 2.22500000000000e+01 9.90603521389808e-02 - 2.27500000000000e+01 9.90603521389808e-02 - 2.32500000000000e+01 9.90603521389808e-02 - 2.37500000000000e+01 9.90603521389808e-02 - 2.42500000000000e+01 9.90603521389808e-02 - 2.47500000000000e+01 9.90603521389808e-02 + 1.47500000000000e+01 7.44570102671401e-02 + 1.52500000000000e+01 9.85667622255897e-02 + 1.57500000000000e+01 9.90599290455859e-02 + 1.62500000000000e+01 9.90603520983742e-02 + 1.67500000000000e+01 9.90603520983742e-02 + 1.72500000000000e+01 9.90603520983742e-02 + 1.77500000000000e+01 9.90603520983742e-02 + 1.82500000000000e+01 9.90603520983742e-02 + 1.87500000000000e+01 9.90603520983742e-02 + 1.92500000000000e+01 9.90603520983742e-02 + 1.97500000000000e+01 9.90603520983742e-02 + 2.02500000000000e+01 9.90603520983742e-02 + 2.07500000000000e+01 9.90603520983742e-02 + 2.12500000000000e+01 9.90603520983742e-02 + 2.17500000000000e+01 9.90603520983742e-02 + 2.22500000000000e+01 9.90603520983742e-02 + 2.27500000000000e+01 9.90603520983742e-02 + 2.32500000000000e+01 9.90603520983742e-02 + 2.37500000000000e+01 9.90603520983742e-02 + 2.42500000000000e+01 9.90603520983742e-02 + 2.47500000000000e+01 9.90603520983742e-02 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state index f6e1b5a1e..f25418e7c 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state @@ -17,9 +17,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 5.90367888432614e-05 - 7.72360342049122e-03 7.98103713126329e-02 6.51481918280550e-02 - 4.20150496559186e-03 2.14098483126557e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 5.90367895903547e-05 + 7.72360347936990e-03 7.98103714989791e-02 6.51481916206231e-02 + 4.20150492815907e-03 2.14098479953629e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -42,9 +42,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 7.25346801924767e-04 - 5.56809955469972e-02 1.70182689379045e-01 -1.91812601541206e-01 - -3.36985920842485e-02 -2.80399679154532e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 7.25346810525990e-04 + 5.56809958916884e-02 1.70182688913198e-01 -1.91812601663509e-01 + -3.36985918329314e-02 -2.80399675255803e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out index c53fc7f3d..239d8d6d2 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep2.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -145,7 +143,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -159,7 +156,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -174,42 +170,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Multiple-walker metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep2r.colvars.state". colvars: The final output state file will be "test.rep2.colvars.state". +colvars: Opening trajectory file "test.rep2.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep2r.colvars.state". colvars: The final output state file will be "test.rep2.colvars.state". colvars: Metadynamics bias "metadynamics1": accessing replica "rep1". -colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". -colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". colvars: Restarting metadynamics bias "metadynamics1" from step number 100. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: Synchronizing (emptying the buffer of) trajectory file "test.rep2.colvars.traj". colvars: Saving collective variables state to "test.rep2.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped index a6354098b..22c1a118b 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 9.94700459880913e+00 + x 9.94700459588437e+00 } metadynamics { @@ -27,9 +27,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 5.90367888432614e-05 - 7.72360342049122e-03 7.98103713126329e-02 6.51481918280550e-02 - 4.20150496559186e-03 2.14098483126557e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 5.90367895903547e-05 + 7.72360347936990e-03 7.98103714989791e-02 6.51481916206231e-02 + 4.20150492815907e-03 2.14098479953629e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -52,9 +52,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 7.25346801924767e-04 - 5.56809955469972e-02 1.70182689379045e-01 -1.91812601541206e-01 - -3.36985920842485e-02 -2.80399679154532e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 7.25346810525990e-04 + 5.56809958916884e-02 1.70182688913198e-01 -1.91812601663509e-01 + -3.36985918329314e-02 -2.80399675255803e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj index 87c724e96..7ebb8134c 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj @@ -1,102 +1,102 @@ # step d fa_d 0 9.92876155419194e+00 0.00000000000000e+00 - 1 9.92863721108117e+00 0.00000000000000e+00 - 2 9.92825734340718e+00 0.00000000000000e+00 - 3 9.92755127525950e+00 0.00000000000000e+00 - 4 9.92667471909311e+00 0.00000000000000e+00 - 5 9.92575034311276e+00 0.00000000000000e+00 - 6 9.92495620963959e+00 0.00000000000000e+00 - 7 9.92461789359752e+00 0.00000000000000e+00 - 8 9.92536305405157e+00 0.00000000000000e+00 - 9 9.92598579851022e+00 0.00000000000000e+00 - 10 9.92698489552914e+00 -1.53692716384904e-02 - 11 9.92813713186745e+00 -1.53692716384904e-02 - 12 9.92958955154718e+00 -1.53692716384904e-02 - 13 9.93146245533469e+00 -1.53692716384904e-02 - 14 9.93387956305109e+00 -1.53692716384904e-02 - 15 9.93625622414012e+00 -1.53692716384904e-02 - 16 9.93875399313412e+00 -1.53692716384904e-02 - 17 9.94136244546042e+00 -1.53692716384904e-02 - 18 9.94440242008114e+00 -1.53692716384904e-02 - 19 9.94723046489032e+00 -1.53692716384904e-02 - 20 9.95024031483397e+00 -3.19982334686605e-02 - 21 9.95290175147503e+00 -3.19982334686605e-02 - 22 9.95500360291990e+00 -3.19982334686605e-02 - 23 9.95625077342743e+00 -3.19982334686605e-02 - 24 9.95679355590983e+00 -3.19982334686605e-02 - 25 9.95732344685766e+00 -3.19982334686605e-02 - 26 9.95731470350271e+00 -3.19982334686605e-02 - 27 9.95681072299199e+00 -3.19982334686605e-02 - 28 9.95602536365077e+00 -3.19982334686605e-02 - 29 9.95531430839414e+00 -3.19982334686605e-02 - 30 9.95424975105506e+00 -4.88206365730334e-02 - 31 9.95332421152467e+00 -4.88206365730334e-02 - 32 9.95229914723985e+00 -4.88206365730334e-02 - 33 9.95131483147978e+00 -4.88206365730334e-02 - 34 9.95060259370787e+00 -4.88206365730334e-02 - 35 9.94987218183758e+00 -4.88206365730334e-02 - 36 9.94977154513057e+00 -4.88206365730334e-02 - 37 9.95025457677085e+00 -4.88206365730334e-02 - 38 9.95141923918344e+00 -4.88206365730334e-02 - 39 9.95216006978580e+00 -4.88206365730334e-02 - 40 9.95360310850276e+00 -6.56123202550344e-02 - 41 9.95547794209557e+00 -6.56123202550344e-02 - 42 9.95752449941017e+00 -6.56123202550344e-02 - 43 9.95986469077451e+00 -6.56123202550344e-02 - 44 9.96229115270165e+00 -6.56123202550344e-02 - 45 9.96422304181782e+00 -6.56123202550344e-02 - 46 9.96619104731396e+00 -6.56123202550344e-02 - 47 9.96771829749829e+00 -6.56123202550344e-02 - 48 9.96865300857455e+00 -6.56123202550344e-02 - 49 9.96983842022116e+00 -6.56123202550344e-02 - 50 9.97072851638560e+00 -8.31549680361093e-02 - 51 9.97176839583889e+00 -8.31549680361093e-02 - 52 9.97294474948930e+00 -8.31549680361093e-02 - 53 9.97393162178829e+00 -8.31549680361093e-02 - 54 9.97422213976697e+00 -8.31549680361093e-02 - 55 9.97427923345291e+00 -8.31549680361093e-02 - 56 9.97509912850479e+00 -8.31549680361093e-02 - 57 9.97598939132573e+00 -8.31549680361093e-02 - 58 9.97736094478977e+00 -8.31549680361093e-02 - 59 9.97908316200223e+00 -8.31549680361093e-02 - 60 9.98144866321475e+00 -1.01101051065911e-01 - 61 9.98418248507440e+00 -1.01101051065911e-01 - 62 9.98724279063945e+00 -1.01101051065911e-01 - 63 9.98983902620720e+00 -1.01101051065911e-01 - 64 9.99205502549511e+00 -1.01101051065911e-01 - 65 9.99396375834268e+00 -1.01101051065911e-01 - 66 9.99521991233981e+00 -1.01101051065911e-01 - 67 9.99552925406132e+00 -1.01101051065911e-01 - 68 9.99539402401249e+00 -1.01101051065911e-01 - 69 9.99477561290164e+00 -1.01101051065911e-01 - 70 9.99375663938557e+00 -1.19446772057086e-01 - 71 9.99241934438575e+00 -1.19446772057086e-01 - 72 9.99028414356615e+00 -1.19446772057086e-01 - 73 9.98782436656130e+00 -1.19446772057086e-01 - 74 9.98501318847694e+00 -1.19446772057086e-01 - 75 9.98166896908869e+00 -1.19446772057086e-01 - 76 9.97818649901180e+00 -1.19446772057086e-01 - 77 9.97405361956510e+00 -1.19446772057086e-01 - 78 9.97043749036436e+00 -1.19446772057086e-01 - 79 9.96680015701972e+00 -1.19446772057086e-01 - 80 9.96387279717675e+00 -1.36704453464043e-01 - 81 9.96115537712523e+00 -1.36704453464043e-01 - 82 9.95917142515307e+00 -1.36704453464043e-01 - 83 9.95805513531301e+00 -1.36704453464043e-01 - 84 9.95728144936743e+00 -1.36704453464043e-01 - 85 9.95684688548056e+00 -1.36704453464043e-01 - 86 9.95695270593551e+00 -1.36704453464043e-01 - 87 9.95764400234754e+00 -1.36704453464043e-01 - 88 9.95799943403282e+00 -1.36704453464043e-01 - 89 9.95808582547394e+00 -1.36704453464043e-01 - 90 9.95829827009459e+00 -1.53714986499153e-01 - 91 9.95900434623497e+00 -1.53714986499153e-01 - 92 9.95935452195446e+00 -1.53714986499153e-01 - 93 9.95926444820010e+00 -1.53714986499153e-01 - 94 9.95895383355610e+00 -1.53714986499153e-01 - 95 9.95787595556106e+00 -1.53714986499153e-01 - 96 9.95651093462575e+00 -1.53714986499153e-01 - 97 9.95450882105866e+00 -1.53714986499153e-01 - 98 9.95215317348883e+00 -1.53714986499153e-01 - 99 9.94953653719804e+00 -1.53714986499153e-01 - 100 9.94700459880913e+00 -1.70182689379045e-01 + 1 9.92863721108118e+00 0.00000000000000e+00 + 2 9.92825734340721e+00 0.00000000000000e+00 + 3 9.92755127525955e+00 0.00000000000000e+00 + 4 9.92667471909320e+00 0.00000000000000e+00 + 5 9.92575034311287e+00 0.00000000000000e+00 + 6 9.92495620963971e+00 0.00000000000000e+00 + 7 9.92461789359763e+00 0.00000000000000e+00 + 8 9.92536305405160e+00 0.00000000000000e+00 + 9 9.92598579851009e+00 0.00000000000000e+00 + 10 9.92698489552874e+00 -1.53692716384669e-02 + 11 9.92813713186662e+00 -1.53692716384669e-02 + 12 9.92958955154570e+00 -1.53692716384669e-02 + 13 9.93146245533227e+00 -1.53692716384669e-02 + 14 9.93387956304736e+00 -1.53692716384669e-02 + 15 9.93625622413464e+00 -1.53692716384669e-02 + 16 9.93875399312634e+00 -1.53692716384669e-02 + 17 9.94136244544969e+00 -1.53692716384669e-02 + 18 9.94440242006668e+00 -1.53692716384669e-02 + 19 9.94723046487128e+00 -1.53692716384669e-02 + 20 9.95024031480938e+00 -3.19982334674286e-02 + 21 9.95290175144380e+00 -3.19982334674286e-02 + 22 9.95500360288087e+00 -3.19982334674286e-02 + 23 9.95625077337936e+00 -3.19982334674286e-02 + 24 9.95679355585141e+00 -3.19982334674286e-02 + 25 9.95732344678751e+00 -3.19982334674286e-02 + 26 9.95731470341938e+00 -3.19982334674286e-02 + 27 9.95681072289397e+00 -3.19982334674286e-02 + 28 9.95602536353651e+00 -3.19982334674286e-02 + 29 9.95531430826202e+00 -3.19982334674286e-02 + 30 9.95424975090340e+00 -4.88206365646183e-02 + 31 9.95332421135175e+00 -4.88206365646183e-02 + 32 9.95229914704390e+00 -4.88206365646183e-02 + 33 9.95131483125902e+00 -4.88206365646183e-02 + 34 9.95060259346046e+00 -4.88206365646183e-02 + 35 9.94987218156172e+00 -4.88206365646183e-02 + 36 9.94977154482446e+00 -4.88206365646183e-02 + 37 9.95025457643273e+00 -4.88206365646183e-02 + 38 9.95141923881165e+00 -4.88206365646183e-02 + 39 9.95216006937876e+00 -4.88206365646183e-02 + 40 9.95360310805905e+00 -6.56123202254770e-02 + 41 9.95547794161392e+00 -6.56123202254770e-02 + 42 9.95752449888952e+00 -6.56123202254770e-02 + 43 9.95986469021403e+00 -6.56123202254770e-02 + 44 9.96229115210074e+00 -6.56123202254770e-02 + 45 9.96422304117613e+00 -6.56123202254770e-02 + 46 9.96619104663140e+00 -6.56123202254770e-02 + 47 9.96771829677501e+00 -6.56123202254770e-02 + 48 9.96865300781088e+00 -6.56123202254770e-02 + 49 9.96983841941765e+00 -6.56123202254770e-02 + 50 9.97072851554298e+00 -8.31549679728180e-02 + 51 9.97176839495805e+00 -8.31549679728180e-02 + 52 9.97294474857124e+00 -8.31549679728180e-02 + 53 9.97393162083410e+00 -8.31549679728180e-02 + 54 9.97422213877777e+00 -8.31549679728180e-02 + 55 9.97427923242988e+00 -8.31549679728180e-02 + 56 9.97509912744913e+00 -8.31549679728180e-02 + 57 9.97598939023862e+00 -8.31549679728180e-02 + 58 9.97736094367233e+00 -8.31549679728180e-02 + 59 9.97908316085552e+00 -8.31549679728180e-02 + 60 9.98144866203979e+00 -1.01101050961226e-01 + 61 9.98418248387209e+00 -1.01101050961226e-01 + 62 9.98724278941060e+00 -1.01101050961226e-01 + 63 9.98983902495251e+00 -1.01101050961226e-01 + 64 9.99205502421520e+00 -1.01101050961226e-01 + 65 9.99396375703816e+00 -1.01101050961226e-01 + 66 9.99521991101117e+00 -1.01101050961226e-01 + 67 9.99552925270898e+00 -1.01101050961226e-01 + 68 9.99539402263682e+00 -1.01101050961226e-01 + 69 9.99477561150299e+00 -1.01101050961226e-01 + 70 9.99375663796423e+00 -1.19446771910169e-01 + 71 9.99241934294185e+00 -1.19446771910169e-01 + 72 9.99028414209973e+00 -1.19446771910169e-01 + 73 9.98782436507227e+00 -1.19446771910169e-01 + 74 9.98501318696502e+00 -1.19446771910169e-01 + 75 9.98166896755343e+00 -1.19446771910169e-01 + 76 9.97818649745244e+00 -1.19446771910169e-01 + 77 9.97405361798055e+00 -1.19446771910169e-01 + 78 9.97043748875320e+00 -1.19446771910169e-01 + 79 9.96680015538000e+00 -1.19446771910169e-01 + 80 9.96387279550620e+00 -1.36704453245133e-01 + 81 9.96115537542108e+00 -1.36704453245133e-01 + 82 9.95917142341217e+00 -1.36704453245133e-01 + 83 9.95805513353189e+00 -1.36704453245133e-01 + 84 9.95728144754225e+00 -1.36704453245133e-01 + 85 9.95684688360727e+00 -1.36704453245133e-01 + 86 9.95695270400995e+00 -1.36704453245133e-01 + 87 9.95764400036554e+00 -1.36704453245133e-01 + 88 9.95799943199032e+00 -1.36704453245133e-01 + 89 9.95808582336709e+00 -1.36704453245133e-01 + 90 9.95829826791995e+00 -1.53714986181138e-01 + 91 9.95900434398949e+00 -1.53714986181138e-01 + 92 9.95935451963563e+00 -1.53714986181138e-01 + 93 9.95926444580604e+00 -1.53714986181138e-01 + 94 9.95895383108549e+00 -1.53714986181138e-01 + 95 9.95787595301329e+00 -1.53714986181138e-01 + 96 9.95651093200075e+00 -1.53714986181138e-01 + 97 9.95450881835695e+00 -1.53714986181138e-01 + 98 9.95215317071137e+00 -1.53714986181138e-01 + 99 9.94953653434610e+00 -1.53714986181138e-01 + 100 9.94700459588437e+00 -1.70182688913198e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf index 2f5afd073..5f62fc1ee 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 9.90603521389808e-02 - 7.50000000000000e-01 9.90603521389808e-02 - 1.25000000000000e+00 9.90603521389808e-02 - 1.75000000000000e+00 9.90603521389808e-02 - 2.25000000000000e+00 9.90603521389808e-02 - 2.75000000000000e+00 9.90603521389808e-02 - 3.25000000000000e+00 9.90603521389808e-02 - 3.75000000000000e+00 9.90603521389808e-02 - 4.25000000000000e+00 9.90603521389808e-02 - 4.75000000000000e+00 9.90603521389808e-02 - 5.25000000000000e+00 9.90603521389808e-02 - 5.75000000000000e+00 9.90603521389808e-02 - 6.25000000000000e+00 9.90603521389808e-02 - 6.75000000000000e+00 9.90603521389808e-02 - 7.25000000000000e+00 9.90603521389808e-02 - 7.75000000000000e+00 9.90603521389808e-02 - 8.25000000000000e+00 9.90603521389808e-02 - 8.75000000000000e+00 9.90013153501375e-02 - 9.25000000000000e+00 9.13367487184896e-02 - 9.75000000000000e+00 1.92499808263479e-02 - 1.02500000000000e+01 3.39121603109258e-02 - 1.07500000000000e+01 9.48588471733889e-02 - 1.12500000000000e+01 9.90389422906681e-02 - 1.17500000000000e+01 9.90603521389808e-02 - 1.22500000000000e+01 9.90603521389808e-02 - 1.27500000000000e+01 9.90588181061136e-02 - 1.32500000000000e+01 9.82171168620079e-02 - 1.37500000000000e+01 6.68675769875806e-02 + 2.50000000000000e-01 9.90603520983742e-02 + 7.50000000000000e-01 9.90603520983742e-02 + 1.25000000000000e+00 9.90603520983742e-02 + 1.75000000000000e+00 9.90603520983742e-02 + 2.25000000000000e+00 9.90603520983742e-02 + 2.75000000000000e+00 9.90603520983742e-02 + 3.25000000000000e+00 9.90603520983742e-02 + 3.75000000000000e+00 9.90603520983742e-02 + 4.25000000000000e+00 9.90603520983742e-02 + 4.75000000000000e+00 9.90603520983742e-02 + 5.25000000000000e+00 9.90603520983742e-02 + 5.75000000000000e+00 9.90603520983742e-02 + 6.25000000000000e+00 9.90603520983742e-02 + 6.75000000000000e+00 9.90603520983742e-02 + 7.25000000000000e+00 9.90603520983742e-02 + 7.75000000000000e+00 9.90603520983742e-02 + 8.25000000000000e+00 9.90603520983742e-02 + 8.75000000000000e+00 9.90013153087839e-02 + 9.25000000000000e+00 9.13367486190043e-02 + 9.75000000000000e+00 1.92499805993951e-02 + 1.02500000000000e+01 3.39121604777511e-02 + 1.07500000000000e+01 9.48588471702151e-02 + 1.12500000000000e+01 9.90389422503788e-02 + 1.17500000000000e+01 9.90603520983742e-02 + 1.22500000000000e+01 9.90603520983742e-02 + 1.27500000000000e+01 9.90588180654791e-02 + 1.32500000000000e+01 9.82171168134545e-02 + 1.37500000000000e+01 6.68675768173003e-02 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 7.44570102130397e-02 - 1.52500000000000e+01 9.85667622630896e-02 - 1.57500000000000e+01 9.90599290861925e-02 - 1.62500000000000e+01 9.90603521389808e-02 - 1.67500000000000e+01 9.90603521389808e-02 - 1.72500000000000e+01 9.90603521389808e-02 - 1.77500000000000e+01 9.90603521389808e-02 - 1.82500000000000e+01 9.90603521389808e-02 - 1.87500000000000e+01 9.90603521389808e-02 - 1.92500000000000e+01 9.90603521389808e-02 - 1.97500000000000e+01 9.90603521389808e-02 - 2.02500000000000e+01 9.90603521389808e-02 - 2.07500000000000e+01 9.90603521389808e-02 - 2.12500000000000e+01 9.90603521389808e-02 - 2.17500000000000e+01 9.90603521389808e-02 - 2.22500000000000e+01 9.90603521389808e-02 - 2.27500000000000e+01 9.90603521389808e-02 - 2.32500000000000e+01 9.90603521389808e-02 - 2.37500000000000e+01 9.90603521389808e-02 - 2.42500000000000e+01 9.90603521389808e-02 - 2.47500000000000e+01 9.90603521389808e-02 + 1.47500000000000e+01 7.44570102671402e-02 + 1.52500000000000e+01 9.85667622255897e-02 + 1.57500000000000e+01 9.90599290455859e-02 + 1.62500000000000e+01 9.90603520983742e-02 + 1.67500000000000e+01 9.90603520983742e-02 + 1.72500000000000e+01 9.90603520983742e-02 + 1.77500000000000e+01 9.90603520983742e-02 + 1.82500000000000e+01 9.90603520983742e-02 + 1.87500000000000e+01 9.90603520983742e-02 + 1.92500000000000e+01 9.90603520983742e-02 + 1.97500000000000e+01 9.90603520983742e-02 + 2.02500000000000e+01 9.90603520983742e-02 + 2.07500000000000e+01 9.90603520983742e-02 + 2.12500000000000e+01 9.90603520983742e-02 + 2.17500000000000e+01 9.90603520983742e-02 + 2.22500000000000e+01 9.90603520983742e-02 + 2.27500000000000e+01 9.90603520983742e-02 + 2.32500000000000e+01 9.90603520983742e-02 + 2.37500000000000e+01 9.90603520983742e-02 + 2.42500000000000e+01 9.90603520983742e-02 + 2.47500000000000e+01 9.90603520983742e-02 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state index 0f90b9de5..30662bcfc 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state @@ -20,9 +20,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.25323465171985e-05 3.48877739229281e-03 - 8.48743669974108e-02 1.87767103667070e-01 3.74493273101570e-02 - 6.54251825834146e-04 4.23052788302019e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.25323473186721e-05 3.48877751270849e-03 + 8.48743679843641e-02 1.87767102998601e-01 3.74493268741002e-02 + 6.54251815918406e-04 4.23052788272303e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -45,9 +45,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.70780739637743e-04 3.06678366244801e-02 - 3.38095245919524e-01 -1.52211785481214e-01 -2.11534386688208e-01 - -6.90290108238559e-03 -6.37695701865853e-06 0.00000000000000e+00 + 0.00000000000000e+00 1.70780749827028e-04 3.06678375007270e-02 + 3.38095246589823e-01 -1.52211789178683e-01 -2.11534384625674e-01 + -6.90290098044747e-03 -6.37695701821339e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out index 051450ff0..2c9517acb 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep1.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -145,7 +143,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -159,7 +156,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -174,49 +170,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Multiple-walker metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.rep1.colvars.state". +colvars: Restarting from file "test.rep1.colvars.state". colvars: Restarting collective variable "d" from value: 14.1657 colvars: Restarting metadynamics bias "metadynamics1" from step number 100. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: Restarting harmonicwalls bias "dw" from step number 100. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testres.rep1r.colvars.state". colvars: The final output state file will be "testres.rep1.colvars.state". +colvars: Opening trajectory file "testres.rep1.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "testres.rep1r.colvars.state". colvars: The final output state file will be "testres.rep1.colvars.state". colvars: Metadynamics bias "metadynamics1": accessing replica "rep2". -colvars: Metadynamics bias "metadynamics1": replica "rep2" has supplied a new state file, "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". -colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep2" from file "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". +colvars: Metadynamics bias "metadynamics1": replica "rep2" has supplied a new state file, "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". +colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep2" from file "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". colvars: Restarting metadynamics bias "metadynamics1" from step number 100. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: Saving collective variables state to "testres.rep1.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped index 3af8b69d2..19d64ce2c 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 1.40671697483701e+01 + x 1.40671697413825e+01 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.25323465171985e-05 3.48877739229281e-03 - 8.48743669974108e-02 1.87767103667070e-01 3.74493273101570e-02 - 6.54251825834146e-04 4.23052788302019e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.25323473186721e-05 3.48877751270849e-03 + 8.48743679843641e-02 1.87767102998601e-01 3.74493268741002e-02 + 6.54251815918406e-04 4.23052788272303e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -55,9 +55,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.70780739637743e-04 3.06678366244801e-02 - 3.38095245919524e-01 -1.52211785481214e-01 -2.11534386688208e-01 - -6.90290108238559e-03 -6.37695701865853e-06 0.00000000000000e+00 + 0.00000000000000e+00 1.70780749827028e-04 3.06678375007270e-02 + 3.38095246589823e-01 -1.52211789178683e-01 -2.11534384625674e-01 + -6.90290098044747e-03 -6.37695701821339e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj index ba8e3a579..62aa833b8 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj @@ -1,102 +1,102 @@ # step d fa_d - 100 1.41656974969458e+01 2.66708902934347e-02 - 101 1.41645168177934e+01 2.66708902934347e-02 - 102 1.41639313723197e+01 2.66708902934347e-02 - 103 1.41639423493949e+01 2.66708902934347e-02 - 104 1.41647561707625e+01 2.66708902934347e-02 - 105 1.41658632142319e+01 2.66708902934347e-02 - 106 1.41673787387882e+01 2.66708902934347e-02 - 107 1.41690285541915e+01 2.66708902934347e-02 - 108 1.41710437199635e+01 2.66708902934347e-02 - 109 1.41735809954887e+01 2.66708902934347e-02 - 110 1.41763514579746e+01 3.39682706157757e-02 - 111 1.41790650979264e+01 3.39682706157757e-02 - 112 1.41816844532206e+01 3.39682706157757e-02 - 113 1.41848030101558e+01 3.39682706157757e-02 - 114 1.41881572686952e+01 3.39682706157757e-02 - 115 1.41914710994669e+01 3.39682706157757e-02 - 116 1.41945076521072e+01 3.39682706157757e-02 - 117 1.41970530487971e+01 3.39682706157757e-02 - 118 1.41993348384181e+01 3.39682706157757e-02 - 119 1.42015324362938e+01 3.39682706157757e-02 - 120 1.42029799155388e+01 3.87040708124342e-02 - 121 1.42039018573139e+01 3.87040708124342e-02 - 122 1.42045497524016e+01 3.87040708124342e-02 - 123 1.42051279143509e+01 3.87040708124342e-02 - 124 1.42057799825133e+01 3.87040708124342e-02 - 125 1.42052035543398e+01 3.87040708124342e-02 - 126 1.42037125406107e+01 3.87040708124342e-02 - 127 1.42013876753793e+01 3.87040708124342e-02 - 128 1.41985000504608e+01 3.87040708124342e-02 - 129 1.41946867955086e+01 3.87040708124342e-02 - 130 1.41907407040072e+01 4.46331785411240e-02 - 131 1.41860814711741e+01 4.46331785411240e-02 - 132 1.41811502776628e+01 4.46331785411240e-02 - 133 1.41759651349297e+01 4.46331785411240e-02 - 134 1.41699530857131e+01 4.46331785411240e-02 - 135 1.41627941484716e+01 4.46331785411240e-02 - 136 1.41557931733251e+01 4.46331785411240e-02 - 137 1.41492699069035e+01 4.46331785411240e-02 - 138 1.41425596947339e+01 4.46331785411240e-02 - 139 1.41364771205764e+01 4.46331785411240e-02 - 140 1.41308683076945e+01 5.59216758917605e-02 - 141 1.41250693714429e+01 5.59216758917605e-02 - 142 1.41191585710561e+01 5.59216758917605e-02 - 143 1.41128806964629e+01 5.59216758917605e-02 - 144 1.41069776769885e+01 5.59216758917605e-02 - 145 1.41013330433959e+01 5.59216758917605e-02 - 146 1.40965351247715e+01 5.59216758917605e-02 - 147 1.40911236046535e+01 5.59216758917605e-02 - 148 1.40860174228665e+01 5.59216758917605e-02 - 149 1.40814707023824e+01 5.59216758917605e-02 - 150 1.40771721143455e+01 7.10415197980919e-02 - 151 1.40727022571165e+01 7.10415197980919e-02 - 152 1.40694284519236e+01 7.10415197980919e-02 - 153 1.40661582239069e+01 7.10415197980919e-02 - 154 1.40627979791840e+01 7.10415197980919e-02 - 155 1.40596112342542e+01 7.10415197980919e-02 - 156 1.40566695308391e+01 7.10415197980919e-02 - 157 1.40540744563696e+01 7.10415197980919e-02 - 158 1.40521880941470e+01 7.10415197980919e-02 - 159 1.40504169101966e+01 7.10415197980919e-02 - 160 1.40490177872330e+01 8.77068087997524e-02 - 161 1.40477627185972e+01 8.77068087997524e-02 - 162 1.40465343759200e+01 8.77068087997524e-02 - 163 1.40459238443624e+01 8.77068087997524e-02 - 164 1.40454989023081e+01 8.77068087997524e-02 - 165 1.40458141277865e+01 8.77068087997524e-02 - 166 1.40462783872865e+01 8.77068087997524e-02 - 167 1.40469230273499e+01 8.77068087997524e-02 - 168 1.40475066692391e+01 8.77068087997524e-02 - 169 1.40479434669772e+01 8.77068087997524e-02 - 170 1.40484684779552e+01 1.04398839016414e-01 - 171 1.40494304130099e+01 1.04398839016414e-01 - 172 1.40500894456774e+01 1.04398839016414e-01 - 173 1.40506811271051e+01 1.04398839016414e-01 - 174 1.40513374594737e+01 1.04398839016414e-01 - 175 1.40524333189262e+01 1.04398839016414e-01 - 176 1.40539698807596e+01 1.04398839016414e-01 - 177 1.40553742441127e+01 1.04398839016414e-01 - 178 1.40565462753219e+01 1.04398839016414e-01 - 179 1.40575157791768e+01 1.04398839016414e-01 - 180 1.40587097821679e+01 1.20570595809343e-01 - 181 1.40600393183434e+01 1.20570595809343e-01 - 182 1.40613410361508e+01 1.20570595809343e-01 - 183 1.40624671262692e+01 1.20570595809343e-01 - 184 1.40634905316866e+01 1.20570595809343e-01 - 185 1.40640000721401e+01 1.20570595809343e-01 - 186 1.40642859325702e+01 1.20570595809343e-01 - 187 1.40639315897108e+01 1.20570595809343e-01 - 188 1.40634945893112e+01 1.20570595809343e-01 - 189 1.40632564819739e+01 1.20570595809343e-01 - 190 1.40631238625021e+01 1.36504067884959e-01 - 191 1.40628238911534e+01 1.36504067884959e-01 - 192 1.40626278632898e+01 1.36504067884959e-01 - 193 1.40620533099285e+01 1.36504067884959e-01 - 194 1.40614884998255e+01 1.36504067884959e-01 - 195 1.40614791769245e+01 1.36504067884959e-01 - 196 1.40625287964965e+01 1.36504067884959e-01 - 197 1.40636172394048e+01 1.36504067884959e-01 - 198 1.40650874989452e+01 1.36504067884959e-01 - 199 1.40663704991439e+01 1.36504067884959e-01 - 200 1.40671697483701e+01 1.52211785481214e-01 + 100 1.41656974949034e+01 2.66708910635591e-02 + 101 1.41645168157006e+01 2.66708910635591e-02 + 102 1.41639313701771e+01 2.66708910635591e-02 + 103 1.41639423472033e+01 2.66708910635591e-02 + 104 1.41647561685229e+01 2.66708910635591e-02 + 105 1.41658632119453e+01 2.66708910635591e-02 + 106 1.41673787364561e+01 2.66708910635591e-02 + 107 1.41690285518153e+01 2.66708910635591e-02 + 108 1.41710437175448e+01 2.66708910635591e-02 + 109 1.41735809930291e+01 2.66708910635591e-02 + 110 1.41763514554758e+01 3.39682716198089e-02 + 111 1.41790650953902e+01 3.39682716198089e-02 + 112 1.41816844506487e+01 3.39682716198089e-02 + 113 1.41848030075499e+01 3.39682716198089e-02 + 114 1.41881572660568e+01 3.39682716198089e-02 + 115 1.41914710967974e+01 3.39682716198089e-02 + 116 1.41945076494076e+01 3.39682716198089e-02 + 117 1.41970530460683e+01 3.39682716198089e-02 + 118 1.41993348356605e+01 3.39682716198089e-02 + 119 1.42015324335073e+01 3.39682716198089e-02 + 120 1.42029799127233e+01 3.87040720936605e-02 + 121 1.42039018544684e+01 3.87040720936605e-02 + 122 1.42045497495248e+01 3.87040720936605e-02 + 123 1.42051279114412e+01 3.87040720936605e-02 + 124 1.42057799795685e+01 3.87040720936605e-02 + 125 1.42052035513576e+01 3.87040720936605e-02 + 126 1.42037125375882e+01 3.87040720936605e-02 + 127 1.42013876723135e+01 3.87040720936605e-02 + 128 1.41985000473486e+01 3.87040720936605e-02 + 129 1.41946867923467e+01 3.87040720936605e-02 + 130 1.41907407007924e+01 4.46331801324967e-02 + 131 1.41860814679033e+01 4.46331801324967e-02 + 132 1.41811502743331e+01 4.46331801324967e-02 + 133 1.41759651315384e+01 4.46331801324967e-02 + 134 1.41699530822577e+01 4.46331801324967e-02 + 135 1.41627941449498e+01 4.46331801324967e-02 + 136 1.41557931697353e+01 4.46331801324967e-02 + 137 1.41492699032442e+01 4.46331801324967e-02 + 138 1.41425596910040e+01 4.46331801324967e-02 + 139 1.41364771167751e+01 4.46331801324967e-02 + 140 1.41308683038212e+01 5.59216777970916e-02 + 141 1.41250693674976e+01 5.59216777970916e-02 + 142 1.41191585670391e+01 5.59216777970916e-02 + 143 1.41128806923745e+01 5.59216777970916e-02 + 144 1.41069776728295e+01 5.59216777970916e-02 + 145 1.41013330391674e+01 5.59216777970916e-02 + 146 1.40965351204746e+01 5.59216777970916e-02 + 147 1.40911236002896e+01 5.59216777970916e-02 + 148 1.40860174184372e+01 5.59216777970916e-02 + 149 1.40814706978895e+01 5.59216777970916e-02 + 150 1.40771721097910e+01 7.10415219806404e-02 + 151 1.40727022525028e+01 7.10415219806404e-02 + 152 1.40694284472531e+01 7.10415219806404e-02 + 153 1.40661582191822e+01 7.10415219806404e-02 + 154 1.40627979744080e+01 7.10415219806404e-02 + 155 1.40596112294300e+01 7.10415219806404e-02 + 156 1.40566695259700e+01 7.10415219806404e-02 + 157 1.40540744514590e+01 7.10415219806404e-02 + 158 1.40521880891984e+01 7.10415219806404e-02 + 159 1.40504169052137e+01 7.10415219806404e-02 + 160 1.40490177822194e+01 8.77068112269737e-02 + 161 1.40477627135566e+01 8.77068112269737e-02 + 162 1.40465343708561e+01 8.77068112269737e-02 + 163 1.40459238392784e+01 8.77068112269737e-02 + 164 1.40454988972072e+01 8.77068112269737e-02 + 165 1.40458141226713e+01 8.77068112269737e-02 + 166 1.40462783821594e+01 8.77068112269737e-02 + 167 1.40469230222126e+01 8.77068112269737e-02 + 168 1.40475066640928e+01 8.77068112269737e-02 + 169 1.40479434618223e+01 8.77068112269737e-02 + 170 1.40484684727914e+01 1.04398841694391e-01 + 171 1.40494304078364e+01 1.04398841694391e-01 + 172 1.40500894404924e+01 1.04398841694391e-01 + 173 1.40506811219062e+01 1.04398841694391e-01 + 174 1.40513374542578e+01 1.04398841694391e-01 + 175 1.40524333136897e+01 1.04398841694391e-01 + 176 1.40539698754981e+01 1.04398841694391e-01 + 177 1.40553742388214e+01 1.04398841694391e-01 + 178 1.40565462699957e+01 1.04398841694391e-01 + 179 1.40575157738103e+01 1.04398841694391e-01 + 180 1.40587097767556e+01 1.20570598774338e-01 + 181 1.40600393128797e+01 1.20570598774338e-01 + 182 1.40613410306303e+01 1.20570598774338e-01 + 183 1.40624671206865e+01 1.20570598774338e-01 + 184 1.40634905260370e+01 1.20570598774338e-01 + 185 1.40640000664191e+01 1.20570598774338e-01 + 186 1.40642859267739e+01 1.20570598774338e-01 + 187 1.40639315838357e+01 1.20570598774338e-01 + 188 1.40634945833543e+01 1.20570598774338e-01 + 189 1.40632564759331e+01 1.20570598774338e-01 + 190 1.40631238563757e+01 1.36504071186495e-01 + 191 1.40628238849401e+01 1.36504071186495e-01 + 192 1.40626278569889e+01 1.36504071186495e-01 + 193 1.40620533035397e+01 1.36504071186495e-01 + 194 1.40614884933489e+01 1.36504071186495e-01 + 195 1.40614791703604e+01 1.36504071186495e-01 + 196 1.40625287898456e+01 1.36504071186495e-01 + 197 1.40636172326678e+01 1.36504071186495e-01 + 198 1.40650874921233e+01 1.36504071186495e-01 + 199 1.40663704922385e+01 1.36504071186495e-01 + 200 1.40671697413825e+01 1.52211789178683e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf index 5728a51c7..6256d0183 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 1.87767103667070e-01 - 7.50000000000000e-01 1.87767103667070e-01 - 1.25000000000000e+00 1.87767103667070e-01 - 1.75000000000000e+00 1.87767103667070e-01 - 2.25000000000000e+00 1.87767103667070e-01 - 2.75000000000000e+00 1.87767103667070e-01 - 3.25000000000000e+00 1.87767103667070e-01 - 3.75000000000000e+00 1.87767103667070e-01 - 4.25000000000000e+00 1.87767103667070e-01 - 4.75000000000000e+00 1.87767103667070e-01 - 5.25000000000000e+00 1.87767103667070e-01 - 5.75000000000000e+00 1.87767103667070e-01 - 6.25000000000000e+00 1.87767103667070e-01 - 6.75000000000000e+00 1.87767103667070e-01 - 7.25000000000000e+00 1.87767103667070e-01 - 7.75000000000000e+00 1.87767103667070e-01 - 8.25000000000000e+00 1.87767103667070e-01 - 8.75000000000000e+00 1.87708066878227e-01 - 9.25000000000000e+00 1.80043500246579e-01 - 9.75000000000000e+00 1.07956732354437e-01 - 1.02500000000000e+01 1.22618911839015e-01 - 1.07500000000000e+01 1.83565598701478e-01 - 1.12500000000000e+01 1.87745693818758e-01 - 1.17500000000000e+01 1.87767103667070e-01 - 1.22500000000000e+01 1.87767103667070e-01 - 1.27500000000000e+01 1.87754571320553e-01 - 1.32500000000000e+01 1.84278326274777e-01 - 1.37500000000000e+01 1.02892736669659e-01 + 2.50000000000000e-01 1.87767102998601e-01 + 7.50000000000000e-01 1.87767102998601e-01 + 1.25000000000000e+00 1.87767102998601e-01 + 1.75000000000000e+00 1.87767102998601e-01 + 2.25000000000000e+00 1.87767102998601e-01 + 2.75000000000000e+00 1.87767102998601e-01 + 3.25000000000000e+00 1.87767102998601e-01 + 3.75000000000000e+00 1.87767102998601e-01 + 4.25000000000000e+00 1.87767102998601e-01 + 4.75000000000000e+00 1.87767102998601e-01 + 5.25000000000000e+00 1.87767102998601e-01 + 5.75000000000000e+00 1.87767102998601e-01 + 6.25000000000000e+00 1.87767102998601e-01 + 6.75000000000000e+00 1.87767102998601e-01 + 7.25000000000000e+00 1.87767102998601e-01 + 7.75000000000000e+00 1.87767102998601e-01 + 8.25000000000000e+00 1.87767102998601e-01 + 8.75000000000000e+00 1.87708066209011e-01 + 9.25000000000000e+00 1.80043499519231e-01 + 9.75000000000000e+00 1.07956731499622e-01 + 1.02500000000000e+01 1.22618911377978e-01 + 1.07500000000000e+01 1.83565598070442e-01 + 1.12500000000000e+01 1.87745693150606e-01 + 1.17500000000000e+01 1.87767102998601e-01 + 1.22500000000000e+01 1.87767102998601e-01 + 1.27500000000000e+01 1.87754570651283e-01 + 1.32500000000000e+01 1.84278325485893e-01 + 1.37500000000000e+01 1.02892735014237e-01 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 1.50317776356913e-01 - 1.52500000000000e+01 1.87112851841236e-01 - 1.57500000000000e+01 1.87766680614282e-01 - 1.62500000000000e+01 1.87767103667070e-01 - 1.67500000000000e+01 1.87767103667070e-01 - 1.72500000000000e+01 1.87767103667070e-01 - 1.77500000000000e+01 1.87767103667070e-01 - 1.82500000000000e+01 1.87767103667070e-01 - 1.87500000000000e+01 1.87767103667070e-01 - 1.92500000000000e+01 1.87767103667070e-01 - 1.97500000000000e+01 1.87767103667070e-01 - 2.02500000000000e+01 1.87767103667070e-01 - 2.07500000000000e+01 1.87767103667070e-01 - 2.12500000000000e+01 1.87767103667070e-01 - 2.17500000000000e+01 1.87767103667070e-01 - 2.22500000000000e+01 1.87767103667070e-01 - 2.27500000000000e+01 1.87767103667070e-01 - 2.32500000000000e+01 1.87767103667070e-01 - 2.37500000000000e+01 1.87767103667070e-01 - 2.42500000000000e+01 1.87767103667070e-01 - 2.47500000000000e+01 1.87767103667070e-01 + 1.47500000000000e+01 1.50317776124501e-01 + 1.52500000000000e+01 1.87112851182683e-01 + 1.57500000000000e+01 1.87766679945813e-01 + 1.62500000000000e+01 1.87767102998601e-01 + 1.67500000000000e+01 1.87767102998601e-01 + 1.72500000000000e+01 1.87767102998601e-01 + 1.77500000000000e+01 1.87767102998601e-01 + 1.82500000000000e+01 1.87767102998601e-01 + 1.87500000000000e+01 1.87767102998601e-01 + 1.92500000000000e+01 1.87767102998601e-01 + 1.97500000000000e+01 1.87767102998601e-01 + 2.02500000000000e+01 1.87767102998601e-01 + 2.07500000000000e+01 1.87767102998601e-01 + 2.12500000000000e+01 1.87767102998601e-01 + 2.17500000000000e+01 1.87767102998601e-01 + 2.22500000000000e+01 1.87767102998601e-01 + 2.27500000000000e+01 1.87767102998601e-01 + 2.32500000000000e+01 1.87767102998601e-01 + 2.37500000000000e+01 1.87767102998601e-01 + 2.42500000000000e+01 1.87767102998601e-01 + 2.47500000000000e+01 1.87767102998601e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state index c2787a073..b13fd85e3 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state @@ -17,9 +17,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 4.94688027692718e-07 4.73585964068546e-04 - 2.87475263076380e-02 1.74745280192386e-01 1.04414172539260e-01 - 5.69106166051415e-03 2.62455924536695e-05 0.00000000000000e+00 + 0.00000000000000e+00 4.94688080523780e-07 4.73585992341132e-04 + 2.87475270508744e-02 1.74745280616823e-01 1.04414171448857e-01 + 5.69106155906453e-03 2.62455918518392e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -42,9 +42,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 7.40502444565457e-06 4.99357118645503e-03 - 1.69663403453012e-01 2.28926007806402e-01 -3.54750303020055e-01 - -4.70268703518904e-02 -3.46867177951536e-04 0.00000000000000e+00 + 0.00000000000000e+00 7.40502520045617e-06 4.99357144931863e-03 + 1.69663406152221e-01 2.28926002246273e-01 -3.54750301243893e-01 + -4.70268695839609e-02 -3.46867170320607e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out index 373c73703..213231cf9 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep2.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -145,7 +143,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -159,7 +156,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -174,49 +170,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Multiple-walker metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.rep2.colvars.state". +colvars: Restarting from file "test.rep2.colvars.state". colvars: Restarting collective variable "d" from value: 9.947 colvars: Restarting metadynamics bias "metadynamics1" from step number 100. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: Restarting harmonicwalls bias "dw" from step number 100. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testres.rep2r.colvars.state". colvars: The final output state file will be "testres.rep2.colvars.state". +colvars: Opening trajectory file "testres.rep2.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "testres.rep2r.colvars.state". colvars: The final output state file will be "testres.rep2.colvars.state". colvars: Metadynamics bias "metadynamics1": accessing replica "rep1". -colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". -colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". colvars: Restarting metadynamics bias "metadynamics1" from step number 200. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: Saving collective variables state to "testres.rep2.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped index ce8f94f06..5f3f08a24 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 9.71175738936231e+00 + x 9.71175738207289e+00 } metadynamics { @@ -27,9 +27,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 4.94688027692718e-07 4.73585964068546e-04 - 2.87475263076380e-02 1.74745280192386e-01 1.04414172539260e-01 - 5.69106166051415e-03 2.62455924536695e-05 0.00000000000000e+00 + 0.00000000000000e+00 4.94688080523780e-07 4.73585992341132e-04 + 2.87475270508744e-02 1.74745280616823e-01 1.04414171448857e-01 + 5.69106155906453e-03 2.62455918518392e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -52,9 +52,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 7.40502444565457e-06 4.99357118645503e-03 - 1.69663403453012e-01 2.28926007806402e-01 -3.54750303020055e-01 - -4.70268703518904e-02 -3.46867177951536e-04 0.00000000000000e+00 + 0.00000000000000e+00 7.40502520045617e-06 4.99357144931863e-03 + 1.69663406152221e-01 2.28926002246273e-01 -3.54750301243893e-01 + -4.70268695839609e-02 -3.46867170320607e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj index 968ab38c3..c28a19f9f 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj @@ -1,102 +1,102 @@ # step d fa_d - 100 9.94700459880913e+00 -1.70182689379045e-01 - 101 9.94458508072563e+00 -1.70182689379045e-01 - 102 9.94237837820968e+00 -1.70182689379045e-01 - 103 9.94046458309169e+00 -1.70182689379045e-01 - 104 9.93917797308190e+00 -1.70182689379045e-01 - 105 9.93831816374525e+00 -1.70182689379045e-01 - 106 9.93730879096641e+00 -1.70182689379045e-01 - 107 9.93672533958771e+00 -1.70182689379045e-01 - 108 9.93648376433042e+00 -1.70182689379045e-01 - 109 9.93652762126550e+00 -1.70182689379045e-01 - 110 9.93706371051391e+00 -1.86126457809144e-01 - 111 9.93776112437344e+00 -1.86126457809144e-01 - 112 9.93854506396815e+00 -1.86126457809144e-01 - 113 9.93918085558668e+00 -1.86126457809144e-01 - 114 9.93937655776149e+00 -1.86126457809144e-01 - 115 9.93893038769523e+00 -1.86126457809144e-01 - 116 9.93789380597970e+00 -1.86126457809144e-01 - 117 9.93662177237539e+00 -1.86126457809144e-01 - 118 9.93489575202623e+00 -1.86126457809144e-01 - 119 9.93264204575408e+00 -1.86126457809144e-01 - 120 9.93021576158670e+00 -2.01684582122971e-01 - 121 9.92745577074879e+00 -2.01684582122971e-01 - 122 9.92406367525066e+00 -2.01684582122971e-01 - 123 9.91986260614685e+00 -2.01684582122971e-01 - 124 9.91533757230742e+00 -2.01684582122971e-01 - 125 9.91093484659609e+00 -2.01684582122971e-01 - 126 9.90665292000386e+00 -2.01684582122971e-01 - 127 9.90211123575625e+00 -2.01684582122971e-01 - 128 9.89781300639078e+00 -2.01684582122971e-01 - 129 9.89406397314085e+00 -2.01684582122971e-01 - 130 9.89014114097385e+00 -2.14600526453355e-01 - 131 9.88640594807955e+00 -2.14600526453355e-01 - 132 9.88226178935358e+00 -2.14600526453355e-01 - 133 9.87820929751591e+00 -2.14600526453355e-01 - 134 9.87355012903898e+00 -2.14600526453355e-01 - 135 9.86875345004836e+00 -2.14600526453355e-01 - 136 9.86400574623842e+00 -2.14600526453355e-01 - 137 9.85896120473937e+00 -2.14600526453355e-01 - 138 9.85422081110592e+00 -2.14600526453355e-01 - 139 9.84970384401704e+00 -2.14600526453355e-01 - 140 9.84571930818557e+00 -2.23905911190324e-01 - 141 9.84162990967742e+00 -2.23905911190324e-01 - 142 9.83714753185596e+00 -2.23905911190324e-01 - 143 9.83237840767275e+00 -2.23905911190324e-01 - 144 9.82753784272710e+00 -2.23905911190324e-01 - 145 9.82322257656238e+00 -2.23905911190324e-01 - 146 9.81960403664628e+00 -2.23905911190324e-01 - 147 9.81638215506584e+00 -2.23905911190324e-01 - 148 9.81411815808055e+00 -2.23905911190324e-01 - 149 9.81186120705696e+00 -2.23905911190324e-01 - 150 9.81023976272379e+00 -2.29929522719298e-01 - 151 9.80895196959333e+00 -2.29929522719298e-01 - 152 9.80803347824830e+00 -2.29929522719298e-01 - 153 9.80725710064431e+00 -2.29929522719298e-01 - 154 9.80685628798525e+00 -2.29929522719298e-01 - 155 9.80643124588796e+00 -2.29929522719298e-01 - 156 9.80651929639905e+00 -2.29929522719298e-01 - 157 9.80658366325459e+00 -2.29929522719298e-01 - 158 9.80608274963996e+00 -2.29929522719298e-01 - 159 9.80533154240805e+00 -2.29929522719298e-01 - 160 9.80408986198415e+00 -2.35357584210514e-01 - 161 9.80243195992594e+00 -2.35357584210514e-01 - 162 9.80032235880316e+00 -2.35357584210514e-01 - 163 9.79828002793355e+00 -2.35357584210514e-01 - 164 9.79526929328518e+00 -2.35357584210514e-01 - 165 9.79205900623106e+00 -2.35357584210514e-01 - 166 9.78836209103374e+00 -2.35357584210514e-01 - 167 9.78427949895649e+00 -2.35357584210514e-01 - 168 9.77985340851435e+00 -2.35357584210514e-01 - 169 9.77597577391508e+00 -2.35357584210514e-01 - 170 9.77231657346676e+00 -2.37624973314339e-01 - 171 9.76872765210230e+00 -2.37624973314339e-01 - 172 9.76445832601357e+00 -2.37624973314339e-01 - 173 9.76039938432572e+00 -2.37624973314339e-01 - 174 9.75645215032161e+00 -2.37624973314339e-01 - 175 9.75287082046772e+00 -2.37624973314339e-01 - 176 9.74968666704269e+00 -2.37624973314339e-01 - 177 9.74684973756385e+00 -2.37624973314339e-01 - 178 9.74348360020917e+00 -2.37624973314339e-01 - 179 9.74030680111914e+00 -2.37624973314339e-01 - 180 9.73711488499836e+00 -2.36313615584043e-01 - 181 9.73433465068754e+00 -2.36313615584043e-01 - 182 9.73173780573565e+00 -2.36313615584043e-01 - 183 9.72947843607525e+00 -2.36313615584043e-01 - 184 9.72710977792195e+00 -2.36313615584043e-01 - 185 9.72467706469478e+00 -2.36313615584043e-01 - 186 9.72244089654436e+00 -2.36313615584043e-01 - 187 9.72029112628186e+00 -2.36313615584043e-01 - 188 9.71845562836040e+00 -2.36313615584043e-01 - 189 9.71680424007266e+00 -2.36313615584043e-01 - 190 9.71521749525137e+00 -2.32792461579337e-01 - 191 9.71413765244917e+00 -2.32792461579337e-01 - 192 9.71307166808760e+00 -2.32792461579337e-01 - 193 9.71195901360456e+00 -2.32792461579337e-01 - 194 9.71186724904802e+00 -2.32792461579337e-01 - 195 9.71169950721007e+00 -2.32792461579337e-01 - 196 9.71157180660297e+00 -2.32792461579337e-01 - 197 9.71177699982444e+00 -2.32792461579337e-01 - 198 9.71199162310558e+00 -2.32792461579337e-01 - 199 9.71215449719626e+00 -2.32792461579337e-01 - 200 9.71175738936231e+00 -2.28926007806402e-01 + 100 9.94700459588437e+00 -1.70182688913198e-01 + 101 9.94458507772995e+00 -1.70182688913198e-01 + 102 9.94237837514508e+00 -1.70182688913198e-01 + 103 9.94046457996010e+00 -1.70182688913198e-01 + 104 9.93917796988520e+00 -1.70182688913198e-01 + 105 9.93831816048514e+00 -1.70182688913198e-01 + 106 9.93730878764442e+00 -1.70182688913198e-01 + 107 9.93672533620511e+00 -1.70182688913198e-01 + 108 9.93648376088839e+00 -1.70182688913198e-01 + 109 9.93652761776498e+00 -1.70182688913198e-01 + 110 9.93706370695588e+00 -1.86126457148131e-01 + 111 9.93776112075882e+00 -1.86126457148131e-01 + 112 9.93854506029798e+00 -1.86126457148131e-01 + 113 9.93918085186220e+00 -1.86126457148131e-01 + 114 9.93937655398418e+00 -1.86126457148131e-01 + 115 9.93893038386686e+00 -1.86126457148131e-01 + 116 9.93789380210237e+00 -1.86126457148131e-01 + 117 9.93662176845159e+00 -1.86126457148131e-01 + 118 9.93489574805879e+00 -1.86126457148131e-01 + 119 9.93264204174611e+00 -1.86126457148131e-01 + 120 9.93021575754143e+00 -2.01684581228258e-01 + 121 9.92745576666947e+00 -2.01684581228258e-01 + 122 9.92406367114035e+00 -2.01684581228258e-01 + 123 9.91986260200830e+00 -2.01684581228258e-01 + 124 9.91533756814292e+00 -2.01684581228258e-01 + 125 9.91093484240737e+00 -2.01684581228258e-01 + 126 9.90665291579182e+00 -2.01684581228258e-01 + 127 9.90211123152112e+00 -2.01684581228258e-01 + 128 9.89781300213203e+00 -2.01684581228258e-01 + 129 9.89406396885698e+00 -2.01684581228258e-01 + 130 9.89014113666249e+00 -2.14600525240779e-01 + 131 9.88640594373758e+00 -2.14600525240779e-01 + 132 9.88226178497735e+00 -2.14600525240779e-01 + 133 9.87820929310142e+00 -2.14600525240779e-01 + 134 9.87355012458204e+00 -2.14600525240779e-01 + 135 9.86875344554473e+00 -2.14600525240779e-01 + 136 9.86400574168410e+00 -2.14600525240779e-01 + 137 9.85896120013053e+00 -2.14600525240779e-01 + 138 9.85422080643946e+00 -2.14600525240779e-01 + 139 9.84970383929048e+00 -2.14600525240779e-01 + 140 9.84571930339719e+00 -2.23905909555689e-01 + 141 9.84162990482619e+00 -2.23905909555689e-01 + 142 9.83714752694151e+00 -2.23905909555689e-01 + 143 9.83237840269532e+00 -2.23905909555689e-01 + 144 9.82753783768742e+00 -2.23905909555689e-01 + 145 9.82322257146133e+00 -2.23905909555689e-01 + 146 9.81960403148490e+00 -2.23905909555689e-01 + 147 9.81638214984508e+00 -2.23905909555689e-01 + 148 9.81411815280101e+00 -2.23905909555689e-01 + 149 9.81186120171889e+00 -2.23905909555689e-01 + 150 9.81023975732696e+00 -2.29929520564960e-01 + 151 9.80895196413704e+00 -2.29929520564960e-01 + 152 9.80803347273143e+00 -2.29929520564960e-01 + 153 9.80725709506516e+00 -2.29929520564960e-01 + 154 9.80685628234177e+00 -2.29929520564960e-01 + 155 9.80643124017792e+00 -2.29929520564960e-01 + 156 9.80651929062019e+00 -2.29929520564960e-01 + 157 9.80658365740485e+00 -2.29929520564960e-01 + 158 9.80608274371768e+00 -2.29929520564960e-01 + 159 9.80533153641205e+00 -2.29929520564960e-01 + 160 9.80408985591389e+00 -2.35357581465163e-01 + 161 9.80243195378187e+00 -2.35357581465163e-01 + 162 9.80032235258663e+00 -2.35357581465163e-01 + 163 9.79828002164672e+00 -2.35357581465163e-01 + 164 9.79526928693096e+00 -2.35357581465163e-01 + 165 9.79205899981332e+00 -2.35357581465163e-01 + 166 9.78836208455697e+00 -2.35357581465163e-01 + 167 9.78427949242546e+00 -2.35357581465163e-01 + 168 9.77985340193428e+00 -2.35357581465163e-01 + 169 9.77597576729126e+00 -2.35357581465163e-01 + 170 9.77231656680436e+00 -2.37624969895514e-01 + 171 9.76872764540608e+00 -2.37624969895514e-01 + 172 9.76445831928769e+00 -2.37624969895514e-01 + 173 9.76039937757358e+00 -2.37624969895514e-01 + 174 9.75645214354585e+00 -2.37624969895514e-01 + 175 9.75287081367028e+00 -2.37624969895514e-01 + 176 9.74968666022476e+00 -2.37624969895514e-01 + 177 9.74684973072586e+00 -2.37624969895514e-01 + 178 9.74348359335075e+00 -2.37624969895514e-01 + 179 9.74030679423950e+00 -2.37624969895514e-01 + 180 9.73711487809642e+00 -2.36313611463974e-01 + 181 9.73433464376223e+00 -2.36313611463974e-01 + 182 9.73173779878573e+00 -2.36313611463974e-01 + 183 9.72947842909980e+00 -2.36313611463974e-01 + 184 9.72710977092031e+00 -2.36313611463974e-01 + 185 9.72467705766697e+00 -2.36313611463974e-01 + 186 9.72244088949095e+00 -2.36313611463974e-01 + 187 9.72029111920384e+00 -2.36313611463974e-01 + 188 9.71845562125918e+00 -2.36313611463974e-01 + 189 9.71680423295022e+00 -2.36313611463974e-01 + 190 9.71521748810981e+00 -2.32792456745213e-01 + 191 9.71413764529071e+00 -2.32792456745213e-01 + 192 9.71307166091424e+00 -2.32792456745213e-01 + 193 9.71195900641790e+00 -2.32792456745213e-01 + 194 9.71186724184931e+00 -2.32792456745213e-01 + 195 9.71169949999982e+00 -2.32792456745213e-01 + 196 9.71157179938086e+00 -2.32792456745213e-01 + 197 9.71177699258930e+00 -2.32792456745213e-01 + 198 9.71199161585537e+00 -2.32792456745213e-01 + 199 9.71215448992823e+00 -2.32792456745213e-01 + 200 9.71175738207289e+00 -2.28926002246273e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf index 403599903..f66c76153 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 1.87767103667070e-01 - 7.50000000000000e-01 1.87767103667070e-01 - 1.25000000000000e+00 1.87767103667070e-01 - 1.75000000000000e+00 1.87767103667070e-01 - 2.25000000000000e+00 1.87767103667070e-01 - 2.75000000000000e+00 1.87767103667070e-01 - 3.25000000000000e+00 1.87767103667070e-01 - 3.75000000000000e+00 1.87767103667070e-01 - 4.25000000000000e+00 1.87767103667070e-01 - 4.75000000000000e+00 1.87767103667070e-01 - 5.25000000000000e+00 1.87767103667070e-01 - 5.75000000000000e+00 1.87767103667070e-01 - 6.25000000000000e+00 1.87767103667070e-01 - 6.75000000000000e+00 1.87767103667070e-01 - 7.25000000000000e+00 1.87767103667070e-01 - 7.75000000000000e+00 1.87767103667070e-01 - 8.25000000000000e+00 1.87766608979042e-01 - 8.75000000000000e+00 1.87293517703001e-01 - 9.25000000000000e+00 1.59019577359432e-01 - 9.75000000000000e+00 1.30218234746837e-02 - 1.02500000000000e+01 8.33529311278102e-02 - 1.07500000000000e+01 1.82076042006556e-01 - 1.12500000000000e+01 1.87740858074616e-01 - 1.17500000000000e+01 1.87767103667070e-01 - 1.22500000000000e+01 1.87767103667070e-01 - 1.27500000000000e+01 1.87754571320553e-01 - 1.32500000000000e+01 1.84278326274777e-01 - 1.37500000000000e+01 1.02892736669659e-01 + 2.50000000000000e-01 1.87767102998601e-01 + 7.50000000000000e-01 1.87767102998601e-01 + 1.25000000000000e+00 1.87767102998601e-01 + 1.75000000000000e+00 1.87767102998601e-01 + 2.25000000000000e+00 1.87767102998601e-01 + 2.75000000000000e+00 1.87767102998601e-01 + 3.25000000000000e+00 1.87767102998601e-01 + 3.75000000000000e+00 1.87767102998601e-01 + 4.25000000000000e+00 1.87767102998601e-01 + 4.75000000000000e+00 1.87767102998601e-01 + 5.25000000000000e+00 1.87767102998601e-01 + 5.75000000000000e+00 1.87767102998601e-01 + 6.25000000000000e+00 1.87767102998601e-01 + 6.75000000000000e+00 1.87767102998601e-01 + 7.25000000000000e+00 1.87767102998601e-01 + 7.75000000000000e+00 1.87767102998601e-01 + 8.25000000000000e+00 1.87766608310520e-01 + 8.75000000000000e+00 1.87293517006260e-01 + 9.25000000000000e+00 1.59019575947726e-01 + 9.75000000000000e+00 1.30218223817775e-02 + 1.02500000000000e+01 8.33529315497443e-02 + 1.07500000000000e+01 1.82076041439536e-01 + 1.12500000000000e+01 1.87740857406749e-01 + 1.17500000000000e+01 1.87767102998601e-01 + 1.22500000000000e+01 1.87767102998601e-01 + 1.27500000000000e+01 1.87754570651282e-01 + 1.32500000000000e+01 1.84278325485893e-01 + 1.37500000000000e+01 1.02892735014237e-01 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 1.50317776356913e-01 - 1.52500000000000e+01 1.87112851841236e-01 - 1.57500000000000e+01 1.87766680614282e-01 - 1.62500000000000e+01 1.87767103667070e-01 - 1.67500000000000e+01 1.87767103667070e-01 - 1.72500000000000e+01 1.87767103667070e-01 - 1.77500000000000e+01 1.87767103667070e-01 - 1.82500000000000e+01 1.87767103667070e-01 - 1.87500000000000e+01 1.87767103667070e-01 - 1.92500000000000e+01 1.87767103667070e-01 - 1.97500000000000e+01 1.87767103667070e-01 - 2.02500000000000e+01 1.87767103667070e-01 - 2.07500000000000e+01 1.87767103667070e-01 - 2.12500000000000e+01 1.87767103667070e-01 - 2.17500000000000e+01 1.87767103667070e-01 - 2.22500000000000e+01 1.87767103667070e-01 - 2.27500000000000e+01 1.87767103667070e-01 - 2.32500000000000e+01 1.87767103667070e-01 - 2.37500000000000e+01 1.87767103667070e-01 - 2.42500000000000e+01 1.87767103667070e-01 - 2.47500000000000e+01 1.87767103667070e-01 + 1.47500000000000e+01 1.50317776124501e-01 + 1.52500000000000e+01 1.87112851182683e-01 + 1.57500000000000e+01 1.87766679945813e-01 + 1.62500000000000e+01 1.87767102998601e-01 + 1.67500000000000e+01 1.87767102998601e-01 + 1.72500000000000e+01 1.87767102998601e-01 + 1.77500000000000e+01 1.87767102998601e-01 + 1.82500000000000e+01 1.87767102998601e-01 + 1.87500000000000e+01 1.87767102998601e-01 + 1.92500000000000e+01 1.87767102998601e-01 + 1.97500000000000e+01 1.87767102998601e-01 + 2.02500000000000e+01 1.87767102998601e-01 + 2.07500000000000e+01 1.87767102998601e-01 + 2.12500000000000e+01 1.87767102998601e-01 + 2.17500000000000e+01 1.87767102998601e-01 + 2.22500000000000e+01 1.87767102998601e-01 + 2.27500000000000e+01 1.87767102998601e-01 + 2.32500000000000e+01 1.87767102998601e-01 + 2.37500000000000e+01 1.87767102998601e-01 + 2.42500000000000e+01 1.87767102998601e-01 + 2.47500000000000e+01 1.87767102998601e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/namd-version.txt b/namd/tests/library/011_multiple_walker_mtd/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/011_multiple_walker_mtd/namd-version.txt +++ b/namd/tests/library/011_multiple_walker_mtd/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out index 3ff945377..6f057103a 100644 --- a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out +++ b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: Warning: no collective variables defined. colvars: Collective variables initialized, 0 in total. colvars: No collective variables biases were defined. @@ -21,6 +19,8 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration: colvars: # units = "" [default] @@ -29,7 +29,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d0" @@ -43,28 +42,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -75,7 +74,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -100,28 +99,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -138,28 +137,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 2 atoms requested: total mass = 15.015, total charge = -0.31. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -176,28 +175,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 3 atoms requested: total mass = 16.023, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -208,7 +207,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -233,28 +232,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -271,28 +270,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 2 atoms requested: total mass = 15.015, total charge = -0.31. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -309,28 +308,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 3 atoms requested: total mass = 16.023, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -347,28 +346,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 28.034, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -385,28 +384,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 5 atoms requested: total mass = 29.042, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -423,28 +422,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 6 atoms requested: total mass = 41.053, total charge = -0.27. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -461,28 +460,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 7 atoms requested: total mass = 42.061, total charge = -0.18. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -493,7 +492,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -514,26 +513,9 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (14 scalable groups, 56 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (14 scalable groups, 56 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d0":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "d0":0/1. 1 atoms: total mass = 1.008, total charge = 0.09. colvars: Re-initialized atom group for variable "d1":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. diff --git a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj index e61993948..764d968c2 100644 --- a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj +++ b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step d0 d1 d2 0 9.68028971673885e+00 2.83439401925857e+01 6.55272039460079e+01 - 1 9.68459329037158e+00 2.83503517848776e+01 6.55348311139462e+01 - 2 9.68863510077707e+00 2.83568986120102e+01 6.55435199472898e+01 - 3 9.69270450128096e+00 2.83637753155840e+01 6.55522671059708e+01 - 4 9.69567146225122e+00 2.83683142733353e+01 6.55581718660859e+01 - 5 9.69861372974800e+00 2.83728360758402e+01 6.55643117777301e+01 - 6 9.69989691772941e+00 2.83755769999054e+01 6.55687963597424e+01 - 7 9.69881248545288e+00 2.83761329500648e+01 6.55711659392461e+01 - 8 9.69696590303006e+00 2.83755659867833e+01 6.55723453523354e+01 - 9 9.69437508769387e+00 2.83738021775598e+01 6.55721051237738e+01 - 10 9.69142876298948e+00 2.83713870793780e+01 6.55715234769294e+01 - 11 9.68736616543871e+00 2.83668242786358e+01 6.55679613897708e+01 - 12 9.68269170466530e+00 2.83619773538931e+01 6.55640905410330e+01 - 13 9.67603219488243e+00 2.83539684890163e+01 6.55557350085058e+01 - 14 9.67131225666176e+00 2.83481344963114e+01 6.55501180057890e+01 - 15 9.66613278096313e+00 2.83417789198344e+01 6.55442094171420e+01 - 16 9.66208835184987e+00 2.83361112760016e+01 6.55383049475210e+01 - 17 9.65853060611532e+00 2.83296225776533e+01 6.55305098868216e+01 - 18 9.65562060404079e+00 2.83230675648197e+01 6.55226790315196e+01 - 19 9.65479770157889e+00 2.83184820767205e+01 6.55167907309241e+01 - 20 9.65474241851144e+00 2.83146389464743e+01 6.55122068151385e+01 + 1 9.68459329037381e+00 2.83503517848797e+01 6.55348311139484e+01 + 2 9.68863510078556e+00 2.83568986120180e+01 6.55435199472981e+01 + 3 9.69270450129925e+00 2.83637753156007e+01 6.55522671059886e+01 + 4 9.69567146228222e+00 2.83683142733634e+01 6.55581718661156e+01 + 5 9.69861372979398e+00 2.83728360758814e+01 6.55643117777734e+01 + 6 9.69989691779190e+00 2.83755769999609e+01 6.55687963598000e+01 + 7 9.69881248553272e+00 2.83761329501348e+01 6.55711659393180e+01 + 8 9.69696590312749e+00 2.83755659868676e+01 6.55723453524207e+01 + 9 9.69437508780854e+00 2.83738021776574e+01 6.55721051238709e+01 + 10 9.69142876312061e+00 2.83713870794876e+01 6.55715234770360e+01 + 11 9.68736616558516e+00 2.83668242787558e+01 6.55679613898842e+01 + 12 9.68269170482564e+00 2.83619773540213e+01 6.55640905411503e+01 + 13 9.67603219505517e+00 2.83539684891505e+01 6.55557350086236e+01 + 14 9.67131225684547e+00 2.83481344964496e+01 6.55501180059041e+01 + 15 9.66613278115654e+00 2.83417789199746e+01 6.55442094172513e+01 + 16 9.66208835205202e+00 2.83361112761420e+01 6.55383049476216e+01 + 17 9.65853060632552e+00 2.83296225777924e+01 6.55305098869110e+01 + 18 9.65562060425861e+00 2.83230675649562e+01 6.55226790315953e+01 + 19 9.65479770180415e+00 2.83184820768533e+01 6.55167907309839e+01 + 20 9.65474241874427e+00 2.83146389466025e+01 6.55122068151804e+01 diff --git a/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out b/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out index 2c7067791..bc4c60690 100644 --- a/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out +++ b/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out @@ -1,100 +1,40 @@ -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013848072 0.0000000003878053 0.0000000094410965 } -TCL: TOTAL TORQUE: { 0.0000000096171986 -0.0000000667110256 0.0000000013296057 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013845900 0.0000000003876409 0.0000000094405268 } -TCL: TOTAL TORQUE: { 0.0000000095852526 -0.0000000666977762 0.0000000013328793 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013847470 0.0000000003876303 0.0000000094408976 } -TCL: TOTAL TORQUE: { 0.0000000095511905 -0.0000000666894295 0.0000000013372524 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013847025 0.0000000003881038 0.0000000094419481 } -TCL: TOTAL TORQUE: { 0.0000000095191286 -0.0000000666852835 0.0000000013450220 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013846686 0.0000000003885957 0.0000000094430159 } -TCL: TOTAL TORQUE: { 0.0000000094870103 -0.0000000666864186 0.0000000013531377 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013843890 0.0000000003892623 0.0000000094432095 } -TCL: TOTAL TORQUE: { 0.0000000094558161 -0.0000000666831221 0.0000000013625325 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013839316 0.0000000003896171 0.0000000094426439 } -TCL: TOTAL TORQUE: { 0.0000000094239665 -0.0000000666716580 0.0000000013697786 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013834814 0.0000000003898117 0.0000000094412102 } -TCL: TOTAL TORQUE: { 0.0000000093931183 -0.0000000666537403 0.0000000013755888 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013832539 0.0000000003898992 0.0000000094391743 } -TCL: TOTAL TORQUE: { 0.0000000093661994 -0.0000000666327935 0.0000000013798055 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013832885 0.0000000003903983 0.0000000094360750 } -TCL: TOTAL TORQUE: { 0.0000000093368824 -0.0000000666050974 0.0000000013869035 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013836644 0.0000000003910720 0.0000000094315508 } -TCL: TOTAL TORQUE: { 0.0000000093077337 -0.0000000665692967 0.0000000013947463 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013839568 0.0000000003916391 0.0000000094269754 } -TCL: TOTAL TORQUE: { 0.0000000092818309 -0.0000000665320030 0.0000000014013880 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013839793 0.0000000003921171 0.0000000094227682 } -TCL: TOTAL TORQUE: { 0.0000000092568291 -0.0000000664963768 0.0000000014075589 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013838283 0.0000000003926106 0.0000000094177920 } -TCL: TOTAL TORQUE: { 0.0000000092346419 -0.0000000664554638 0.0000000014134884 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013835781 0.0000000003927679 0.0000000094127447 } -TCL: TOTAL TORQUE: { 0.0000000092166221 -0.0000000664099504 0.0000000014163500 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013833556 0.0000000003930108 0.0000000094071154 } -TCL: TOTAL TORQUE: { 0.0000000091982395 -0.0000000663596005 0.0000000014197321 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013832197 0.0000000003935579 0.0000000094012935 } -TCL: TOTAL TORQUE: { 0.0000000091779127 -0.0000000663086817 0.0000000014254637 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013833440 0.0000000003940628 0.0000000093949191 } -TCL: TOTAL TORQUE: { 0.0000000091557357 -0.0000000662538246 0.0000000014308384 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013834062 0.0000000003941312 0.0000000093895322 } -TCL: TOTAL TORQUE: { 0.0000000091350936 -0.0000000662080812 0.0000000014332043 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013834729 0.0000000003936539 0.0000000093840155 } -TCL: TOTAL TORQUE: { 0.0000000091166648 -0.0000000661598230 0.0000000014313052 } +TCL: TOTAL FORCE: ( 1.384807019055856e-9 3.878058707496024e-10 9.441096737727861e-9 ) +TCL: TOTAL TORQUE: ( 9.617198148959005e-9 -6.671102603661438e-8 1.3296069245605224e-9 ) +TCL: TOTAL FORCE: ( 1.3845898871878148e-9 3.876407805858406e-10 9.440526915760472e-9 ) +TCL: TOTAL TORQUE: ( 9.58525481209449e-9 -6.669777796730614e-8 1.3328811387935957e-9 ) +TCL: TOTAL FORCE: ( 1.384747011501375e-9 3.876299281557749e-10 9.440897230650336e-9 ) +TCL: TOTAL TORQUE: ( 9.551191837431361e-9 -6.668942509335807e-8 1.3372550289325602e-9 ) +TCL: TOTAL FORCE: ( 1.3847027136026924e-9 3.8810379909826054e-10 9.441948223276597e-9 ) +TCL: TOTAL TORQUE: ( 9.519129040569396e-9 -6.668528440556543e-8 1.3450211500121156e-9 ) +TCL: TOTAL FORCE: ( 1.3846692126229243e-9 3.8859587769835e-10 9.44301592475938e-9 ) +TCL: TOTAL TORQUE: ( 9.487008512110151e-9 -6.668641860940738e-8 1.3531361586771595e-9 ) +TCL: TOTAL FORCE: ( 1.3843895196874456e-9 3.892627331580911e-10 9.443209769699479e-9 ) +TCL: TOTAL TORQUE: ( 9.455814797831863e-9 -6.668312035884583e-8 1.3625308659115376e-9 ) +TCL: TOTAL FORCE: ( 1.3839312196228803e-9 3.896173383921564e-10 9.442643722490374e-9 ) +TCL: TOTAL TORQUE: ( 9.423963831522997e-9 -6.66716588604288e-8 1.3697779022159295e-9 ) +TCL: TOTAL FORCE: ( 1.3834813572533022e-9 3.8981154415473895e-10 9.441210035987524e-9 ) +TCL: TOTAL TORQUE: ( 9.39311961545286e-9 -6.665373897263294e-8 1.375589642194086e-9 ) +TCL: TOTAL FORCE: ( 1.383253483977498e-9 3.8989927952925996e-10 9.43917471962763e-9 ) +TCL: TOTAL TORQUE: ( 9.36619892755175e-9 -6.663279394913957e-8 1.3798079900873006e-9 ) +TCL: TOTAL FORCE: ( 1.383288567025076e-9 3.903983525344046e-10 9.43607558756554e-9 ) +TCL: TOTAL TORQUE: ( 9.336882378363498e-9 -6.660509610512122e-8 1.3869025372592603e-9 ) +TCL: TOTAL FORCE: ( 1.3836645162967898e-9 3.910716472876885e-10 9.431551373229041e-9 ) +TCL: TOTAL TORQUE: ( 9.307735915342619e-9 -6.656929452120153e-8 1.3947462074170858e-9 ) +TCL: TOTAL FORCE: ( 1.383956810263598e-9 3.916388602309695e-10 9.426974978410385e-9 ) +TCL: TOTAL TORQUE: ( 9.281833523999694e-9 -6.653200479433963e-8 1.4013895599518378e-9 ) +TCL: TOTAL FORCE: ( 1.3839795143244515e-9 3.9211683899864624e-10 9.422767954792022e-9 ) +TCL: TOTAL TORQUE: ( 9.256830413306716e-9 -6.64963777374794e-8 1.4075592358331335e-9 ) +TCL: TOTAL FORCE: ( 1.3838287182821318e-9 3.9261055517769705e-10 9.417791990706803e-9 ) +TCL: TOTAL TORQUE: ( 9.234642384114977e-9 -6.64554629103975e-8 1.4134880488292367e-9 ) +TCL: TOTAL FORCE: ( 1.3835778911452934e-9 3.927678460247108e-10 9.412744972348008e-9 ) +TCL: TOTAL TORQUE: ( 9.216622132157681e-9 -6.640994820727997e-8 1.4163497041863593e-9 ) +TCL: TOTAL FORCE: ( 1.3833555689846122e-9 3.9301065180019634e-10 9.407115364457042e-9 ) +TCL: TOTAL TORQUE: ( 9.198239947494358e-9 -6.635960181355927e-8 1.4197321096531823e-9 ) +TCL: TOTAL FORCE: ( 1.3832198719754274e-9 3.9355749215097546e-10 9.401293632471663e-9 ) +TCL: TOTAL TORQUE: ( 9.17791531662715e-9 -6.630868121249023e-8 1.425466855664581e-9 ) +TCL: TOTAL FORCE: ( 1.3833443557320635e-9 3.940626436271799e-10 9.394919009420022e-9 ) +TCL: TOTAL TORQUE: ( 9.155735281041189e-9 -6.625382553693271e-8 1.4308377815908102e-9 ) +TCL: TOTAL FORCE: ( 1.383406056376657e-9 3.941313664324042e-10 9.38953176321533e-9 ) +TCL: TOTAL TORQUE: ( 9.135093126388938e-9 -6.620808390422894e-8 1.4332044995235549e-9 ) +TCL: TOTAL FORCE: ( 1.3834732248696469e-9 3.936540260429666e-10 9.384015065005968e-9 ) +TCL: TOTAL TORQUE: ( 9.11666298009095e-9 -6.615982339752691e-8 1.4313049634395725e-9 ) diff --git a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out index 90737e554..c84bb7e88 100644 --- a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out +++ b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "r" @@ -27,25 +25,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 5 atoms requested: total mass = 60.055, total charge = 0.35. @@ -66,7 +64,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -94,7 +92,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "r" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -105,29 +102,13 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (6 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "r":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (6 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "r":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: The final output state file will be "test.colvars.state". colvars: Debugging gradients for cvc rmsd0001 @@ -151,11 +132,11 @@ colvars: dx(interp) = -1.35149604087641e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.75153e-07 colvars: refPosGroup atom 0, component 0: colvars: dx(actual) = -1.32256818830001e-08 -colvars: dx(interp) = -1.32256806784028e-08 +colvars: dx(interp) = -1.32256806784027e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.10802e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.65148816633609e-09 -colvars: dx(interp) = 5.65148916474421e-09 +colvars: dx(interp) = 5.65148916474418e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.76663e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70015094119935e-08 @@ -183,7 +164,7 @@ colvars: dx(interp) = 1.64047652855846e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.00693e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44798905777589e-09 -colvars: dx(interp) = 9.44799082028362e-09 +colvars: dx(interp) = 9.44799082028361e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.86548e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.49833905283003e-08 @@ -209,7 +190,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02938776286510e-08 colvars: dx(interp) = 3.02938806702505e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.00403e-07. -colvars: Gradient sum: ( 0.973323 , -0.185412 , -0.13515 ) Fit gradient sum: ( -0.973323 , 0.185412 , 0.13515 ) Total ( -3.33067e-16 , 3.05311e-16 , 5.55112e-17 ) +colvars: Gradient sum: ( 0.973323 , -0.185412 , -0.13515 ) Fit gradient sum: ( -0.973323 , 0.185412 , 0.13515 ) Total ( -1.11022e-16 , -5.55112e-17 , -2.22045e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234785 , 0.269301 , -0.173026 ) @@ -251,7 +232,7 @@ colvars: dx(interp) = 8.53838213116278e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.71227e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.15095546613520e-10 -colvars: dx(interp) = 8.15096690566031e-10 +colvars: dx(interp) = 8.15096690566021e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.40346e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26069001693941e-08 @@ -271,11 +252,11 @@ colvars: dx(interp) = -1.49873663013446e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.94117e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.07673869820246e-09 -colvars: dx(interp) = 1.07674116921778e-09 +colvars: dx(interp) = 1.07674116921777e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.29491e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.95859750219097e-09 -colvars: dx(interp) = 9.95860073923380e-09 +colvars: dx(interp) = 9.95860073923379e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.25050e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43292595566891e-08 @@ -289,7 +270,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02918081729331e-08 colvars: dx(interp) = 3.02918110782712e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.59117e-08. -colvars: Gradient sum: ( 0.973303 , -0.185528 , -0.135131 ) Fit gradient sum: ( -0.973303 , 0.185528 , 0.135131 ) Total ( 0 , -2.22045e-16 , 1.94289e-16 ) +colvars: Gradient sum: ( 0.973303 , -0.185528 , -0.135131 ) Fit gradient sum: ( -0.973303 , 0.185528 , 0.135131 ) Total ( 1.11022e-16 , -1.11022e-16 , 2.77556e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234756 , 0.269374 , -0.172978 ) @@ -331,7 +312,7 @@ colvars: dx(interp) = 8.53613239284918e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.92870e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.18408452119002e-10 -colvars: dx(interp) = 8.18402186831441e-10 +colvars: dx(interp) = 8.18402186831449e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.65545e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26106322951136e-08 @@ -343,7 +324,7 @@ colvars: dx(interp) = 1.64127071165021e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.64922e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44612565945135e-09 -colvars: dx(interp) = 9.44611973805957e-09 +colvars: dx(interp) = 9.44611973805956e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.26859e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.49949652694659e-08 @@ -351,7 +332,7 @@ colvars: dx(interp) = -1.49949667603800e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.94276e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.08642161933403e-09 -colvars: dx(interp) = 1.08642112294382e-09 +colvars: dx(interp) = 1.08642112294384e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.56904e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.95594184871607e-09 @@ -359,7 +340,7 @@ colvars: dx(interp) = 9.95594165715356e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.92410e-08. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43341960523458e-08 -colvars: dx(interp) = 1.43341893744116e-08 +colvars: dx(interp) = 1.43341893744115e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.65874e-07. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.30965638334146e-08 @@ -369,7 +350,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02961637999033e-08 colvars: dx(interp) = 3.02961588118116e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.64644e-07. -colvars: Gradient sum: ( 0.973277 , -0.185665 , -0.135133 ) Fit gradient sum: ( -0.973277 , 0.185665 , 0.135133 ) Total ( 0 , -2.77556e-17 , -1.66533e-16 ) +colvars: Gradient sum: ( 0.973277 , -0.185665 , -0.135133 ) Fit gradient sum: ( -0.973277 , 0.185665 , 0.135133 ) Total ( 0 , 2.77556e-16 , -5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234717 , 0.269457 , -0.172922 ) @@ -391,11 +372,11 @@ colvars: dx(interp) = -1.35095571144321e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.93919e-08 colvars: refPosGroup atom 0, component 0: colvars: dx(actual) = -1.32276785080876e-08 -colvars: dx(interp) = -1.32276807821041e-08 +colvars: dx(interp) = -1.32276807821042e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.71914e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.61136204169088e-09 -colvars: dx(interp) = 5.61135643011218e-09 +colvars: dx(interp) = 5.61135643011219e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.00004e-06. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70074335620529e-08 @@ -403,19 +384,19 @@ colvars: dx(interp) = -3.70074373671765e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.02821e-07. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.08169099128008e-08 -colvars: dx(interp) = -3.08169108969143e-08 +colvars: dx(interp) = -3.08169108969144e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.19342e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53347614793165e-09 -colvars: dx(interp) = 8.53347204237835e-09 +colvars: dx(interp) = 8.53347204237836e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.81111e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.19884604652543e-10 -colvars: dx(interp) = 8.19880913108474e-10 +colvars: dx(interp) = 8.19880913108477e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.50252e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26149719348723e-08 -colvars: dx(interp) = -5.26149677696460e-08 +colvars: dx(interp) = -5.26149677696461e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.91643e-08. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64202287322723e-08 @@ -423,7 +404,7 @@ colvars: dx(interp) = 1.64202293878008e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.99220e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44173628170120e-09 -colvars: dx(interp) = 9.44173782371806e-09 +colvars: dx(interp) = 9.44173782371807e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.63319e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50037209323273e-08 @@ -449,7 +430,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03022300585098e-08 colvars: dx(interp) = 3.03022309014118e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.78165e-08. -colvars: Gradient sum: ( 0.973258 , -0.185792 , -0.135096 ) Fit gradient sum: ( -0.973258 , 0.185792 , 0.135096 ) Total ( 0 , -1.38778e-16 , -5.55112e-17 ) +colvars: Gradient sum: ( 0.973258 , -0.185792 , -0.135096 ) Fit gradient sum: ( -0.973258 , 0.185792 , 0.135096 ) Total ( -2.22045e-16 , -2.77556e-17 , 0 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234673 , 0.269532 , -0.172868 ) @@ -479,11 +460,11 @@ colvars: dx(interp) = 5.59468663743374e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.84774e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70104338287547e-08 -colvars: dx(interp) = -3.70104348510150e-08 +colvars: dx(interp) = -3.70104348510151e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.76209e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.08071026466905e-08 -colvars: dx(interp) = -3.08070979989617e-08 +colvars: dx(interp) = -3.08070979989616e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.50865e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53082937624094e-09 @@ -491,11 +472,11 @@ colvars: dx(interp) = 8.53082896971171e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.76541e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.21989587507232e-10 -colvars: dx(interp) = 8.21992304895591e-10 +colvars: dx(interp) = 8.21992304895594e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.30587e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26181160864780e-08 -colvars: dx(interp) = -5.26181139628721e-08 +colvars: dx(interp) = -5.26181139628722e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.03588e-08. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64276485747905e-08 @@ -503,7 +484,7 @@ colvars: dx(interp) = 1.64276457374503e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.72717e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43767197725265e-09 -colvars: dx(interp) = 9.43767316290166e-09 +colvars: dx(interp) = 9.43767316290167e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.25629e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50121302056050e-08 @@ -511,11 +492,11 @@ colvars: dx(interp) = -1.50121288821272e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.81606e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.10627063065749e-09 -colvars: dx(interp) = 1.10626880712029e-09 +colvars: dx(interp) = 1.10626880712028e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.64836e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94974769241708e-09 -colvars: dx(interp) = 9.94974605686307e-09 +colvars: dx(interp) = 9.94974605686308e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.64381e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43403262597985e-08 @@ -529,7 +510,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03069658258437e-08 colvars: dx(interp) = 3.03069655364643e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.54828e-09. -colvars: Gradient sum: ( 0.973239 , -0.185915 , -0.135059 ) Fit gradient sum: ( -0.973239 , 0.185915 , 0.135059 ) Total ( 0 , 2.22045e-16 , -1.38778e-16 ) +colvars: Gradient sum: ( 0.973239 , -0.185915 , -0.135059 ) Fit gradient sum: ( -0.973239 , 0.185915 , 0.135059 ) Total ( -2.22045e-16 , 2.77556e-17 , -1.11022e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234607 , 0.269564 , -0.172831 ) @@ -555,7 +536,7 @@ colvars: dx(interp) = -1.32278620619718e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.45370e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.58072343892491e-09 -colvars: dx(interp) = 5.58072846304628e-09 +colvars: dx(interp) = 5.58072846304627e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.00263e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70086290502059e-08 @@ -567,11 +548,11 @@ colvars: dx(interp) = -3.07984711538700e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.33569e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.52902282133527e-09 -colvars: dx(interp) = 8.52902381842602e-09 +colvars: dx(interp) = 8.52902381842601e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.16906e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.21517076587952e-10 -colvars: dx(interp) = 8.21520935813326e-10 +colvars: dx(interp) = 8.21520935813319e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.69768e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26158636660057e-08 @@ -583,7 +564,7 @@ colvars: dx(interp) = 1.64322611396739e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.85733e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43348865689586e-09 -colvars: dx(interp) = 9.43349355322967e-09 +colvars: dx(interp) = 9.43349355322966e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.19037e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50185890390730e-08 @@ -591,7 +572,7 @@ colvars: dx(interp) = -1.50185908462051e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.20326e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.11479359077293e-09 -colvars: dx(interp) = 1.11479734212101e-09 +colvars: dx(interp) = 1.11479734212100e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.36506e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94741355953010e-09 @@ -609,7 +590,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03068983242838e-08 colvars: dx(interp) = 3.03068956667397e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.76878e-08. -colvars: Gradient sum: ( 0.973222 , -0.186041 , -0.135007 ) Fit gradient sum: ( -0.973222 , 0.186041 , 0.135007 ) Total ( -1.11022e-16 , 1.66533e-16 , 1.11022e-16 ) +colvars: Gradient sum: ( 0.973222 , -0.186041 , -0.135007 ) Fit gradient sum: ( -0.973222 , 0.186041 , 0.135007 ) Total ( -1.11022e-16 , -2.498e-16 , 0 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234537 , 0.269561 , -0.17281 ) @@ -647,11 +628,11 @@ colvars: dx(interp) = -3.07916615664810e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.56497e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.52869419531999e-09 -colvars: dx(interp) = 8.52868892238300e-09 +colvars: dx(interp) = 8.52868892238299e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.18258e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.19877499225186e-10 -colvars: dx(interp) = 8.19875243528284e-10 +colvars: dx(interp) = 8.19875243528287e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.75126e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26105150555622e-08 @@ -683,13 +664,13 @@ colvars: dx(interp) = 1.43339758956300e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.78098e-09. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.30378747797977e-08 -colvars: dx(interp) = -1.30378745728901e-08 +colvars: dx(interp) = -1.30378745728902e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.58697e-08. colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03053191430536e-08 colvars: dx(interp) = 3.03053173599431e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.88382e-08. -colvars: Gradient sum: ( 0.973204 , -0.186178 , -0.134953 ) Fit gradient sum: ( -0.973204 , 0.186178 , 0.134953 ) Total ( 0 , 0 , -4.16334e-16 ) +colvars: Gradient sum: ( 0.973204 , -0.186178 , -0.134953 ) Fit gradient sum: ( -0.973204 , 0.186178 , 0.134953 ) Total ( 3.33067e-16 , -1.66533e-16 , -1.94289e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234465 , 0.26953 , -0.172803 ) @@ -727,11 +708,11 @@ colvars: dx(interp) = -3.07862418575286e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.39617e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.52950954310927e-09 -colvars: dx(interp) = 8.52950262791878e-09 +colvars: dx(interp) = 8.52950262791877e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.10737e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.18326739704389e-10 -colvars: dx(interp) = 8.18323711303208e-10 +colvars: dx(interp) = 8.18323711303201e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.70072e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26022727598274e-08 @@ -743,7 +724,7 @@ colvars: dx(interp) = 1.64395237187071e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.28199e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.42581479534965e-09 -colvars: dx(interp) = 9.42581605591191e-09 +colvars: dx(interp) = 9.42581605591192e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.33735e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50253089969965e-08 @@ -751,7 +732,7 @@ colvars: dx(interp) = -1.50253124431236e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.29355e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.12816245234626e-09 -colvars: dx(interp) = 1.12815789618417e-09 +colvars: dx(interp) = 1.12815789618418e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.03857e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94434401491162e-09 @@ -769,7 +750,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03002405388497e-08 colvars: dx(interp) = 3.03002411548953e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.03314e-08. -colvars: Gradient sum: ( 0.973182 , -0.186322 , -0.134914 ) Fit gradient sum: ( -0.973182 , 0.186322 , 0.134914 ) Total ( -2.22045e-16 , 8.32667e-17 , 0 ) +colvars: Gradient sum: ( 0.973182 , -0.186322 , -0.134914 ) Fit gradient sum: ( -0.973182 , 0.186322 , 0.134914 ) Total ( -3.33067e-16 , 1.38778e-16 , -8.32667e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.2344 , 0.269471 , -0.172812 ) @@ -795,7 +776,7 @@ colvars: dx(interp) = -1.32356119387801e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.51720e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.55776402677566e-09 -colvars: dx(interp) = 5.55776415678252e-09 +colvars: dx(interp) = 5.55776415678251e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.33919e-08. