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update more references that unintentionally include shake bond counts
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@akohlmey
akohlmey committed Oct 27, 2020
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207 changes: 108 additions & 99 deletions ...lvars/log.16Jul20.linux.8.peptide-colvars → ...lvars/log.22Oct20.linux.8.peptide-colvars
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
LAMMPS (30 Jun 2020)
LAMMPS (22 Oct 2020)
# Solvated 5-mer peptide

units real
Expand All @@ -12,6 +12,7 @@ improper_style harmonic
kspace_style pppm 0.0001

read_data data.peptide
Reading data file ...
orthogonal box = (36.840194 41.013691 29.768095) to (64.211560 68.385058 57.139462)
2 by 2 by 2 MPI processor grid
reading atoms ...
Expand All @@ -34,12 +35,15 @@ read_data data.peptide
207 dihedrals
reading impropers ...
12 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.014 seconds
read_data CPU = 0.018 seconds

neighbor 2.0 bin
neigh_modify delay 5
Expand Down Expand Up @@ -68,7 +72,7 @@ fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000 seconds
find clusters CPU = 0.001 seconds

#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
Expand All @@ -79,7 +83,7 @@ thermo 10

run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:330)
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
Expand All @@ -101,12 +105,12 @@ Neighbor list info ...
bin: standard
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version "2020-02-25".
colvars: Initializing the collective variables module, version "2020-09-17".
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: https://dx.doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: This version was built with the C++11 standard or higher.
colvars: Using LAMMPS interface, version "2019-12-04".
colvars: Using LAMMPS interface, version "2020-04-07".
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars":
colvars: # units = "" [default]
Expand Down Expand Up @@ -231,7 +235,9 @@ colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "h_pot"
colvars: # colvars = { one, two }
colvars: # stepZeroData = off [default]
colvars: # outputEnergy = off [default]
colvars: # outputFreq = 1000 [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
Expand All @@ -249,21 +255,22 @@ colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out.colvars.state".
colvars: Writing to colvar trajectory file "out.colvars.traj".
colvars: Opening trajectory file "out.colvars.traj".
colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
colvars: Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
colvars: Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
SHAKE stats (type/ave/delta/count) on step 0
4 1.11100 1.44264e-05 36
6 0.996998 7.26967e-06 12
8 1.08000 1.32536e-05 18
10 1.11100 1.22749e-05 24
12 1.08000 1.11767e-05 18
14 0.96 0.00000 2
18 0.957206 4.37979e-05 3840
31 104.519 0.00396029 1920
Per MPI rank memory allocation (min/avg/max) = 15.39 | 15.5 | 15.78 Mbytes
4 2.22200 1.44264e-05 18
6 1.99400 7.26967e-06 6
8 2.16000 1.32536e-05 9
10 2.22200 1.22749e-05 12
12 2.16000 1.11767e-05 9
14 1.92000 0.00000 1
18 1.91441 4.37979e-05 1920
31 313.558 0.00396029 640
Per MPI rank memory allocation (min/avg/max) = 15.39 | 15.50 | 15.78 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
Expand All @@ -276,32 +283,32 @@ Step Temp TotEng PotEng KinEng E_pair E_bond f_2
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
SHAKE stats (type/ave/delta/count) on step 100
4 1.11098 8.97155e-05 36
6 0.996996 1.00568e-05 12
8 1.08000 6.02345e-06 18
10 1.11100 1.84253e-05 24
12 1.08000 7.27130e-06 18
14 0.959996 0.00000 2
18 0.957198 3.36079e-05 3840
31 104.520 0.0030599 1920
4 2.22196 8.97155e-05 18
6 1.99399 1.00568e-05 6
8 2.15999 6.02345e-06 9
10 2.22199 1.84253e-05 12
12 2.15999 7.27130e-06 9
14 1.91999 0.00000 1
18 1.91440 3.36079e-05 1920
31 313.560 0.0030599 640
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 0.37081 on 8 procs for 100 steps with 2004 atoms
Loop time of 0.348581 on 8 procs for 100 steps with 2004 atoms

