LAMMPS (4 May 2017) 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 pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 # switch to tabulated potential pair_style table linear 2000 pppm pair_coeff 1 1 spce.table OW-OW pair_coeff 1 2 spce.table OW-HW pair_coeff 2 2 spce.table HW-HW 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) = 9.962 | 9.963 | 9.963 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18284.922 0 -18284.922 -2080.7739 10 146.83806 -19552.072 0 -18239.421 -4865.31 20 183.15761 -18706.872 0 -17069.543 -4865.6695 30 205.96203 -18901.541 0 -17060.354 -4454.8634 40 241.62768 -18323.117 0 -16163.099 -3269.1475 50 265.98384 -19883.562 0 -17505.813 -2788.5194 60 274.01897 -21320.575 0 -18870.996 -2387.0708 70 288.7601 -19849.269 0 -17267.913 -1235.818 80 300.64724 -20958.602 0 -18270.981 -1714.7988 90 304.19113 -21580.4 0 -18861.099 -2144.1614 100 304.22027 -21239.014 0 -18519.452 -2092.6759 Loop time of 1.7361 on 4 procs for 100 steps with 4500 atoms Performance: 4.977 ns/day, 4.823 hours/ns, 57.600 timesteps/s 99.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4424 | 1.5149 | 1.6066 | 5.3 | 87.26 Bond | 8.9407e-05 | 0.00010258 | 0.00012374 | 0.0 | 0.01 Neigh | 0.064205 | 0.064241 | 0.064295 | 0.0 | 3.70 Comm | 0.023643 | 0.1155 | 0.18821 | 19.2 | 6.65 Output | 0.00038004 | 0.00042355 | 0.00054145 | 0.0 | 0.02 Modify | 0.037507 | 0.037787 | 0.038042 | 0.1 | 2.18 Other | | 0.003148 | | | 0.18 Nlocal: 1125 ave 1162 max 1098 min Histogram: 1 1 0 0 0 1 0 0 0 1 Nghost: 12267.8 ave 12302 max 12238 min Histogram: 2 0 0 0 0 0 0 0 1 1 Neighs: 649416 ave 681458 max 630541 min Histogram: 1 0 2 0 0 0 0 0 0 1 Total # of neighbors = 2597662 Ave neighs/atom = 577.258 Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 shell rm spce.table Total wall time: 0:00:01