Update LAMMPS regression tests for TI/ABF fix

Colvars · Dec 17, 2024 · b35427e · b35427e
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diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out
@@ -1,10 +1,12 @@
-colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
 colvars: This version was built with the C++11 standard or higher.
-colvars: Using LAMMPS interface, version "2020-04-07".
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 2)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: not available
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -56,27 +58,27 @@ colvars:     # forceNoPBC = off [default]
 colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = 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.
 colvars:       Initializing atom group "group2".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = 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.
@@ -104,19 +106,20 @@ colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "abf" instance.
 colvars:   # name = "abf1" [default]
 colvars:   # colvars = { one }
-colvars:   # zeroStepData = off [default]
+colvars:   # stepZeroData = off [default]
 colvars:   # outputEnergy = off [default]
 colvars:   # outputFreq = 10 [default]
 colvars:   # timeStepFactor = 1 [default]
 colvars:   WARNING: ABF should not be run without a thermostat or at 0 Kelvin!
 colvars:   # applyBias = on [default]
-colvars:   # updateBias = on [default]
 colvars:   # hideJacobian = off [default]
 colvars:   Jacobian (geometric) forces will be included in reported free energy gradients.
 colvars:   # fullSamples = 10
+colvars:   # minSamples = 5 [default]
 colvars:   # inputPrefix =  [default]
 colvars:   # historyFreq = 0 [default]
 colvars:   # shared = off [default]
+colvars:   # updateBias = on [default]
 colvars:   # maxForce =  [default]
 colvars:   # integrate = on [default]
 colvars:   Finished ABF setup.
@@ -125,16 +128,14 @@ colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "test.colvars.state".
-colvars: Opening trajectory file "test.colvars.traj".
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
 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:   Prepared sample and gradient buffers at step 0.
+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 "rest.colvars.state".
+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 "rest.colvars.state".
 colvars: Saving collective variables state to "test.colvars.state".
-colvars: Resetting the Collective Variables module.
+colvars: Saving collective variables state to "test.colvars.state".
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped
@@ -5,13 +5,13 @@ configuration {
 
 colvar {
   name one
-  x  3.20036069218762e+00
+  x       3.2003843562355
 }
 
 abf {
   configuration {
-    step 20
-    name abf1
+step 20
+name abf1
   }
 
 samples
@@ -20,8 +20,8 @@ samples
  0 0 0 0
 
 gradient
- 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.12776581376024e-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 0 0 0 0 0 -0.10385485654788 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0
 }
 
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj
@@ -5,18 +5,18 @@
            3    3.20405779931486e+00  0.00000000000000e+00 
            4    3.20488715757478e+00  0.00000000000000e+00 
            5    3.20630753860023e+00  0.00000000000000e+00 
-           6    3.20822521484009e+00 -6.61626791923408e+00 
-           7    3.21041717634450e+00 -1.27156541500808e+01 
-           8    3.21265147474750e+00 -1.78199101059935e+01 
-           9    3.21470018041825e+00 -2.15984911523814e+01 
-          10    3.21635524474136e+00 -2.38649655797079e+01 
-          11    3.21744175542164e+00 -2.04771085292232e+01 
-          12    3.21789227153408e+00 -1.70074606132688e+01 
-          13    3.21766748124389e+00 -1.36104049871579e+01 
-          14    3.21676135390922e+00 -1.04308363259766e+01 
-          15    3.21520071953742e+00 -7.58252414070870e+00 
-          16    3.21304286766655e+00 -5.14775867496289e+00 
-          17    3.21037093904356e+00 -3.17629358378122e+00 
-          18    3.20728794724505e+00 -1.68764750172374e+00 
-          19    3.20391020908566e+00 -6.75514681148352e-01 
-          20    3.20036069218762e+00 -1.12776581376024e-01 
+           6    3.20822521484009e+00 -6.61157190854750e+00 
+           7    3.21041724907750e+00 -1.27050301328157e+01 
+           8    3.21265178240395e+00 -1.78028628544160e+01 
+           9    3.21470098068744e+00 -2.15753129933168e+01 
+          10    3.21635688320852e+00 -2.38366465889628e+01 
+          11    3.21744464629897e+00 -2.04504671342194e+01 
+          12    3.21789678756116e+00 -1.69832533952049e+01 
+          13    3.21767393972780e+00 -1.35890910889714e+01 
+          14    3.21677000635471e+00 -1.04125653142527e+01 
+          15    3.21521174831218e+00 -7.56715843574337e+00 
+          16    3.21305638863422e+00 -5.13491652636543e+00 
+          17    3.21038700938995e+00 -3.16541313007834e+00 
+          18    3.20730657726304e+00 -1.67806747099744e+00 
+          19    3.20393137633088e+00 -6.66563054214209e-01 
+          20    3.20038435623547e+00 -1.03854856547883e-01 
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.grad b/lammps/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  -1.12776581375979e-01
+  3.25000000000000e+00  -1.03854856547883e-01
   3.75000000000000e+00   0.00000000000000e+00
   4.25000000000000e+00   0.00000000000000e+00
   4.75000000000000e+00   0.00000000000000e+00

diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.pmf b/lammps/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   5.63882906879895e-02
-  5.00000000000000e-01   5.63882906879895e-02
-  1.00000000000000e+00   5.63882906879895e-02
-  1.50000000000000e+00   5.63882906879895e-02
-  2.00000000000000e+00   5.63882906879895e-02
-  2.50000000000000e+00   5.63882906879895e-02
-  3.00000000000000e+00   5.63882906879895e-02
+  0.00000000000000e+00   5.19274282739416e-02
+  5.00000000000000e-01   5.19274282739416e-02
+  1.00000000000000e+00   5.19274282739416e-02
+  1.50000000000000e+00   5.19274282739416e-02
+  2.00000000000000e+00   5.19274282739416e-02
+  2.50000000000000e+00   5.19274282739416e-02
+  3.00000000000000e+00   5.19274282739416e-02
   3.50000000000000e+00   0.00000000000000e+00
   4.00000000000000e+00   0.00000000000000e+00
   4.50000000000000e+00   0.00000000000000e+00

diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out
@@ -1,10 +1,13 @@
-colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
 colvars: This version was built with the C++11 standard or higher.
-colvars: Using LAMMPS interface, version "2020-04-07".
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 2)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: not available
+colvars: Will read input state from file "test.colvars.state"
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -56,27 +59,27 @@ colvars:     # forceNoPBC = off [default]
 colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = 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.
 colvars:       Initializing atom group "group2".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = 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.
@@ -104,19 +107,20 @@ colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "abf" instance.
 colvars:   # name = "abf1" [default]
 colvars:   # colvars = { one }
-colvars:   # zeroStepData = off [default]
+colvars:   # stepZeroData = off [default]
 colvars:   # outputEnergy = off [default]
 colvars:   # outputFreq = 10 [default]
 colvars:   # timeStepFactor = 1 [default]
 colvars:   WARNING: ABF should not be run without a thermostat or at 0 Kelvin!
 colvars:   # applyBias = on [default]
-colvars:   # updateBias = on [default]
 colvars:   # hideJacobian = off [default]
 colvars:   Jacobian (geometric) forces will be included in reported free energy gradients.
 colvars:   # fullSamples = 10
+colvars:   # minSamples = 5 [default]
 colvars:   # inputPrefix =  [default]
 colvars:   # historyFreq = 0 [default]
 colvars:   # shared = off [default]
+colvars:   # updateBias = on [default]
 colvars:   # maxForce =  [default]
 colvars:   # integrate = on [default]
 colvars:   Finished ABF setup.
@@ -125,21 +129,19 @@ colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+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: Restarting from file "test.colvars.state".
-colvars:   Restarting collective variable "one" from value: 3.20036
-colvars:   Restarting abf bias "abf1" from step number 20.
+colvars: Loading state from text file "test.colvars.state".
+colvars:   Restarting collective variable "one" from value: 3.20038
+colvars:   Restarted abf bias "abf1" with step number 20.
 colvars: ----------------------------------------------------------------------
-colvars: The restart output state file will be "rest.colvars.state".
 colvars: The final output state file will be "test.restart.colvars.state".
-colvars: Opening trajectory file "test.restart.colvars.traj".
-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:   Prepared sample and gradient buffers at step 20.
 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 "rest.colvars.state".
+colvars: Saving collective variables state to "test.restart.colvars.state".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
 colvars: Saving collective variables state to "test.restart.colvars.state".
-colvars: Resetting the Collective Variables module.
+colvars: Saving collective variables state to "test.restart.colvars.state".
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped
@@ -5,13 +5,13 @@ configuration {
 
 colvar {
   name one
-  x  3.17582252688381e+00
+  x       3.1758939206034
 }
 
 abf {
   configuration {
-    step 40
-    name abf1
+step 40
+name abf1
   }
 
 samples
@@ -20,8 +20,8 @@ samples
  0 0 0 0
 
 gradient
- 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -8.67716293178495e+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 0 0 0 0 0 -8.6637911275798 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0
 }
 