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.69885455597796e-08 @@ -803,15 +784,15 @@ colvars: dx(interp) = -3.69885421692242e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.16650e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.07832497270510e-08 -colvars: dx(interp) = -3.07832430368368e-08 +colvars: dx(interp) = -3.07832430368367e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.17333e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53208881324008e-09 -colvars: dx(interp) = 8.53209051317432e-09 +colvars: dx(interp) = 8.53209051317431e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.99240e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.16180900642394e-10 -colvars: dx(interp) = 8.16182049051563e-10 +colvars: dx(interp) = 8.16182049051574e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.40705e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25918135707570e-08 @@ -827,7 +808,7 @@ colvars: dx(interp) = 9.42484522140630e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.10575e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50250638597527e-08 -colvars: dx(interp) = -1.50250574958697e-08 +colvars: dx(interp) = -1.50250574958698e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.23551e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.13177911487128e-09 @@ -835,11 +816,11 @@ colvars: dx(interp) = 1.13178194955547e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.50463e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94482007854458e-09 -colvars: dx(interp) = 9.94482275879587e-09 +colvars: dx(interp) = 9.94482275879586e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.69512e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43201948077376e-08 -colvars: dx(interp) = 1.43202002666372e-08 +colvars: dx(interp) = 1.43202002666371e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.81203e-07. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.30169226508769e-08 @@ -849,7 +830,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02934708429348e-08 colvars: dx(interp) = 3.02934722035031e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.49129e-08. -colvars: Gradient sum: ( 0.973155 , -0.186464 , -0.134908 ) Fit gradient sum: ( -0.973155 , 0.186464 , 0.134908 ) Total ( -1.11022e-16 , 1.11022e-16 , 2.77556e-16 ) +colvars: Gradient sum: ( 0.973155 , -0.186464 , -0.134908 ) Fit gradient sum: ( -0.973155 , 0.186464 , 0.134908 ) Total ( 3.33067e-16 , 0 , -5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234296 , 0.269417 , -0.172808 ) @@ -875,7 +856,7 @@ colvars: dx(interp) = -1.32422526736177e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.36098e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.55336931995498e-09 -colvars: dx(interp) = 5.55337024450270e-09 +colvars: dx(interp) = 5.55337024450271e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.66484e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.69760897456217e-08 @@ -887,11 +868,11 @@ colvars: dx(interp) = -3.07767415223223e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.03519e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53379233944906e-09 -colvars: dx(interp) = 8.53379552462336e-09 +colvars: dx(interp) = 8.53379552462335e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.73243e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.17991008261743e-10 -colvars: dx(interp) = 8.17993039794563e-10 +colvars: dx(interp) = 8.17993039794562e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.48356e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25781533866621e-08 @@ -903,7 +884,7 @@ colvars: dx(interp) = 1.64451465632283e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.31202e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.42628552991209e-09 -colvars: dx(interp) = 9.42628948602318e-09 +colvars: dx(interp) = 9.42628948602319e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.19689e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50267567278206e-08 @@ -911,11 +892,11 @@ colvars: dx(interp) = -1.50267515866314e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.42136e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.13714904159679e-09 -colvars: dx(interp) = 1.13714937112551e-09 +colvars: dx(interp) = 1.13714937112552e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.89785e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94296200929057e-09 -colvars: dx(interp) = 9.94296464169271e-09 +colvars: dx(interp) = 9.94296464169270e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.64750e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43117819817462e-08 @@ -929,7 +910,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02822567022076e-08 colvars: dx(interp) = 3.02822597447637e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.00473e-07. -colvars: Gradient sum: ( 0.973121 , -0.186623 , -0.134934 ) Fit gradient sum: ( -0.973121 , 0.186623 , 0.134934 ) Total ( -2.22045e-16 , 1.11022e-16 , -8.32667e-17 ) +colvars: Gradient sum: ( 0.973121 , -0.186623 , -0.134934 ) Fit gradient sum: ( -0.973121 , 0.186623 , 0.134934 ) Total ( -1.11022e-16 , 1.11022e-16 , -3.88578e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234174 , 0.269337 , -0.172813 ) @@ -963,15 +944,15 @@ colvars: dx(interp) = -3.69593977936285e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.28040e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.07704990376578e-08 -colvars: dx(interp) = -3.07704988193405e-08 +colvars: dx(interp) = -3.07704988193406e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.09502e-09. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53549586565805e-09 -colvars: dx(interp) = 8.53549862619538e-09 +colvars: dx(interp) = 8.53549862619539e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.23419e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.20783441213280e-10 -colvars: dx(interp) = 8.20780197348801e-10 +colvars: dx(interp) = 8.20780197348790e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.95216e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25603880419112e-08 @@ -983,7 +964,7 @@ colvars: dx(interp) = 1.64463866462574e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.80441e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43124334185086e-09 -colvars: dx(interp) = 9.43124625857663e-09 +colvars: dx(interp) = 9.43124625857664e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.09262e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50269396925751e-08 @@ -995,7 +976,7 @@ colvars: dx(interp) = 1.14190518785238e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.20873e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94215909599916e-09 -colvars: dx(interp) = 9.94215964550208e-09 +colvars: dx(interp) = 9.94215964550207e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.52700e-08. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43026106513844e-08 @@ -1009,7 +990,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02664240336981e-08 colvars: dx(interp) = 3.02664253559446e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.36869e-08. -colvars: Gradient sum: ( 0.973081 , -0.186777 , -0.135012 ) Fit gradient sum: ( -0.973081 , 0.186777 , 0.135012 ) Total ( 1.11022e-16 , 8.32667e-17 , 2.498e-16 ) +colvars: Gradient sum: ( 0.973081 , -0.186777 , -0.135012 ) Fit gradient sum: ( -0.973081 , 0.186777 , 0.135012 ) Total ( 0 , 2.77556e-16 , -2.22045e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234049 , 0.269251 , -0.172818 ) @@ -1035,7 +1016,7 @@ colvars: dx(interp) = -1.32624504625399e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.50484e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.54771517613517e-09 -colvars: dx(interp) = 5.54771226834331e-09 +colvars: dx(interp) = 5.54771226834333e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.24142e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.69424064672330e-08 @@ -1047,11 +1028,11 @@ colvars: dx(interp) = -3.07644895154988e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.47710e-09. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53744630546771e-09 -colvars: dx(interp) = 8.53744794265352e-09 +colvars: dx(interp) = 8.53744794265350e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.91765e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.23895618395909e-10 -colvars: dx(interp) = 8.23894751207842e-10 +colvars: dx(interp) = 8.23894751207838e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.05255e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25424947994679e-08 @@ -1063,7 +1044,7 @@ colvars: dx(interp) = 1.64481466417069e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.82325e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43529698815837e-09 -colvars: dx(interp) = 9.43529750666335e-09 +colvars: dx(interp) = 9.43529750666334e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.49538e-08. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50270977883338e-08 @@ -1075,7 +1056,7 @@ colvars: dx(interp) = 1.14616428729916e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.44466e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94072202331608e-09 -colvars: dx(interp) = 9.94071820020490e-09 +colvars: dx(interp) = 9.94071820020491e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.84591e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42922811363633e-08 @@ -1089,7 +1070,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02509981509047e-08 colvars: dx(interp) = 3.02509964189633e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.72524e-08. -colvars: Gradient sum: ( 0.973043 , -0.186923 , -0.135085 ) Fit gradient sum: ( -0.973043 , 0.186923 , 0.135085 ) Total ( -1.11022e-16 , 5.55112e-17 , 5.55112e-17 ) +colvars: Gradient sum: ( 0.973043 , -0.186923 , -0.135085 ) Fit gradient sum: ( -0.973043 , 0.186923 , 0.135085 ) Total ( 1.11022e-16 , 2.22045e-16 , 2.77556e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233924 , 0.269169 , -0.17282 ) @@ -1127,11 +1108,11 @@ colvars: dx(interp) = -3.07585788706113e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.46834e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53809289935725e-09 -colvars: dx(interp) = 8.53808936876943e-09 +colvars: dx(interp) = 8.53808936876944e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.13510e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.26105406304123e-10 -colvars: dx(interp) = 8.26104904082130e-10 +colvars: dx(interp) = 8.26104904082126e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.07939e-07. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25262713324537e-08 @@ -1143,7 +1124,7 @@ colvars: dx(interp) = 1.64489014094928e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.75055e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43667011199523e-09 -colvars: dx(interp) = 9.43666776859373e-09 +colvars: dx(interp) = 9.43666776859372e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.48329e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50279149124799e-08 @@ -1151,7 +1132,7 @@ colvars: dx(interp) = -1.50279164684174e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.03536e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.15079323848022e-09 -colvars: dx(interp) = 1.15079570362507e-09 +colvars: dx(interp) = 1.15079570362508e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.14213e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.93875737265171e-09 @@ -1169,7 +1150,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02379525862762e-08 colvars: dx(interp) = 3.02379521612961e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.40545e-08. -colvars: Gradient sum: ( 0.973014 , -0.187041 , -0.135129 ) Fit gradient sum: ( -0.973014 , 0.187041 , 0.135129 ) Total ( 1.11022e-16 , -1.11022e-16 , 0 ) +colvars: Gradient sum: ( 0.973014 , -0.187041 , -0.135129 ) Fit gradient sum: ( -0.973014 , 0.187041 , 0.135129 ) Total ( 0 , 8.32667e-17 , 1.11022e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233783 , 0.269072 , -0.172824 ) @@ -1211,7 +1192,7 @@ colvars: dx(interp) = 8.53851757305771e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.45711e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.28652702011823e-10 -colvars: dx(interp) = 8.28651094684910e-10 +colvars: dx(interp) = 8.28651094684908e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.93969e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25080263713562e-08 @@ -1219,7 +1200,7 @@ colvars: dx(interp) = -5.25080262626950e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.06942e-09. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64482276687750e-08 -colvars: dx(interp) = 1.64482285289397e-08 +colvars: dx(interp) = 1.64482285289396e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.22953e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43820843701815e-09 @@ -1243,13 +1224,13 @@ colvars: dx(interp) = 1.42696604177533e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.65875e-07. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.29644650570526e-08 -colvars: dx(interp) = -1.29644631624477e-08 +colvars: dx(interp) = -1.29644631624476e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.46138e-07. colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02220222181404e-08 colvars: dx(interp) = 3.02220270034202e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.58338e-07. -colvars: Gradient sum: ( 0.972987 , -0.187152 , -0.135166 ) Fit gradient sum: ( -0.972987 , 0.187152 , 0.135166 ) Total ( -1.11022e-16 , 5.55112e-17 , -8.32667e-17 ) +colvars: Gradient sum: ( 0.972987 , -0.187152 , -0.135166 ) Fit gradient sum: ( -0.972987 , 0.187152 , 0.135166 ) Total ( -2.22045e-16 , 5.55112e-17 , -2.498e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233652 , 0.268975 , -0.172829 ) @@ -1275,7 +1256,7 @@ colvars: dx(interp) = -1.32848260553267e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.79536e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.53572121475554e-09 -colvars: dx(interp) = 5.53571877378612e-09 +colvars: dx(interp) = 5.53571877378613e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.40949e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68913646298097e-08 @@ -1287,11 +1268,11 @@ colvars: dx(interp) = -3.07470135653119e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.93636e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53970405501059e-09 -colvars: dx(interp) = 8.53970370599940e-09 +colvars: dx(interp) = 8.53970370599939e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.08692e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.31423818681287e-10 -colvars: dx(interp) = 8.31424273287314e-10 +colvars: dx(interp) = 8.31424273287319e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.46780e-07. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24915630961686e-08 @@ -1303,7 +1284,7 @@ colvars: dx(interp) = 1.64490443312681e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.36057e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43796862884483e-09 -colvars: dx(interp) = 9.43796707135715e-09 +colvars: dx(interp) = 9.43796707135716e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.65024e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50295562661995e-08 @@ -1315,7 +1296,7 @@ colvars: dx(interp) = 1.15783892166374e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.03950e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.93288296058381e-09 -colvars: dx(interp) = 9.93288148106967e-09 +colvars: dx(interp) = 9.93288148106965e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.48951e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42566420890944e-08 @@ -1329,7 +1310,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02093123849545e-08 colvars: dx(interp) = 3.02093113112382e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.55426e-08. -colvars: Gradient sum: ( 0.972963 , -0.187251 , -0.135202 ) Fit gradient sum: ( -0.972963 , 0.187251 , 0.135202 ) Total ( 0 , 0 , 5.55112e-17 ) +colvars: Gradient sum: ( 0.972963 , -0.187251 , -0.135202 ) Fit gradient sum: ( -0.972963 , 0.187251 , 0.135202 ) Total ( 0 , -2.77556e-17 , -5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233501 , 0.268891 , -0.17282 ) @@ -1383,7 +1364,7 @@ colvars: dx(interp) = 1.64524625852538e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.02999e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43822975330022e-09 -colvars: dx(interp) = 9.43822725654554e-09 +colvars: dx(interp) = 9.43822725654555e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.64536e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50321763925376e-08 @@ -1400,7 +1381,7 @@ colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.12540e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42431844096791e-08 colvars: dx(interp) = 1.42431843748016e-08 -colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.44872e-09. +colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.44871e-09. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.29516273261743e-08 colvars: dx(interp) = -1.29516244952331e-08 @@ -1409,7 +1390,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01953040349190e-08 colvars: dx(interp) = 3.01953067756868e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.07680e-08. -colvars: Gradient sum: ( 0.972936 , -0.18736 , -0.135247 ) Fit gradient sum: ( -0.972936 , 0.18736 , 0.135247 ) Total ( -1.11022e-16 , 1.11022e-16 , -5.55112e-17 ) +colvars: Gradient sum: ( 0.972936 , -0.18736 , -0.135247 ) Fit gradient sum: ( -0.972936 , 0.18736 , 0.135247 ) Total ( -3.33067e-16 , 1.94289e-16 , 2.77556e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233334 , 0.268839 , -0.172792 ) @@ -1435,7 +1416,7 @@ colvars: dx(interp) = -1.32982975870102e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.68116e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.52796031172420e-09 -colvars: dx(interp) = 5.52796395730564e-09 +colvars: dx(interp) = 5.52796395730563e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.59480e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68559884833530e-08 @@ -1451,7 +1432,7 @@ colvars: dx(interp) = 8.54029141083031e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.23973e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.48276116016677e-10 -colvars: dx(interp) = 8.48275187664032e-10 +colvars: dx(interp) = 8.48275187664044e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.09440e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24580787697460e-08 @@ -1463,7 +1444,7 @@ colvars: dx(interp) = 1.64581994897726e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.86623e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44032407801387e-09 -colvars: dx(interp) = 9.44032745458435e-09 +colvars: dx(interp) = 9.44032745458434e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.57675e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50375996099683e-08 @@ -1471,7 +1452,7 @@ colvars: dx(interp) = -1.50376008458710e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.21875e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.16808074324126e-09 -colvars: dx(interp) = 1.16807984581743e-09 +colvars: dx(interp) = 1.16807984581744e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.68289e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.91784787629513e-09 @@ -1489,7 +1470,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01791249768257e-08 colvars: dx(interp) = 3.01791291797173e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.39265e-07. -colvars: Gradient sum: ( 0.972906 , -0.187482 , -0.135296 ) Fit gradient sum: ( -0.972906 , 0.187482 , 0.135296 ) Total ( -1.11022e-16 , -1.66533e-16 , 5.55112e-17 ) +colvars: Gradient sum: ( 0.972906 , -0.187482 , -0.135296 ) Fit gradient sum: ( -0.972906 , 0.187482 , 0.135296 ) Total ( -3.33067e-16 , 1.66533e-16 , -5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233163 , 0.26881 , -0.172755 ) @@ -1515,7 +1496,7 @@ colvars: dx(interp) = -1.33079579182108e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.61708e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.52538281795023e-09 -colvars: dx(interp) = 5.52538365273264e-09 +colvars: dx(interp) = 5.52538365273265e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.51081e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68380721482708e-08 @@ -1527,11 +1508,11 @@ colvars: dx(interp) = -3.07143629147814e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.96154e-09. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.54108606063164e-09 -colvars: dx(interp) = 8.54108462786948e-09 +colvars: dx(interp) = 8.54108462786949e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.67749e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.63986215904333e-10 -colvars: dx(interp) = 8.63984483685957e-10 +colvars: dx(interp) = 8.63984483685953e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.00491e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24407806068439e-08 @@ -1551,7 +1532,7 @@ colvars: dx(interp) = -1.50443213074023e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.15626e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.17551302025731e-09 -colvars: dx(interp) = 1.17551172995610e-09 +colvars: dx(interp) = 1.17551172995609e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.09765e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.90585391491550e-09 @@ -1569,7 +1550,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01599225593918e-08 colvars: dx(interp) = 3.01599231791652e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.05496e-08. -colvars: Gradient sum: ( 0.972861 , -0.187655 , -0.135377 ) Fit gradient sum: ( -0.972861 , 0.187655 , 0.135377 ) Total ( 0 , -1.66533e-16 , -2.22045e-16 ) +colvars: Gradient sum: ( 0.972861 , -0.187655 , -0.135377 ) Fit gradient sum: ( -0.972861 , 0.187655 , 0.135377 ) Total ( -4.44089e-16 , -2.77556e-17 , -8.32667e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233016 , 0.268793 , -0.172714 ) @@ -1603,7 +1584,7 @@ colvars: dx(interp) = -3.68237786462595e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.36274e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.07013916511778e-08 -colvars: dx(interp) = -3.07013933891594e-08 +colvars: dx(interp) = -3.07013933891593e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.66092e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.54437764985505e-09 @@ -1611,11 +1592,11 @@ colvars: dx(interp) = 8.54437233935429e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.21520e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.80977069073197e-10 -colvars: dx(interp) = 8.80974516357789e-10 +colvars: dx(interp) = 8.80974516357787e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.89760e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24269960777701e-08 -colvars: dx(interp) = -5.24269988263056e-08 +colvars: dx(interp) = -5.24269988263055e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.24260e-08. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64836180260863e-08 @@ -1623,7 +1604,7 @@ colvars: dx(interp) = 1.64836152925342e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.65834e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44961797699762e-09 -colvars: dx(interp) = 9.44961894491783e-09 +colvars: dx(interp) = 9.44961894491784e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.02430e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50513521646189e-08 @@ -1631,11 +1612,11 @@ colvars: dx(interp) = -1.50513524198364e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.69564e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.18215304212299e-09 -colvars: dx(interp) = 1.18215354891988e-09 +colvars: dx(interp) = 1.18215354891989e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.28707e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.89235360293605e-09 -colvars: dx(interp) = 9.89235145488877e-09 +colvars: dx(interp) = 9.89235145488878e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.17142e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42107428047211e-08 @@ -1649,7 +1630,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01451859030522e-08 colvars: dx(interp) = 3.01451822120947e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.22439e-07. -colvars: Gradient sum: ( 0.972812 , -0.187862 , -0.135443 ) Fit gradient sum: ( -0.972812 , 0.187862 , 0.135443 ) Total ( -3.33067e-16 , 2.22045e-16 , -3.88578e-16 ) +colvars: Gradient sum: ( 0.972812 , -0.187862 , -0.135443 ) Fit gradient sum: ( -0.972812 , 0.187862 , 0.135443 ) Total ( 0 , 8.32667e-17 , -2.77556e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.232895 , 0.268756 , -0.172689 ) @@ -1675,7 +1656,7 @@ colvars: dx(interp) = -1.33145349553423e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.89118e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.53619017296114e-09 -colvars: dx(interp) = 5.53619602088125e-09 +colvars: dx(interp) = 5.53619602088123e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.05631e-06. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68101620296102e-08 @@ -1703,7 +1684,7 @@ colvars: dx(interp) = 1.64991576726264e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.27652e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.45344957870020e-09 -colvars: dx(interp) = 9.45345422358396e-09 +colvars: dx(interp) = 9.45345422358397e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.91343e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50559547051898e-08 @@ -1711,7 +1692,7 @@ colvars: dx(interp) = -1.50559499577201e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.15322e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.18710907770492e-09 -colvars: dx(interp) = 1.18711101841253e-09 +colvars: dx(interp) = 1.18711101841254e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.63482e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.88098136645021e-09 @@ -1729,7 +1710,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01317442108484e-08 colvars: dx(interp) = 3.01317461182275e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.33013e-08. -colvars: Gradient sum: ( 0.972755 , -0.188099 , -0.135521 ) Fit gradient sum: ( -0.972755 , 0.188099 , 0.135521 ) Total ( 0 , 2.77556e-17 , 8.32667e-17 ) +colvars: Gradient sum: ( 0.972755 , -0.188099 , -0.135521 ) Fit gradient sum: ( -0.972755 , 0.188099 , 0.135521 ) Total ( -1.11022e-16 , -8.32667e-17 , 2.77556e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.232767 , 0.268736 , -0.172656 ) @@ -1755,7 +1736,7 @@ colvars: dx(interp) = -1.33169569565328e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.26978e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.54423351672995e-09 -colvars: dx(interp) = 5.54423349146830e-09 +colvars: dx(interp) = 5.54423349146829e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.55638e-09. