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jheningiacomofiorin
jhenin
authored and
giacomofiorin
committed
Update LAMMPS regression tests for TI/ABF fix
1 parent f7337be commit b35427e

31 files changed

+329
-305
lines changed

‎lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out

+20-19
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,12 @@
1-
colvars: Creating proxy instance
21
colvars: ----------------------------------------------------------------------
32
colvars: Please cite Fiorin et al, Mol Phys 2013:
4-
colvars: https://dx.doi.org/10.1080/00268976.2013.813594
5-
colvars: in any publication based on this calculation.
3+
colvars: https://doi.org/10.1080/00268976.2013.813594
4+
colvars: as well as all other papers listed below for individual features used.
65
colvars: This version was built with the C++11 standard or higher.
7-
colvars: Using LAMMPS interface, version "2020-04-07".
6+
colvars: Summary of compile-time features available in this build:
7+
colvars: - SMP parallelism: enabled (num. threads = 2)
8+
colvars: - Lepton custom functions: available
9+
colvars: - Tcl interpreter: not available
810
colvars: ----------------------------------------------------------------------
911
colvars: Reading new configuration from file "test.in":
1012
colvars: # units = "" [default]
@@ -56,27 +58,27 @@ colvars: # forceNoPBC = off [default]
5658
colvars: # scalable = on [default]
5759
colvars: Initializing atom group "group1".
5860
colvars: # name = "" [default]
59-
colvars: # centerReference = off [default]
60-
colvars: # rotateReference = off [default]
61+
colvars: # centerToOrigin = off [default]
62+
colvars: # centerToReference = off [default]
63+
colvars: # rotateToReference = off [default]
6164
colvars: # atomsOfGroup = "" [default]
6265
colvars: # indexGroup = "group1"
6366
colvars: # psfSegID = [default]
6467
colvars: # atomsFile = "" [default]
6568
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
66-
colvars: # enableForces = on [default]
6769
colvars: # enableFitGradients = on [default]
6870
colvars: # printAtomIDs = off [default]
6971
colvars: Atom group "group1" defined with 4 atoms requested.
7072
colvars: Initializing atom group "group2".
7173
colvars: # name = "" [default]
72-
colvars: # centerReference = off [default]
73-
colvars: # rotateReference = off [default]
74+
colvars: # centerToOrigin = off [default]
75+
colvars: # centerToReference = off [default]
76+
colvars: # rotateToReference = off [default]
7477
colvars: # atomsOfGroup = "" [default]
7578
colvars: # indexGroup = "group2"
7679
colvars: # psfSegID = [default]
7780
colvars: # atomsFile = "" [default]
7881
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
79-
colvars: # enableForces = on [default]
8082
colvars: # enableFitGradients = on [default]
8183
colvars: # printAtomIDs = off [default]
8284
colvars: Atom group "group2" defined with 4 atoms requested.
@@ -104,19 +106,20 @@ colvars: ----------------------------------------------------------------------
104106
colvars: Initializing a new "abf" instance.
105107
colvars: # name = "abf1" [default]
106108
colvars: # colvars = { one }
107-
colvars: # zeroStepData = off [default]
109+
colvars: # stepZeroData = off [default]
108110
colvars: # outputEnergy = off [default]
109111
colvars: # outputFreq = 10 [default]
110112
colvars: # timeStepFactor = 1 [default]
111113
colvars: WARNING: ABF should not be run without a thermostat or at 0 Kelvin!
112114
colvars: # applyBias = on [default]
113-
colvars: # updateBias = on [default]
114115
colvars: # hideJacobian = off [default]
115116
colvars: Jacobian (geometric) forces will be included in reported free energy gradients.
116117
colvars: # fullSamples = 10
118+
colvars: # minSamples = 5 [default]
117119
colvars: # inputPrefix = [default]
118120
colvars: # historyFreq = 0 [default]
119121
colvars: # shared = off [default]
122+
colvars: # updateBias = on [default]
120123
colvars: # maxForce = [default]
121124
colvars: # integrate = on [default]
122125
colvars: Finished ABF setup.
@@ -125,16 +128,14 @@ colvars: Collective variables biases initialized, 1 in total.
125128
colvars: ----------------------------------------------------------------------
126129
colvars: Collective variables module (re)initialized.
127130
colvars: ----------------------------------------------------------------------
128-
colvars: The restart output state file will be "rest.colvars.state".
129-
colvars: The final output state file will be "test.colvars.state".
130-
colvars: Opening trajectory file "test.colvars.traj".
131+
colvars: Current simulation parameters: initial step = 0, integration timestep = 1
132+
colvars: Updating atomic parameters (masses, charges, etc).
131133
colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
132134
colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
133-
colvars: Prepared sample and gradient buffers at step 0.
135+
colvars: The final output state file will be "test.colvars.state".
134136
colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
135137
colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
136-
colvars: Saving collective variables state to "rest.colvars.state".
138+
colvars: Saving collective variables state to "test.colvars.state".
137139
colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
138-
colvars: Saving collective variables state to "rest.colvars.state".
139140
colvars: Saving collective variables state to "test.colvars.state".
140-
colvars: Resetting the Collective Variables module.
141+
colvars: Saving collective variables state to "test.colvars.state".