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj
@@ -1,22 +1,22 @@
 # step         one                   fa_one                
-          20    3.20036076583879e+00 -1.12776581376024e-01 
-          21    3.19676250595523e+00 -1.12776581376024e-01 
-          22    3.19323015858381e+00 -2.99226657105897e-01 
-          23    3.18986878033029e+00 -7.71570670388436e-01 
-          24    3.18676635816465e+00 -1.45966444381162e+00 
-          25    3.18399012323985e+00 -2.29255009605800e+00 
-          26    3.18158461659959e+00 -3.20291155852885e+00 
-          27    3.17957172980453e+00 -4.13119762789999e+00 
-          28    3.17795242533882e+00 -5.02830487271041e+00 
-          29    3.17670962516017e+00 -5.85665418044438e+00 
-          30    3.17581173522468e+00 -6.58995308174671e+00 
-          31    3.17521643416185e+00 -7.21224165778954e+00 
-          32    3.17487456266985e+00 -7.71677976467746e+00 
-          33    3.17473400751618e+00 -8.10491399457095e+00 
-          34    3.17474340422162e+00 -8.38478985628265e+00 
-          35    3.17485538125568e+00 -8.56974337269324e+00 
-          36    3.17502906896877e+00 -8.67642273989548e+00 
-          37    3.17523173654562e+00 -8.72292739505557e+00 
-          38    3.17543964478384e+00 -8.72734418672621e+00 
-          39    3.17563832893481e+00 -8.70683028310459e+00 
-          40    3.17582252688381e+00 -8.67716293178495e+00 
+          20    3.20038442890979e+00 -1.03854856547880e-01 
+          21    3.19678862154174e+00 -1.03854856547880e-01 
+          22    3.19325868201096e+00 -2.89577637067747e-01 
+          23    3.18989968114783e+00 -7.61101440554271e-01 
+          24    3.18679962469704e+00 -1.44844736047144e+00 
+          25    3.18402576202599e+00 -2.28077446479501e+00 
+          26    3.18162264923830e+00 -3.19083007934240e+00 
+          27    3.17961218770411e+00 -4.11907208902965e+00 
+          28    3.17799534343587e+00 -5.01636137209204e+00 
+          29    3.17675503558160e+00 -5.84505314310151e+00 
+          30    3.17585966166561e+00 -6.57877537042113e+00 
+          31    3.17526688749274e+00 -7.20148861595175e+00 
+          32    3.17492753806785e+00 -7.70638297502586e+00 
+          33    3.17478948326253e+00 -8.09475011416048e+00 
+          34    3.17480134217557e+00 -8.37469681855967e+00 
+          35    3.17491572893043e+00 -8.55953599790606e+00 
+          36    3.17509176298755e+00 -8.66590727775137e+00 
+          37    3.17529670713715e+00 -8.71191545508902e+00 
+          38    3.17550682085422e+00 -8.71566657237990e+00 
+          39    3.17570764320513e+00 -8.69435074482412e+00 
+          40    3.17589392060342e+00 -8.66379112757977e+00 
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad b/lammps/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  -8.67716293178499e+00
+  3.25000000000000e+00  -8.66379112757977e+00
   3.75000000000000e+00   0.00000000000000e+00
   4.25000000000000e+00   0.00000000000000e+00
   4.75000000000000e+00   0.00000000000000e+00

diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf b/lammps/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   4.33858146589250e+00
-  5.00000000000000e-01   4.33858146589250e+00
-  1.00000000000000e+00   4.33858146589250e+00
-  1.50000000000000e+00   4.33858146589250e+00
-  2.00000000000000e+00   4.33858146589250e+00
-  2.50000000000000e+00   4.33858146589250e+00
-  3.00000000000000e+00   4.33858146589250e+00
+  0.00000000000000e+00   4.33189556378988e+00
+  5.00000000000000e-01   4.33189556378988e+00
+  1.00000000000000e+00   4.33189556378988e+00
+  1.50000000000000e+00   4.33189556378988e+00
+  2.00000000000000e+00   4.33189556378988e+00
+  2.50000000000000e+00   4.33189556378988e+00
+  3.00000000000000e+00   4.33189556378988e+00
   3.50000000000000e+00   0.00000000000000e+00
   4.00000000000000e+00   0.00000000000000e+00
   4.50000000000000e+00   0.00000000000000e+00