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Update regtest for extended Lagrangian bugfix
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@jhenin @giacomofiorin
jhenin authored and giacomofiorin committed Jan 17, 2019
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48 changes: 26 additions & 22 deletions lammps/tests/library/000_distance-extended/AutoDiff/test.colvars.out
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Expand Up @@ -3,10 +3,9 @@ colvars: ----------------------------------------------------------------------
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: Using LAMMPS interface, version 2017-01-09.
colvars: Using LAMMPS interface, version 2018-08-29.
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).
Expand Down Expand Up @@ -37,80 +36,85 @@ 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 = on [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
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: Initializing atom group "group1".
colvars: # name = "" [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: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
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: # atomsOfGroup = "" [default]
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: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: # forceNoPBC = off [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined with 4 atoms requested.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 0.5
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # extendedLagrangian = on
colvars: Enabling the extended Lagrangian term for colvar "one".
colvars: # extendedTemp = 500
colvars: # extendedFluctuation = 0.1
colvars: Computed extended system force constant: 99.3603 kcal/mol/U^2
colvars: Computed extended system force constant: 99.3603 [E]/U^2
colvars: # extendedTimeConstant = 200
colvars: Computed fictitious mass: 100673 kcal/mol/(U/fs)^2 (U: colvar unit)
colvars: Computed fictitious mass: 100673 [E]/(U/fs)^2 (U: colvar unit)
colvars: # outputEnergy = off [default]
colvars: # extendedLangevinDamping = 0
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: No collective variables biases were defined.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "test.colvars.state".
colvars: Writing to colvar trajectory file "test.colvars.traj".
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 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: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
colvars: Writing the state file "rest.colvars.state".
colvars: Saving collective variables state to "rest.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
colvars: Writing the state file "rest.colvars.state".
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: Resetting the Collective Variables module.
6 changes: 3 additions & 3 deletions lammps/tests/library/000_distance-extended/AutoDiff/test.colvars.state.stripped
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@ configuration {

colvar {
name one
x 3.21778304084605e+00
extended_x 3.20685063863908e+00
extended_v 1.94067245864449e-04
x 3.21778294380433e+00
extended_x 3.20685063455126e+00
extended_v 1.94066490737836e-04
}

