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update examples for pair style local/density

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Axel Kohlmeyer
2021-12-09 18:21:32 -05:00
parent 146c6fe5ff
commit a975d0506a
8 changed files with 1117 additions and 493 deletions
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examples/PACKAGES/local_density/benzene_water/benzene_water.in → examples/PACKAGES/local_density/benzene_water/in.benzene_water
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examples/PACKAGES/local_density/benzene_water/log.04Sep19.g++.1
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LAMMPS (7 Aug 2019)
# LAMMPS input file for 26.5% benzene mole fraction solution
# with 380 benzene and 1000 water molecules,
# using all possible local density potentials
# between benzene and water
#
# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
#
# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data benzene_water.data
orthogonal box = (-12.865 -12.865 -64.829) to (12.865 12.865 64.829)
1 by 1 by 8 MPI processor grid
reading atoms ...
1380 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000566959 secs
read_data CPU = 0.00661397 secs
velocity all create 3.0000e+02 16611 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table benzene_water.pair.table PairBB
WARNING: 33 of 500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:483)
WARNING: 150 of 500 distance values in table with relative error
over 1e-06 to re-computed values (../pair_table.cpp:492)
pair_coeff 1 2 table benzene_water.pair.table PairWW
WARNING: 61 of 500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:483)
WARNING: 90 of 500 distance values in table with relative error
over 1e-06 to re-computed values (../pair_table.cpp:492)
pair_coeff 2 2 table benzene_water.pair.table PairBW
WARNING: 108 of 500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:483)
WARNING: 135 of 500 distance values in table with relative error
over 1e-06 to re-computed values (../pair_table.cpp:492)
pair_coeff * * local/density benzene_water.localdensity.table
# Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
# Thermostat & time integration
timestep 2.0
thermo 100
thermo_style custom temp ke pe etotal ebond eangle edihed evdwl
# Minimization
minimize 1.e-4 0.0 10000 10000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.25
ghost atom cutoff = 15.25
binsize = 7.625, bins = 4 4 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.061 | 8.32 | 8.674 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 4162.3053 5395.4665 0 0 0 4162.3053
300 1233.1611 2275.526 3508.6871 0 0 0 2275.526
Loop time of 0.352822 on 8 procs for 40 steps with 1380 atoms
71.3% CPU use with 8 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
4162.30533361 2208.86525108 2275.52597861
Force two-norm initial, final = 259.364 69.3915
Force max component initial, final = 22.2077 8.31436
Final line search alpha, max atom move = 2.90022e-12 2.41135e-11
Iterations, force evaluations = 40 110
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.053192 | 0.23903 | 0.32779 | 17.2 | 67.75
Bond | 9.0599e-06 | 1.6302e-05 | 2.5272e-05 | 0.0 | 0.00
Neigh | 0.00044513 | 0.0023614 | 0.0063851 | 5.1 | 0.67
Comm | 0.015469 | 0.090432 | 0.20295 | 20.0 | 25.63
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02098 | | | 5.95
Nlocal: 172.5 ave 348 max 72 min
Histogram: 5 0 0 0 0 0 0 0 1 2
Nghost: 2193.62 ave 4352 max 932 min
Histogram: 3 0 0 2 0 0 2 0 0 1
Neighs: 9700.5 ave 20535 max 3685 min
Histogram: 5 0 0 0 0 0 0 1 0 2
Total # of neighbors = 77604
Ave neighs/atom = 56.2348
Ave special neighs/atom = 0
Neighbor list builds = 2
Dangerous builds = 0
# Set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 81890
# Equilibration (for realistic results, run for 5000000 steps)
reset_timestep 0
run 5000
WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
Per MPI rank memory allocation (min/avg/max) = 6.936 | 7.195 | 7.552 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 2866.9109 4100.0721 0 0 0 2866.9109
273.33541 1123.5553 3983.2007 5106.756 0 0 0 3983.2007
293.68078 1207.1857 3319.6601 4526.8458 0 0 0 3319.6601
314.21462 1291.5908 3389.2178 4680.8086 0 0 0 3389.2178
323.77563 1330.8917 3332.9828 4663.8745 0 0 0 3332.9828
302.5902 1243.8082 3461.7692 4705.5774 0 0 0 3461.7692
295.39324 1214.2249 3411.5727 4625.7976 0 0 0 3411.5727
320.52341 1317.5234 3453.1931 4770.7164 0 0 0 3453.1931
312.00777 1282.5195 3403.3443 4685.8638 0 0 0 3403.3443
307.96774 1265.9128 3429.7809 4695.6937 0 0 0 3429.7809
294.75922 1211.6187 3388.8404 4600.4591 0 0 0 3388.8404
311.24567 1279.3869 3514.9603 4794.3472 0 0 0 3514.9603
306.6152 1260.3531 3447.2011 4707.5542 0 0 0 3447.2011
305.23306 1254.6718 3375.5092 4630.181 0 0 0 3375.5092
321.62889 1322.0675 3460.2581 4782.3256 0 0 0 3460.2581
316.37725 1300.4804 3437.0312 4737.5116 0 0 0 3437.0312
322.90522 1327.3139 3389.1262 4716.44 0 0 0 3389.1262
307.57893 1264.3146 3359.8491 4624.1637 0 0 0 3359.8491
302.22607 1242.3115 3406.1711 4648.4826 0 0 0 3406.1711
302.73997 1244.4239 3220.2582 4464.6821 0 0 0 3220.2582
