Allow reusing computation and data between CVC objects

namd/tests/library/000_spinangle-reuse_harmonic-fixed/AutoDiff/test.colvars.out

@@ -0,0 +1,186 @@
+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 (num threads = 1).
+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: # 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 = "ori"
+colvars:   Initializing a new "orientation" 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:     # reuseComponent = "" [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:       # 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 = "rmsd_atoms_refpos.xyz"
+colvars:     # refPositionsCol = "" [default]
+colvars:     Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units.
+colvars:     # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default]
+colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 0.5
+colvars:   # hardLowerBoundary = off [default]
+colvars:   # hardUpperBoundary = off [default]
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = off [default]
+colvars:   # outputValue = off
+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:   Initializing a new collective variable.
+colvars:   # name = "one"
+colvars:   Initializing a new "spinAngle" component.
+colvars:     # name = "" [default]
+colvars:     # componentCoeff = 1 [default]
+colvars:     # componentExp = 1 [default]
+colvars:     # period = 360 [default]
+colvars:     # wrapAround = 0 [default]
+colvars:     # forceNoPBC = off [default]
+colvars:     # scalable = on [default]
+colvars:     # reuseComponent = "ori/orientation0001"
+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:   # expandBoundaries = off [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, 2 in total.
+colvars: List of variables:  ori one
+colvars: List of components:  one/spinAngle0001 ori/orientation0001
+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:   # 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: ----------------------------------------------------------------------
+colvars: Collective variables biases initialized, 1 in total.
+colvars: List of biases:  harmonic1
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables module (re)initialized.
+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: - orientationProj colvar component (derived from orientationAngle):
+colvars: - spinAngle colvar component (derived from tilt):
+colvars: - tilt colvar component (derived from orientationProj):
+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: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+colvars: Re-initialized atom group for variable "ori":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: 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".
+colvars: Saving collective variables state to "test.colvars.state".

namd/tests/library/000_spinangle-reuse_harmonic-fixed/AutoDiff/test.colvars.state.stripped

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+configuration {
+  step           20
+  dt 1.000000e+00
+}
+
+colvar {
+  name ori
+  x (      0.99504759124548 ,    -0.089421878144897 ,     0.010350023726748 ,    -0.042153242751538 )
+}
+
+colvar {
+  name one
+  x      -6.5219617552899
+}
+
+restraint {
+  configuration {
+step 20
+name harmonic1
+  }
+}
+

namd/tests/library/000_spinangle-reuse_harmonic-fixed/AutoDiff/test.colvars.traj

@@ -0,0 +1,22 @@
+# step         one                   fa_one                
+           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