‎lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped

+6-6
Original file line numberDiff line numberDiff line change
@@ -5,13 +5,13 @@ configuration {
55

66
colvar {
77
name one
8-
x 3.20036069218762e+00
8+
x 3.2003843562355
99
}
1010

1111
abf {
1212
configuration {
13-
step 20
14-
name abf1
13+
step 20
14+
name abf1
1515
}
1616

1717
samples
@@ -20,8 +20,8 @@ samples
2020
0 0 0 0
2121

2222
gradient
23-
0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.12776581376024e-01 0.00000000000000e+00
24-
0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
25-
0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
23+
0 0 0 0 0 0 -0.10385485654788 0
24+
0 0 0 0 0 0 0 0
25+
0 0 0 0
2626
}
2727

‎lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj

+15-15
Original file line numberDiff line numberDiff line change
@@ -5,18 +5,18 @@
55
3 3.20405779931486e+00 0.00000000000000e+00
66
4 3.20488715757478e+00 0.00000000000000e+00
77
5 3.20630753860023e+00 0.00000000000000e+00
8-
6 3.20822521484009e+00 -6.61626791923408e+00
9-
7 3.21041717634450e+00 -1.27156541500808e+01
10-
8 3.21265147474750e+00 -1.78199101059935e+01
11-
9 3.21470018041825e+00 -2.15984911523814e+01
12-
10 3.21635524474136e+00 -2.38649655797079e+01
13-
11 3.21744175542164e+00 -2.04771085292232e+01
14-
12 3.21789227153408e+00 -1.70074606132688e+01
15-
13 3.21766748124389e+00 -1.36104049871579e+01
16-
14 3.21676135390922e+00 -1.04308363259766e+01
17-
15 3.21520071953742e+00 -7.58252414070870e+00
18-
16 3.21304286766655e+00 -5.14775867496289e+00
19-
17 3.21037093904356e+00 -3.17629358378122e+00
20-
18 3.20728794724505e+00 -1.68764750172374e+00
21-
19 3.20391020908566e+00 -6.75514681148352e-01
22-
20 3.20036069218762e+00 -1.12776581376024e-01
8+
6 3.20822521484009e+00 -6.61157190854750e+00
9+
7 3.21041724907750e+00 -1.27050301328157e+01
10+
8 3.21265178240395e+00 -1.78028628544160e+01
11+
9 3.21470098068744e+00 -2.15753129933168e+01
12+
10 3.21635688320852e+00 -2.38366465889628e+01
13+
11 3.21744464629897e+00 -2.04504671342194e+01
14+
12 3.21789678756116e+00 -1.69832533952049e+01
15+
13 3.21767393972780e+00 -1.35890910889714e+01
16+
14 3.21677000635471e+00 -1.04125653142527e+01
17+
15 3.21521174831218e+00 -7.56715843574337e+00
18+
16 3.21305638863422e+00 -5.13491652636543e+00
19+
17 3.21038700938995e+00 -3.16541313007834e+00
20+
18 3.20730657726304e+00 -1.67806747099744e+00
21+
19 3.20393137633088e+00 -6.66563054214209e-01
22+
20 3.20038435623547e+00 -1.03854856547883e-01