303.66194 1248.2137 3318.4629 4566.6765 0 0 0 3318.4629
308.73862 1269.0815 3369.5894 4638.671 0 0 0 3369.5894
315.60294 1297.2976 3411.2405 4708.5381 0 0 0 3411.2405
310.0113 1274.3129 3360.1054 4634.4183 0 0 0 3360.1054
302.36229 1242.8714 3326.9845 4569.8559 0 0 0 3326.9845
317.78659 1306.2735 3355.4976 4661.7711 0 0 0 3355.4976
302.50479 1243.4571 3317.6846 4561.1417 0 0 0 3317.6846
304.29249 1250.8056 3423.5068 4674.3124 0 0 0 3423.5068
305.99948 1257.8222 3432.9395 4690.7617 0 0 0 3432.9395
309.93363 1273.9937 3393.657 4667.6506 0 0 0 3393.657
316.14884 1299.5415 3463.0636 4762.6051 0 0 0 3463.0636
300.38817 1234.7567 3309.2495 4544.0062 0 0 0 3309.2495
311.05735 1278.6128 3304.4418 4583.0546 0 0 0 3304.4418
311.11872 1278.865 3291.1891 4570.0542 0 0 0 3291.1891
315.74338 1297.8749 3341.3063 4639.1812 0 0 0 3341.3063
297.5658 1223.1552 3316.3862 4539.5414 0 0 0 3316.3862
311.79033 1281.6257 3357.4556 4639.0813 0 0 0 3357.4556
310.93666 1278.1167 3414.7694 4692.8861 0 0 0 3414.7694
307.37298 1263.468 3337.3889 4600.8569 0 0 0 3337.3889
298.84185 1228.4005 3329.6173 4558.0178 0 0 0 3329.6173
310.54684 1276.5143 3351.0852 4627.5995 0 0 0 3351.0852
300.0871 1233.5191 3302.2315 4535.7506 0 0 0 3302.2315
304.69078 1252.4427 3324.2508 4576.6935 0 0 0 3324.2508
313.50714 1288.6827 3330.4088 4619.0915 0 0 0 3330.4088
329.80018 1355.6559 3301.86 4657.5159 0 0 0 3301.86
304.57609 1251.9713 3365.2938 4617.2652 0 0 0 3365.2938
308.73584 1269.0701 3344.4155 4613.4856 0 0 0 3344.4155
306.90951 1261.5629 3304.4698 4566.0327 0 0 0 3304.4698
308.85761 1269.5707 3392.1511 4661.7218 0 0 0 3392.1511
302.78788 1244.6208 3317.0849 4561.7057 0 0 0 3317.0849
321.68092 1322.2813 3321.5755 4643.8568 0 0 0 3321.5755
Loop time of 16.3061 on 8 procs for 5000 steps with 1380 atoms
Performance: 52.986 ns/day, 0.453 hours/ns, 306.634 timesteps/s
69.6% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1872 | 10.542 | 14.607 | 116.7 | 64.65
Bond | 0.00044084 | 0.00069669 | 0.00095081 | 0.0 | 0.00
Neigh | 0.026948 | 0.15225 | 0.44344 | 42.0 | 0.93
Comm | 0.63452 | 4.2953 | 9.49 | 133.9 | 26.34
Output | 0.0016391 | 0.012378 | 0.050919 | 13.9 | 0.08
Modify | 0.45894 | 1.2107 | 4.4629 | 116.4 | 7.42
Other | | 0.09292 | | | 0.57
Nlocal: 172.5 ave 380 max 70 min
Histogram: 5 0 0 0 0 0 0 1 1 1
Nghost: 2213 ave 4440 max 903 min
Histogram: 3 0 0 2 0 0 2 0 0 1
Neighs: 10042.5 ave 24051 max 3500 min
Histogram: 5 0 0 0 0 0 0 1 1 1
Total # of neighbors = 80340
Ave neighs/atom = 58.2174
Ave special neighs/atom = 0
Neighbor list builds = 123
Dangerous builds = 1
# Turn off recentering during production phase
unfix recentering
# Setup trajectory output
dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
dump_modify myDump element B W
dump_modify myDump sort id
# Production (for realistic results, run for 10000000 steps)
reset_timestep 0
run 1000
Per MPI rank memory allocation (min/avg/max) = 8.232 | 8.492 | 8.851 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
321.68092 1322.2813 3784.0834 5106.3647 0 0 0 3784.0834
310.59763 1276.7231 3318.3283 4595.0513 0 0 0 3318.3283
303.39445 1247.1141 3324.1191 4571.2332 0 0 0 3324.1191
311.37275 1279.9092 3305.0901 4584.9993 0 0 0 3305.0901
311.29071 1279.572 3248.216 4527.788 0 0 0 3248.216
314.53456 1292.906 3283.4563 4576.3623 0 0 0 3283.4563
316.52595 1301.0916 3258.9171 4560.0087 0 0 0 3258.9171
318.92447 1310.9509 3235.6256 4546.5765 0 0 0 3235.6256
311.79212 1281.6331 3308.099 4589.7321 0 0 0 3308.099
305.52477 1255.8709 3267.6907 4523.5616 0 0 0 3267.6907
301.07457 1237.5782 3206.3997 4443.9779 0 0 0 3206.3997
Loop time of 4.44139 on 8 procs for 1000 steps with 1380 atoms
Performance: 38.907 ns/day, 0.617 hours/ns, 225.155 timesteps/s
60.8% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.656 | 2.5078 | 3.5775 | 57.7 | 56.46
Bond | 0.00013375 | 0.0001854 | 0.0002377 | 0.0 | 0.00
Neigh | 0.0048757 | 0.029188 | 0.090432 | 18.9 | 0.66
Comm | 0.51836 | 1.4427 | 2.6285 | 56.9 | 32.48
Output | 0.083084 | 0.089199 | 0.10333 | 2.3 | 2.01
Modify | 0.0087376 | 0.019705 | 0.038437 | 8.4 | 0.44
Other | | 0.3526 | | | 7.94
Nlocal: 172.5 ave 388 max 69 min
Histogram: 5 0 0 0 0 0 0 2 0 1
Nghost: 2207.88 ave 4429 max 896 min
Histogram: 3 0 0 2 0 0 2 0 0 1
Neighs: 10094.1 ave 24847 max 3403 min
Histogram: 5 0 0 0 0 0 1 1 0 1
Total # of neighbors = 80753
Ave neighs/atom = 58.5167
Ave special neighs/atom = 0
Neighbor list builds = 23
Dangerous builds = 0
Total wall time: 0:00:21

300
examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.1 Normal file
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LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 26.5% benzene mole fraction solution
# with 380 benzene and 1000 water molecules,
# using all possible local density potentials
# between benzene and water
#
# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
#
# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data benzene_water.data
Reading data file ...
orthogonal box = (-12.865000 -12.865000 -64.829000) to (12.865000 12.865000 64.829000)
1 by 1 by 1 MPI processor grid
reading atoms ...
