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jheningiacomofiorin
jhenin
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giacomofiorin
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Update GROMACS test for coordnum fix
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‎gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out‎

Lines changed: 58 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,16 @@
11
colvars: ----------------------------------------------------------------------
22
colvars: Please cite Fiorin et al, Mol Phys 2013:
3-
colvars: SMP parallelism is enabled; if needed, use "smp off" to override this.
3+
colvars: https://doi.org/10.1080/00268976.2013.813594
4+
colvars: as well as all other papers listed below for individual features used.
5+
colvars: Summary of compile-time features available in this build:
6+
colvars: - C++ language version: 201703
7+
colvars: - Multiple replicas: not available
8+
colvars: - Lepton custom functions: available
9+
colvars: - Tcl interpreter: not available
410
colvars: ----------------------------------------------------------------------
5-
colvars: Reading new configuration from file "test.dat":
11+
colvars: Start colvars Initialization.
12+
colvars: ----------------------------------------------------------------------
13+
colvars: Reading new configuration:
614
colvars: # units = "" [default]
715
colvars: # indexFile = "index.ndx"
816
colvars: The following index groups are currently defined:
@@ -34,15 +42,22 @@ colvars: group9 (4 atoms)
3442
colvars: Protein_C-alpha_10 (1 atoms)
3543
colvars: group10 (4 atoms)
3644
colvars: heavy_atoms (51 atoms)
37-
colvars: # smp = on [default]
45+
colvars: prot_N (10 atoms)
46+
colvars: prot_CA (10 atoms)
47+
colvars: prot_C (10 atoms)
48+
colvars: prot_O (10 atoms)
49+
colvars: # smp = "cvcs" [default]
50+
colvars: SMP parallelism will be applied to Colvars components.
51+
colvars: - SMP parallelism: enabled (num. threads = 2)
3852
colvars: # colvarsTrajFrequency = 1
3953
colvars: # colvarsRestartFrequency = 10
4054
colvars: # scriptedColvarForces = off [default]
4155
colvars: # scriptingAfterBiases = off [default]
56+
colvars: # defaultInputStateFile = "" [default]
4257
colvars: ----------------------------------------------------------------------
4358
colvars: Initializing a new collective variable.
4459
colvars: # name = "one"
45-
colvars: Initializing a new "coordNum" component.
60+
colvars: Initializing a new "coordNum" component.
4661
colvars: # name = "" [default]
4762
colvars: # componentCoeff = 1 [default]
4863
colvars: # componentExp = 1 [default]
@@ -52,27 +67,27 @@ colvars: # forceNoPBC = off [default]
5267
colvars: # scalable = on [default]
5368
colvars: Initializing atom group "group1".
5469
colvars: # name = "" [default]
55-
colvars: # centerReference = off [default]
56-
colvars: # rotateReference = off [default]
70+
colvars: # centerToOrigin = off [default]
71+
colvars: # centerToReference = off [default]
72+
colvars: # rotateToReference = off [default]
5773
colvars: # atomsOfGroup = "" [default]
5874
colvars: # indexGroup = "group1"
5975
colvars: # psfSegID = [default]
6076
colvars: # atomsFile = "" [default]
6177
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
62-
colvars: # enableForces = on [default]
6378
colvars: # enableFitGradients = on [default]
6479
colvars: # printAtomIDs = off [default]
6580
colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72.
6681
colvars: Initializing atom group "group2".
6782
colvars: # name = "" [default]
68-
colvars: # centerReference = off [default]
69-
colvars: # rotateReference = off [default]
83+
colvars: # centerToOrigin = off [default]
84+
colvars: # centerToReference = off [default]
85+
colvars: # rotateToReference = off [default]
7086
colvars: # atomsOfGroup = "" [default]
7187
colvars: # indexGroup = "group2"
7288
colvars: # psfSegID = [default]
7389
colvars: # atomsFile = "" [default]
7490
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
75-
colvars: # enableForces = on [default]
7691
colvars: # enableFitGradients = on [default]
7792
colvars: # printAtomIDs = off [default]
7893
colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4.
@@ -87,7 +102,9 @@ colvars: All components initialized.
87102
colvars: # timeStepFactor = 1 [default]
88103
colvars: # width = 0.5
89104
colvars: # lowerBoundary = 0 [default]
90-
colvars: # upperBoundary = 0 [default]
105+
colvars: # upperBoundary = 16 [default]
106+
colvars: # hardLowerBoundary = on [default]
107+
colvars: # hardUpperBoundary = on [default]
91108
colvars: # expandBoundaries = off [default]
92109
colvars: # extendedLagrangian = off [default]
93110
colvars: # outputValue = on [default]
@@ -103,29 +120,53 @@ colvars: ----------------------------------------------------------------------
103120
colvars: Initializing a new "harmonic" instance.
104121
colvars: # name = "harmonic1" [default]
105122
colvars: # colvars = { one }
106-
colvars: # outputEnergy = off [default]
123+
colvars: # stepZeroData = off [default]
107124
colvars: # timeStepFactor = 1 [default]
125+
colvars: # outputEnergy = off [default]
126+
colvars: # outputFreq = 10 [default]
108127
colvars: # writeTISamples = off [default]
109128
colvars: # writeTIPMF = off [default]
110129
colvars: # centers = { 0.01 }
111130
colvars: # targetCenters = { 0.01 } [default]
112131
colvars: # outputCenters = off [default]
113132
colvars: # forceConstant = 0.004184
133+
colvars: # decoupling = off [default]
114134
colvars: # targetForceConstant = -1 [default]
115135
colvars: The force constant for colvar "one" will be rescaled to 0.016736 according to the specified width (0.5).
116136
colvars: ----------------------------------------------------------------------
117137
colvars: Collective variables biases initialized, 1 in total.
118138
colvars: ----------------------------------------------------------------------
119139
colvars: Collective variables module (re)initialized.
120140
colvars: ----------------------------------------------------------------------
141+
colvars: Current simulation parameters: initial step = 0, integration timestep = 1
142+
colvars: Updating atomic parameters (masses, charges, etc).
121143
colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
122144
colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
123-
colvars: The restart output state file will be "test.restart.colvars.state".
145+
colvars:
146+
colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS:
147+
colvars:
148+
colvars: - GROMACS engine:
149+
colvars: Abraham2015 https://doi.org/10.1016/j.softx.2015.06.001
150+
colvars:
151+
colvars: - Colvars module:
152+
colvars: - Harmonic colvar bias implementation:
153+
colvars: - Optimal rotation via flexible fitting:
154+
colvars: - coordNum colvar component:
155+
colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594
156+
colvars:
157+
colvars: - Colvars-GROMACS interface:
158+
colvars: Fiorin2024 https://doi.org/10.1021/acs.jpcb.4c05604
159+
colvars:
160+
colvars: - coordNum pairlist:
161+
colvars: n/a
162+
colvars:
124163
colvars: The final output state file will be "test.colvars.state".
125-
colvars: Writing to colvar trajectory file "test.colvars.traj".
164+
colvars: ----------------------------------------------------------------------
165+
colvars: End colvars Initialization.
166+
colvars:
126167
colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
127-
colvars: Saving collective variables state to "test.restart.colvars.state".
128168
colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
129-
colvars: Saving collective variables state to "test.restart.colvars.state".
130169
colvars: Saving collective variables state to "test.colvars.state".
131-
colvars: Resetting the Collective Variables module.
170+
colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
171+
colvars: Saving collective variables state to "test.colvars.state".
172+
colvars: Saving collective variables state to "test.colvars.state".

