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) 1 by 1 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 python 12.0 pair_coeff * * py_pot.LJCutSPCE OW HW 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 only lj/cut table for the oxygen atoms from python shell rm -f spce.table WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW 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 python, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard # switch to tabulated potential with long-range coulomb as overlay pair_style hybrid/overlay coul/long 12.0 table linear 2000 kspace_style pppm 1.0e-6 pair_coeff * * coul/long pair_coeff 1 1 table spce.table OW-OW thermo 10 run 100 PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.279652 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.000394674 estimated relative force accuracy = 1.18855e-06 using double precision FFTs 3d grid and FFT values/proc = 103823 64000 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/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) pair table, perpetual, skip from (1) attributes: half, newton on pair build: skip stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 36.47 | 36.47 | 36.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16690.032 0 -16690.032 -1268.9538 10 120.58553 -17767.504 0 -16689.536 -4063.8589 20 136.11736 -17882.557 0 -16665.742 -5124.6758 30 137.00764 -17872.318 0 -16647.545 -5337.2022 40 153.38868 -17999.269 0 -16628.059 -5213.6001 50 167.70342 -18103.06 0 -16603.883 -4460.6632 60 163.07134 -18034.856 0 -16577.088 -3285.0037 70 169.59286 -18064.636 0 -16548.57 -2606.407 80 182.92893 -18153.499 0 -16518.215 -2385.5152 90 191.2793 -18195.356 0 -16485.425 -2235.3701 100 194.68587 -18192.458 0 -16452.073 -1948.3746 Loop time of 7.90705 on 1 procs for 100 steps with 4500 atoms Performance: 1.093 ns/day, 21.964 hours/ns, 12.647 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0343 | 6.0343 | 6.0343 | 0.0 | 76.32 Bond | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.00 Kspace | 1.5311 | 1.5311 | 1.5311 | 0.0 | 19.36 Neigh | 0.246 | 0.246 | 0.246 | 0.0 | 3.11 Comm | 0.023937 | 0.023937 | 0.023937 | 0.0 | 0.30 Output | 0.00060368 | 0.00060368 | 0.00060368 | 0.0 | 0.01 Modify | 0.065543 | 0.065543 | 0.065543 | 0.0 | 0.83 Other | | 0.005364 | | | 0.07 Nlocal: 4500 ave 4500 max 4500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21216 ave 21216 max 21216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2601769 Ave neighs/atom = 578.171 Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 shell rm spce.table Total wall time: 0:00:08