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.67969441583682e-08 @@ -1763,15 +1744,15 @@ colvars: dx(interp) = -3.67969415711082e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.03118e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.06796579252477e-08 -colvars: dx(interp) = -3.06796542496762e-08 +colvars: dx(interp) = -3.06796542496761e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.19805e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.55582804604182e-09 -colvars: dx(interp) = 8.55583619604505e-09 +colvars: dx(interp) = 8.55583619604507e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.52567e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 9.12068642833219e-10 -colvars: dx(interp) = 9.12071277135839e-10 +colvars: dx(interp) = 9.12071277135838e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.88827e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.23999084123261e-08 @@ -1791,11 +1772,11 @@ colvars: dx(interp) = -1.50616518663852e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.10329e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.19267085096908e-09 -colvars: dx(interp) = 1.19267017999369e-09 +colvars: dx(interp) = 1.19267017999368e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.62582e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.86899095778426e-09 -colvars: dx(interp) = 9.86899596501447e-09 +colvars: dx(interp) = 9.86899596501446e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.07370e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.41884619608845e-08 @@ -1809,5 +1790,5 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01179419182063e-08 colvars: dx(interp) = 3.01179465384051e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.53404e-07. -colvars: Gradient sum: ( 0.972697 , -0.188344 , -0.135599 ) Fit gradient sum: ( -0.972697 , 0.188344 , 0.135599 ) Total ( -2.22045e-16 , 1.11022e-16 , -1.11022e-16 ) +colvars: Gradient sum: ( 0.972697 , -0.188344 , -0.135599 ) Fit gradient sum: ( -0.972697 , 0.188344 , 0.135599 ) Total ( 0 , -8.32667e-17 , -3.05311e-16 ) colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj index 0aee73595..92e7f7f59 100644 --- a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj +++ b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step r fa_r 0 1.42934254297405e+01 -1.42934254297405e+00 - 1 1.42933316010584e+01 -1.42933316010584e+00 - 2 1.42929135723284e+01 -1.42929135723284e+00 - 3 1.42923486101213e+01 -1.42923486101213e+00 - 4 1.42923026875853e+01 -1.42923026875853e+00 - 5 1.42924344310511e+01 -1.42924344310511e+00 - 6 1.42922522296169e+01 -1.42922522296169e+00 - 7 1.42921269629819e+01 -1.42921269629819e+00 - 8 1.42921521124067e+01 -1.42921521124067e+00 - 9 1.42925995746785e+01 -1.42925995746785e+00 - 10 1.42932888390403e+01 -1.42932888390403e+00 - 11 1.42938611783336e+01 -1.42938611783336e+00 - 12 1.42940308415500e+01 -1.42940308415500e+00 - 13 1.42939753495075e+01 -1.42939753495075e+00 - 14 1.42930019085500e+01 -1.42930019085500e+00 - 15 1.42917673901443e+01 -1.42917673901443e+00 - 16 1.42906595563889e+01 -1.42906595563889e+00 - 17 1.42898165380577e+01 -1.42898165380577e+00 - 18 1.42887881291995e+01 -1.42887881291995e+00 - 19 1.42873640416024e+01 -1.42873640416024e+00 - 20 1.42859393553853e+01 -1.42859393553853e+00 + 1 1.42933316010585e+01 -1.42933316010585e+00 + 2 1.42929135723286e+01 -1.42929135723286e+00 + 3 1.42923486101217e+01 -1.42923486101217e+00 + 4 1.42923026875859e+01 -1.42923026875859e+00 + 5 1.42924344310521e+01 -1.42924344310521e+00 + 6 1.42922522296184e+01 -1.42922522296184e+00 + 7 1.42921269629840e+01 -1.42921269629840e+00 + 8 1.42921521124096e+01 -1.42921521124096e+00 + 9 1.42925995746822e+01 -1.42925995746822e+00 + 10 1.42932888390452e+01 -1.42932888390452e+00 + 11 1.42938611783395e+01 -1.42938611783396e+00 + 12 1.42940308415572e+01 -1.42940308415572e+00 + 13 1.42939753495160e+01 -1.42939753495160e+00 + 14 1.42930019085598e+01 -1.42930019085598e+00 + 15 1.42917673901553e+01 -1.42917673901553e+00 + 16 1.42906595564010e+01 -1.42906595564010e+00 + 17 1.42898165380707e+01 -1.42898165380707e+00 + 18 1.42887881292130e+01 -1.42887881292130e+00 + 19 1.42873640416160e+01 -1.42873640416160e+00 + 20 1.42859393553985e+01 -1.42859393553985e+00 diff --git a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped index 8c6776e10..b42918a80 100644 --- a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name angle - x 9.03916964165211e+01 + x 9.03916964164922e+01 } restraint { diff --git a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj index b71ea85f2..5e9454d4b 100644 --- a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj +++ b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step angle fa_angle 0 8.94641033519923e+01 2.92663795777991e+00 - 1 8.94912729262455e+01 2.91909085382069e+00 - 2 8.95442152151541e+01 2.90438466245720e+00 - 3 8.96073749974988e+01 2.88684027847255e+00 - 4 8.96877844443296e+01 2.86450432101956e+00 - 5 8.97771650948167e+01 2.83967636255091e+00 - 6 8.98769301106577e+01 2.81196385815065e+00 - 7 8.99890383094453e+01 2.78082269182076e+00 - 8 9.01041412594469e+01 2.74884965015365e+00 - 9 9.02399071760806e+01 2.71113689553318e+00 - 10 9.03916964165211e+01 2.66897321763303e+00 + 1 8.94912729262462e+01 2.91909085382051e+00 + 2 8.95442152151567e+01 2.90438466245647e+00 + 3 8.96073749975041e+01 2.88684027847108e+00 + 4 8.96877844443377e+01 2.86450432101732e+00 + 5 8.97771650948268e+01 2.83967636254810e+00 + 6 8.98769301106680e+01 2.81196385814778e+00 + 7 8.99890383094529e+01 2.78082269181864e+00 + 8 9.01041412594477e+01 2.74884965015340e+00 + 9 9.02399071760696e+01 2.71113689553622e+00 + 10 9.03916964164922e+01 2.66897321764106e+00 diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out index 8b2c94159..6bf9ea6a6 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 0 colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,27 +125,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped index f96f926f7..f7587bf73 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685416853788e+00 + x 3.21685416874363e+00 } restraint { diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj index 450a1752e..8aaf17fd1 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hp_one - 0 3.20554673468334e+00 -4.96887477549335e-02 1.92888410426048e-02 - 1 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 - 2 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 - 3 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 - 4 3.20472669829003e+00 -4.96756271726405e-02 1.92786557421498e-02 - 5 3.20472669829003e+00 0.00000000000000e+00 1.92786557421498e-02 - 6 3.20472669829003e+00 0.00000000000000e+00 1.92786557421498e-02 - 7 3.20472669829003e+00 0.00000000000000e+00 1.92786557421498e-02 - 8 3.21245897755043e+00 -4.97993436408069e-02 1.93748017738685e-02 - 9 3.21245897755043e+00 0.00000000000000e+00 1.93748017738685e-02 - 10 3.21245897755043e+00 0.00000000000000e+00 1.93748017738685e-02 - 11 3.21245897755043e+00 0.00000000000000e+00 1.93748017738685e-02 - 12 3.22129314143762e+00 -4.99406902630019e-02 1.94849417495711e-02 - 13 3.22129314143762e+00 0.00000000000000e+00 1.94849417495711e-02 - 14 3.22129314143762e+00 0.00000000000000e+00 1.94849417495711e-02 - 15 3.22129314143762e+00 0.00000000000000e+00 1.94849417495711e-02 - 16 3.22320461230820e+00 -4.99712737969313e-02 1.95088141006865e-02 - 17 3.22320461230820e+00 0.00000000000000e+00 1.95088141006865e-02 - 18 3.22320461230820e+00 0.00000000000000e+00 1.95088141006865e-02 - 19 3.22320461230820e+00 0.00000000000000e+00 1.95088141006865e-02 - 20 3.21685416853788e+00 -4.98696666966061e-02 1.94295598158639e-02 + 0 3.20554673468334e+00 -4.96887477549335e-02 1.92888410426048e-02 + 1 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 + 2 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 + 3 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 + 4 3.20472669830023e+00 -4.96756271728037e-02 1.92786557422765e-02 + 5 3.20472669830023e+00 0.00000000000000e+00 1.92786557422765e-02 + 6 3.20472669830023e+00 0.00000000000000e+00 1.92786557422765e-02 + 7 3.20472669830023e+00 0.00000000000000e+00 1.92786557422765e-02 + 8 3.21245897759072e+00 -4.97993436414515e-02 1.93748017743701e-02 + 9 3.21245897759072e+00 0.00000000000000e+00 1.93748017743701e-02 + 10 3.21245897759072e+00 0.00000000000000e+00 1.93748017743701e-02 + 11 3.21245897759072e+00 0.00000000000000e+00 1.93748017743701e-02 + 12 3.22129314152384e+00 -4.99406902643814e-02 1.94849417506475e-02 + 13 3.22129314152384e+00 0.00000000000000e+00 1.94849417506475e-02 + 14 3.22129314152384e+00 0.00000000000000e+00 1.94849417506475e-02 + 15 3.22129314152384e+00 0.00000000000000e+00 1.94849417506475e-02 + 16 3.22320461245070e+00 -4.99712737992112e-02 1.95088141024666e-02 + 17 3.22320461245070e+00 0.00000000000000e+00 1.95088141024666e-02 + 18 3.22320461245070e+00 0.00000000000000e+00 1.95088141024666e-02 + 19 3.22320461245070e+00 0.00000000000000e+00 1.95088141024666e-02 + 20 3.21685416874363e+00 -4.98696666998981e-02 1.94295598184291e-02 diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out index ca317540a..6f4f440d6 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 0 colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,32 +125,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "hp_one" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped index c5c46002b..566d795a4 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397142146894e+00 + x 3.21397142195016e+00 } restraint { diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj index 25e47276b..e5c68ffe3 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hp_one - 20 3.21685416853788e+00 -4.98696666966061e-02 1.94295598158639e-02 - 21 3.21685416853788e+00 0.00000000000000e+00 1.94295598158639e-02 - 22 3.21685416853788e+00 0.00000000000000e+00 1.94295598158639e-02 - 23 3.21685416853788e+00 0.00000000000000e+00 1.94295598158639e-02 - 24 3.20781524498993e+00 -4.97250439198388e-02 1.93170311939836e-02 - 25 3.20781524498993e+00 0.00000000000000e+00 1.93170311939836e-02 - 26 3.20781524498993e+00 0.00000000000000e+00 1.93170311939836e-02 - 27 3.20781524498993e+00 0.00000000000000e+00 1.93170311939836e-02 - 28 3.20267947244878e+00 -4.96428715591806e-02 1.92532398175101e-02 - 29 3.20267947244878e+00 0.00000000000000e+00 1.92532398175101e-02 - 30 3.20267947244878e+00 0.00000000000000e+00 1.92532398175101e-02 - 31 3.20267947244878e+00 0.00000000000000e+00 1.92532398175101e-02 - 32 3.20367252455682e+00 -4.96587603929091e-02 1.92655662793778e-02 - 33 3.20367252455682e+00 0.00000000000000e+00 1.92655662793778e-02 - 34 3.20367252455682e+00 0.00000000000000e+00 1.92655662793778e-02 - 35 3.20367252455682e+00 0.00000000000000e+00 1.92655662793778e-02 - 36 3.20851202025206e+00 -4.97361923240330e-02 1.93256939601031e-02 - 37 3.20851202025206e+00 0.00000000000000e+00 1.93256939601031e-02 - 38 3.20851202025206e+00 0.00000000000000e+00 1.93256939601031e-02 - 39 3.20851202025206e+00 0.00000000000000e+00 1.93256939601031e-02 - 40 3.21397142146894e+00 -4.98235427435031e-02 1.93936360274506e-02 + 20 3.21685416874363e+00 -4.98696666998981e-02 1.94295598184291e-02 + 21 3.21685416874363e+00 0.00000000000000e+00 1.94295598184291e-02 + 22 3.21685416874363e+00 0.00000000000000e+00 1.94295598184291e-02 + 23 3.21685416874363e+00 0.00000000000000e+00 1.94295598184291e-02 + 24 3.20781524526346e+00 -4.97250439242154e-02 1.93170311973840e-02 + 25 3.20781524526346e+00 0.00000000000000e+00 1.93170311973840e-02 + 26 3.20781524526346e+00 0.00000000000000e+00 1.93170311973840e-02 + 27 3.20781524526346e+00 0.00000000000000e+00 1.93170311973840e-02 + 28 3.20267947278925e+00 -4.96428715646280e-02 1.92532398217355e-02 + 29 3.20267947278925e+00 0.00000000000000e+00 1.92532398217355e-02 + 30 3.20267947278925e+00 0.00000000000000e+00 1.92532398217355e-02 + 31 3.20267947278925e+00 0.00000000000000e+00 1.92532398217355e-02 + 32 3.20367252495752e+00 -4.96587603993203e-02 1.92655662843524e-02 + 33 3.20367252495752e+00 0.00000000000000e+00 1.92655662843524e-02 + 34 3.20367252495752e+00 0.00000000000000e+00 1.92655662843524e-02 + 35 3.20367252495752e+00 0.00000000000000e+00 1.92655662843524e-02 + 36 3.20851202070242e+00 -4.97361923312387e-02 1.93256939657028e-02 + 37 3.20851202070242e+00 0.00000000000000e+00 1.93256939657028e-02 + 38 3.20851202070242e+00 0.00000000000000e+00 1.93256939657028e-02 + 39 3.20851202070242e+00 0.00000000000000e+00 1.93256939657028e-02 + 40 3.21397142195016e+00 -4.98235427512026e-02 1.93936360334447e-02 diff --git a/namd/tests/library/016_mts_bias/namd-version.txt b/namd/tests/library/016_mts_bias/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/016_mts_bias/namd-version.txt +++ b/namd/tests/library/016_mts_bias/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out index e9eb1b9a5..90ba327a0 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out +++ b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -15,7 +12,6 @@ colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -29,28 +25,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -67,28 +63,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = 0.51. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -101,6 +97,37 @@ colvars: Warning: Variable r1 is absent from expression "x". colvars: Warning: Variable r2 is absent from expression "x". colvars: Warning: Variable r3 is absent from expression "x". colvars: Warning: Variable r2 is absent from expression "cos(x) + r1 + r3". +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r3. colvars: Expecting colvar value of type n-dimensional vector of size 2. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] @@ -131,7 +158,6 @@ colvars: # centers = { ( 20 , -5 ) } colvars: # targetCenters = { ( 20 , -5 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 100 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 100 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -142,31 +168,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. +colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "c":1/0. 1 atoms: total mass = 12.011, total charge = 0.51. +colvars: Re-initialized atom group for variable "c":1/1. 1 atoms: total mass = 12.011, total charge = 0.51. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "c":1/0. 1 atoms: total mass = 12.011, total charge = 0.51. diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped index aff97d707..cb77abf4e 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name c - x ( 1.65450803779147e+01 , -2.58120974399207e+00 ) + x ( 1.65450803775141e+01 , -2.58120974253005e+00 ) } restraint { diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj index bfd90c361..d7ab641d2 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj +++ b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj @@ -1,4 +1,4 @@ # step c 0 ( 1.47736880982107e+01 , 5.47598531906441e-01 ) - 10 ( 1.64732268956376e+01 , -1.86635727005636e+00 ) - 20 ( 1.65450803779147e+01 , -2.58120974399207e+00 ) + 10 ( 1.64732268956053e+01 , -1.86635726975950e+00 ) + 20 ( 1.65450803775141e+01 , -2.58120974253006e+00 ) diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped index e7fddb9d1..5b04314b5 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name c - x ( 1.75996935761212e+01 , -3.48707549970946e+00 ) + x ( 1.75996935759052e+01 , -3.48707550156878e+00 ) } restraint { diff --git a/namd/tests/library/017_custom_function/namd-version.txt b/namd/tests/library/017_custom_function/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/017_custom_function/namd-version.txt +++ b/namd/tests/library/017_custom_function/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/018_pathCV/namd-version.txt b/namd/tests/library/018_pathCV/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/018_pathCV/namd-version.txt +++ b/namd/tests/library/018_pathCV/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out index 8f6da7076..4d96ba271 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_dihed" @@ -34,56 +32,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -99,56 +97,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -164,56 +162,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -455,7 +453,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -487,53 +485,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -548,53 +546,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -609,53 +607,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -898,7 +896,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -919,25 +917,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - gspathCV colvar component: -colvars: - gzpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -964,11 +943,11 @@ colvars: Re-initialized atom group for variable "gpath_z_dihed":0/10. 1 atoms: t colvars: Re-initialized atom group for variable "gpath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped index d940cb619..0a6f34748 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped @@ -10,6 +10,6 @@ colvar { colvar { name gpath_z_dihed - x 9.55645131452191e+01 + x 9.55645131452184e+01 } diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj index ddaf3721c..5fac76756 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step gpath_s_dihed gpath_z_dihed 0 7.83123228264734e-01 3.83533978043175e+01 - 1 7.82945678970628e-01 4.29689076394212e+01 - 2 7.82818444070286e-01 4.79082192050887e+01 - 3 7.82680619902823e-01 5.32968526519466e+01 - 4 7.82481029251750e-01 5.95665170545919e+01 - 5 7.82394193117627e-01 6.58557656139231e+01 - 6 7.82260880668904e-01 7.22764122107677e+01 - 7 7.82016364258954e-01 7.87726707676510e+01 - 8 7.81934087543136e-01 8.51257353163676e+01 - 9 7.81821580461319e-01 8.98923615763005e+01 - 10 7.81811987245692e-01 9.36566870572311e+01 + 1 7.82945678970628e-01 4.29689076394209e+01 + 2 7.82818444070286e-01 4.79082192050889e+01 + 3 7.82680619902823e-01 5.32968526519463e+01 + 4 7.82481029251750e-01 5.95665170545922e+01 + 5 7.82394193117627e-01 6.58557656139234e+01 + 6 7.82260880668904e-01 7.22764122107678e+01 + 7 7.82016364258954e-01 7.87726707676512e+01 + 8 7.81934087543136e-01 8.51257353163675e+01 + 9 7.81821580461319e-01 8.98923615763004e+01 + 10 7.81811987245692e-01 9.36566870572305e+01 11 7.81676091324908e-01 9.70906581768438e+01 12 7.81497401408420e-01 1.00284195800025e+02 13 7.81382447528542e-01 1.01730136329478e+02 - 14 7.81310203934944e-01 1.02632785559219e+02 + 14 7.81310203934944e-01 1.02632785559218e+02 15 7.81107670050000e-01 1.02580995635213e+02 16 7.81000240562519e-01 1.01690738350632e+02 17 7.81032069099019e-01 1.00431749174877e+02 - 18 7.81089334289029e-01 9.86347657918943e+01 + 18 7.81089334289029e-01 9.86347657918941e+01 19 7.81314767005367e-01 9.68745522484514e+01 - 20 7.81476379939767e-01 9.55645131452191e+01 + 20 7.81476379939767e-01 9.55645131452184e+01 diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out index 591e79589..ac4527f9d 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_dihed" @@ -34,56 +32,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -99,56 +97,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -164,56 +162,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -455,7 +453,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -487,53 +485,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -548,53 +546,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -609,53 +607,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -898,7 +896,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -919,25 +917,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - gspathCV colvar component: -colvars: - gzpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -963,17 +942,17 @@ colvars: Re-initialized atom group for variable "gpath_z_dihed":0/9. 1 atoms: to colvars: Re-initialized atom group for variable "gpath_z_dihed":0/10. 1 atoms: total mass = 12.01, total charge = 0.0337. colvars: Re-initialized atom group for variable "gpath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "gpath_s_dihed" from value: 0.781476 colvars: Restarting collective variable "gpath_z_dihed" from value: 95.5645 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj index d5ec83feb..5b9068d9b 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step gpath_s_dihed gpath_z_dihed - 20 7.81476379939767e-01 9.55645131452191e+01 - 21 7.81240698201971e-01 1.06229693509577e+02 + 20 7.81476379939767e-01 9.55645131452184e+01 + 21 7.81240698201971e-01 1.06229693509576e+02 22 7.81005545091406e-01 1.17334167235362e+02 - 23 7.80723779014191e-01 1.28845704977404e+02 + 23 7.80723779014191e-01 1.28845704977403e+02 24 7.80348823600053e-01 1.41207832230497e+02 - 25 7.80052868542975e-01 1.53573472293347e+02 + 25 7.80052868542975e-01 1.53573472293346e+02 26 7.79695411661275e-01 1.65225530758384e+02 27 7.79227129868925e-01 1.75833882118768e+02 28 7.78924791555966e-01 1.85072740224480e+02 - 29 7.78616822792614e-01 1.91408513274007e+02 - 30 7.78445744037639e-01 1.96072266414115e+02 + 29 7.78616822792614e-01 1.91408513274006e+02 + 30 7.78445744037639e-01 1.96072266414114e+02 31 7.78198587511674e-01 1.99830728112820e+02 - 32 7.77969198638703e-01 2.02348834208334e+02 - 33 7.77870454975722e-01 2.01925240313579e+02 + 32 7.77969198638703e-01 2.02348834208335e+02 + 33 7.77870454975722e-01 2.01925240313578e+02 34 7.77892445039517e-01 2.00152956848502e+02 - 35 7.77861620836214e-01 1.96872674617573e+02 - 36 7.78012144635351e-01 1.92375777763847e+02 + 35 7.77861620836214e-01 1.96872674617572e+02 + 36 7.78012144635351e-01 1.92375777763846e+02 37 7.78402492011077e-01 1.87024840666577e+02 38 7.78909881410184e-01 1.81082923676999e+02 - 39 7.79681670070840e-01 1.75290823442271e+02 + 39 7.79681670070840e-01 1.75290823442270e+02 40 7.80475723743606e-01 1.69997870041256e+02 diff --git a/namd/tests/library/019_gpathCV/namd-version.txt b/namd/tests/library/019_gpathCV/namd-version.txt index 157cac038..90b3a010a 100644 --- a/namd/tests/library/019_gpathCV/namd-version.txt +++ b/namd/tests/library/019_gpathCV/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA +colvars: Initializing the collective variables module, version "2019-10-21". +colvars: Using NAMD interface, version "2019-10-21". diff --git a/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj b/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj index f4d864ba8..a2d265a65 100644 --- a/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj +++ b/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step gpath_s_cartesian gpath_z_cartesian 0 5.30720368611864e-01 8.61059914994141e-02 - 1 5.30717690590865e-01 8.54273375358692e-02 - 2 5.30714251957229e-01 8.51458403558880e-02 - 3 5.30710055975446e-01 8.51321853522883e-02 - 4 5.30704973571852e-01 8.52949333585580e-02 - 5 5.30697460621445e-01 8.55508921045213e-02 - 6 5.30685286827787e-01 8.56177474112287e-02 - 7 5.30670902617345e-01 8.57812083900462e-02 - 8 5.30652367951073e-01 8.59993861857884e-02 - 9 5.30632081382459e-01 8.62909912963241e-02 - 10 5.30606987319570e-01 8.66946366005643e-02 + 1 5.30717690590865e-01 8.54273375358691e-02 + 2 5.30714251957229e-01 8.51458403558881e-02 + 3 5.30710055975446e-01 8.51321853522884e-02 + 4 5.30704973571852e-01 8.52949333585581e-02 + 5 5.30697460621445e-01 8.55508921045210e-02 + 6 5.30685286827787e-01 8.56177474112286e-02 + 7 5.30670902617345e-01 8.57812083900463e-02 + 8 5.30652367951073e-01 8.59993861857883e-02 + 9 5.30632081382459e-01 8.62909912963239e-02 + 10 5.30606987319570e-01 8.66946366005642e-02 11 5.30579540524640e-01 8.73047828339237e-02 - 12 5.30552631793952e-01 8.81730152476006e-02 - 13 5.30524058862923e-01 8.91926063197971e-02 + 12 5.30552631793952e-01 8.81730152476007e-02 + 13 5.30524058862923e-01 8.91926063197970e-02 14 5.30493980557183e-01 9.03283581585283e-02 15 5.30463117047670e-01 9.15212996991972e-02 16 5.30431734419221e-01 9.30006426174987e-02 - 17 5.30399413235259e-01 9.44575442040143e-02 - 18 5.30368252449657e-01 9.62800980538578e-02 + 17 5.30399413235259e-01 9.44575442040145e-02 + 18 5.30368252449657e-01 9.62800980538579e-02 19 5.30333234090156e-01 9.82010258065717e-02 20 5.30301765703773e-01 1.00592004206710e-01 diff --git a/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj b/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj index 44c3cc8ee..0b4049f9a 100644 --- a/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj @@ -1,6 +1,6 @@ # step gpath_s_cartesian gpath_z_cartesian 20 5.30301765703773e-01 1.00592004206710e-01 - 21 5.30299068311154e-01 1.01776105919982e-01 + 21 5.30299068311154e-01 1.01776105919981e-01 22 5.30296225733479e-01 1.02913020025282e-01 23 5.30293151382629e-01 1.03888660431483e-01 24 5.30289871026115e-01 1.04670153673202e-01 @@ -10,9 +10,9 @@ 28 5.30250537018860e-01 1.05411857890215e-01 29 5.30235512500134e-01 1.05013013758426e-01 30 5.30216395990587e-01 1.04566807352862e-01 - 31 5.30195586650359e-01 1.04225738170003e-01 + 31 5.30195586650359e-01 1.04225738170004e-01 32 5.30176202069296e-01 1.03881270572137e-01 - 33 5.30155909450721e-01 1.03435901761179e-01 + 33 5.30155909450721e-01 1.03435901761180e-01 34 5.30134759237002e-01 1.02902765055984e-01 35 5.30113387291624e-01 1.02318158639028e-01 36 5.30092042017102e-01 1.01828820799264e-01 diff --git a/namd/tests/library/020_gpath/namd-version.txt b/namd/tests/library/020_gpath/namd-version.txt index 157cac038..355758d76 100644 --- a/namd/tests/library/020_gpath/namd-version.txt +++ b/namd/tests/library/020_gpath/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +Info: NAMD 3.0b3 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-18. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out index 8b007336e..2825984f5 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_distanceVec" @@ -34,9 +32,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -47,14 +44,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -70,9 +67,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -83,14 +79,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -106,9 +102,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -119,14 +114,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -142,9 +137,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -155,14 +149,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -178,9 +172,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -191,14 +184,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -214,9 +207,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -227,14 +219,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -250,9 +242,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -263,14 +254,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -286,9 +277,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -299,14 +289,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -322,9 +312,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -335,14 +324,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -358,9 +347,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -371,14 +359,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -394,9 +382,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -407,14 +394,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -430,9 +417,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -443,14 +429,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -466,9 +452,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -479,14 +464,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -502,9 +487,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -515,14 +499,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -538,9 +522,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -551,14 +534,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -574,9 +557,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -587,14 +569,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -610,9 +592,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -623,14 +604,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -646,9 +627,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -659,14 +639,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -682,9 +662,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -695,14 +674,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -718,9 +697,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -731,14 +709,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3182,11 +3160,12 @@ colvars: # useSecondClosestFrame = on [default] colvars: Geometric path s(σ) will use the second closest frame to compute s_(m-1) colvars: # useThirdClosestFrame = off [default] colvars: Geometric path s(σ) will use the neighbouring frame to compute s_(m+1) +colvars: Geometric path s(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3218,9 +3197,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3231,14 +3209,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3254,9 +3232,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3267,14 +3244,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3290,9 +3267,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3303,14 +3279,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3326,9 +3302,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3339,14 +3314,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3362,9 +3337,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3375,14 +3349,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3398,9 +3372,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3411,14 +3384,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3434,9 +3407,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3447,14 +3419,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3470,9 +3442,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3483,14 +3454,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3506,9 +3477,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3519,14 +3489,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3542,9 +3512,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3555,14 +3524,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3578,9 +3547,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3591,14 +3559,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3614,9 +3582,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3627,14 +3594,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3650,9 +3617,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3663,14 +3629,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3686,9 +3652,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3699,14 +3664,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3722,9 +3687,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3735,14 +3699,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3758,9 +3722,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3771,14 +3734,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3794,9 +3757,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3807,14 +3769,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3830,9 +3792,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3843,14 +3804,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3866,9 +3827,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3879,14 +3839,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3902,9 +3862,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3915,14 +3874,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6368,11 +6327,12 @@ colvars: # useThirdClosestFrame = off [default] colvars: Geometric path z(σ) will use the neighbouring frame to compute s_(m+1) colvars: # useZsquare = on colvars: Geometric path z(σ) will use the square of distance from current frame to path compute z +colvars: Geometric path z(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6393,26 +6353,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - gspathCV colvar component: -colvars: - gzpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6495,11 +6435,11 @@ colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/38. 