‎gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ configuration {
55

66
colvar {
77
name one
8-
x 1.01440692492519e+01
8+
x 10.144043682546
99
}
1010

1111
restraint {

‎gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj‎

Lines changed: 20 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,22 +1,22 @@
11
# step one fa_one
22
0 1.01481356885925e+01 -1.69671838884284e-01
3-
1 1.01532198191674e+01 -1.69756926893585e-01
4-
2 1.01557545931500e+01 -1.69799348870958e-01
5-
3 1.01557319137895e+01 -1.69798969309181e-01
6-
4 1.01533142217901e+01 -1.69758506815879e-01
7-
5 1.01488170635086e+01 -1.69683242374880e-01
8-
6 1.01426774487970e+01 -1.69580489783066e-01
9-
7 1.01354254524201e+01 -1.69459120371702e-01
10-
8 1.01276434072835e+01 -1.69328880064296e-01
11-
9 1.01199313368170e+01 -1.69199810852969e-01
12-
10 1.01128718388556e+01 -1.69081663095087e-01
13-
11 1.01069979199802e+01 -1.68983357188788e-01
14-
12 1.01027494826722e+01 -1.68912255342002e-01
15-
13 1.01004810673464e+01 -1.68874291143109e-01
16-
14 1.01004273653748e+01 -1.68873392386913e-01
17-
15 1.01026950922535e+01 -1.68911345063955e-01
18-
16 1.01072620475184e+01 -1.68987777627267e-01
19-
17 1.01139827912872e+01 -1.69100255994983e-01
20-
18 1.01226024425788e+01 -1.69244514478999e-01
21-
19 1.01327705014571e+01 -1.69414687112385e-01
22-
20 1.01440692492519e+01 -1.69603782955480e-01
3+
1 1.01532196515848e+01 -1.69756924088922e-01
4+
2 1.01557540929563e+01 -1.69799340499717e-01
5+
3 1.01557309204432e+01 -1.69798952684538e-01
6+
4 1.01533125810296e+01 -1.69758479356112e-01
7+
5 1.01488146290092e+01 -1.69683201631098e-01
8+
6 1.01426740836049e+01 -1.69580433463212e-01
9+
7 1.01354210298558e+01 -1.69459046355667e-01
10+
8 1.01276378116210e+01 -1.69328786415290e-01
11+
9 1.01199244633384e+01 -1.69199695818432e-01
12+
10 1.01128635934176e+01 -1.69081525099437e-01
13+
11 1.01069882181287e+01 -1.68983194818602e-01
14+
12 1.01027382484634e+01 -1.68912067326284e-01
15+
13 1.01004682319993e+01 -1.68874076330741e-01
16+
14 1.01004128659236e+01 -1.68873149724098e-01
17+
15 1.01026788707835e+01 -1.68911073581432e-01
18+
16 1.01072440500357e+01 -1.68987476421397e-01
19+
17 1.01139629675644e+01 -1.69099924225157e-01
20+
18 1.01225807464515e+01 -1.69244151372612e-01
21+
19 1.01327468896246e+01 -1.69414291944757e-01
22+
20 1.01440436825462e+01 -1.69603355071092e-01