‎lammps/tests/library/000_distance-grid_abf/AutoDiff/test.grad

+1-1
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
1.75000000000000e+00 0.00000000000000e+00
88
2.25000000000000e+00 0.00000000000000e+00
99
2.75000000000000e+00 0.00000000000000e+00
10-
3.25000000000000e+00 -1.12776581375979e-01
10+
3.25000000000000e+00 -1.03854856547883e-01
1111
3.75000000000000e+00 0.00000000000000e+00
1212
4.25000000000000e+00 0.00000000000000e+00
1313
4.75000000000000e+00 0.00000000000000e+00

‎lammps/tests/library/000_distance-grid_abf/AutoDiff/test.pmf

+7-7
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,13 @@
11
# 1
22
# -2.50000000000000e-01 5.00000000000000e-01 21 0
33

4-
0.00000000000000e+00 5.63882906879895e-02
5-
5.00000000000000e-01 5.63882906879895e-02
6-
1.00000000000000e+00 5.63882906879895e-02
7-
1.50000000000000e+00 5.63882906879895e-02
8-
2.00000000000000e+00 5.63882906879895e-02
9-
2.50000000000000e+00 5.63882906879895e-02
10-
3.00000000000000e+00 5.63882906879895e-02
4+
0.00000000000000e+00 5.19274282739416e-02
5+
5.00000000000000e-01 5.19274282739416e-02
6+
1.00000000000000e+00 5.19274282739416e-02
7+
1.50000000000000e+00 5.19274282739416e-02
8+
2.00000000000000e+00 5.19274282739416e-02
9+
2.50000000000000e+00 5.19274282739416e-02
10+
3.00000000000000e+00 5.19274282739416e-02
1111
3.50000000000000e+00 0.00000000000000e+00
1212
4.00000000000000e+00 0.00000000000000e+00
1313
4.50000000000000e+00 0.00000000000000e+00