0 at colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj index e5d0bb3cf..8e7ee67dd 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj @@ -2,15 +2,15 @@ 0 3.77171678533515e-02 6.76736838399185e+02 1 3.77408160662234e-02 6.76814886658536e+02 2 3.77652902052649e-02 6.76904118559529e+02 - 3 3.77885901836011e-02 6.77002173338060e+02 + 3 3.77885901836011e-02 6.77002173338061e+02 4 3.78148176804083e-02 6.77104722272709e+02 5 3.78372534576845e-02 6.77211769234532e+02 - 6 3.78552413890631e-02 6.77324430169634e+02 + 6 3.78552413890631e-02 6.77324430169633e+02 7 3.78833685463047e-02 6.77427790438348e+02 - 8 3.79119516235524e-02 6.77529691393681e+02 + 8 3.79119516235519e-02 6.77529691393681e+02 9 3.79430521380542e-02 6.77636436765019e+02 - 10 3.79763962901917e-02 6.77753499558135e+02 - 11 3.80148985287524e-02 6.77879781194716e+02 + 10 3.79763962901923e-02 6.77753499558135e+02 + 11 3.80148985287519e-02 6.77879781194716e+02 12 3.80574676219839e-02 6.77995499164433e+02 13 3.80958506694046e-02 6.78083025670623e+02 14 3.81395612603290e-02 6.78153378635457e+02 diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out index 1d14cbe04..e11c82e21 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_distanceVec" @@ -34,9 +32,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -47,14 +44,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -70,9 +67,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -83,14 +79,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -106,9 +102,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -119,14 +114,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -142,9 +137,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -155,14 +149,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -178,9 +172,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -191,14 +184,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -214,9 +207,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -227,14 +219,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -250,9 +242,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -263,14 +254,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -286,9 +277,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -299,14 +289,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -322,9 +312,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -335,14 +324,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -358,9 +347,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -371,14 +359,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -394,9 +382,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -407,14 +394,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -430,9 +417,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -443,14 +429,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -466,9 +452,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -479,14 +464,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -502,9 +487,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -515,14 +499,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -538,9 +522,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -551,14 +534,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -574,9 +557,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -587,14 +569,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -610,9 +592,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -623,14 +604,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -646,9 +627,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -659,14 +639,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -682,9 +662,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -695,14 +674,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -718,9 +697,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -731,14 +709,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3182,11 +3160,12 @@ colvars: # useSecondClosestFrame = on [default] colvars: Geometric path s(σ) will use the second closest frame to compute s_(m-1) colvars: # useThirdClosestFrame = off [default] colvars: Geometric path s(σ) will use the neighbouring frame to compute s_(m+1) +colvars: Geometric path s(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3218,9 +3197,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3231,14 +3209,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3254,9 +3232,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3267,14 +3244,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3290,9 +3267,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3303,14 +3279,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3326,9 +3302,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3339,14 +3314,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3362,9 +3337,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3375,14 +3349,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3398,9 +3372,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3411,14 +3384,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3434,9 +3407,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3447,14 +3419,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3470,9 +3442,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3483,14 +3454,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3506,9 +3477,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3519,14 +3489,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3542,9 +3512,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3555,14 +3524,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3578,9 +3547,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3591,14 +3559,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3614,9 +3582,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3627,14 +3594,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3650,9 +3617,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3663,14 +3629,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3686,9 +3652,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3699,14 +3664,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3722,9 +3687,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3735,14 +3699,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3758,9 +3722,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3771,14 +3734,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3794,9 +3757,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3807,14 +3769,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3830,9 +3792,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3843,14 +3804,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3866,9 +3827,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3879,14 +3839,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3902,9 +3862,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3915,14 +3874,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6368,11 +6327,12 @@ colvars: # useThirdClosestFrame = off [default] colvars: Geometric path z(σ) will use the neighbouring frame to compute s_(m+1) colvars: # useZsquare = on colvars: Geometric path z(σ) will use the square of distance from current frame to path compute z +colvars: Geometric path z(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6393,26 +6353,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - gspathCV colvar component: -colvars: - gzpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6494,17 +6434,17 @@ colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/37. 1 at colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/38. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "gpath_s_distanceVec" from value: 0.0384565 colvars: Restarting collective variable "gpath_z_distanceVec" from value: 678.131 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj index 81de6b0bc..defbf6a45 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj @@ -10,10 +10,10 @@ 28 3.86084059020791e-02 6.78925279191111e+02 29 3.86298828548808e-02 6.79025716470530e+02 30 3.86527796201097e-02 6.79134948406694e+02 - 31 3.86798568836978e-02 6.79251839399435e+02 + 31 3.86798568836977e-02 6.79251839399435e+02 32 3.87098949985802e-02 6.79356485630484e+02 33 3.87343129795344e-02 6.79430860596411e+02 - 34 3.87624579979551e-02 6.79485989524982e+02 + 34 3.87624579979557e-02 6.79485989524982e+02 35 3.87892874098554e-02 6.79502594982682e+02 36 3.88193203791849e-02 6.79495678267542e+02 37 3.88506047395243e-02 6.79480901306783e+02 diff --git a/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt b/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt index 157cac038..90b3a010a 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt +++ b/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA +colvars: Initializing the collective variables module, version "2019-10-21". +colvars: Using NAMD interface, version "2019-10-21". diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out index 4dbd24972..27624c699 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_distanceVec" @@ -34,9 +32,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -47,14 +44,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -70,9 +67,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -83,14 +79,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -106,9 +102,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -119,14 +114,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -142,9 +137,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -155,14 +149,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -178,9 +172,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -191,14 +184,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -214,9 +207,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -227,14 +219,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -250,9 +242,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -263,14 +254,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -286,9 +277,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -299,14 +289,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -322,9 +312,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -335,14 +324,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -358,9 +347,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -371,14 +359,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -394,9 +382,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -407,14 +394,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -430,9 +417,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -443,14 +429,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -466,9 +452,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -479,14 +464,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -502,9 +487,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -515,14 +499,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -538,9 +522,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -551,14 +534,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -574,9 +557,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -587,14 +569,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -610,9 +592,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -623,14 +604,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -646,9 +627,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -659,14 +639,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -682,9 +662,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -695,14 +674,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -718,9 +697,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -731,14 +709,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3179,6 +3157,35 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 1.24993 +colvars: Distance between frame 2 and 3 is 1.22263 +colvars: Distance between frame 3 and 4 is 1.15797 +colvars: Distance between frame 4 and 5 is 1.20671 +colvars: Distance between frame 5 and 6 is 1.22068 +colvars: Distance between frame 6 and 7 is 1.27376 +colvars: Distance between frame 7 and 8 is 1.16679 +colvars: Distance between frame 8 and 9 is 1.23641 +colvars: Distance between frame 9 and 10 is 1.23647 +colvars: Distance between frame 10 and 11 is 1.24224 +colvars: Distance between frame 11 and 12 is 1.21755 +colvars: Distance between frame 12 and 13 is 1.2113 +colvars: Distance between frame 13 and 14 is 1.25829 +colvars: Distance between frame 14 and 15 is 1.14361 +colvars: Distance between frame 15 and 16 is 1.25482 +colvars: Distance between frame 16 and 17 is 1.19127 +colvars: Distance between frame 17 and 18 is 1.21515 +colvars: Distance between frame 18 and 19 is 1.28854 +colvars: Distance between frame 19 and 20 is 1.21558 +colvars: Distance between frame 20 and 21 is 1.18825 +colvars: Distance between frame 21 and 22 is 1.29888 +colvars: Distance between frame 22 and 23 is 1.23365 +colvars: Distance between frame 23 and 24 is 1.17305 +colvars: Distance between frame 24 and 25 is 1.32493 +colvars: Distance between frame 25 and 26 is 1.21926 +colvars: Distance between frame 26 and 27 is 1.1941 +colvars: Distance between frame 27 and 28 is 1.28306 +colvars: Distance between frame 28 and 29 is 1.24978 +colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -3205,7 +3212,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3237,9 +3244,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3250,14 +3256,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3273,9 +3279,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3286,14 +3291,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3309,9 +3314,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3322,14 +3326,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3345,9 +3349,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3358,14 +3361,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3381,9 +3384,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3394,14 +3396,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3417,9 +3419,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3430,14 +3431,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3453,9 +3454,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3466,14 +3466,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3489,9 +3489,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3502,14 +3501,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3525,9 +3524,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3538,14 +3536,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3561,9 +3559,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3574,14 +3571,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3597,9 +3594,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3610,14 +3606,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3633,9 +3629,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3646,14 +3641,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3669,9 +3664,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3682,14 +3676,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3705,9 +3699,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3718,14 +3711,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3741,9 +3734,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3754,14 +3746,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3777,9 +3769,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3790,14 +3781,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3813,9 +3804,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3826,14 +3816,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3849,9 +3839,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3862,14 +3851,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3885,9 +3874,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3898,14 +3886,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3921,9 +3909,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3934,14 +3921,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6382,6 +6369,35 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 1.24993 +colvars: Distance between frame 2 and 3 is 1.22263 +colvars: Distance between frame 3 and 4 is 1.15797 +colvars: Distance between frame 4 and 5 is 1.20671 +colvars: Distance between frame 5 and 6 is 1.22068 +colvars: Distance between frame 6 and 7 is 1.27376 +colvars: Distance between frame 7 and 8 is 1.16679 +colvars: Distance between frame 8 and 9 is 1.23641 +colvars: Distance between frame 9 and 10 is 1.23647 +colvars: Distance between frame 10 and 11 is 1.24224 +colvars: Distance between frame 11 and 12 is 1.21755 +colvars: Distance between frame 12 and 13 is 1.2113 +colvars: Distance between frame 13 and 14 is 1.25829 +colvars: Distance between frame 14 and 15 is 1.14361 +colvars: Distance between frame 15 and 16 is 1.25482 +colvars: Distance between frame 16 and 17 is 1.19127 +colvars: Distance between frame 17 and 18 is 1.21515 +colvars: Distance between frame 18 and 19 is 1.28854 +colvars: Distance between frame 19 and 20 is 1.21558 +colvars: Distance between frame 20 and 21 is 1.18825 +colvars: Distance between frame 21 and 22 is 1.29888 +colvars: Distance between frame 22 and 23 is 1.23365 +colvars: Distance between frame 23 and 24 is 1.17305 +colvars: Distance between frame 24 and 25 is 1.32493 +colvars: Distance between frame 25 and 26 is 1.21926 +colvars: Distance between frame 26 and 27 is 1.1941 +colvars: Distance between frame 27 and 28 is 1.28306 +colvars: Distance between frame 28 and 29 is 1.24978 +colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -6408,7 +6424,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6429,26 +6445,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - aspathCV colvar component: -colvars: - azpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6531,11 +6527,11 @@ colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/38. 0 at colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj index 358b06848..8c3fd2f17 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj @@ -7,10 +7,10 @@ 5 3.71951763458571e-02 6.76437235131064e+02 6 3.72110087084931e-02 6.76548721440867e+02 7 3.72351763642007e-02 6.76650733895917e+02 - 8 3.72595960457660e-02 6.76751383624712e+02 + 8 3.72595960457659e-02 6.76751383624712e+02 9 3.72860044867264e-02 6.76856908644382e+02 - 10 3.73141938916311e-02 6.76972778630392e+02 - 11 3.73465707477626e-02 6.77097844460360e+02 + 10 3.73141938916315e-02 6.76972778630392e+02 + 11 3.73465707477625e-02 6.77097844460360e+02 12 3.73823307193035e-02 6.77212255632268e+02 13 3.74145603254307e-02 6.77298631416326e+02 14 3.74510510199529e-02 6.77367872060677e+02 diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out index 81cb87adf..a31a3d332 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_distanceVec" @@ -34,9 +32,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -47,14 +44,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -70,9 +67,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -83,14 +79,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -106,9 +102,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -119,14 +114,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -142,9 +137,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -155,14 +149,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -178,9 +172,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -191,14 +184,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -214,9 +207,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -227,14 +219,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -250,9 +242,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -263,14 +254,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -286,9 +277,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -299,14 +289,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -322,9 +312,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -335,14 +324,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -358,9 +347,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -371,14 +359,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -394,9 +382,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -407,14 +394,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -430,9 +417,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -443,14 +429,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -466,9 +452,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -479,14 +464,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -502,9 +487,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -515,14 +499,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -538,9 +522,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -551,14 +534,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -574,9 +557,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -587,14 +569,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -610,9 +592,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -623,14 +604,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -646,9 +627,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -659,14 +639,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -682,9 +662,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -695,14 +674,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -718,9 +697,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -731,14 +709,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3179,6 +3157,35 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 1.24993 +colvars: Distance between frame 2 and 3 is 1.22263 +colvars: Distance between frame 3 and 4 is 1.15797 +colvars: Distance between frame 4 and 5 is 1.20671 +colvars: Distance between frame 5 and 6 is 1.22068 +colvars: Distance between frame 6 and 7 is 1.27376 +colvars: Distance between frame 7 and 8 is 1.16679 +colvars: Distance between frame 8 and 9 is 1.23641 +colvars: Distance between frame 9 and 10 is 1.23647 +colvars: Distance between frame 10 and 11 is 1.24224 +colvars: Distance between frame 11 and 12 is 1.21755 +colvars: Distance between frame 12 and 13 is 1.2113 +colvars: Distance between frame 13 and 14 is 1.25829 +colvars: Distance between frame 14 and 15 is 1.14361 +colvars: Distance between frame 15 and 16 is 1.25482 +colvars: Distance between frame 16 and 17 is 1.19127 +colvars: Distance between frame 17 and 18 is 1.21515 +colvars: Distance between frame 18 and 19 is 1.28854 +colvars: Distance between frame 19 and 20 is 1.21558 +colvars: Distance between frame 20 and 21 is 1.18825 +colvars: Distance between frame 21 and 22 is 1.29888 +colvars: Distance between frame 22 and 23 is 1.23365 +colvars: Distance between frame 23 and 24 is 1.17305 +colvars: Distance between frame 24 and 25 is 1.32493 +colvars: Distance between frame 25 and 26 is 1.21926 +colvars: Distance between frame 26 and 27 is 1.1941 +colvars: Distance between frame 27 and 28 is 1.28306 +colvars: Distance between frame 28 and 29 is 1.24978 +colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -3205,7 +3212,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3237,9 +3244,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3250,14 +3256,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3273,9 +3279,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3286,14 +3291,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3309,9 +3314,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3322,14 +3326,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3345,9 +3349,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3358,14 +3361,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3381,9 +3384,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3394,14 +3396,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3417,9 +3419,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3430,14 +3431,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3453,9 +3454,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3466,14 +3466,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3489,9 +3489,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3502,14 +3501,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3525,9 +3524,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3538,14 +3536,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3561,9 +3559,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3574,14 +3571,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3597,9 +3594,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3610,14 +3606,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3633,9 +3629,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3646,14 +3641,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3669,9 +3664,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3682,14 +3676,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3705,9 +3699,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3718,14 +3711,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3741,9 +3734,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3754,14 +3746,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3777,9 +3769,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3790,14 +3781,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3813,9 +3804,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3826,14 +3816,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3849,9 +3839,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3862,14 +3851,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3885,9 +3874,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3898,14 +3886,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3921,9 +3909,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3934,14 +3921,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6382,6 +6369,35 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 1.24993 +colvars: Distance between frame 2 and 3 is 1.22263 +colvars: Distance between frame 3 and 4 is 1.15797 +colvars: Distance between frame 4 and 5 is 1.20671 +colvars: Distance between frame 5 and 6 is 1.22068 +colvars: Distance between frame 6 and 7 is 1.27376 +colvars: Distance between frame 7 and 8 is 1.16679 +colvars: Distance between frame 8 and 9 is 1.23641 +colvars: Distance between frame 9 and 10 is 1.23647 +colvars: Distance between frame 10 and 11 is 1.24224 +colvars: Distance between frame 11 and 12 is 1.21755 +colvars: Distance between frame 12 and 13 is 1.2113 +colvars: Distance between frame 13 and 14 is 1.25829 +colvars: Distance between frame 14 and 15 is 1.14361 +colvars: Distance between frame 15 and 16 is 1.25482 +colvars: Distance between frame 16 and 17 is 1.19127 +colvars: Distance between frame 17 and 18 is 1.21515 +colvars: Distance between frame 18 and 19 is 1.28854 +colvars: Distance between frame 19 and 20 is 1.21558 +colvars: Distance between frame 20 and 21 is 1.18825 +colvars: Distance between frame 21 and 22 is 1.29888 +colvars: Distance between frame 22 and 23 is 1.23365 +colvars: Distance between frame 23 and 24 is 1.17305 +colvars: Distance between frame 24 and 25 is 1.32493 +colvars: Distance between frame 25 and 26 is 1.21926 +colvars: Distance between frame 26 and 27 is 1.1941 +colvars: Distance between frame 27 and 28 is 1.28306 +colvars: Distance between frame 28 and 29 is 1.24978 +colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -6408,7 +6424,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6429,26 +6445,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - aspathCV colvar component: -colvars: - azpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6530,17 +6526,17 @@ colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/37. 