1380 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
velocity all create 3.0000e+02 16611 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table benzene_water.pair.table PairBB
WARNING: 33 of 500 force values in table PairBB are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 150 of 500 distance values in table 1e-06 with relative error
WARNING: over PairBB to re-computed values (src/pair_table.cpp:473)
pair_coeff 1 2 table benzene_water.pair.table PairWW
WARNING: 61 of 500 force values in table PairWW are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 90 of 500 distance values in table 1e-06 with relative error
WARNING: over PairWW to re-computed values (src/pair_table.cpp:473)
pair_coeff 2 2 table benzene_water.pair.table PairBW
WARNING: 108 of 500 force values in table PairBW are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 135 of 500 distance values in table 1e-06 with relative error
WARNING: over PairBW to re-computed values (src/pair_table.cpp:473)
pair_coeff * * local/density benzene_water.localdensity.table
# Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
# Thermostat & time integration
timestep 2.0
thermo 100
thermo_style custom temp ke pe etotal ebond eangle edihed evdwl
# Minimization
minimize 1.e-4 0.0 10000 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair_style local/density command:
@Article{Sanyal16,
author = {T.Sanyal and M.Scott Shell},
title = {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
journal = {J.~Chem.~Phys.},
year = 2016,
DOI = doi.org/10.1063/1.4958629}
@Article{Sanyal18,
author = {T.Sanyal and M.Scott Shell},
title = {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
journal = {J.~Phys.~Chem. B},
year = 2018,
DOI = doi.org/10.1021/acs.jpcb.7b12446}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.25
ghost atom cutoff = 15.25
binsize = 7.625, bins = 4 4 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.754 | 8.754 | 8.754 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 2374.6749 3607.836 0 0 0 2374.6749
300 1233.1611 1007.0651 2240.2262 0 0 0 1007.0651
300 1233.1611 1003.7985 2236.9596 0 0 0 1003.7985
Loop time of 0.728266 on 1 procs for 108 steps with 1380 atoms
97.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2374.67491482358 1003.82993060848 1003.798492926
Force two-norm initial, final = 264.30145 15.134143
Force max component initial, final = 25.270244 6.2440444
Final line search alpha, max atom move = 0.035941700 0.22442157
Iterations, force evaluations = 108 187
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.70292 | 0.70292 | 0.70292 | 0.0 | 96.52
Bond | 2.6803e-05 | 2.6803e-05 | 2.6803e-05 | 0.0 | 0.00
Neigh | 0.015295 | 0.015295 | 0.015295 | 0.0 | 2.10
Comm | 0.0043677 | 0.0043677 | 0.0043677 | 0.0 | 0.60
Output | 3.6465e-05 | 3.6465e-05 | 3.6465e-05 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005623 | | | 0.77
Nlocal: 1380.00 ave 1380 max 1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5817.00 ave 5817 max 5817 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 77865.0 ave 77865 max 77865 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 77865
Ave neighs/atom = 56.423913
Ave special neighs/atom = 0.0000000
Neighbor list builds = 4
Dangerous builds = 0
# Set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 81890
# Equilibration (for realistic results, run for 5000000 steps)
reset_timestep 0
run 5000
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 7.629 | 7.629 | 7.629 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 1003.7985 2236.9596 0 0 0 1003.7985
250.59531 1030.0813 1862.9804 2893.0617 0 0 0 1862.9804
294.88945 1212.154 2073.2032 3285.3572 0 0 0 2073.2032
305.20132 1254.5413 2163.282 3417.8234 0 0 0 2163.282
304.53795 1251.8145 2213.378 3465.1926 0 0 0 2213.378
294.57091 1210.8446 2264.186 3475.0306 0 0 0 2264.186
298.76658 1228.0911 2263.969 3492.0601 0 0 0 2263.969
305.54588 1255.9576 2265.5593 3521.5169 0 0 0 2265.5593
303.79048 1248.742 2298.1483 3546.8904 0 0 0 2298.1483
305.27436 1254.8416 2341.7086 3596.5502 0 0 0 2341.7086
295.72401 1215.5845 2353.1525 3568.737 0 0 0 2353.1525
311.92354 1282.1733 2330.0971 3612.2704 0 0 0 2330.0971
295.64719 1215.2687 2357.4742 3572.7429 0 0 0 2357.4742
304.1022 1250.0234 2351.4664 3601.4898 0 0 0 2351.4664
287.75335 1182.8208 2308.6084 3491.4292 0 0 0 2308.6084
302.38356 1242.9588 2320.4797 3563.4385 0 0 0 2320.4797
311.87862 1281.9886 2314.8858 3596.8744 0 0 0 2314.8858
304.83172 1253.0221 2326.7945 3579.8166 0 0 0 2326.7945
312.30448 1283.7391 2338.373 3622.1121 0 0 0 2338.373
307.88048 1265.5541 2330.3168 3595.871 0 0 0 2330.3168
299.36592 1230.5547 2353.9626 3584.5173 0 0 0 2353.9626
306.95405 1261.746 2321.3201 3583.0661 0 0 0 2321.3201
302.25732 1242.4399 2373.7417 3616.1816 0 0 0 2373.7417
302.50301 1243.4498 2386.453 3629.9029 0 0 0 2386.453
298.21873 1225.8391 2374.4162 3600.2554 0 0 0 2374.4162
295.11396 1213.0769 2353.4284 3566.5053 0 0 0 2353.4284
318.23487 1308.1162 2348.8039 3656.9201 0 0 0 2348.8039
311.7761 1281.5672 2370.2622 3651.8295 0 0 0 2370.2622
315.98584 1298.8715 2408.0705 3706.9419 0 0 0 2408.0705
302.72107 1244.3462 2371.5641 3615.9103 0 0 0 2371.5641
301.04285 1237.4478 2360.4977 3597.9455 0 0 0 2360.4977
299.6202 1231.5999 2365.4272 3597.0272 0 0 0 2365.4272
305.18681 1254.4817 2373.1731 3627.6548 0 0 0 2373.1731
301.10791 1237.7152 2384.3091 3622.0244 0 0 0 2384.3091
311.01973 1278.4581 2343.4387 3621.8969 0 0 0 2343.4387
294.65697 1211.1984 2404.8895 3616.0879 0 0 0 2404.8895
293.49218 1206.4105 2382.3375 3588.7479 0 0 0 2382.3375
300.87208 1236.7458 2366.731 3603.4768 0 0 0 2366.731
303.87832 1249.1031 2394.8683 3643.9714 0 0 0 2394.8683
312.03203 1282.6192 2359.5805 3642.1998 0 0 0 2359.5805
294.64316 1211.1416 2391.1496 3602.2913 0 0 0 2391.1496
307.10402 1262.3624 2361.5883 3623.9508 0 0 0 2361.5883
300.99003 1237.2307 2362.7573 3599.988 0 0 0 2362.7573
297.1091 1221.278 2376.6407 3597.9187 0 0 0 2376.6407
306.5047 1259.8989 2373.2659 3633.1648 0 0 0 2373.2659
302.58147 1243.7723 2314.387 3558.1593 0 0 0 2314.387
315.87503 1298.416 2367.4739 3665.89 0 0 0 2367.4739
301.8964 1240.9563 2384.9153 3625.8717 0 0 0 2384.9153
299.65454 1231.7411 2349.3482 3581.0893 0 0 0 2349.3482
308.81015 1269.3756 2364.1622 3633.5378 0 0 0 2364.1622
293.75579 1207.4941 2380.9551 3588.4492 0 0 0 2380.9551
Loop time of 21.8496 on 1 procs for 5000 steps with 1380 atoms
Performance: 39.543 ns/day, 0.607 hours/ns, 228.837 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 20.643 | 20.643 | 20.643 | 0.0 | 94.48