Performance: 46.601 ns/day, 0.515 hours/ns, 269.680 timesteps/s
94.3% CPU use with 8 MPI tasks x no OpenMP threads
Performance: 49.572 ns/day, 0.484 hours/ns, 286.878 timesteps/s
94.0% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14242 | 0.21103 | 0.23881 | 8.6 | 56.91
Bond | 6.6575e-05 | 0.00081926 | 0.0025508 | 0.0 | 0.22
Kspace | 0.042432 | 0.068538 | 0.13477 | 14.6 | 18.48
Neigh | 0.040982 | 0.041167 | 0.041452 | 0.1 | 11.10
Comm | 0.01803 | 0.019509 | 0.022843 | 1.3 | 5.26
Output | 0.00034259 | 0.00036492 | 0.00050298 | 0.0 | 0.10
Modify | 0.027939 | 0.028112 | 0.028307 | 0.1 | 7.58
Other | | 0.001267 | | | 0.34
Pair | 0.19353 | 0.20727 | 0.21673 | 1.7 | 59.46
Bond | 4.9349e-05 | 0.00059958 | 0.0020139 | 0.0 | 0.17
Kspace | 0.048286 | 0.057429 | 0.071356 | 3.2 | 16.47
Neigh | 0.038413 | 0.038516 | 0.038608 | 0.0 | 11.05
Comm | 0.020058 | 0.020532 | 0.021127 | 0.2 | 5.89
Output | 0.00033634 | 0.00035522 | 0.00045565 | 0.0 | 0.10
Modify | 0.021584 | 0.021675 | 0.021731 | 0.0 | 6.22
Other | | 0.002207 | | | 0.63

Nlocal: 250.500 ave 263 max 235 min
Histogram: 1 0 1 1 0 1 2 0 0 2
Expand All @@ -318,7 +325,7 @@ Dangerous builds = 2

run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:330)
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
Expand All @@ -331,15 +338,15 @@ colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass =
colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
colvars: Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
SHAKE stats (type/ave/delta/count) on step 100
4 1.11098 8.97155e-05 36
6 0.996996 1.00568e-05 12
8 1.08000 6.02345e-06 18
10 1.11100 1.84253e-05 24
12 1.08000 7.27130e-06 18
14 0.959996 0.00000 2
18 0.957198 3.36079e-05 3840
31 104.520 0.0030599 1920
Per MPI rank memory allocation (min/avg/max) = 15.39 | 15.5 | 15.78 Mbytes
4 2.22196 8.97155e-05 18
6 1.99399 1.00568e-05 6
8 2.15999 6.02345e-06 9
10 2.22199 1.84253e-05 12
12 2.15999 7.27130e-06 9
14 1.91999 0.00000 1
18 1.91440 3.36079e-05 1920
31 313.560 0.0030599 640
Per MPI rank memory allocation (min/avg/max) = 15.39 | 15.50 | 15.78 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
Expand All @@ -352,32 +359,32 @@ Step Temp TotEng PotEng KinEng E_pair E_bond f_2
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4235 26.200127 3.4336037
190 250.80862 -5555.2554 -6564.2835 1009.0281 -6666.1639 25.53634 3.3494286
SHAKE stats (type/ave/delta/count) on step 200
4 1.11100 1.81266e-06 36
6 0.997 7.79424e-07 12
8 1.08000 1.08903e-06 18
10 1.11100 2.96503e-07 24
12 1.08000 4.69038e-07 18
14 0.960001 0.00000 2
18 0.957201 3.76471e-06 3840
31 104.520 0.000411055 1920
4 2.22200 1.81266e-06 18
6 1.99400 7.79424e-07 6
8 2.16000 1.08903e-06 9
10 2.22200 2.96503e-07 12
12 2.16000 4.69038e-07 9
14 1.92000 0.00000 1
18 1.91440 3.76471e-06 1920
31 313.560 0.000411055 640
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 0.35371 on 8 procs for 100 steps with 2004 atoms
Loop time of 0.327564 on 8 procs for 100 steps with 2004 atoms