‎lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out

+25-23
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,13 @@
1-
colvars: Creating proxy instance
21
colvars: ----------------------------------------------------------------------
32
colvars: Please cite Fiorin et al, Mol Phys 2013:
4-
colvars: https://dx.doi.org/10.1080/00268976.2013.813594
5-
colvars: in any publication based on this calculation.
3+
colvars: https://doi.org/10.1080/00268976.2013.813594
4+
colvars: as well as all other papers listed below for individual features used.
65
colvars: This version was built with the C++11 standard or higher.
7-
colvars: Using LAMMPS interface, version "2020-04-07".
6+
colvars: Summary of compile-time features available in this build:
7+
colvars: - SMP parallelism: enabled (num. threads = 2)
8+
colvars: - Lepton custom functions: available
9+
colvars: - Tcl interpreter: not available
10+
colvars: Will read input state from file "test.colvars.state"
811
colvars: ----------------------------------------------------------------------
912
colvars: Reading new configuration from file "test.in":
1013
colvars: # units = "" [default]
@@ -56,27 +59,27 @@ colvars: # forceNoPBC = off [default]
5659
colvars: # scalable = on [default]
5760
colvars: Initializing atom group "group1".
5861
colvars: # name = "" [default]
59-
colvars: # centerReference = off [default]
60-
colvars: # rotateReference = off [default]
62+
colvars: # centerToOrigin = off [default]
63+
colvars: # centerToReference = off [default]
64+
colvars: # rotateToReference = off [default]
6165
colvars: # atomsOfGroup = "" [default]
6266
colvars: # indexGroup = "group1"
6367
colvars: # psfSegID = [default]
6468
colvars: # atomsFile = "" [default]
6569
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
66-
colvars: # enableForces = on [default]
6770
colvars: # enableFitGradients = on [default]
6871
colvars: # printAtomIDs = off [default]
6972
colvars: Atom group "group1" defined with 4 atoms requested.
7073
colvars: Initializing atom group "group2".
7174
colvars: # name = "" [default]
72-
colvars: # centerReference = off [default]
73-
colvars: # rotateReference = off [default]
75+
colvars: # centerToOrigin = off [default]
76+
colvars: # centerToReference = off [default]
77+
colvars: # rotateToReference = off [default]
7478
colvars: # atomsOfGroup = "" [default]
7579
colvars: # indexGroup = "group2"
7680
colvars: # psfSegID = [default]
7781
colvars: # atomsFile = "" [default]
7882
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
79-
colvars: # enableForces = on [default]
8083
colvars: # enableFitGradients = on [default]
8184
colvars: # printAtomIDs = off [default]
8285
colvars: Atom group "group2" defined with 4 atoms requested.
@@ -104,19 +107,20 @@ colvars: ----------------------------------------------------------------------
104107
colvars: Initializing a new "abf" instance.
105108
colvars: # name = "abf1" [default]
106109
colvars: # colvars = { one }
107-
colvars: # zeroStepData = off [default]
110+
colvars: # stepZeroData = off [default]
108111
colvars: # outputEnergy = off [default]
109112
colvars: # outputFreq = 10 [default]
110113
colvars: # timeStepFactor = 1 [default]
111114
colvars: WARNING: ABF should not be run without a thermostat or at 0 Kelvin!
112115
colvars: # applyBias = on [default]
113-
colvars: # updateBias = on [default]
114116
colvars: # hideJacobian = off [default]
115117
colvars: Jacobian (geometric) forces will be included in reported free energy gradients.
116118
colvars: # fullSamples = 10
119+
colvars: # minSamples = 5 [default]
117120
colvars: # inputPrefix = [default]
118121
colvars: # historyFreq = 0 [default]
119122
colvars: # shared = off [default]
123+
colvars: # updateBias = on [default]
120124
colvars: # maxForce = [default]
121125
colvars: # integrate = on [default]
122126
colvars: Finished ABF setup.
@@ -125,21 +129,19 @@ colvars: Collective variables biases initialized, 1 in total.
125129
colvars: ----------------------------------------------------------------------
126130
colvars: Collective variables module (re)initialized.
127131
colvars: ----------------------------------------------------------------------
132+
colvars: Current simulation parameters: initial step = 0, integration timestep = 1
133+
colvars: Updating atomic parameters (masses, charges, etc).
134+
colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
135+
colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
128136
colvars: ----------------------------------------------------------------------
129-
colvars: Restarting from file "test.colvars.state".
130-
colvars: Restarting collective variable "one" from value: 3.20036
131-
colvars: Restarting abf bias "abf1" from step number 20.
137+
colvars: Loading state from text file "test.colvars.state".
138+
colvars: Restarting collective variable "one" from value: 3.20038
139+
colvars: Restarted abf bias "abf1" with step number 20.
132140
colvars: ----------------------------------------------------------------------
133-
colvars: The restart output state file will be "rest.colvars.state".
134141
colvars: The final output state file will be "test.restart.colvars.state".
135-
colvars: Opening trajectory file "test.restart.colvars.traj".
136-
colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
137-
colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
138-
colvars: Prepared sample and gradient buffers at step 20.
139142
colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
140143
colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
141-
colvars: Saving collective variables state to "rest.colvars.state".
144+
colvars: Saving collective variables state to "test.restart.colvars.state".
142145
colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
143-
colvars: Saving collective variables state to "rest.colvars.state".
144146
colvars: Saving collective variables state to "test.restart.colvars.state".
145-
colvars: Resetting the Collective Variables module.
147+
colvars: Saving collective variables state to "test.restart.colvars.state".

‎lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped

+6-6
Original file line numberDiff line numberDiff line change
@@ -5,13 +5,13 @@ configuration {
55

66
colvar {
77
name one
8-
x 3.17582252688381e+00
8+
x 3.1758939206034
99
}
1010

1111
abf {
1212
configuration {
13-
step 40
14-
name abf1
13+
step 40
14+
name abf1
1515
}
1616

1717
samples
@@ -20,8 +20,8 @@ samples
2020
0 0 0 0
2121

2222
gradient
23-
0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -8.67716293178495e+00 0.00000000000000e+00
24-
0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
25-
0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
23+
0 0 0 0 0 0 -8.6637911275798 0
24+
0 0 0 0 0 0 0 0
25+
0 0 0 0
2626
}
2727