Bond | 0.00086668 | 0.00086668 | 0.00086668 | 0.0 | 0.00
Neigh | 0.56747 | 0.56747 | 0.56747 | 0.0 | 2.60
Comm | 0.17074 | 0.17074 | 0.17074 | 0.0 | 0.78
Output | 0.0020671 | 0.0020671 | 0.0020671 | 0.0 | 0.01
Modify | 0.43257 | 0.43257 | 0.43257 | 0.0 | 1.98
Other | | 0.03296 | | | 0.15
Nlocal: 1380.00 ave 1380 max 1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5865.00 ave 5865 max 5865 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 77120.0 ave 77120 max 77120 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 77120
Ave neighs/atom = 55.884058
Ave special neighs/atom = 0.0000000
Neighbor list builds = 122
Dangerous builds = 1
# Turn off recentering during production phase
unfix recentering
# Setup trajectory output
dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
dump_modify myDump element B W
dump_modify myDump sort id
# Production (for realistic results, run for 10000000 steps)
reset_timestep 0
run 1000
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.022 | 9.022 | 9.022 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
293.75579 1207.4941 2380.9551 3588.4492 0 0 0 2380.9551
298.7158 1227.8824 2359.3991 3587.2814 0 0 0 2359.3991
302.80266 1244.6815 2388.4042 3633.0858 0 0 0 2388.4042
307.6188 1264.4785 2353.3305 3617.8089 0 0 0 2353.3305
296.67416 1219.4901 2355.8078 3575.2979 0 0 0 2355.8078
293.79477 1207.6543 2402.8039 3610.4582 0 0 0 2402.8039
310.5565 1276.554 2401.0407 3677.5947 0 0 0 2401.0407
308.50884 1268.137 2353.619 3621.756 0 0 0 2353.619
298.84758 1228.4241 2392.9054 3621.3295 0 0 0 2392.9054
299.81424 1232.3975 2386.9653 3619.3628 0 0 0 2386.9653
310.94967 1278.1702 2361.9869 3640.1571 0 0 0 2361.9869
Loop time of 3.85351 on 1 procs for 1000 steps with 1380 atoms
Performance: 44.842 ns/day, 0.535 hours/ns, 259.504 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6349 | 3.6349 | 3.6349 | 0.0 | 94.33
Bond | 0.00018364 | 0.00018364 | 0.00018364 | 0.0 | 0.00
Neigh | 0.10319 | 0.10319 | 0.10319 | 0.0 | 2.68
Comm | 0.025723 | 0.025723 | 0.025723 | 0.0 | 0.67
Output | 0.016269 | 0.016269 | 0.016269 | 0.0 | 0.42
Modify | 0.066304 | 0.066304 | 0.066304 | 0.0 | 1.72
Other | | 0.006982 | | | 0.18
Nlocal: 1380.00 ave 1380 max 1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5894.00 ave 5894 max 5894 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 77157.0 ave 77157 max 77157 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 77157
Ave neighs/atom = 55.910870
Ave special neighs/atom = 0.0000000
Neighbor list builds = 24
Dangerous builds = 0
Total wall time: 0:00:26

299
examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.4 Normal file
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@ -0,0 +1,299 @@
LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 26.5% benzene mole fraction solution
# with 380 benzene and 1000 water molecules,
# using all possible local density potentials
# between benzene and water
#
# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
#
# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data benzene_water.data
Reading data file ...
orthogonal box = (-12.865000 -12.865000 -64.829000) to (12.865000 12.865000 64.829000)
1 by 1 by 4 MPI processor grid
reading atoms ...
1380 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
velocity all create 3.0000e+02 16611 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table benzene_water.pair.table PairBB
WARNING: 33 of 500 force values in table PairBB are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 150 of 500 distance values in table 1e-06 with relative error
WARNING: over PairBB to re-computed values (src/pair_table.cpp:473)
pair_coeff 1 2 table benzene_water.pair.table PairWW
WARNING: 61 of 500 force values in table PairWW are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 90 of 500 distance values in table 1e-06 with relative error
WARNING: over PairWW to re-computed values (src/pair_table.cpp:473)
pair_coeff 2 2 table benzene_water.pair.table PairBW
WARNING: 108 of 500 force values in table PairBW are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 135 of 500 distance values in table 1e-06 with relative error
WARNING: over PairBW to re-computed values (src/pair_table.cpp:473)
pair_coeff * * local/density benzene_water.localdensity.table
# Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
# Thermostat & time integration
timestep 2.0
thermo 100
thermo_style custom temp ke pe etotal ebond eangle edihed evdwl
# Minimization
minimize 1.e-4 0.0 10000 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair_style local/density command:
@Article{Sanyal16,
author = {T.Sanyal and M.Scott Shell},
title = {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
journal = {J.~Chem.~Phys.},
year = 2016,
DOI = doi.org/10.1063/1.4958629}
@Article{Sanyal18,
author = {T.Sanyal and M.Scott Shell},
title = {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
journal = {J.~Phys.~Chem. B},
year = 2018,
DOI = doi.org/10.1021/acs.jpcb.7b12446}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.25
ghost atom cutoff = 15.25
binsize = 7.625, bins = 4 4 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.441 | 8.589 | 8.688 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 2374.6749 3607.836 0 0 0 2374.6749
300 1233.1611 1029.2315 2262.3926 0 0 0 1029.2315
Loop time of 0.465159 on 4 procs for 90 steps with 1380 atoms
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
2374.67491482358 1029.2314829893 1029.2314829893
Force two-norm initial, final = 264.24130 21.036662
Force max component initial, final = 25.270244 7.5408301
Final line search alpha, max atom move = 4.3177150e-11 3.2559155e-10
Iterations, force evaluations = 90 202
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.30938 | 0.36161 | 0.44348 | 8.9 | 77.74
Bond | 7.496e-06 | 1.2981e-05 | 1.8699e-05 | 0.0 | 0.00
Neigh | 0.00086721 | 0.0042845 | 0.0093341 | 5.4 | 0.92
Comm | 0.0080858 | 0.075631 | 0.14089 | 17.1 | 16.26
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02362 | | | 5.08
Nlocal: 345.000 ave 664 max 145 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 2836.75 ave 4443 max 1191 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 19429.0 ave 37734 max 7312 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 77716
Ave neighs/atom = 56.315942
Ave special neighs/atom = 0.0000000
Neighbor list builds = 4
Dangerous builds = 0
# Set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 81890
# Equilibration (for realistic results, run for 5000000 steps)
reset_timestep 0