‎gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out‎

Lines changed: 62 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,16 @@
11
colvars: ----------------------------------------------------------------------
22
colvars: Please cite Fiorin et al, Mol Phys 2013:
3-
colvars: SMP parallelism is enabled; if needed, use "smp off" to override this.
3+
colvars: https://doi.org/10.1080/00268976.2013.813594
4+
colvars: as well as all other papers listed below for individual features used.
5+
colvars: Summary of compile-time features available in this build:
6+
colvars: - C++ language version: 201703
7+
colvars: - Multiple replicas: not available
8+
colvars: - Lepton custom functions: available
9+
colvars: - Tcl interpreter: not available
410
colvars: ----------------------------------------------------------------------
5-
colvars: Reading new configuration from file "test.dat":
11+
colvars: Start colvars Initialization.
12+
colvars: ----------------------------------------------------------------------
13+
colvars: Reading new configuration:
614
colvars: # units = "" [default]
715
colvars: # indexFile = "index.ndx"
816
colvars: The following index groups are currently defined:
@@ -34,15 +42,22 @@ colvars: group9 (4 atoms)
3442
colvars: Protein_C-alpha_10 (1 atoms)
3543
colvars: group10 (4 atoms)
3644
colvars: heavy_atoms (51 atoms)
37-
colvars: # smp = on [default]
45+
colvars: prot_N (10 atoms)
46+
colvars: prot_CA (10 atoms)
47+
colvars: prot_C (10 atoms)
48+
colvars: prot_O (10 atoms)
49+
colvars: # smp = "cvcs" [default]
50+
colvars: SMP parallelism will be applied to Colvars components.
51+
colvars: - SMP parallelism: enabled (num. threads = 2)
3852
colvars: # colvarsTrajFrequency = 1
3953
colvars: # colvarsRestartFrequency = 10
4054
colvars: # scriptedColvarForces = off [default]
4155
colvars: # scriptingAfterBiases = off [default]
56+
colvars: # defaultInputStateFile = "" [default]
4257
colvars: ----------------------------------------------------------------------
4358
colvars: Initializing a new collective variable.
4459
colvars: # name = "one"
45-
colvars: Initializing a new "coordNum" component.
60+
colvars: Initializing a new "coordNum" component.
4661
colvars: # name = "" [default]
4762
colvars: # componentCoeff = 1 [default]
4863
colvars: # componentExp = 1 [default]
@@ -52,27 +67,27 @@ colvars: # forceNoPBC = off [default]
5267
colvars: # scalable = on [default]
5368
colvars: Initializing atom group "group1".
5469
colvars: # name = "" [default]
55-
colvars: # centerReference = off [default]
56-
colvars: # rotateReference = off [default]
70+
colvars: # centerToOrigin = off [default]
71+
colvars: # centerToReference = off [default]
72+
colvars: # rotateToReference = off [default]
5773
colvars: # atomsOfGroup = "" [default]
5874
colvars: # indexGroup = "group1"
5975
colvars: # psfSegID = [default]
6076
colvars: # atomsFile = "" [default]
6177
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
62-
colvars: # enableForces = on [default]
6378
colvars: # enableFitGradients = on [default]
6479
colvars: # printAtomIDs = off [default]
6580
colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72.
6681
colvars: Initializing atom group "group2".
6782
colvars: # name = "" [default]
68-
colvars: # centerReference = off [default]
69-
colvars: # rotateReference = off [default]
83+
colvars: # centerToOrigin = off [default]
84+
colvars: # centerToReference = off [default]
85+
colvars: # rotateToReference = off [default]
7086
colvars: # atomsOfGroup = "" [default]
7187
colvars: # indexGroup = "group2"
7288
colvars: # psfSegID = [default]
7389
colvars: # atomsFile = "" [default]
7490
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
75-
colvars: # enableForces = on [default]
7691
colvars: # enableFitGradients = on [default]
7792
colvars: # printAtomIDs = off [default]
7893
colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4.
@@ -87,7 +102,9 @@ colvars: All components initialized.
87102
colvars: # timeStepFactor = 1 [default]
88103
colvars: # width = 0.5
89104
colvars: # lowerBoundary = 0 [default]
90-
colvars: # upperBoundary = 0 [default]
105+
colvars: # upperBoundary = 16 [default]
106+
colvars: # hardLowerBoundary = on [default]
107+
colvars: # hardUpperBoundary = on [default]
91108
colvars: # expandBoundaries = off [default]
92109
colvars: # extendedLagrangian = off [default]
93110