1 at colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/38. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "apath_s_distanceVec" from value: 0.0377147 colvars: Restarting collective variable "apath_z_distanceVec" from value: 677.339 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj index 2a0e6503c..9306d59e6 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj @@ -13,10 +13,10 @@ 31 3.79086164652580e-02 6.78450434800659e+02 32 3.79338795931516e-02 6.78554453096444e+02 33 3.79543432866692e-02 6.78628383973525e+02 - 34 3.79777414197508e-02 6.78683148858527e+02 + 34 3.79777414197512e-02 6.78683148858527e+02 35 3.79999682058412e-02 6.78699467676242e+02 36 3.80248319961822e-02 6.78692254801370e+02 - 37 3.80506503259602e-02 6.78677248372969e+02 + 37 3.80506503259599e-02 6.78677248372969e+02 38 3.80831517398857e-02 6.78640840179385e+02 39 3.81094518561156e-02 6.78584570499380e+02 40 3.81323012651889e-02 6.78535020169896e+02 diff --git a/namd/tests/library/022_apathCV_distanceVec/namd-version.txt b/namd/tests/library/022_apathCV_distanceVec/namd-version.txt index 157cac038..90b3a010a 100644 --- a/namd/tests/library/022_apathCV_distanceVec/namd-version.txt +++ b/namd/tests/library/022_apathCV_distanceVec/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA +colvars: Initializing the collective variables module, version "2019-10-21". +colvars: Using NAMD interface, version "2019-10-21". diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out index e7178f688..833f3b0c7 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out +++ b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_dihed" @@ -34,56 +32,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -99,56 +97,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -164,56 +162,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -448,6 +446,37 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 13.3844 +colvars: Distance between frame 2 and 3 is 13.3844 +colvars: Distance between frame 3 and 4 is 13.4029 +colvars: Distance between frame 4 and 5 is 13.4142 +colvars: Distance between frame 5 and 6 is 13.4056 +colvars: Distance between frame 6 and 7 is 13.42 +colvars: Distance between frame 7 and 8 is 13.3375 +colvars: Distance between frame 8 and 9 is 13.4007 +colvars: Distance between frame 9 and 10 is 13.0106 +colvars: Distance between frame 10 and 11 is 13.3842 +colvars: Distance between frame 11 and 12 is 11.9956 +colvars: Distance between frame 12 and 13 is 13.2179 +colvars: Distance between frame 13 and 14 is 13.2532 +colvars: Distance between frame 14 and 15 is 13.4171 +colvars: Distance between frame 15 and 16 is 13.4199 +colvars: Distance between frame 16 and 17 is 13.4188 +colvars: Distance between frame 17 and 18 is 13.3433 +colvars: Distance between frame 18 and 19 is 13.2697 +colvars: Distance between frame 19 and 20 is 13.0715 +colvars: Distance between frame 20 and 21 is 13.3511 +colvars: Distance between frame 21 and 22 is 12.7202 +colvars: Distance between frame 22 and 23 is 13.2064 +colvars: Distance between frame 23 and 24 is 13.3364 +colvars: Distance between frame 24 and 25 is 13.3914 +colvars: Distance between frame 25 and 26 is 13.4199 +colvars: Distance between frame 26 and 27 is 13.4148 +colvars: Distance between frame 27 and 28 is 13.3844 +colvars: Distance between frame 28 and 29 is 13.3858 +colvars: Distance between frame 29 and 30 is 13.204 +colvars: Distance between frame 30 and 31 is 13.2614 +colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -457,7 +486,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -489,56 +518,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -554,56 +583,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -619,56 +648,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -903,6 +932,37 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 13.3844 +colvars: Distance between frame 2 and 3 is 13.3844 +colvars: Distance between frame 3 and 4 is 13.4029 +colvars: Distance between frame 4 and 5 is 13.4142 +colvars: Distance between frame 5 and 6 is 13.4056 +colvars: Distance between frame 6 and 7 is 13.42 +colvars: Distance between frame 7 and 8 is 13.3375 +colvars: Distance between frame 8 and 9 is 13.4007 +colvars: Distance between frame 9 and 10 is 13.0106 +colvars: Distance between frame 10 and 11 is 13.3842 +colvars: Distance between frame 11 and 12 is 11.9956 +colvars: Distance between frame 12 and 13 is 13.2179 +colvars: Distance between frame 13 and 14 is 13.2532 +colvars: Distance between frame 14 and 15 is 13.4171 +colvars: Distance between frame 15 and 16 is 13.4199 +colvars: Distance between frame 16 and 17 is 13.4188 +colvars: Distance between frame 17 and 18 is 13.3433 +colvars: Distance between frame 18 and 19 is 13.2697 +colvars: Distance between frame 19 and 20 is 13.0715 +colvars: Distance between frame 20 and 21 is 13.3511 +colvars: Distance between frame 21 and 22 is 12.7202 +colvars: Distance between frame 22 and 23 is 13.2064 +colvars: Distance between frame 23 and 24 is 13.3364 +colvars: Distance between frame 24 and 25 is 13.3914 +colvars: Distance between frame 25 and 26 is 13.4199 +colvars: Distance between frame 26 and 27 is 13.4148 +colvars: Distance between frame 27 and 28 is 13.3844 +colvars: Distance between frame 28 and 29 is 13.3858 +colvars: Distance between frame 29 and 30 is 13.204 +colvars: Distance between frame 30 and 31 is 13.2614 +colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -912,7 +972,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -933,25 +993,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - aspathCV colvar component: -colvars: - azpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -978,11 +1019,11 @@ colvars: Re-initialized atom group for variable "apath_z_dihed":0/10. 1 atoms: t colvars: Re-initialized atom group for variable "apath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped index 36fd4bb55..2279fe2bc 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped @@ -10,6 +10,6 @@ colvar { colvar { name apath_z_dihed - x 4.37232316380885e+00 + x 4.37232316380883e+00 } diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj index 815ea7a8e..f2cfedfcc 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj +++ b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj @@ -9,14 +9,14 @@ 7 7.81951384906762e-01 -1.12708542497330e+01 8 7.81862402327513e-01 -5.04973060370784e+00 9 7.81744790117315e-01 -4.11017372635214e-01 - 10 7.81727932105477e-01 3.23713799393060e+00 - 11 7.81587394970700e-01 6.52501229704586e+00 + 10 7.81727932105477e-01 3.23713799393062e+00 + 11 7.81587394970700e-01 6.52501229704612e+00 12 7.81406177092293e-01 9.56998059334305e+00 - 13 7.81288506120401e-01 1.08957744034999e+01 + 13 7.81288506120401e-01 1.08957744035001e+01 14 7.81213577479822e-01 1.17023277179725e+01 15 7.81012363824849e-01 1.15317460999164e+01 - 16 7.80904107517137e-01 1.05479253244908e+01 - 17 7.80932778795886e-01 9.25509175496143e+00 - 18 7.80986172825268e-01 7.43274003628036e+00 + 16 7.80904107517137e-01 1.05479253244909e+01 + 17 7.80932778795886e-01 9.25509175496145e+00 + 18 7.80986172825268e-01 7.43274003628034e+00 19 7.81202292537037e-01 5.68220000516656e+00 - 20 7.81356397470272e-01 4.37232316380885e+00 + 20 7.81356397470272e-01 4.37232316380883e+00 diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out index 9828f21a4..813a12275 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_dihed" @@ -34,56 +32,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -99,56 +97,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -164,56 +162,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -448,6 +446,37 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 13.3844 +colvars: Distance between frame 2 and 3 is 13.3844 +colvars: Distance between frame 3 and 4 is 13.4029 +colvars: Distance between frame 4 and 5 is 13.4142 +colvars: Distance between frame 5 and 6 is 13.4056 +colvars: Distance between frame 6 and 7 is 13.42 +colvars: Distance between frame 7 and 8 is 13.3375 +colvars: Distance between frame 8 and 9 is 13.4007 +colvars: Distance between frame 9 and 10 is 13.0106 +colvars: Distance between frame 10 and 11 is 13.3842 +colvars: Distance between frame 11 and 12 is 11.9956 +colvars: Distance between frame 12 and 13 is 13.2179 +colvars: Distance between frame 13 and 14 is 13.2532 +colvars: Distance between frame 14 and 15 is 13.4171 +colvars: Distance between frame 15 and 16 is 13.4199 +colvars: Distance between frame 16 and 17 is 13.4188 +colvars: Distance between frame 17 and 18 is 13.3433 +colvars: Distance between frame 18 and 19 is 13.2697 +colvars: Distance between frame 19 and 20 is 13.0715 +colvars: Distance between frame 20 and 21 is 13.3511 +colvars: Distance between frame 21 and 22 is 12.7202 +colvars: Distance between frame 22 and 23 is 13.2064 +colvars: Distance between frame 23 and 24 is 13.3364 +colvars: Distance between frame 24 and 25 is 13.3914 +colvars: Distance between frame 25 and 26 is 13.4199 +colvars: Distance between frame 26 and 27 is 13.4148 +colvars: Distance between frame 27 and 28 is 13.3844 +colvars: Distance between frame 28 and 29 is 13.3858 +colvars: Distance between frame 29 and 30 is 13.204 +colvars: Distance between frame 30 and 31 is 13.2614 +colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -457,7 +486,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -489,56 +518,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -554,56 +583,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -619,56 +648,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -903,6 +932,37 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 13.3844 +colvars: Distance between frame 2 and 3 is 13.3844 +colvars: Distance between frame 3 and 4 is 13.4029 +colvars: Distance between frame 4 and 5 is 13.4142 +colvars: Distance between frame 5 and 6 is 13.4056 +colvars: Distance between frame 6 and 7 is 13.42 +colvars: Distance between frame 7 and 8 is 13.3375 +colvars: Distance between frame 8 and 9 is 13.4007 +colvars: Distance between frame 9 and 10 is 13.0106 +colvars: Distance between frame 10 and 11 is 13.3842 +colvars: Distance between frame 11 and 12 is 11.9956 +colvars: Distance between frame 12 and 13 is 13.2179 +colvars: Distance between frame 13 and 14 is 13.2532 +colvars: Distance between frame 14 and 15 is 13.4171 +colvars: Distance between frame 15 and 16 is 13.4199 +colvars: Distance between frame 16 and 17 is 13.4188 +colvars: Distance between frame 17 and 18 is 13.3433 +colvars: Distance between frame 18 and 19 is 13.2697 +colvars: Distance between frame 19 and 20 is 13.0715 +colvars: Distance between frame 20 and 21 is 13.3511 +colvars: Distance between frame 21 and 22 is 12.7202 +colvars: Distance between frame 22 and 23 is 13.2064 +colvars: Distance between frame 23 and 24 is 13.3364 +colvars: Distance between frame 24 and 25 is 13.3914 +colvars: Distance between frame 25 and 26 is 13.4199 +colvars: Distance between frame 26 and 27 is 13.4148 +colvars: Distance between frame 27 and 28 is 13.3844 +colvars: Distance between frame 28 and 29 is 13.3858 +colvars: Distance between frame 29 and 30 is 13.204 +colvars: Distance between frame 30 and 31 is 13.2614 +colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -912,7 +972,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -933,25 +993,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - aspathCV colvar component: -colvars: - azpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -977,17 +1018,17 @@ colvars: Re-initialized atom group for variable "apath_z_dihed":0/9. 1 atoms: to colvars: Re-initialized atom group for variable "apath_z_dihed":0/10. 1 atoms: total mass = 12.01, total charge = 0.0337. colvars: Re-initialized atom group for variable "apath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "apath_s_dihed" from value: 0.781356 colvars: Restarting collective variable "apath_z_dihed" from value: 4.37232 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj index c7068744f..5c831af6c 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step apath_s_dihed apath_z_dihed - 20 7.81356397470272e-01 4.37232316380885e+00 + 20 7.81356397470272e-01 4.37232316380883e+00 21 7.81121297977296e-01 1.48408014536711e+01 22 7.80887161764356e-01 2.57385064204216e+01 - 23 7.80608432401527e-01 3.70202491380729e+01 - 24 7.80239933131218e-01 4.91093814693695e+01 - 25 7.79948040898093e-01 6.12096791457022e+01 + 23 7.80608432401527e-01 3.70202491380727e+01 + 24 7.80239933131218e-01 4.91093814693698e+01 + 25 7.79948040898093e-01 6.12096791457024e+01 26 7.79597382762391e-01 7.25781789569762e+01 - 27 7.79139962688763e-01 8.28720619927340e+01 - 28 7.78844243269635e-01 9.18816600988179e+01 - 29 7.78543385360186e-01 9.80096734023500e+01 + 27 7.79139962688763e-01 8.28720619927337e+01 + 28 7.78844243269635e-01 9.18816600988182e+01 + 29 7.78543385360186e-01 9.80096734023498e+01 30 7.78375612820579e-01 1.02527289564776e+02 31 7.78133685857404e-01 1.06109051968502e+02 32 7.77909386932695e-01 1.08483291935737e+02 - 33 7.77812868144173e-01 1.08011291253484e+02 - 34 7.77834700404172e-01 1.06277606048478e+02 - 35 7.77805205280960e-01 1.03033626610267e+02 - 36 7.77952856594698e-01 9.86638072614039e+01 + 33 7.77812868144174e-01 1.08011291253484e+02 + 34 7.77834700404172e-01 1.06277606048477e+02 + 35 7.77805205280961e-01 1.03033626610267e+02 + 36 7.77952856594698e-01 9.86638072614035e+01 37 7.78335111156798e-01 9.35772864178580e+01 38 7.78830800008326e-01 8.79413506004191e+01 - 39 7.79581636252493e-01 8.25355761517521e+01 + 39 7.79581636252493e-01 8.25355761517518e+01 40 7.80351655557853e-01 7.76247569132204e+01 diff --git a/namd/tests/library/023_apathCV/namd-version.txt b/namd/tests/library/023_apathCV/namd-version.txt index 157cac038..90b3a010a 100644 --- a/namd/tests/library/023_apathCV/namd-version.txt +++ b/namd/tests/library/023_apathCV/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA +colvars: Initializing the collective variables module, version "2019-10-21". +colvars: Using NAMD interface, version "2019-10-21". diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out index 054d4b4fb..584abb889 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -89,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -114,28 +112,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -146,7 +144,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -174,7 +172,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.001 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -185,33 +182,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped index dc898032e..1500d4fef 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name one - x 3.21687540035845e+00 + x 3.21687540056419e+00 } colvar { name two - x 3.24433796460560e+00 + x 3.24433796455973e+00 } restraint { diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj index 6a7d2b487..b7cc76f65 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one two 0 3.20554673468334e+00 -3.10554673468334e-03 3.24960869251665e+00 - 1 3.20437145934513e+00 -3.10437145934513e-03 3.24790015328133e+00 - 2 3.20384019096481e+00 -3.10384019096481e-03 3.24647131781550e+00 - 3 3.20396699951790e+00 -3.10396699951790e-03 3.24540254818910e+00 - 4 3.20472779827294e+00 -3.10472779827294e-03 3.24474238729463e+00 - 5 3.20606250099130e+00 -3.10606250099130e-03 3.24450566312591e+00 - 6 3.20787906478401e+00 -3.10787906478401e-03 3.24467445124469e+00 - 7 3.21005887073584e+00 -3.11005887073584e-03 3.24520146026858e+00 - 8 3.21246317927417e+00 -3.11246317927417e-03 3.24601517487763e+00 - 9 3.21494069574114e+00 -3.11494069574114e-03 3.24702593004012e+00 - 10 3.21733635383034e+00 -3.11733635383034e-03 3.24813222863437e+00 - 11 3.21950110803244e+00 -3.11950110803244e-03 3.24922682020241e+00 - 12 3.22130200104731e+00 -3.12130200104731e-03 3.25020238852994e+00 - 13 3.22263134337672e+00 -3.12263134337672e-03 3.25095680349705e+00 - 14 3.22341377052897e+00 -3.12341377052897e-03 3.25139789468993e+00 - 15 3.22361031714383e+00 -3.12361031714383e-03 3.25144752038385e+00 - 16 3.22321924431675e+00 -3.12321924431675e-03 3.25104461582539e+00 - 17 3.22227396694008e+00 -3.12227396694008e-03 3.25014689320737e+00 - 18 3.22083879561905e+00 -3.12083879561905e-03 3.24873103007473e+00 - 19 3.21900323728982e+00 -3.11900323728982e-03 3.24679144034112e+00 - 20 3.21687540035845e+00 -3.11687540035845e-03 3.24433796460560e+00 + 1 3.20437145934575e+00 -3.10437145934575e-03 3.24790015328139e+00 + 2 3.20384019096733e+00 -3.10384019096733e-03 3.24647131781566e+00 + 3 3.20396699952362e+00 -3.10396699952362e-03 3.24540254818933e+00 + 4 3.20472779828314e+00 -3.10472779828314e-03 3.24474238729480e+00 + 5 3.20606250100725e+00 -3.10606250100725e-03 3.24450566312581e+00 + 6 3.20787906480694e+00 -3.10787906480694e-03 3.24467445124404e+00 + 7 3.21005887076690e+00 -3.11005887076690e-03 3.24520146026706e+00 + 8 3.21246317931445e+00 -3.11246317931445e-03 3.24601517487488e+00 + 9 3.21494069579163e+00 -3.11494069579163e-03 3.24702593003580e+00 + 10 3.21733635389196e+00 -3.11733635389196e-03 3.24813222862814e+00 + 11 3.21950110810599e+00 -3.11950110810599e-03 3.24922682019398e+00 + 12 3.22130200113352e+00 -3.12130200113352e-03 3.25020238851898e+00 + 13 3.22263134347621e+00 -3.12263134347621e-03 3.25095680348327e+00 + 14 3.22341377064230e+00 -3.12341377064230e-03 3.25139789467301e+00 + 15 3.22361031727151e+00 -3.12361031727151e-03 3.25144752036343e+00 + 16 3.22321924445923e+00 -3.12321924445923e-03 3.25104461580106e+00 + 17 3.22227396709780e+00 -3.12227396709780e-03 3.25014689317864e+00 + 18 3.22083879579240e+00 -3.12083879579240e-03 3.24873103004102e+00 + 19 3.21900323747919e+00 -3.11900323747919e-03 3.24679144030174e+00 + 20 3.21687540056419e+00 -3.11687540056419e-03 3.24433796455973e+00 diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out index 924e11490..4ef6865a5 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.new.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "two" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -89,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -117,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "two" will be rescaled to 0.001 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -128,35 +125,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "two" from value: 3.24434 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped index fdc8f77c4..e7f40a07f 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name two - x 3.14862665177989e+00 + x 3.14862665152884e+00 } restraint { diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj index 105050dcc..7ce7af5cf 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step two - 20 3.24433796460560e+00 - 21 3.24139291207264e+00 - 22 3.23798801582996e+00 - 23 3.23416154810177e+00 - 24 3.22995568096637e+00 - 25 3.22541422333673e+00 - 26 3.22058076826608e+00 - 27 3.21549743768062e+00 - 28 3.21020446914023e+00 - 29 3.20474085873977e+00 - 30 3.19914608370685e+00 - 31 3.19346261304852e+00 - 32 3.18773858987485e+00 - 33 3.18202996232668e+00 - 34 3.17640140687287e+00 - 35 3.17092573613846e+00 - 36 3.16568187395172e+00 - 37 3.16075175422443e+00 - 38 3.15621655979123e+00 - 39 3.15215255867285e+00 - 40 3.14862665177989e+00 + 20 3.24433796455973e+00 + 21 3.24139291201932e+00 + 22 3.23798801576814e+00 + 23 3.23416154803027e+00 + 24 3.22995568088397e+00 + 25 3.22541422324222e+00 + 26 3.22058076815832e+00 + 27 3.21549743755863e+00 + 28 3.21020446900326e+00 + 29 3.20474085858739e+00 + 30 3.19914608353898e+00 + 31 3.19346261286550e+00 + 32 3.18773858967743e+00 + 33 3.18202996211599e+00 + 34 3.17640140665043e+00 + 35 3.17092573590606e+00 + 36 3.16568187371138e+00 + 37 3.16075175397829e+00 + 38 3.15621655954144e+00 + 39 3.15215255842149e+00 + 40 3.14862665152884e+00 diff --git a/namd/tests/library/024_flexible_restart/namd-version.txt b/namd/tests/library/024_flexible_restart/namd-version.txt index 157cac038..47e185902 100644 --- a/namd/tests/library/024_flexible_restart/namd-version.txt +++ b/namd/tests/library/024_flexible_restart/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-01-27". +colvars: Using NAMD interface, version "2019-12-04". diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out index 622c1934d..c7ba00d0a 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -15,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -29,25 +25,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -67,7 +63,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -92,25 +88,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -132,7 +128,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -157,25 +153,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -201,25 +197,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -245,25 +241,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -286,7 +282,7 @@ colvars: # period = 0 [default] colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -304,7 +300,6 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { rmsd_sym } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] @@ -314,7 +309,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 100 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd_sym" will be rescaled to 100 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -325,33 +319,18 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Symmetry-adapted RMSD: -colvars: Ebrahimi2022 https://doi.org/10.1021/acs.jctc.1c01235 -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":1/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":2/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped index 0067e4445..993abc8ee 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped @@ -5,17 +5,17 @@ configuration { colvar { name rmsd - x 1.67010101996502e+00 + x 1.67010101996501e+00 } colvar { name rmsd_sym - x 1.06269628600355e+00 + x 1.06269628600354e+00 } colvar { name rmsd_min - x 1.06269628600355e+00 + x 1.06269628600354e+00 } restraint { diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj index 652bfe40b..6974d2232 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj @@ -3,20 +3,20 @@ 1 2.65583548116796e+00 2.49357076354985e+00 2.49357076354985e+00 2 1.74533483223524e+00 1.47077556782424e+00 1.47077556782424e+00 3 1.40555434624453e+00 1.03079831602729e+00 1.03079831602729e+00 - 4 2.06648653553549e+00 1.82627061136782e+00 1.82627061136782e+00 - 5 2.54017219029395e+00 2.33735720111240e+00 2.33735720111240e+00 - 6 2.44511763951317e+00 2.20810814129125e+00 2.20810814129125e+00 + 4 2.06648653553550e+00 1.82627061136782e+00 1.82627061136782e+00 + 5 2.54017219029394e+00 2.33735720111240e+00 2.33735720111240e+00 + 6 2.44511763951316e+00 2.20810814129124e+00 2.20810814129124e+00 7 1.90917369343023e+00 1.54370117101215e+00 1.54370117101215e+00 - 8 1.46846059624425e+00 8.57092838197608e-01 8.57092838197608e-01 + 8 1.46846059624425e+00 8.57092838197605e-01 8.57092838197605e-01 9 1.73306101411381e+00 1.20805207461003e+00 1.20805207461003e+00 10 2.23122614737732e+00 1.83168666851452e+00 1.83168666851452e+00 11 2.40879160755837e+00 2.03136190092487e+00 2.03136190092487e+00 - 12 2.16660397964881e+00 1.72654978561156e+00 1.72654978561156e+00 - 13 1.72124086387257e+00 1.10943093382589e+00 1.10943093382589e+00 - 14 1.54507113594669e+00 8.13315046570523e-01 8.13315046570523e-01 - 15 1.84201976466438e+00 1.30057662388300e+00 1.30057662388300e+00 - 16 2.18866124657310e+00 1.76429607011378e+00 1.76429607011378e+00 + 12 2.16660397964880e+00 1.72654978561155e+00 1.72654978561155e+00 + 13 1.72124086387256e+00 1.10943093382589e+00 1.10943093382589e+00 + 14 1.54507113594670e+00 8.13315046570531e-01 8.13315046570531e-01 + 15 1.84201976466439e+00 1.30057662388302e+00 1.30057662388302e+00 + 16 2.18866124657311e+00 1.76429607011380e+00 1.76429607011380e+00 17 2.26240711868798e+00 1.85743190829637e+00 1.85743190829637e+00 18 1.99090416866217e+00 1.51280845285182e+00 1.51280845285182e+00 - 19 1.59604958772557e+00 9.31109046188018e-01 9.31109046188018e-01 - 20 1.67010101996502e+00 1.06269628600355e+00 1.06269628600355e+00 + 19 1.59604958772556e+00 9.31109046188012e-01 9.31109046188012e-01 + 20 1.67010101996501e+00 1.06269628600354e+00 1.06269628600354e+00 diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out index 0b153b893..8b384c5c1 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -15,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -29,25 +25,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -67,7 +63,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -92,25 +88,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -132,7 +128,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -157,25 +153,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -201,25 +197,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -245,25 +241,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -286,7 +282,7 @@ colvars: # period = 0 [default] colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -304,7 +300,6 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { rmsd_sym } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] @@ -314,7 +309,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 100 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd_sym" will be rescaled to 100 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -325,40 +319,25 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Symmetry-adapted RMSD: -colvars: Ebrahimi2022 https://doi.org/10.1021/acs.jctc.1c01235 -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":1/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":2/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "rmsd" from value: 1.6701 colvars: Restarting collective variable "rmsd_sym" from value: 1.0627 colvars: Restarting collective variable "rmsd_min" from value: 1.0627 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped index 512353c31..fdae84add 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped @@ -10,12 +10,12 @@ colvar { colvar { name rmsd_sym - x 7.26619298562140e-01 + x 7.26619298562136e-01 } colvar { name rmsd_min - x 7.26619298562140e-01 + x 7.26619298562136e-01 } restraint { diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj index c1832014e..b66d34d1e 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step rmsd rmsd_sym rmsd_min - 20 1.67010101996502e+00 1.06269628600355e+00 1.06269628600355e+00 - 21 2.04433892429580e+00 1.60292722878384e+00 1.60292722878384e+00 - 22 2.06240612835231e+00 1.64334625236225e+00 1.64334625236225e+00 - 23 1.72479860434135e+00 1.21752251761604e+00 1.21752251761604e+00 - 24 1.45281664722968e+00 8.31805423263470e-01 8.31805423263470e-01 - 25 1.62193082908379e+00 1.13819710156541e+00 1.13819710156541e+00 - 26 1.91428771037452e+00 1.54849490838443e+00 1.54849490838443e+00 - 27 1.93241576009646e+00 1.57970290898645e+00 1.57970290898645e+00 - 28 1.64032456570088e+00 1.19887684608300e+00 1.19887684608300e+00 - 29 1.42831104802460e+00 8.67878207872016e-01 8.67878207872016e-01 - 30 1.71179394524437e+00 1.27004409838276e+00 1.27004409838276e+00 - 31 2.10204997402061e+00 1.75291645597029e+00 1.75291645597029e+00 - 32 2.16523333046788e+00 1.81717671975523e+00 1.81717671975523e+00 - 33 1.85227206897976e+00 1.41097165384594e+00 1.41097165384594e+00 - 34 1.51283191580260e+00 8.90242598276090e-01 8.90242598276090e-01 - 35 1.65809367768181e+00 1.09671669300780e+00 1.09671669300780e+00 - 36 2.03497663158024e+00 1.59379893021682e+00 1.59379893021682e+00 - 37 2.17858401892652e+00 1.75248645511792e+00 1.75248645511792e+00 - 38 1.99046986313611e+00 1.48057223445696e+00 1.48057223445696e+00 - 39 1.64708037387981e+00 9.18991758873730e-01 9.18991758873730e-01 - 40 1.57261614568718e+00 7.26619298562140e-01 7.26619298562140e-01 + 20 1.67010101996501e+00 1.06269628600354e+00 1.06269628600354e+00 + 21 2.04433892429578e+00 1.60292722878381e+00 1.60292722878381e+00 + 22 2.06240612835228e+00 1.64334625236222e+00 1.64334625236222e+00 + 23 1.72479860434134e+00 1.21752251761603e+00 1.21752251761603e+00 + 24 1.45281664722968e+00 