run 5000
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 7.316 | 7.464 | 7.563 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 1029.2315 2262.3926 0 0 0 1029.2315
265.18991 1090.073 1878.3252 2968.3982 0 0 0 1878.3252
304.12211 1250.1052 2105.69 3355.7952 0 0 0 2105.69
302.61467 1243.9088 2227.4415 3471.3503 0 0 0 2227.4415
308.1928 1266.8379 2226.2374 3493.0754 0 0 0 2226.2374
300.17421 1233.8772 2296.803 3530.6802 0 0 0 2296.803
292.06857 1200.5587 2335.7126 3536.2713 0 0 0 2335.7126
297.90952 1224.5681 2345.6702 3570.2383 0 0 0 2345.6702
294.85752 1212.0228 2355.4448 3567.4676 0 0 0 2355.4448
301.15823 1237.9221 2370.264 3608.1861 0 0 0 2370.264
314.40489 1292.3729 2376.5416 3668.9145 0 0 0 2376.5416
310.72125 1277.2312 2390.4042 3667.6355 0 0 0 2390.4042
311.57912 1280.7575 2349.4496 3630.2071 0 0 0 2349.4496
321.68234 1322.2872 2363.3692 3685.6564 0 0 0 2363.3692
291.23554 1197.1345 2342.8227 3539.9572 0 0 0 2342.8227
284.55116 1169.6581 2359.9129 3529.571 0 0 0 2359.9129
304.73247 1252.6141 2315.7628 3568.3769 0 0 0 2315.7628
306.94929 1261.7264 2290.5539 3552.2804 0 0 0 2290.5539
297.78932 1224.074 2296.9762 3521.0503 0 0 0 2296.9762
294.69384 1211.3499 2358.1814 3569.5313 0 0 0 2358.1814
299.74519 1232.1137 2353.0172 3585.131 0 0 0 2353.0172
305.14969 1254.3291 2387.2078 3641.5369 0 0 0 2387.2078
308.89809 1269.737 2370.2676 3640.0046 0 0 0 2370.2676
314.78405 1293.9315 2350.5471 3644.4786 0 0 0 2350.5471
295.55098 1214.8732 2411.8143 3626.6875 0 0 0 2411.8143
297.87014 1224.4062 2388.5545 3612.9608 0 0 0 2388.5545
299.39609 1230.6787 2368.4147 3599.0934 0 0 0 2368.4147
304.67061 1252.3598 2379.1491 3631.509 0 0 0 2379.1491
306.45428 1259.6917 2372.4715 3632.1632 0 0 0 2372.4715
305.28844 1254.8995 2366.3995 3621.299 0 0 0 2366.3995
310.45396 1276.1325 2348.2931 3624.4256 0 0 0 2348.2931
309.11136 1270.6137 2343.1454 3613.7591 0 0 0 2343.1454
294.53472 1210.6959 2341.6814 3552.3773 0 0 0 2341.6814
302.25322 1242.4231 2328.8413 3571.2644 0 0 0 2328.8413
297.03265 1220.9637 2312.6769 3533.6406 0 0 0 2312.6769
287.46871 1181.6508 2335.725 3517.3758 0 0 0 2335.725
305.57746 1256.0875 2337.5497 3593.6372 0 0 0 2337.5497
298.19499 1225.7416 2352.2051 3577.9467 0 0 0 2352.2051
303.96866 1249.4744 2358.772 3608.2464 0 0 0 2358.772
312.66902 1285.2376 2345.9235 3631.1611 0 0 0 2345.9235
310.89912 1277.9623 2346.6294 3624.5918 0 0 0 2346.6294
294.47888 1210.4664 2349.5528 3560.0191 0 0 0 2349.5528
314.31262 1291.9937 2345.1845 3637.1782 0 0 0 2345.1845
305.20881 1254.5721 2416.0554 3670.6275 0 0 0 2416.0554
303.25745 1246.551 2438.1155 3684.6665 0 0 0 2438.1155
305.6354 1256.3257 2396.2654 3652.591 0 0 0 2396.2654
314.31965 1292.0226 2399.552 3691.5745 0 0 0 2399.552
307.04169 1262.1063 2402.2739 3664.3802 0 0 0 2402.2739
290.46881 1193.9828 2382.3388 3576.3216 0 0 0 2382.3388
305.23755 1254.6903 2405.19 3659.8803 0 0 0 2405.19
307.7561 1265.0429 2386.6581 3651.701 0 0 0 2386.6581
Loop time of 17.4554 on 4 procs for 5000 steps with 1380 atoms
Performance: 49.498 ns/day, 0.485 hours/ns, 286.445 timesteps/s
95.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.548 | 13.243 | 15.862 | 48.1 | 75.87
Bond | 0.00034133 | 0.00041399 | 0.00051148 | 0.0 | 0.00
Neigh | 0.040843 | 0.19583 | 0.431 | 36.7 | 1.12
Comm | 0.6407 | 2.8387 | 4.9175 | 89.8 | 16.26
Output | 0.0014477 | 0.010298 | 0.032363 | 12.6 | 0.06
Modify | 0.40772 | 1.0577 | 2.8132 | 98.7 | 6.06
Other | | 0.1098 | | | 0.63
Nlocal: 345.000 ave 683 max 143 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Nghost: 2860.00 ave 4457 max 1216 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 19372.2 ave 38813 max 7144 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 77489
Ave neighs/atom = 56.151449
Ave special neighs/atom = 0.0000000
Neighbor list builds = 123
Dangerous builds = 1
# Turn off recentering during production phase
unfix recentering
# Setup trajectory output
dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
dump_modify myDump element B W
dump_modify myDump sort id
# Production (for realistic results, run for 10000000 steps)
reset_timestep 0
run 1000
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.640 | 8.791 | 8.895 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
307.7561 1265.0429 2386.6581 3651.701 0 0 0 2386.6581
306.2186 1258.7229 2371.3144 3630.0373 0 0 0 2371.3144
309.32547 1271.4938 2358.0777 3629.5715 0 0 0 2358.0777
303.23297 1246.4504 2394.0277 3640.4781 0 0 0 2394.0277
299.98244 1233.0889 2372.4799 3605.5689 0 0 0 2372.4799
303.00349 1245.5071 2378.7054 3624.2125 0 0 0 2378.7054
300.25892 1234.2254 2375.314 3609.5394 0 0 0 2375.314
299.66684 1231.7917 2350.7012 3582.4928 0 0 0 2350.7012
300.19054 1233.9443 2353.5112 3587.4556 0 0 0 2353.5112
295.45586 1214.4823 2367.8741 3582.3564 0 0 0 2367.8741
301.37866 1238.8281 2353.9228 3592.7509 0 0 0 2353.9228
Loop time of 3.11832 on 4 procs for 1000 steps with 1380 atoms
Performance: 55.414 ns/day, 0.433 hours/ns, 320.685 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1016 | 2.4316 | 2.9115 | 22.0 | 77.98
Bond | 5.7434e-05 | 7.7061e-05 | 9.8781e-05 | 0.0 | 0.00
Neigh | 0.0085809 | 0.04009 | 0.080657 | 15.8 | 1.29
Comm | 0.063574 | 0.51668 | 0.94055 | 45.3 | 16.57
Output | 0.010522 | 0.011868 | 0.01519 | 1.8 | 0.38
Modify | 0.01113 | 0.025305 | 0.045851 | 9.0 | 0.81
Other | | 0.09266 | | | 2.97
Nlocal: 345.000 ave 682 max 143 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Nghost: 2858.25 ave 4424 max 1221 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 19316.5 ave 38673 max 7133 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 77266
Ave neighs/atom = 55.989855
Ave special neighs/atom = 0.0000000
Neighbor list builds = 24
Dangerous builds = 0
Total wall time: 0:00:21

0
examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.in → examples/PACKAGES/local_density/methanol_implicit_water/in.methanol_implicit_water
View File

226
examples/PACKAGES/local_density/methanol_implicit_water/log.04Sep19.g++.1
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@ -1,226 +0,0 @@
LAMMPS (7 Aug 2019)
# LAMMPS input file for 50.0% methanol mole fraction solution
# with 2500 methanol molecules in implicit water.
#
#
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
#
# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data methanol_implicit_water.data
orthogonal box = (-31.123 -31.123 -31.123) to (31.123 31.123 31.123)
2 by 2 by 2 MPI processor grid
reading atoms ...