Performance: 48.854 ns/day, 0.491 hours/ns, 282.717 timesteps/s
92.1% CPU use with 8 MPI tasks x no OpenMP threads
Performance: 52.753 ns/day, 0.455 hours/ns, 305.284 timesteps/s
97.1% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14228 | 0.20919 | 0.24117 | 8.5 | 59.14
Bond | 6.5351e-05 | 0.00082216 | 0.0025287 | 0.0 | 0.23
Kspace | 0.042284 | 0.072782 | 0.13728 | 13.8 | 20.58
Neigh | 0.024121 | 0.024217 | 0.024347 | 0.1 | 6.85
Comm | 0.01612 | 0.017894 | 0.02125 | 1.4 | 5.06
Output | 0.00033606 | 0.00035649 | 0.00047083 | 0.0 | 0.10
Modify | 0.026886 | 0.027075 | 0.02727 | 0.1 | 7.65
Other | | 0.001375 | | | 0.39
Pair | 0.19464 | 0.20787 | 0.21743 | 1.8 | 63.46
Bond | 4.9595e-05 | 0.00058829 | 0.0019724 | 0.0 | 0.18
Kspace | 0.044601 | 0.053396 | 0.066362 | 3.5 | 16.30
Neigh | 0.022539 | 0.0226 | 0.022683 | 0.0 | 6.90
Comm | 0.018733 | 0.019325 | 0.01973 | 0.2 | 5.90
Output | 0.00033555 | 0.00035296 | 0.00044201 | 0.0 | 0.11
Modify | 0.020998 | 0.02112 | 0.021177 | 0.0 | 6.45
Other | | 0.002317 | | | 0.71

Nlocal: 250.500 ave 261 max 238 min
Histogram: 1 0 1 1 1 0 1 1 0 2
Expand All @@ -397,7 +404,7 @@ colvars: Resetting the Collective Variables module.