40 changes: 20 additions & 20 deletions lammps/tests/library/000_distance-extended/AutoDiff/test.colvars.traj
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Original file line number Diff line number Diff line change
@@ -1,22 +1,22 @@
# step one r_one fa_one
0 3.20554673729024e+00 3.20554673729024e+00 0.00000000000000e+00
1 3.20438171380941e+00 3.20554673729024e+00 0.00000000000000e+00
2 3.20388273215229e+00 3.20554558745816e+00 0.00000000000000e+00
3 3.20406388498896e+00 3.20554279645367e+00 0.00000000000000e+00
4 3.20489969829559e+00 3.20553854582206e+00 0.00000000000000e+00
5 3.20632733605908e+00 3.20553366467323e+00 0.00000000000000e+00
6 3.20825080423986e+00 3.20552956684665e+00 0.00000000000000e+00
7 3.21054657441751e+00 3.20552815477373e+00 0.00000000000000e+00
8 3.21307035658245e+00 3.20553169568246e+00 0.00000000000000e+00
9 3.21566504763335e+00 3.20554267695128e+00 0.00000000000000e+00
10 3.21816992448880e+00 3.20556364859952e+00 0.00000000000000e+00
11 3.22043083206112e+00 3.20559706214336e+00 0.00000000000000e+00
12 3.22231059402696e+00 3.20564511603129e+00 0.00000000000000e+00
13 3.22369845338746e+00 3.20570961808671e+00 0.00000000000000e+00
14 3.22451727908619e+00 3.20579187441094e+00 0.00000000000000e+00
15 3.22472766116353e+00 3.20589261196881e+00 0.00000000000000e+00
16 3.22432864521884e+00 3.20601193897513e+00 0.00000000000000e+00
17 3.22335548479862e+00 3.20614934384589e+00 0.00000000000000e+00
18 3.22187515928638e+00 3.20630373049711e+00 0.00000000000000e+00
19 3.21998043546551e+00 3.20647348553253e+00 0.00000000000000e+00
20 3.21778304084605e+00 3.20665657139321e+00 0.00000000000000e+00
1 3.20438171378811e+00 3.20554558745814e+00 0.00000000000000e+00
2 3.20388273201193e+00 3.20554279645348e+00 0.00000000000000e+00
3 3.20406388447918e+00 3.20553854582122e+00 0.00000000000000e+00
4 3.20489969696127e+00 3.20553366467040e+00 0.00000000000000e+00
5 3.20632733322629e+00 3.20552956683905e+00 0.00000000000000e+00
6 3.20825079903897e+00 3.20552815475624e+00 0.00000000000000e+00
7 3.21054656583369e+00 3.20553169564662e+00 0.00000000000000e+00
8 3.21307034351980e+00 3.20554267688423e+00 0.00000000000000e+00
9 3.21566502898008e+00 3.20556364848292e+00 0.00000000000000e+00
10 3.21816989917650e+00 3.20559706195234e+00 0.00000000000000e+00
11 3.22043079911796e+00 3.20564511573352e+00 0.00000000000000e+00
12 3.22231055263007e+00 3.20570961764164e+00 0.00000000000000e+00
13 3.22369840292301e+00 3.20579187376919e+00 0.00000000000000e+00
14 3.22451721922192e+00 3.20589261107194e+00 0.00000000000000e+00
15 3.22472759193434e+00 3.20601193775568e+00 0.00000000000000e+00
16 3.22432856711887e+00 3.20614934222801e+00 0.00000000000000e+00
17 3.22335539886678e+00 3.20630372839756e+00 0.00000000000000e+00
18 3.22187506716916e+00 3.20647348286248e+00 0.00000000000000e+00
19 3.21998033944187e+00 3.20665656806052e+00 0.00000000000000e+00
20 3.21778294380433e+00 3.20685063455126e+00 0.00000000000000e+00
48 changes: 26 additions & 22 deletions lammps/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.out
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Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,9 @@ colvars: ----------------------------------------------------------------------
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: Using LAMMPS interface, version 2017-01-09.
colvars: Using LAMMPS interface, version 2018-08-29.
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).
Expand Down Expand Up @@ -37,84 +36,89 @@ 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 = on [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
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: Initializing atom group "group1".
colvars: # name = "" [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: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
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: # atomsOfGroup = "" [default]
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: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: # forceNoPBC = off [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined with 4 atoms requested.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 0.5
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # extendedLagrangian = on
colvars: Enabling the extended Lagrangian term for colvar "one".
colvars: # extendedTemp = 500
colvars: # extendedFluctuation = 0.1
colvars: Computed extended system force constant: 99.3603 kcal/mol/U^2
colvars: Computed extended system force constant: 99.3603 [E]/U^2
colvars: # extendedTimeConstant = 200
colvars: Computed fictitious mass: 100673 kcal/mol/(U/fs)^2 (U: colvar unit)
colvars: Computed fictitious mass: 100673 [E]/(U/fs)^2 (U: colvar unit)
colvars: # outputEnergy = off [default]
colvars: # extendedLangevinDamping = 0
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: No collective variables biases were defined.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
colvars: ----------------------------------------------------------------------
colvars: Restarting from file "test.colvars.state".
colvars: Restarting collective variable "one" from value: 3.21778
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: Writing to colvar trajectory file "test.restart.colvars.traj".
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 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: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
colvars: Writing the state file "rest.colvars.state".
colvars: Saving collective variables state to "rest.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
colvars: Writing the state file "rest.colvars.state".
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: Resetting the Collective Variables module.
6 changes: 3 additions & 3 deletions lammps/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.state.stripped
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@ configuration {

colvar {
name one
x 3.21432092080871e+00
extended_x 3.20718650755556e+00
extended_v 2.46916734757320e-05
x 3.21432129898711e+00
extended_x 3.20718650988919e+00
extended_v 2.46940822129498e-05
}

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