2500 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.00063014 secs
read_data CPU = 0.00599909 secs
velocity all create 3.0000e+02 12142 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM
WARNING: 93 of 500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:483)
WARNING: 254 of 500 distance values in table with relative error
over 1e-06 to re-computed values (../pair_table.cpp:492)
pair_coeff * * local/density methanol_implicit_water.localdensity.table
#Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
#Thermostat & time integration
timestep 1.0
thermo 100
thermo_style custom etotal ke pe temp evdwl
#minimization
minimize 1.e-4 0.0 1000 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 8 8 8
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.411 | 7.411 | 7.412 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1470.3564 2234.7133 -764.35689 300 -764.35689
46.496766 2234.7133 -2188.2165 300 -2188.2165
7.9030246 2234.7133 -2226.8103 300 -2226.8103
Loop time of 0.463996 on 8 procs for 121 steps with 2500 atoms
91.4% CPU use with 8 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-764.356892369 -2227.85589084 -2226.81026984
Force two-norm initial, final = 134.911 3.83896
Force max component initial, final = 14.1117 1.07422
Final line search alpha, max atom move = 5.06747e-10 5.44356e-10
Iterations, force evaluations = 121 154
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.41442 | 0.41976 | 0.42434 | 0.5 | 90.47
Bond | 1.1683e-05 | 2.0713e-05 | 3.5048e-05 | 0.0 | 0.00
Neigh | 0.0084722 | 0.0090862 | 0.010038 | 0.5 | 1.96
Comm | 0.022712 | 0.028157 | 0.034072 | 1.9 | 6.07
Output | 3.1948e-05 | 3.6925e-05 | 6.6996e-05 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006937 | | | 1.50
Nlocal: 312.5 ave 333 max 299 min
Histogram: 2 2 0 0 1 0 2 0 0 1
Nghost: 2546 ave 2580 max 2517 min
Histogram: 1 1 0 3 0 1 0 0 0 2
Neighs: 33215.4 ave 37251 max 29183 min
Histogram: 1 0 0 1 2 2 0 1 0 1
Total # of neighbors = 265723
Ave neighs/atom = 106.289
Ave special neighs/atom = 0
Neighbor list builds = 6
Dangerous builds = 0
#set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 59915
#Equilibration (for realistic results, run for 2000000 steps)
reset_timestep 0
thermo 200
thermo_style custom etotal ke pe temp evdwl
#run equilibration
run 2000
WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
Per MPI rank memory allocation (min/avg/max) = 6.286 | 6.286 | 6.287 Mbytes
TotEng KinEng PotEng Temp E_vdwl
177.26822 2234.7133 -2057.4451 300 -2057.4451
736.24287 2151.2608 -1415.0179 288.79688 -1415.0179
963.07617 2090.6433 -1127.5671 280.65926 -1127.5671
1148.9049 2173.1327 -1024.2279 291.73309 -1024.2279
1303.6409 2279.8586 -976.21767 306.06055 -976.21767
1355.42 2281.0383 -925.61826 306.21892 -925.61826
1394.5206 2276.2093 -881.68863 305.57064 -881.68863
1346.9764 2215.2973 -868.32091 297.3935 -868.32091
1381.3654 2248.8061 -867.44063 301.89189 -867.44063
1315.8059 2189.3193 -873.51332 293.90606 -873.51332
1314.4456 2209.7431 -895.29752 296.64787 -895.29752
Loop time of 6.38989 on 8 procs for 2000 steps with 2500 atoms
Performance: 27.043 ns/day, 0.887 hours/ns, 312.994 timesteps/s
80.5% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.2693 | 5.3572 | 5.457 | 2.1 | 83.84
Bond | 0.00028825 | 0.00033835 | 0.00039148 | 0.0 | 0.01
Neigh | 0.0296 | 0.032337 | 0.035071 | 0.9 | 0.51
Comm | 0.64679 | 0.73397 | 0.80847 | 5.2 | 11.49
Output | 0.00033498 | 0.00051582 | 0.0015228 | 0.0 | 0.01
Modify | 0.16395 | 0.18919 | 0.21056 | 3.9 | 2.96
Other | | 0.07636 | | | 1.19
Nlocal: 312.5 ave 337 max 295 min
Histogram: 2 2 0 1 0 0 0 1 1 1
Nghost: 2551.62 ave 2582 max 2525 min
Histogram: 2 1 0 0 1 1 1 0 1 1
Neighs: 33241.8 ave 37659 max 29705 min
Histogram: 2 0 0 2 2 0 0 0 1 1
Total # of neighbors = 265934
Ave neighs/atom = 106.374
Ave special neighs/atom = 0
Neighbor list builds = 21
Dangerous builds = 0
#turn off recentering during production run
unfix recentering
#setup trajectory output
dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
dump_modify myDump element M
dump_modify myDump sort id
#run production (for realistic results, run for 10000000 steps)
reset_timestep 0
thermo 1000
thermo_style custom etotal ke pe temp evdwl
run 10000
Per MPI rank memory allocation (min/avg/max) = 7.588 | 7.589 | 7.589 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1442.5428 2209.7431 -767.20027 296.64787 -767.20027
1391.8624 2262.6889 -870.82656 303.7556 -870.82656
1375.914 2244.6176 -868.7036 301.3296 -868.7036
1345.9064 2227.2324 -881.32599 298.99573 -881.32599
1379.2334 2278.1156 -898.88222 305.82657 -898.88222
1389.7928 2255.8062 -866.01341 302.83163 -866.01341
1380.4549 2258.2108 -877.75582 303.15443 -877.75582
1380.8489 2256.9432 -876.09428 302.98426 -876.09428
1326.5151 2225.7408 -899.22577 298.79549 -899.22577
1376.6025 2253.0128 -876.41028 302.45662 -876.41028
1331.0008 2218.1033 -887.10258 297.77019 -887.10258
Loop time of 25.4591 on 8 procs for 10000 steps with 2500 atoms
Performance: 33.937 ns/day, 0.707 hours/ns, 392.787 timesteps/s
89.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.635 | 21.916 | 22.237 | 3.9 | 86.08
Bond | 0.0011308 | 0.0013149 | 0.0016932 | 0.5 | 0.01
Neigh | 0.14593 | 0.15675 | 0.16667 | 1.9 | 0.62
Comm | 1.3789 | 1.7502 | 1.9558 | 13.7 | 6.87
Output | 0.34664 | 0.82927 | 1.2013 | 32.8 | 3.26
Modify | 0.24904 | 0.25842 | 0.26907 | 1.2 | 1.02
Other | | 0.5475 | | | 2.15
Nlocal: 312.5 ave 327 max 298 min
Histogram: 2 0 0 1 1 0 1 1 1 1
Nghost: 2575 ave 2601 max 2559 min
Histogram: 2 0 3 1 0 0 0 0 1 1
Neighs: 33223.2 ave 35920 max 30303 min
Histogram: 1 1 1 1 0 1 0 0 0 3
Total # of neighbors = 265786
Ave neighs/atom = 106.314
Ave special neighs/atom = 0
Neighbor list builds = 103
Dangerous builds = 0
Total wall time: 0:00:32

259
examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.1 Normal file
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@ -0,0 +1,259 @@
LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 50.0% methanol mole fraction solution
# with 2500 methanol molecules in implicit water.
#
#
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
#
# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data methanol_implicit_water.data
Reading data file ...
orthogonal box = (-31.123000 -31.123000 -31.123000) to (31.123000 31.123000 31.123000)
1 by 1 by 1 MPI processor grid
reading atoms ...