8.31805423263468e-01 8.31805423263468e-01 + 25 1.62193082908377e+00 1.13819710156539e+00 1.13819710156539e+00 + 26 1.91428771037449e+00 1.54849490838439e+00 1.54849490838439e+00 + 27 1.93241576009644e+00 1.57970290898642e+00 1.57970290898642e+00 + 28 1.64032456570087e+00 1.19887684608299e+00 1.19887684608299e+00 + 29 1.42831104802460e+00 8.67878207872020e-01 8.67878207872020e-01 + 30 1.71179394524434e+00 1.27004409838273e+00 1.27004409838273e+00 + 31 2.10204997402056e+00 1.75291645597024e+00 1.75291645597024e+00 + 32 2.16523333046785e+00 1.81717671975520e+00 1.81717671975520e+00 + 33 1.85227206897975e+00 1.41097165384593e+00 1.41097165384593e+00 + 34 1.51283191580260e+00 8.90242598276096e-01 8.90242598276096e-01 + 35 1.65809367768181e+00 1.09671669300779e+00 1.09671669300779e+00 + 36 2.03497663158023e+00 1.59379893021680e+00 1.59379893021680e+00 + 37 2.17858401892649e+00 1.75248645511788e+00 1.75248645511788e+00 + 38 1.99046986313608e+00 1.48057223445693e+00 1.48057223445693e+00 + 39 1.64708037387980e+00 9.18991758873705e-01 9.18991758873705e-01 + 40 1.57261614568718e+00 7.26619298562136e-01 7.26619298562136e-01 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out b/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out index 75a651d7a..d6f4b9ad4 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -134,29 +130,16 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.grad b/namd/tests/library/026_ABF_energy/AutoDiff/test.grad index 46dea61eb..16cf7fcda 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.grad +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.17682469793588e+01 + 3.25000000000000e+00 -1.17682470708695e+01 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf b/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf index 665e2643f..d27977925 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 5.88412348967941e+00 - 5.00000000000000e-01 5.88412348967941e+00 - 1.00000000000000e+00 5.88412348967941e+00 - 1.50000000000000e+00 5.88412348967941e+00 - 2.00000000000000e+00 5.88412348967941e+00 - 2.50000000000000e+00 5.88412348967941e+00 - 3.00000000000000e+00 5.88412348967941e+00 + 0.00000000000000e+00 5.88412353543475e+00 + 5.00000000000000e-01 5.88412353543475e+00 + 1.00000000000000e+00 5.88412353543475e+00 + 1.50000000000000e+00 5.88412353543475e+00 + 2.00000000000000e+00 5.88412353543475e+00 + 2.50000000000000e+00 5.88412353543475e+00 + 3.00000000000000e+00 5.88412353543475e+00 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out index 865f10f4c..8def9ee51 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -134,34 +130,21 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.14228 colvars: Restarting abf bias "abf1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad index d348c12f2..8b57bb739 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -2.34801644956595e+01 + 3.25000000000000e+00 -2.34801645799521e+01 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf index 08a4d3d5b..d2eb54957 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 1.17400822478297e+01 - 5.00000000000000e-01 1.17400822478297e+01 - 1.00000000000000e+00 1.17400822478297e+01 - 1.50000000000000e+00 1.17400822478297e+01 - 2.00000000000000e+00 1.17400822478297e+01 - 2.50000000000000e+00 1.17400822478297e+01 - 3.00000000000000e+00 1.17400822478297e+01 + 0.00000000000000e+00 1.17400822899760e+01 + 5.00000000000000e-01 1.17400822899760e+01 + 1.00000000000000e+00 1.17400822899760e+01 + 1.50000000000000e+00 1.17400822899760e+01 + 2.00000000000000e+00 1.17400822899760e+01 + 2.50000000000000e+00 1.17400822899760e+01 + 3.00000000000000e+00 1.17400822899760e+01 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/namd-version.txt b/namd/tests/library/026_ABF_energy/namd-version.txt index 157cac038..402dbcc14 100644 --- a/namd/tests/library/026_ABF_energy/namd-version.txt +++ b/namd/tests/library/026_ABF_energy/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-06-02". +colvars: Using NAMD interface, version "2020-05-04". diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state index ac87bdbc5..ad2a42cd1 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state +++ b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state @@ -11,10 +11,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 8.70939574046587e-05 - 2.70056900312946e-03 3.08054911230446e-02 1.29272634625682e-01 - 1.99567890849616e-01 1.13339251307472e-01 2.36796683760721e-02 - 1.82002141052347e-03 5.14615641849260e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 8.70939573129658e-05 + 2.70056900100952e-03 3.08054911071083e-02 1.29272634593393e-01 + 1.99567890853138e-01 1.13339251339767e-01 2.36796683891457e-02 + 1.82002141201432e-03 5.14615642408155e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -26,10 +26,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 6.85295349016874e-04 - 1.58481831440929e-02 1.19169844943943e-01 2.41540944181510e-01 - -2.62507763713641e-02 -2.41586884549233e-01 -9.78334326726952e-02 - -1.11595284046322e-02 -4.18461586694560e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 6.85295348342052e-04 + 1.58481831330982e-02 1.19169844898782e-01 2.41540944190337e-01 + -2.62507762651161e-02 -2.41586884557496e-01 -9.78334327140598e-02 + -1.11595284128016e-02 -4.18461587121564e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state index ac87bdbc5..ad2a42cd1 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state +++ b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state @@ -11,10 +11,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 8.70939574046587e-05 - 2.70056900312946e-03 3.08054911230446e-02 1.29272634625682e-01 - 1.99567890849616e-01 1.13339251307472e-01 2.36796683760721e-02 - 1.82002141052347e-03 5.14615641849260e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 8.70939573129658e-05 + 2.70056900100952e-03 3.08054911071083e-02 1.29272634593393e-01 + 1.99567890853138e-01 1.13339251339767e-01 2.36796683891457e-02 + 1.82002141201432e-03 5.14615642408155e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -26,10 +26,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 6.85295349016874e-04 - 1.58481831440929e-02 1.19169844943943e-01 2.41540944181510e-01 - -2.62507763713641e-02 -2.41586884549233e-01 -9.78334326726952e-02 - -1.11595284046322e-02 -4.18461586694560e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 6.85295348342052e-04 + 1.58481831330982e-02 1.19169844898782e-01 2.41540944190337e-01 + -2.62507762651161e-02 -2.41586884557496e-01 -9.78334327140598e-02 + -1.11595284128016e-02 -4.18461587121564e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state index 30f1b680a..8dcab87f9 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state +++ b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state @@ -11,10 +11,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.80472755097040e-04 - 5.54447036223268e-03 6.26727288407827e-02 2.60655276117922e-01 - 3.98862365610485e-01 2.24567790690383e-01 4.65199212276517e-02 - 3.54565765284328e-03 9.94306268035517e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.80472754695334e-04 + 5.54447035307032e-03 6.26727287728974e-02 2.60655275982959e-01 + 3.98862365627901e-01 2.24567790825392e-01 4.65199212813745e-02 + 3.54565765888724e-03 9.94306270273247e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -26,10 +26,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.41667561487056e-03 - 3.24357195248848e-02 2.41314964024310e-01 4.82392264917098e-01 - -5.94386861724842e-02 -4.82536712977343e-01 -1.92985724018794e-01 - -2.17993242036534e-02 -8.10150852681438e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.41667561192491e-03 + 3.24357194776196e-02 2.41314963834041e-01 4.82392264961036e-01 + -5.94386857287638e-02 -4.82536713017911e-01 -1.92985724190331e-01 + -2.17993242369277e-02 -8.10150854396533e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out index 5a868114a..93db4f3a8 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -115,34 +113,7 @@ colvars: # outputFile = "" [default] colvars: # outputFileDX = "none" [default] colvars: # gatherVectorColvars = off [default] colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "metadynamics" instance. -colvars: # name = "metadynamics1" [default] -colvars: # colvars = { one } -colvars: # stepZeroData = off [default] -colvars: # outputEnergy = off [default] -colvars: # outputFreq = 10 [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] -colvars: # hillWeight = 0.1 -colvars: # newHillFrequency = 10 -colvars: # gaussianSigmas = [default] -colvars: # hillWidth = 2 -colvars: Half-widths of the Gaussian hills (sigma's): -colvars: one: 0.5 -colvars: # multipleReplicas = off [default] -colvars: # useGrids = on [default] -colvars: # gridsUpdateFrequency = 10 [default] -colvars: # rebinGrids = off [default] -colvars: # writeFreeEnergyFile = on [default] -colvars: # keepHills = off [default] -colvars: # keepFreeEnergyFiles = off [default] -colvars: # writeHillsTrajectory = off [default] -colvars: # wellTempered = off [default] -colvars: # biasTemperature = -1 [default] -colvars: # ebMeta = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 2 in total. +colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- @@ -150,31 +121,16 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Histogram colvar bias implementation: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". @@ -191,6 +147,12 @@ colvars: Saving collective variables state to "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". colvars: Writing the histogram file "test.histogram1.dat". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Writing the histogram file "test.histogram1.dat". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Writing the histogram file "test.histogram1.dat". colvars: Saving collective variables state to "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped index eb8fb4fb7..b62b4fcd0 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21415030858830e+00 + x 3.21415030906913e+00 } histogram { @@ -32,10 +32,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.80472755097040e-04 - 5.54447036223268e-03 6.26727288407827e-02 2.60655276117922e-01 - 3.98862365610485e-01 2.24567790690383e-01 4.65199212276517e-02 - 3.54565765284328e-03 9.94306268035517e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.80472754695334e-04 + 5.54447035307032e-03 6.26727287728974e-02 2.60655275982959e-01 + 3.98862365627901e-01 2.24567790825392e-01 4.65199212813745e-02 + 3.54565765888724e-03 9.94306270273247e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -47,10 +47,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.41667561487056e-03 - 3.24357195248848e-02 2.41314964024310e-01 4.82392264917098e-01 - -5.94386861724842e-02 -4.82536712977343e-01 -1.92985724018794e-01 - -2.17993242036534e-02 -8.10150852681438e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.41667561192491e-03 + 3.24357194776196e-02 2.41314963834041e-01 4.82392264961036e-01 + -5.94386857287638e-02 -4.82536713017911e-01 -1.92985724190331e-01 + -2.17993242369277e-02 -8.10150854396533e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj index 31091a629..e04394664 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj @@ -1,44 +1,44 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 1.30367508844061e-02 - 11 3.21950387395255e+00 1.30367508844061e-02 - 12 3.22130559658681e+00 1.30367508844061e-02 - 13 3.22263598353165e+00 1.30367508844061e-02 - 14 3.22341966109109e+00 1.30367508844061e-02 - 15 3.22361765299886e+00 1.30367508844061e-02 - 16 3.22322820813411e+00 1.30367508844061e-02 - 17 3.22228472829020e+00 1.30367508844061e-02 - 18 3.22085151053088e+00 1.30367508844061e-02 - 19 3.21901804823901e+00 1.30367508844061e-02 - 20 3.21689243666711e+00 2.62507763713641e-02 - 20 3.21689243666711e+00 2.62507763713641e-02 - 20 3.21689243666711e+00 2.62507763713641e-02 - 21 3.21459439240045e+00 2.62507763713641e-02 - 22 3.21224726535912e+00 2.62507763713641e-02 - 23 3.20997056365207e+00 2.62507763713641e-02 - 24 3.20787270637879e+00 2.62507763713641e-02 - 25 3.20604492520325e+00 2.62507763713641e-02 - 26 3.20455694842083e+00 2.62507763713641e-02 - 27 3.20345479563379e+00 2.62507763713641e-02 - 28 3.20276061061291e+00 2.62507763713641e-02 - 29 3.20247408259157e+00 2.62507763713641e-02 - 30 3.20257503670478e+00 4.51356215063288e-02 - 31 3.20302710728970e+00 4.51356215063288e-02 - 32 3.20378117591190e+00 4.51356215063288e-02 - 33 3.20478014892865e+00 4.51356215063288e-02 - 34 3.20596369561551e+00 4.51356215063288e-02 - 35 3.20727281779169e+00 4.51356215063288e-02 - 36 3.20865380534294e+00 4.51356215063288e-02 - 37 3.21006125723226e+00 4.51356215063288e-02 - 38 3.21146012394088e+00 4.51356215063288e-02 - 39 3.21282692105120e+00 4.51356215063288e-02 - 40 3.21415030858830e+00 5.94386861724842e-02 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 1.30367508599117e-02 + 11 3.21950387402611e+00 1.30367508599117e-02 + 12 3.22130559667303e+00 1.30367508599117e-02 + 13 3.22263598363115e+00 1.30367508599117e-02 + 14 3.22341966120443e+00 1.30367508599117e-02 + 15 3.22361765312655e+00 1.30367508599117e-02 + 16 3.22322820827659e+00 1.30367508599117e-02 + 17 3.22228472844791e+00 1.30367508599117e-02 + 18 3.22085151070423e+00 1.30367508599117e-02 + 19 3.21901804842838e+00 1.30367508599117e-02 + 20 3.21689243687284e+00 2.62507762651161e-02 + 20 3.21689243687284e+00 2.62507762651161e-02 + 20 3.21689243687284e+00 2.62507762651161e-02 + 21 3.21459439262285e+00 2.62507762651161e-02 + 22 3.21224726559843e+00 2.62507762651161e-02 + 23 3.20997056390844e+00 2.62507762651161e-02 + 24 3.20787270665228e+00 2.62507762651161e-02 + 25 3.20604492549381e+00 2.62507762651161e-02 + 26 3.20455694872830e+00 2.62507762651161e-02 + 27 3.20345479595789e+00 2.62507762651161e-02 + 28 3.20276061095329e+00 2.62507762651161e-02 + 29 3.20247408294778e+00 2.62507762651161e-02 + 30 3.20257503707633e+00 4.51356212534586e-02 + 31 3.20302710767604e+00 4.51356212534586e-02 + 32 3.20378117631245e+00 4.51356212534586e-02 + 33 3.20478014934277e+00 4.51356212534586e-02 + 34 3.20596369604249e+00 4.51356212534586e-02 + 35 3.20727281823071e+00 4.51356212534586e-02 + 36 3.20865380579304e+00 4.51356212534586e-02 + 37 3.21006125769230e+00 4.51356212534586e-02 + 38 3.21146012440951e+00 4.51356212534586e-02 + 39 3.21282692152683e+00 4.51356212534586e-02 + 40 3.21415030906913e+00 5.94386857287638e-02 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf b/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf index af5f3fa27..d85393c4f 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.98862365610485e-01 - 7.50000000000000e-01 3.98862365610485e-01 - 1.25000000000000e+00 3.98681892855388e-01 - 1.75000000000000e+00 3.93317895248252e-01 - 2.25000000000000e+00 3.36189636769702e-01 - 2.75000000000000e+00 1.38207089492563e-01 + 2.50000000000000e-01 3.98862365627901e-01 + 7.50000000000000e-01 3.98862365627901e-01 + 1.25000000000000e+00 3.98681892873206e-01 + 1.75000000000000e+00 3.93317895274831e-01 + 2.25000000000000e+00 3.36189636855004e-01 + 2.75000000000000e+00 1.38207089644942e-01 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.74294574920103e-01 - 4.25000000000000e+00 3.52342444382833e-01 - 4.75000000000000e+00 3.95316707957642e-01 - 5.25000000000000e+00 3.98762934983682e-01 - 5.75000000000000e+00 3.98862365610485e-01 - 6.25000000000000e+00 3.98862365610485e-01 - 6.75000000000000e+00 3.98862365610485e-01 - 7.25000000000000e+00 3.98862365610485e-01 - 7.75000000000000e+00 3.98862365610485e-01 - 8.25000000000000e+00 3.98862365610485e-01 - 8.75000000000000e+00 3.98862365610485e-01 - 9.25000000000000e+00 3.98862365610485e-01 - 9.75000000000000e+00 3.98862365610485e-01 + 3.75000000000000e+00 1.74294574802509e-01 + 4.25000000000000e+00 3.52342444346527e-01 + 4.75000000000000e+00 3.95316707969014e-01 + 5.25000000000000e+00 3.98762935000874e-01 + 5.75000000000000e+00 3.98862365627901e-01 + 6.25000000000000e+00 3.98862365627901e-01 + 6.75000000000000e+00 3.98862365627901e-01 + 7.25000000000000e+00 3.98862365627901e-01 + 7.75000000000000e+00 3.98862365627901e-01 + 8.25000000000000e+00 3.98862365627901e-01 + 8.75000000000000e+00 3.98862365627901e-01 + 9.25000000000000e+00 3.98862365627901e-01 + 9.75000000000000e+00 3.98862365627901e-01 diff --git a/namd/tests/library/027_multiple_runs/namd-version.txt b/namd/tests/library/027_multiple_runs/namd-version.txt index 157cac038..402dbcc14 100644 --- a/namd/tests/library/027_multiple_runs/namd-version.txt +++ b/namd/tests/library/027_multiple_runs/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-06-02". +colvars: Using NAMD interface, version "2020-05-04". diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out index 9a80820be..f8931d8a7 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out @@ -1,21 +1,17 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "test.in": +colvars: Reading new configuration from file "test.legacy.in": colvars: # units = "" [default] colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -60,13 +56,18 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. colvars: Warning: Variable r2 is absent from expression "atan2(r3, r1) * 180 / 3.1415926". +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r1. +colvars: Warning: Variable r1 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r3 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r3. colvars: Expecting colvar value of type scalar number. colvars: # period = 360 colvars: # wrapAround = 0 colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -94,7 +95,6 @@ colvars: # centers = { -179 } colvars: # targetCenters = { -179 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.01 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 0.01 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -105,31 +105,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. +colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out index b5c095d75..fc34e52ef 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out @@ -1,21 +1,17 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "test.in": +colvars: Reading new configuration from file "test.legacy.in": colvars: # units = "" [default] colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -60,13 +56,18 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. colvars: Warning: Variable r2 is absent from expression "atan2(r3, r1) * 180 / 3.1415926". +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r1. +colvars: Warning: Variable r1 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r3 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r3. colvars: Expecting colvar value of type scalar number. colvars: # period = 360 colvars: # wrapAround = 0 colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -94,7 +95,6 @@ colvars: # centers = { -179 } colvars: # targetCenters = { -179 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.01 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 0.01 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -105,36 +105,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. +colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "c" from value: 157.339 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/028_periodic_custom_function/namd-version.txt b/namd/tests/library/028_periodic_custom_function/namd-version.txt index 157cac038..fb5cc08df 100644 --- a/namd/tests/library/028_periodic_custom_function/namd-version.txt +++ b/namd/tests/library/028_periodic_custom_function/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 3.0alpha8 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2021-03-09". +colvars: Using NAMD interface, version "2021-03-02". diff --git a/namd/tests/library/029_reweightamd/namd-version.txt b/namd/tests/library/029_reweightamd/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/029_reweightamd/namd-version.txt +++ b/namd/tests/library/029_reweightamd/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out index e3bbc2221..1152d4a8f 100644 --- a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out +++ b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out @@ -4,7 +4,6 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "end_to_end_distance" @@ -88,6 +86,7 @@ colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # scaledBiasingForce = on colvars: # scaledBiasingForceFactorsGrid = "factors.grid" +colvars: Reading scaling factors for the forces of bias production_abf from factors.grid colvars: # applyBias = on [default] colvars: # updateBias = on [default] colvars: # hideJacobian = off [default] @@ -109,6 +108,7 @@ colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # scaledBiasingForce = on colvars: # scaledBiasingForceFactorsGrid = "factors.grid" +colvars: Reading scaling factors for the forces of bias production_mtd from factors.grid colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # hillWeight = 2 @@ -142,7 +142,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -156,7 +155,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 13 } colvars: # upperWalls = { 15 } @@ -196,17 +194,17 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "end_to_end_distance":0/0. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "end_to_end_distance":0/1. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: Warning: enabling wrapAll can lead to inconsistent results for Colvars calculations: please disable wrapAll, as is the default option in NAMD. colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "end_to_end_distance":0/0. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "end_to_end_distance":0/1. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.colvars.state". diff --git a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped index aaafe01d2..2983b7392 100644 --- a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped @@ -61,9 +61,9 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 -2.46034201565941e+01 -1.71228758550381e+01 -4.35028348233383e+00 8.77100343862926e+00 0.00000000000000e+00 2.41578842132070e+01 - 0.00000000000000e+00 3.67760957979660e+01 0.00000000000000e+00 0.00000000000000e+00 4.03080315984188e+01 0.00000000000000e+00 4.91740802690052e+01 0.00000000000000e+00 - 4.58607749339768e+01 0.00000000000000e+00 5.28741550375003e+01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 -2.46034201565942e+01 -1.71228758550407e+01 -4.35028348233554e+00 8.77100343862862e+00 0.00000000000000e+00 2.41578842131827e+01 + 0.00000000000000e+00 3.67760957979561e+01 0.00000000000000e+00 0.00000000000000e+00 4.03080315983995e+01 0.00000000000000e+00 4.91740802690014e+01 0.00000000000000e+00 + 4.58607749339655e+01 0.00000000000000e+00 5.28741550375132e+01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -129,20 +129,20 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 2.61587935067117e-05 1.94683970632333e-04 - 1.08251565030012e-03 5.09475130902687e-03 2.04659308796424e-02 - 7.06125286654209e-02 2.09435976415536e-01 5.34918613697524e-01 - 1.17861358817339e+00 2.24504431300101e+00 3.70656454838329e+00 - 5.32145917169711e+00 6.67261938563254e+00 7.35195926071128e+00 - 7.18021399808668e+00 6.29685877472027e+00 5.06102998507674e+00 - 3.86183081585070e+00 2.97265484622017e+00 2.49720984195920e+00 - 2.38143486949621e+00 2.47333896395547e+00 2.62156486038421e+00 - 2.76069831296951e+00 2.91199826509797e+00 3.10017196004795e+00 - 3.27504048000548e+00 3.31818588496202e+00 3.12189683918950e+00 - 2.66602374122956e+00 2.03536975844399e+00 1.37396310594800e+00 - 8.12936839978680e-01 4.18576183807702e-01 1.86468431860140e-01 - 7.15657207976055e-02 2.35824489722632e-02 6.65642098671754e-03 - 1.60673261084200e-03 3.28034119054257e-04 5.79178127981109e-05 + 0.00000000000000e+00 2.61587935066948e-05 1.94683970632219e-04 + 1.08251565029956e-03 5.09475130902452e-03 2.04659308796341e-02 + 7.06125286653960e-02 2.09435976415474e-01 5.34918613697393e-01 + 1.17861358817316e+00 2.24504431300069e+00 3.70656454838293e+00 + 5.32145917169682e+00 6.67261938563242e+00 7.35195926071138e+00 + 7.18021399808696e+00 6.29685877472059e+00 5.06102998507698e+00 + 3.86183081585080e+00 2.97265484622012e+00 2.49720984195906e+00 + 2.38143486949602e+00 2.47333896395524e+00 2.62156486038390e+00 + 2.76069831296907e+00 2.91199826509736e+00 3.10017196004723e+00 + 3.27504048000479e+00 3.31818588496156e+00 3.12189683918944e+00 + 2.66602374122993e+00 2.03536975844466e+00 1.37396310594875e+00 + 8.12936839979314e-01 4.18576183808133e-01 1.86468431860379e-01 + 7.15657207977159e-02 2.35824489723058e-02 6.65642098673127e-03 + 1.60673261084573e-03 3.28034119055107e-04 5.79178127982759e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -204,20 +204,20 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 4.98572553752462e-03 3.44543416760259e-02 - 1.75326645541183e-01 7.47482721295256e-01 2.68947029660910e+00 - 8.20870614494615e+00 2.11986301747035e+01 4.61909880344223e+01 - 8.44826248580398e+01 1.28506873925876e+02 1.59712391231044e+02 - 1.55977235774206e+02 1.07039391871361e+02 2.56744580180974e+01 - -5.75055838168977e+01 -1.12829758918543e+02 -1.27599236648709e+02 - -1.07606408348117e+02 -6.85243194218725e+01 -2.75641170223360e+01 - 1.69829679656285e+00 1.39955997855656e+01 1.45571151643531e+01 - 1.37895289828742e+01 1.70425441756613e+01 1.97475224737415e+01 - 1.31056573124731e+01 -6.41279019649712e+00 -3.32095989551511e+01 - -5.64631191592674e+01 -6.71337049514181e+01 -6.28686158484828e+01 - -4.82254030908254e+01 -3.07787466326868e+01 -1.64540466072889e+01 - -7.39576145057542e+00 -2.79968734690709e+00 -8.93905835951089e-01 - -2.41013764581217e-01 -5.42598821858858e-02 -1.05068277897643e-02 + 0.00000000000000e+00 4.98572553752153e-03 3.44543416760067e-02 + 1.75326645541099e-01 7.47482721294938e-01 2.68947029660812e+00 + 8.20870614494365e+00 2.11986301746983e+01 4.61909880344138e+01 + 8.44826248580294e+01 1.28506873925868e+02 1.59712391231045e+02 + 1.55977235774219e+02 1.07039391871382e+02 2.56744580181185e+01 + -5.75055838168864e+01 -1.12829758918545e+02 -1.27599236648721e+02 + -1.07606408348132e+02 -6.85243194218847e+01 -2.75641170223432e+01 + 1.69829679655862e+00 1.39955997855602e+01 1.45571151643426e+01 + 1.37895289828585e+01 1.70425441756459e+01 1.97475224737359e+01 + 1.31056573124861e+01 -6.41279019646412e+00 -3.32095989551069e+01 + -5.64631191592285e+01 -6.71337049513984e+01 -6.28686158484858e+01 + -4.82254030908433e+01 -3.07787466327079e+01 -1.64540466073052e+01 + -7.39576145058497e+00 -2.79968734691153e+00 -8.93905835952760e-01 + -2.41013764581735e-01 -5.42598821860181e-02 -1.05068277897928e-02 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj index d76c74714..90721e014 100644 --- a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj +++ b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj @@ -3,20 +3,20 @@ 1 1.45695261014138e+01 0.00000000000000e+00 2 1.45635632664853e+01 0.00000000000000e+00 3 1.45582489261713e+01 -2.58411685289576e+01 - 4 1.45527923170544e+01 -2.07125939557695e+01 + 4 1.45527923170544e+01 -2.07125939557735e+01 5 1.45473541901844e+01 0.00000000000000e+00 6 1.45442591718140e+01 0.00000000000000e+00 7 1.45431535519741e+01 0.00000000000000e+00 8 1.45439619694008e+01 0.00000000000000e+00 9 1.45475029536962e+01 0.00000000000000e+00 - 10 1.45537536789397e+01 1.61692398556099e+01 - 11 1.45592642275934e+01 1.61692398556099e+01 + 10 1.45537536789397e+01 1.61692398555902e+01 + 11 1.45592642275934e+01 1.61692398555902e+01 12 1.45670515013898e+01 0.00000000000000e+00 - 13 1.45744569915016e+01 1.47925560209934e+02 - 14 1.45916606161846e+01 1.32015920190288e+02 - 15 1.46158023047859e+01 7.80198886000781e+01 + 13 1.45744569915016e+01 1.47925560209933e+02 + 14 1.45916606161846e+01 1.32015920190301e+02 + 15 1.46158023047859e+01 7.80198886000819e+01 16 1.46427017872138e+01 0.00000000000000e+00 - 17 1.46664306062949e+01 0.00000000000000e+00 + 17 1.46664306062950e+01 0.00000000000000e+00 18 1.46862961461938e+01 0.00000000000000e+00 19 1.47010927350238e+01 0.00000000000000e+00 - 20 1.47116192100262e+01 5.64631191592674e+01 + 20 1.47116192100262e+01 5.64631191592285e+01 diff --git a/namd/tests/library/030_scaledBiasingForce/namd-version.txt b/namd/tests/library/030_scaledBiasingForce/namd-version.txt index 157cac038..a8b4c8892 100644 --- a/namd/tests/library/030_scaledBiasingForce/namd-version.txt +++ b/namd/tests/library/030_scaledBiasingForce/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2022-01-19. +colvars: Using NAMD interface, version "2021-10-13". diff --git a/namd/tests/library/031_neuralnetwork/namd-version.txt b/namd/tests/library/031_neuralnetwork/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/031_neuralnetwork/namd-version.txt +++ b/namd/tests/library/031_neuralnetwork/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06".