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Add distanceZ and distanceXY regression tests
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Amazingly enough, nobody had set them up earlier.  Note that the fittingGroup versions are a bit sensitive to the choice of axis/ref2.
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@giacomofiorin
giacomofiorin committed Jul 22, 2017
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107 changes: 107 additions & 0 deletions namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out
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colvars: ----------------------------------------------------------------------
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "test.in":
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: # colvarsTrajAppend = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = one
colvars: Initializing a new "distanceXY" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: Initializing atom group "main".
colvars: # indexGroup = group5
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: Atom group "main" defined, 4 atoms initialized: total mass = 54.028.
colvars: Initializing atom group "ref".
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: Atom group "ref" defined, 4 atoms initialized: total mass = 54.028.
colvars: # axis = ( 0.3 , -0.4 , 0.5 )
colvars: The normalized axis is: ( 0.424264 , -0.565685 , 0.707107 ).
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: All components initialized.
colvars: # width = 0.5
colvars: # lowerBoundary = 0 [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: # outputSystemForce = off [default]
colvars: # outputAppliedForce = on
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "harmonic1" [default]
colvars: # colvars = { one }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 0.001
colvars: # centers = { 0.1 }
colvars: # targetCenters = { 0.1 } [default]
colvars: # targetForceConstant = 0 [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: 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: Writing the state file "test.tmp.colvars.state".
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.colvars.state".
16 changes: 16 additions & 0 deletions namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped
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configuration {
step 20
dt 1.000000e+00
}

colvar {
name one
x 6.10714243551413e+00
}

restraint {
configuration {
name harmonic1
}
}

22 changes: 22 additions & 0 deletions namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj
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# step one fa_one
0 6.28105056411478e+00 -2.47242022564591e-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
111 changes: 111 additions & 0 deletions namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out
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colvars: ----------------------------------------------------------------------
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "test.in":
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: # colvarsTrajAppend = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = one
colvars: Initializing a new "distanceXY" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: Initializing atom group "main".
colvars: # indexGroup = group5
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: Atom group "main" defined, 4 atoms initialized: total mass = 54.028.
colvars: Initializing atom group "ref".
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: Atom group "ref" defined, 4 atoms initialized: total mass = 54.028.
colvars: # axis = ( 0.3 , -0.4 , 0.5 )
colvars: The normalized axis is: ( 0.424264 , -0.565685 , 0.707107 ).
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: All components initialized.
colvars: # width = 0.5
colvars: # lowerBoundary = 0 [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: # outputSystemForce = off [default]
colvars: # outputAppliedForce = on
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "harmonic1" [default]
colvars: # colvars = { one }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 0.001
colvars: # centers = { 0.1 }
colvars: # targetCenters = { 0.1 } [default]
colvars: # targetForceConstant = 0 [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: Restarting from file "test.colvars.state".
colvars: Restarting collective variable "one" from value: 6.10714
colvars: Restarting restraint bias "harmonic1".
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: Writing to colvar 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: 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.colvars.state".
16 changes: 16 additions & 0 deletions ...s/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped
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configuration {
step 40
dt 1.000000e+00
}

colvar {
name one
x 5.98331278931269e+00
}

restraint {
configuration {
name harmonic1
}
}

22 changes: 22 additions & 0 deletions namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj
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# step one fa_one
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
1 change: 1 addition & 0 deletions namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt
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Info: NAMD 2.11 for Linux-x86_64-multicore
28 changes: 28 additions & 0 deletions namd/tests/library/000_distancexy-axis_harmonic-fixed/test.in
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colvarsTrajFrequency 1
colvarsRestartFrequency 10
indexFile index.ndx

colvar {

name one

outputAppliedForce on

width 0.5

distanceXY {
axis (0.3, -0.4, 0.5)
main {
indexGroup group5
}
ref {
indexGroup group1
}
}
}

harmonic {
colvars one
centers 0.1
forceConstant 0.001
}
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