2500 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.013 seconds
velocity all create 3.0000e+02 12142 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM
WARNING: 93 of 500 force values in table PairMM are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 254 of 500 distance values in table 1e-06 with relative error
WARNING: over PairMM to re-computed values (src/pair_table.cpp:473)
pair_coeff * * local/density methanol_implicit_water.localdensity.table
#Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
#Thermostat & time integration
timestep 1.0
thermo 100
thermo_style custom etotal ke pe temp evdwl
#minimization
minimize 1.e-4 0.0 1000 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair_style local/density command:
@Article{Sanyal16,
author = {T.Sanyal and M.Scott Shell},
title = {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
journal = {J.~Chem.~Phys.},
year = 2016,
DOI = doi.org/10.1063/1.4958629}
@Article{Sanyal18,
author = {T.Sanyal and M.Scott Shell},
title = {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
journal = {J.~Phys.~Chem. B},
year = 2018,
DOI = doi.org/10.1021/acs.jpcb.7b12446}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 8 8 8
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.535 | 9.535 | 9.535 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1283.8556 2234.7133 -950.85771 300 -950.85771
-9.7958217 2234.7133 -2244.5091 300 -2244.5091
-124.06884 2234.7133 -2358.7821 300 -2358.7821
-147.62166 2234.7133 -2382.335 300 -2382.335
Loop time of 1.62821 on 1 procs for 241 steps with 2500 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-950.857712502514 -2382.10870675249 -2382.33495251609
Force two-norm initial, final = 135.23808 2.6585717
Force max component initial, final = 14.083102 1.1756489
Final line search alpha, max atom move = 0.17024312 0.20014614
Iterations, force evaluations = 241 265
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5428 | 1.5428 | 1.5428 | 0.0 | 94.75
Bond | 2.5869e-05 | 2.5869e-05 | 2.5869e-05 | 0.0 | 0.00
Neigh | 0.063379 | 0.063379 | 0.063379 | 0.0 | 3.89
Comm | 0.0064436 | 0.0064436 | 0.0064436 | 0.0 | 0.40
Output | 6.1984e-05 | 6.1984e-05 | 6.1984e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01554 | | | 0.95
Nlocal: 2500.00 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6692.00 ave 6692 max 6692 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 265654.0 ave 265654 max 265654 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 265654
Ave neighs/atom = 106.26160
Ave special neighs/atom = 0.0000000
Neighbor list builds = 12
Dangerous builds = 0
#set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 59915
#Equilibration (for realistic results, run for 2000000 steps)
reset_timestep 0
thermo 200
thermo_style custom etotal ke pe temp evdwl
#run equilibration
run 2000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 8.410 | 8.410 | 8.410 Mbytes
TotEng KinEng PotEng Temp E_vdwl
-147.62166 2234.7133 -2382.335 300 -2382.335
537.85671 2048.4261 -1510.5694 274.9918 -1510.5694
965.63232 2159.0283 -1193.396 289.83963 -1193.396
1134.2224 2219.4775 -1085.2551 297.95466 -1085.2551
1179.7829 2223.7806 -1043.9976 298.53233 -1043.9976
1283.8992 2276.5007 -992.60147 305.60976 -992.60147
1258.5839 2233.2201 -974.63621 299.79954 -974.63621
1284.986 2226.9462 -941.96019 298.95731 -941.96019
1283.0707 2242.5034 -959.43275 301.04579 -959.43275
1243.5964 2234.6938 -991.09745 299.99739 -991.09745
1268.8458 2223.4431 -954.59731 298.48702 -954.59731
Loop time of 9.51867 on 1 procs for 2000 steps with 2500 atoms
Performance: 18.154 ns/day, 1.322 hours/ns, 210.113 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.1412 | 9.1412 | 9.1412 | 0.0 | 96.03
Bond | 0.00018215 | 0.00018215 | 0.00018215 | 0.0 | 0.00
Neigh | 0.10535 | 0.10535 | 0.10535 | 0.0 | 1.11
Comm | 0.040353 | 0.040353 | 0.040353 | 0.0 | 0.42
Output | 0.00030119 | 0.00030119 | 0.00030119 | 0.0 | 0.00
Modify | 0.21926 | 0.21926 | 0.21926 | 0.0 | 2.30
Other | | 0.01203 | | | 0.13
Nlocal: 2500.00 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6694.00 ave 6694 max 6694 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 265940.0 ave 265940 max 265940 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 265940
Ave neighs/atom = 106.37600
Ave special neighs/atom = 0.0000000
Neighbor list builds = 20
Dangerous builds = 0
#turn off recentering during production run
unfix recentering
#setup trajectory output
dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
dump_modify myDump element M
dump_modify myDump sort id
#run production (for realistic results, run for 10000000 steps)
reset_timestep 0
thermo 1000
thermo_style custom etotal ke pe temp evdwl
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.917 | 9.917 | 9.917 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1268.8458 2223.4431 -954.59731 298.48702 -954.59731
1316.5359 2251.6787 -935.14283 302.27753 -935.14283
1354.5001 2297.0836 -942.5835 308.37293 -942.5835
1310.7793 2244.4215 -933.64213 301.30328 -933.64213
1240.9316 2199.0235 -958.09194 295.20881 -958.09194
1322.2028 2224.6711 -902.46825 298.65188 -902.46825
1295.6764 2239.5464 -943.87002 300.64882 -943.87002
1264.7686 2193.8137 -929.04513 294.50942 -929.04513
1332.726 2225.0636 -892.33763 298.70457 -892.33763
1300.8091 2245.0291 -944.22001 301.38485 -944.22001
1283.7858 2263.1178 -979.33199 303.81317 -979.33199
Loop time of 48.4805 on 1 procs for 10000 steps with 2500 atoms
Performance: 17.822 ns/day, 1.347 hours/ns, 206.269 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 46.382 | 46.382 | 46.382 | 0.0 | 95.67
Bond | 0.00067195 | 0.00067195 | 0.00067195 | 0.0 | 0.00
Neigh | 0.5527 | 0.5527 | 0.5527 | 0.0 | 1.14
Comm | 0.20936 | 0.20936 | 0.20936 | 0.0 | 0.43
Output | 0.3089 | 0.3089 | 0.3089 | 0.0 | 0.64
Modify | 0.96229 | 0.96229 | 0.96229 | 0.0 | 1.98
Other | | 0.06462 | | | 0.13
Nlocal: 2500.00 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6717.00 ave 6717 max 6717 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 265687.0 ave 265687 max 265687 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 265687
Ave neighs/atom = 106.27480
Ave special neighs/atom = 0.0000000
Neighbor list builds = 104
Dangerous builds = 0
Total wall time: 0:00:59

259
examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.4 Normal file
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@ -0,0 +1,259 @@
LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 50.0% methanol mole fraction solution
# with 2500 methanol molecules in implicit water.
#
#
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
#
# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data methanol_implicit_water.data
Reading data file ...
orthogonal box = (-31.123000 -31.123000 -31.123000) to (31.123000 31.123000 31.123000)
1 by 2 by 2 MPI processor grid
reading atoms ...