run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:330)
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
Expand All @@ -407,12 +414,12 @@ PPPM initialization ...
3d grid and FFT values/proc = 2744 512
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version "2020-02-25".
colvars: Initializing the collective variables module, version "2020-09-17".
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: https://dx.doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: This version was built with the C++11 standard or higher.
colvars: Using LAMMPS interface, version "2019-12-04".
colvars: Using LAMMPS interface, version "2020-04-07".
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars":
colvars: # units = "" [default]
Expand Down Expand Up @@ -537,7 +544,9 @@ colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "h_pot"
colvars: # colvars = { one, two }
colvars: # stepZeroData = off [default]
colvars: # outputEnergy = off [default]
colvars: # outputFreq = 1000 [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
Expand All @@ -554,29 +563,29 @@ colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: ----------------------------------------------------------------------
colvars: Restarting from file "out.colvars.state".
colvars: Loading state from file "out.colvars.state".
colvars: Restarting collective variable "one" from value: 10.0128
colvars: Restarting collective variable "two" from value: 9.62236
colvars: Restarting harmonic bias "h_pot" from step number 200.
colvars: ----------------------------------------------------------------------
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out2.colvars.state".
colvars: Writing to colvar trajectory file "out2.colvars.traj".
colvars: Opening trajectory file "out2.colvars.traj".
colvars: Setting initial step number from LAMMPS: 200
colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
colvars: Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
SHAKE stats (type/ave/delta/count) on step 200
4 1.11100 1.81266e-06 36
6 0.997 7.79424e-07 12
8 1.08000 1.08903e-06 18
10 1.11100 2.96503e-07 24
12 1.08000 4.69038e-07 18
14 0.960001 0.00000 2
18 0.957201 3.76471e-06 3840
31 104.520 0.000411055 1920
Per MPI rank memory allocation (min/avg/max) = 15.4 | 15.52 | 15.78 Mbytes
4 2.22200 1.81266e-06 18
6 1.99400 7.79424e-07 6
8 2.16000 1.08903e-06 9
10 2.22200 2.96503e-07 12
12 2.16000 4.69038e-07 9
14 1.92000 0.00000 1
18 1.91440 3.76471e-06 1920
31 313.560 0.000411055 640
Per MPI rank memory allocation (min/avg/max) = 15.40 | 15.52 | 15.78 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
210 253.15303 -5538.5615 -6557.0214 1018.4599 -6672.0497 37.676621 0.61219488
Expand All @@ -589,32 +598,32 @@ Step Temp TotEng PotEng KinEng E_pair E_bond f_2
280 279.42264 -5307.9799 -6432.1251 1124.1452 -6557.3368 33.644022 8.5490489
290 286.85168 -5260.8409 -6414.8739 1154.033 -6515.6796 28.574838 5.9100102
SHAKE stats (type/ave/delta/count) on step 300
4 1.11100 1.79793e-05 36
6 0.997005 1.02512e-05 12
8 1.08000 1.85103e-05 18
10 1.11100 9.98839e-06 24
12 1.08000 8.84114e-06 18
14 0.960008 0.00000 2
18 0.957203 1.84450e-05 3840
31 104.520 0.00168383 1920
4 2.22201 1.79793e-05 18
6 1.99401 1.02512e-05 6
8 2.16001 1.85103e-05 9
10 2.22201 9.98839e-06 12
12 2.16001 8.84114e-06 9
14 1.92002 0.00000 1
18 1.91441 1.84450e-05 1920
31 313.559 0.00168383 640
300 291.52795 -5216.2878 -6389.1339 1172.8461 -6503.1274 27.889149 2.2482427
colvars: Saving collective variables state to "out2.colvars.state".
Loop time of 0.364351 on 8 procs for 100 steps with 2004 atoms
Loop time of 0.342261 on 8 procs for 100 steps with 2004 atoms

Performance: 47.427 ns/day, 0.506 hours/ns, 274.461 timesteps/s
94.4% CPU use with 8 MPI tasks x no OpenMP threads
Performance: 50.488 ns/day, 0.475 hours/ns, 292.175 timesteps/s
90.5% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15168 | 0.21065 | 0.24871 | 7.6 | 57.81
Bond | 7.9118e-05 | 0.0008286 | 0.0026193 | 0.0 | 0.23
Kspace | 0.040882 | 0.076563 | 0.13382 | 12.2 | 21.01
Neigh | 0.027605 | 0.027729 | 0.027912 | 0.1 | 7.61
Comm | 0.016442 | 0.018351 | 0.021096 | 1.2 | 5.04
Output | 0.00034201 | 0.00036986 | 0.00048564 | 0.0 | 0.10
Modify | 0.02831 | 0.028418 | 0.028519 | 0.0 | 7.80
Other | | 0.001445 | | | 0.40
Pair | 0.19722 | 0.21118 | 0.22596 | 1.9 | 61.70
Bond | 5.118e-05 | 0.0006023 | 0.0020252 | 0.0 | 0.18
Kspace | 0.045324 | 0.05919 | 0.072866 | 3.3 | 17.29
Neigh | 0.026356 | 0.026455 | 0.026492 | 0.0 | 7.73
Comm | 0.019712 | 0.020124 | 0.02084 | 0.2 | 5.88
Output | 0.00036238 | 0.00038436 | 0.00049658 | 0.0 | 0.11
Modify | 0.021787 | 0.021863 | 0.021954 | 0.0 | 6.39
Other | | 0.002457 | | | 0.72

Nlocal: 250.500 ave 264 max 226 min
Histogram: 1 0 0 0 0 2 2 0 1 2
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