colvars: # outputValue = on [default]
@@ -103,34 +120,58 @@ colvars: ----------------------------------------------------------------------
103120
colvars: Initializing a new "harmonic" instance.
104121
colvars: # name = "harmonic1" [default]
105122
colvars: # colvars = { one }
106-
colvars: # outputEnergy = off [default]
123+
colvars: # stepZeroData = off [default]
107124
colvars: # timeStepFactor = 1 [default]
125+
colvars: # outputEnergy = off [default]
126+
colvars: # outputFreq = 10 [default]
108127
colvars: # writeTISamples = off [default]
109128
colvars: # writeTIPMF = off [default]
110129
colvars: # centers = { 0.01 }
111130
colvars: # targetCenters = { 0.01 } [default]
112131
colvars: # outputCenters = off [default]
113132
colvars: # forceConstant = 0.004184
133+
colvars: # decoupling = off [default]
114134
colvars: # targetForceConstant = -1 [default]
115135
colvars: The force constant for colvar "one" will be rescaled to 0.016736 according to the specified width (0.5).
116136
colvars: ----------------------------------------------------------------------
117137
colvars: Collective variables biases initialized, 1 in total.
118138
colvars: ----------------------------------------------------------------------
119139
colvars: Collective variables module (re)initialized.
120140
colvars: ----------------------------------------------------------------------
141+
colvars: Current simulation parameters: initial step = 0, integration timestep = 1
142+
colvars: Updating atomic parameters (masses, charges, etc).
121143
colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
122144
colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
145+
colvars:
146+
colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS:
147+
colvars:
148+
colvars: - GROMACS engine:
149+
colvars: Abraham2015 https://doi.org/10.1016/j.softx.2015.06.001
150+
colvars:
151+
colvars: - Colvars module:
152+
colvars: - Harmonic colvar bias implementation:
153+
colvars: - Optimal rotation via flexible fitting:
154+
colvars: - coordNum colvar component:
155+
colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594
156+
colvars:
157+
colvars: - Colvars-GROMACS interface:
158+
colvars: Fiorin2024 https://doi.org/10.1021/acs.jpcb.4c05604
159+
colvars:
160+
colvars: - coordNum pairlist:
161+
colvars: n/a
162+
colvars:
163+
colvars: The final output state file will be "test.restart.part0002.colvars.state".
123164
colvars: ----------------------------------------------------------------------
124-
colvars: Restarting from file "test.colvars.state.dat".
125-
colvars: Restarting collective variable "one" from value: 10.1441
165+
colvars: Loading state from unformatted memory.
166+
colvars: Restarting collective variable "one" from value: 10.144
167+
colvars: Restarted harmonic bias "harmonic1" with step number 20.
126168
colvars: ----------------------------------------------------------------------
127-
colvars: The restart output state file will be "test.restart.part0002.restart.colvars.state".
128-
colvars: The final output state file will be "test.restart.part0002.colvars.state".
129-
colvars: Writing to colvar trajectory file "test.restart.part0002.colvars.traj".
130-
colvars: Initializing step number to 20.
169+
colvars: ----------------------------------------------------------------------
170+
colvars: End colvars Initialization.
171+
colvars:
172+
colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.part0002.colvars.traj".
131173
colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.part0002.colvars.traj".
132-
colvars: Saving collective variables state to "test.restart.part0002.restart.colvars.state".
174+
colvars: Saving collective variables state to "test.restart.part0002.colvars.state".
133175
colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.part0002.colvars.traj".
134-
colvars: Saving collective variables state to "test.restart.part0002.restart.colvars.state".
135176
colvars: Saving collective variables state to "test.restart.part0002.colvars.state".
136-
colvars: Resetting the Collective Variables module.
177+
colvars: Saving collective variables state to "test.restart.part0002.colvars.state".

‎gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ configuration {
55

66
colvar {
77
name one
8-
x 1.01859775648354e+01
8+
x 10.185911509183
99
}
1010

1111
restraint {

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