2500 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
velocity all create 3.0000e+02 12142 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM
WARNING: 93 of 500 force values in table PairMM are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 254 of 500 distance values in table 1e-06 with relative error
WARNING: over PairMM to re-computed values (src/pair_table.cpp:473)
pair_coeff * * local/density methanol_implicit_water.localdensity.table
#Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
#Thermostat & time integration
timestep 1.0
thermo 100
thermo_style custom etotal ke pe temp evdwl
#minimization
minimize 1.e-4 0.0 1000 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair_style local/density command:
@Article{Sanyal16,
author = {T.Sanyal and M.Scott Shell},
title = {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
journal = {J.~Chem.~Phys.},
year = 2016,
DOI = doi.org/10.1063/1.4958629}
@Article{Sanyal18,
author = {T.Sanyal and M.Scott Shell},
title = {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
journal = {J.~Phys.~Chem. B},
year = 2018,
DOI = doi.org/10.1021/acs.jpcb.7b12446}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 8 8 8
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.855 | 7.855 | 7.855 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1283.8556 2234.7133 -950.85771 300 -950.85771
-9.4401685 2234.7133 -2244.1535 300 -2244.1535
-122.80029 2234.7133 -2357.5136 300 -2357.5136
-146.96064 2234.7133 -2381.6739 300 -2381.6739
Loop time of 0.498841 on 4 procs for 241 steps with 2500 atoms
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-950.857712502527 -2381.44072433077 -2381.67393909809
Force two-norm initial, final = 135.21195 1.9890578
Force max component initial, final = 14.083102 0.35498472
Final line search alpha, max atom move = 0.22126422 0.078545415
Iterations, force evaluations = 241 266
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.45851 | 0.46126 | 0.46421 | 0.3 | 92.47
Bond | 8.964e-06 | 1.0965e-05 | 1.3252e-05 | 0.0 | 0.00
Neigh | 0.017003 | 0.017754 | 0.018391 | 0.4 | 3.56
Comm | 0.010352 | 0.013856 | 0.017292 | 2.1 | 2.78
Output | 3.7232e-05 | 4.2203e-05 | 5.6379e-05 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005917 | | | 1.19
Nlocal: 625.000 ave 643 max 609 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 3592.25 ave 3614 max 3560 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 66421.2 ave 71727 max 62557 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 265685
Ave neighs/atom = 106.27400
Ave special neighs/atom = 0.0000000
Neighbor list builds = 12
Dangerous builds = 0
#set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 59915
#Equilibration (for realistic results, run for 2000000 steps)
reset_timestep 0
thermo 200
thermo_style custom etotal ke pe temp evdwl
#run equilibration
run 2000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 6.730 | 6.730 | 6.731 Mbytes
TotEng KinEng PotEng Temp E_vdwl
-146.96064 2234.7133 -2381.6739 300 -2381.6739
599.48689 2124.6561 -1525.1692 285.22532 -1525.1692
951.02252 2176.9553 -1225.9328 292.24625 -1225.9328
1124.1537 2216.3745 -1092.2209 297.53811 -1092.2209
1255.0922 2291.8755 -1036.7833 307.67376 -1036.7833
1214.4874 2210.1494 -995.66199 296.7024 -995.66199
1271.549 2224.6855 -953.13648 298.65381 -953.13648
1307.661 2233.6901 -926.02913 299.86264 -926.02913
1240.6625 2196.6116 -955.94904 294.88502 -955.94904
1323.5685 2270.4712 -946.90268 304.80033 -946.90268
1303.6912 2251.0445 -947.35323 302.19239 -947.35323
Loop time of 2.95451 on 4 procs for 2000 steps with 2500 atoms
Performance: 58.487 ns/day, 0.410 hours/ns, 676.931 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7367 | 2.756 | 2.7834 | 1.0 | 93.28
Bond | 6.6059e-05 | 7.0557e-05 | 7.8303e-05 | 0.0 | 0.00
Neigh | 0.028439 | 0.029542 | 0.030829 | 0.5 | 1.00
Comm | 0.068091 | 0.096506 | 0.1167 | 5.8 | 3.27
Output | 0.00018063 | 0.00020758 | 0.00027798 | 0.0 | 0.01
Modify | 0.0654 | 0.065679 | 0.065809 | 0.1 | 2.22
Other | | 0.006553 | | | 0.22
Nlocal: 625.000 ave 637 max 616 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 3605.00 ave 3622 max 3584 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 66474.2 ave 71000 max 62801 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 265897
Ave neighs/atom = 106.35880
Ave special neighs/atom = 0.0000000
Neighbor list builds = 20
Dangerous builds = 0
#turn off recentering during production run
unfix recentering
#setup trajectory output
dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
dump_modify myDump element M
dump_modify myDump sort id
#run production (for realistic results, run for 10000000 steps)
reset_timestep 0
thermo 1000
thermo_style custom etotal ke pe temp evdwl
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.071 | 8.071 | 8.071 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1303.6912 2251.0445 -947.35323 302.19239 -947.35323
1303.261 2239.1583 -935.89729 300.59672 -935.89729
1424.774 2323.5004 -898.72637 311.91926 -898.72637
1284.1578 2196.6712 -912.51339 294.89302 -912.51339
1300.0421 2226.2016 -926.15949 298.85735 -926.15949
1312.6498 2256.5133 -943.86352 302.92655 -943.86352
1336.2952 2266.6579 -930.36267 304.28841 -930.36267
1301.8361 2248.4166 -946.58057 301.83961 -946.58057
1311.1461 2231.3093 -920.16317 299.54303 -920.16317
1379.406 2276.2942 -896.88827 305.58205 -896.88827
1305.5794 2241.899 -936.31962 300.96465 -936.31962
Loop time of 20.352 on 4 procs for 10000 steps with 2500 atoms
Performance: 42.453 ns/day, 0.565 hours/ns, 491.352 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.732 | 18.812 | 19.031 | 2.9 | 92.43
Bond | 0.00040507 | 0.00043028 | 0.00046819 | 0.0 | 0.00
Neigh | 0.18389 | 0.19009 | 0.20356 | 1.8 | 0.93
Comm | 0.54247 | 0.76034 | 0.84695 | 14.5 | 3.74
Output | 0.099103 | 0.11843 | 0.17457 | 9.4 | 0.58
Modify | 0.31601 | 0.33337 | 0.35741 | 2.9 | 1.64
Other | | 0.1378 | | | 0.68
Nlocal: 625.000 ave 649 max 609 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 3606.75 ave 3631 max 3571 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 66515.0 ave 72591 max 63412 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 266060
Ave neighs/atom = 106.42400
Ave special neighs/atom = 0.0000000
Neighbor list builds = 104
Dangerous builds = 0
Total wall time: 0:00:23