LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real atom_style full read_data data.spce orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) 2 by 2 by 1 MPI processor grid reading atoms ... 4500 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 3000 bonds reading angles ... 1500 angles 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors pair_style hybrid/overlay coul/cut 12.0 python 12.0 pair_coeff * * coul/cut pair_coeff * * python py_pot.LJCutSPCE OW NULL bond_style harmonic angle_style harmonic dihedral_style none improper_style none bond_coeff 1 1000.00 1.000 angle_coeff 1 100.0 109.47 special_bonds lj/coul 0.0 0.0 1.0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 2 = max # of special neighbors neighbor 2.0 bin fix 1 all shake 0.0001 20 0 b 1 a 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 # create combined lj/coul table for all atom types # generate tabulated potential from python variant pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) pair python, perpetual, skip from (1) attributes: half, newton on pair build: skip stencil: none bin: none pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) pair python, perpetual, skip from (1) attributes: half, newton on pair build: skip stencil: none bin: none pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) pair python, perpetual, skip from (1) attributes: half, newton on pair build: skip stencil: none bin: none # switch to tabulated potential pair_style table linear 2000 pppm pair_coeff 1 1 spce.table OW-OW WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (src/pair_table.cpp:481) pair_coeff 1 2 spce.table OW-HW WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (src/pair_table.cpp:481) pair_coeff 2 2 spce.table HW-HW WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (src/pair_table.cpp:481) thermo 10 run 100 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair table, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 10.01 | 10.01 | 10.01 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18173.499 0 -18173.499 -2019.6011 10 146.87683 -19431.334 0 -18118.336 -4804.774 20 183.13008 -19192.694 0 -17555.612 -5105.075 30 205.91102 -18124.567 0 -16283.836 -4052.5955 40 241.34432 -18154.089 0 -15996.604 -3187.3994 50 265.93905 -19712.779 0 -17335.431 -2716.3264 60 273.67861 -21092.479 0 -18645.943 -2266.2648 70 288.39213 -19794.592 0 -17216.526 -1207.5782 80 300.36209 -20235.73 0 -17550.658 -1345.2669 90 303.8567 -21670.331 0 -18954.02 -2207.0831 100 304.10875 -19847.214 0 -17128.649 -1431.7749 Loop time of 1.64676 on 4 procs for 100 steps with 4500 atoms Performance: 5.247 ns/day, 4.574 hours/ns, 60.725 timesteps/s 98.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4241 | 1.4506 | 1.5134 | 3.0 | 88.09 Bond | 9.8705e-05 | 0.00010312 | 0.00010729 | 0.0 | 0.01 Neigh | 0.071698 | 0.071712 | 0.07172 | 0.0 | 4.35 Comm | 0.027696 | 0.090501 | 0.11691 | 12.1 | 5.50 Output | 0.00032783 | 0.00048846 | 0.00096679 | 0.0 | 0.03 Modify | 0.030543 | 0.030691 | 0.030788 | 0.1 | 1.86 Other | | 0.002627 | | | 0.16 Nlocal: 1125 ave 1163 max 1097 min Histogram: 1 1 0 0 0 1 0 0 0 1 Nghost: 12265.5 ave 12299 max 12233 min Histogram: 1 1 0 0 0 0 0 0 1 1 Neighs: 649430 ave 681781 max 630283 min Histogram: 1 0 2 0 0 0 0 0 0 1 Total # of neighbors = 2597720 Ave neighs/atom = 577.271 Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 shell rm spce.table Total wall time: 0:00:01