‎lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj

+21-21
Original file line numberDiff line numberDiff line change
@@ -1,22 +1,22 @@
11
# step one fa_one
2-
20 3.20036076583879e+00 -1.12776581376024e-01
3-
21 3.19676250595523e+00 -1.12776581376024e-01
4-
22 3.19323015858381e+00 -2.99226657105897e-01
5-
23 3.18986878033029e+00 -7.71570670388436e-01
6-
24 3.18676635816465e+00 -1.45966444381162e+00
7-
25 3.18399012323985e+00 -2.29255009605800e+00
8-
26 3.18158461659959e+00 -3.20291155852885e+00
9-
27 3.17957172980453e+00 -4.13119762789999e+00
10-
28 3.17795242533882e+00 -5.02830487271041e+00
11-
29 3.17670962516017e+00 -5.85665418044438e+00
12-
30 3.17581173522468e+00 -6.58995308174671e+00
13-
31 3.17521643416185e+00 -7.21224165778954e+00
14-
32 3.17487456266985e+00 -7.71677976467746e+00
15-
33 3.17473400751618e+00 -8.10491399457095e+00
16-
34 3.17474340422162e+00 -8.38478985628265e+00
17-
35 3.17485538125568e+00 -8.56974337269324e+00
18-
36 3.17502906896877e+00 -8.67642273989548e+00
19-
37 3.17523173654562e+00 -8.72292739505557e+00
20-
38 3.17543964478384e+00 -8.72734418672621e+00
21-
39 3.17563832893481e+00 -8.70683028310459e+00
22-
40 3.17582252688381e+00 -8.67716293178495e+00
2+
20 3.20038442890979e+00 -1.03854856547880e-01
3+
21 3.19678862154174e+00 -1.03854856547880e-01
4+
22 3.19325868201096e+00 -2.89577637067747e-01
5+
23 3.18989968114783e+00 -7.61101440554271e-01
6+
24 3.18679962469704e+00 -1.44844736047144e+00
7+
25 3.18402576202599e+00 -2.28077446479501e+00
8+
26 3.18162264923830e+00 -3.19083007934240e+00
9+
27 3.17961218770411e+00 -4.11907208902965e+00
10+
28 3.17799534343587e+00 -5.01636137209204e+00
11+
29 3.17675503558160e+00 -5.84505314310151e+00
12+
30 3.17585966166561e+00 -6.57877537042113e+00
13+
31 3.17526688749274e+00 -7.20148861595175e+00
14+
32 3.17492753806785e+00 -7.70638297502586e+00
15+
33 3.17478948326253e+00 -8.09475011416048e+00
16+
34 3.17480134217557e+00 -8.37469681855967e+00
17+
35 3.17491572893043e+00 -8.55953599790606e+00
18+
36 3.17509176298755e+00 -8.66590727775137e+00
19+
37 3.17529670713715e+00 -8.71191545508902e+00
20+
38 3.17550682085422e+00 -8.71566657237990e+00
21+
39 3.17570764320513e+00 -8.69435074482412e+00
22+
40 3.17589392060342e+00 -8.66379112757977e+00

‎lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad

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1.75000000000000e+00 0.00000000000000e+00
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2.25000000000000e+00 0.00000000000000e+00
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10-
3.25000000000000e+00 -8.67716293178499e+00
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3.25000000000000e+00 -8.66379112757977e+00
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3.75000000000000e+00 0.00000000000000e+00
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4.25000000000000e+00 0.00000000000000e+00
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4.75000000000000e+00 0.00000000000000e+00

‎lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf

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# 1
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# -2.50000000000000e-01 5.00000000000000e-01 21 0
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4-
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1.50000000000000e+00 4.33858146589250e+00
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2.00000000000000e+00 4.33858146589250e+00
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2.50000000000000e+00 4.33858146589250e+00
10-
3.00000000000000e+00 4.33858146589250e+00
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0.00000000000000e+00 4.33189556378988e+00
5+
5.00000000000000e-01 4.33189556378988e+00
6+
1.00000000000000e+00 4.33189556378988e+00
7+
1.50000000000000e+00 4.33189556378988e+00
8+
2.00000000000000e+00 4.33189556378988e+00
9+
2.50000000000000e+00 4.33189556378988e+00
10+
3.00000000000000e+00 4.33189556378988e+00
1111
3.50000000000000e+00 0.00000000000000e+00
1212
4.00000000000000e+00 0.00000000000000e+00
1313
4.50000000000000e+00 0.00000000000000e+00

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