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move examples away from USER-MISC now that the package folder is gone

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This commit is contained in:
Axel Kohlmeyer
2021-07-24 20:53:23 -04:00
parent add7565d9f
commit f192102da9
216 changed files with 7 additions and 12 deletions
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examples/PACKAGES/local_density/benzene_water/benzene_water.data Normal file
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examples/PACKAGES/local_density/benzene_water/benzene_water.in Normal file
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# 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
velocity all create 3.0000e+02 16611 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table benzene_water.pair.table PairBB
pair_coeff 1 2 table benzene_water.pair.table PairWW
pair_coeff 2 2 table benzene_water.pair.table PairBW
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
# 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
# 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

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examples/PACKAGES/local_density/benzene_water/benzene_water.localdensity.table Normal file
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examples/PACKAGES/local_density/benzene_water/benzene_water.pair.table Normal file
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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

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examples/PACKAGES/local_density/methanol_implicit_water/log.04Sep19.g++.1 Normal file
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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

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# 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
velocity all create 3.0000e+02 12142 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM
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
#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
#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

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#LOCAL DENSITY POTENTIALS
1 500
5.3000000e+00 6.3000000e+00
1
1
0.0000000e+00 2.6000000e+01 5.2104208e-02
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
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1.4810000e-01
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1.4810000e-01
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1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4810000e-01
1.4807157e-01
1.4782582e-01
1.4711763e-01
1.4570179e-01
1.4333312e-01
1.3976643e-01
1.3478059e-01
1.2856173e-01
1.2163552e-01
1.1453802e-01
1.0780525e-01
1.0197328e-01
9.7575837e-02
9.4875548e-02
9.3613063e-02
9.3469690e-02
9.4126738e-02
9.5265515e-02
9.6567329e-02
9.7735007e-02
9.8575495e-02
9.8927186e-02
9.8628481e-02
9.7517779e-02
9.5433481e-02
9.2235018e-02
8.8072568e-02
8.3308496e-02
7.8309990e-02
7.3444241e-02
6.9078438e-02
6.5577180e-02
6.3110699e-02
6.1523109e-02
6.0627357e-02
6.0236386e-02
6.0163144e-02
6.0220573e-02
6.0233006e-02
6.0072080e-02
5.9621717e-02
5.8765838e-02
5.7388366e-02
5.5373224e-02
5.2623498e-02
4.9261717e-02
4.5550390e-02
4.1754290e-02
3.8138193e-02
3.4966871e-02
3.2501662e-02
3.0825931e-02
2.9762256e-02
2.9112455e-02
2.8678347e-02
2.8261751e-02
2.7664487e-02
2.6737788e-02
2.5509284e-02
2.4045951e-02
2.2414767e-02
2.0682707e-02
1.8916748e-02
1.7179645e-02
1.5493687e-02
1.3858641e-02
1.2274032e-02
1.0739385e-02
9.2542252e-03
7.8179601e-03
6.4255437e-03
5.0662231e-03
3.7288715e-03
2.4023618e-03
1.0755673e-03
-2.6263394e-04
-1.6141074e-03
-2.9522803e-03
-4.2451362e-03
-5.4606586e-03
-6.5668312e-03
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-1.0078658e-02
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-1.3781467e-02
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-2.9367192e-02
-3.0187085e-02
-3.0712590e-02
-3.0944560e-02
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-3.0018416e-02
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-2.2620686e-02
-1.8367122e-02
-1.2765600e-02
-6.3400224e-03
3.8564733e-04
6.8874449e-03
1.2641406e-02
1.7151899e-02
2.0334733e-02
2.2416173e-02
2.3630118e-02
2.4210466e-02
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2.4405000e-02
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2.4405000e-02
2.4405000e-02
2.4405000e-02
2.4405000e-02
2.4405000e-02

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