diff --git a/examples/PACKAGES/local_density/benzene_water/benzene_water.in b/examples/PACKAGES/local_density/benzene_water/in.benzene_water similarity index 100% rename from examples/PACKAGES/local_density/benzene_water/benzene_water.in rename to examples/PACKAGES/local_density/benzene_water/in.benzene_water diff --git a/examples/PACKAGES/local_density/benzene_water/log.04Sep19.g++.1 b/examples/PACKAGES/local_density/benzene_water/log.04Sep19.g++.1 deleted file mode 100644 index 928906edbd..0000000000 --- a/examples/PACKAGES/local_density/benzene_water/log.04Sep19.g++.1 +++ /dev/null @@ -1,267 +0,0 @@ -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 diff --git a/examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.1 b/examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.1 new file mode 100644 index 0000000000..386aaced0e --- /dev/null +++ b/examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.1 @@ -0,0 +1,300 @@ +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 diff --git a/examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.4 b/examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.4 new file mode 100644 index 0000000000..2a89780b40 --- /dev/null +++ b/examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.4 @@ -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 diff --git a/examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.in b/examples/PACKAGES/local_density/methanol_implicit_water/in.methanol_implicit_water similarity index 100% rename from examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.in rename to examples/PACKAGES/local_density/methanol_implicit_water/in.methanol_implicit_water diff --git a/examples/PACKAGES/local_density/methanol_implicit_water/log.04Sep19.g++.1 b/examples/PACKAGES/local_density/methanol_implicit_water/log.04Sep19.g++.1 deleted file mode 100644 index 618e994946..0000000000 --- a/examples/PACKAGES/local_density/methanol_implicit_water/log.04Sep19.g++.1 +++ /dev/null @@ -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 diff --git a/examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.1 b/examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.1 new file mode 100644 index 0000000000..2e2cfe00da --- /dev/null +++ b/examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.1 @@ -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 diff --git a/examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.4 b/examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.4 new file mode 100644 index 0000000000..7b6b97ad61 --- /dev/null +++ b/examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.4 @@ -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