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 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' (src/input.cpp:1308) WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308) 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 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 PPPM initialization ... using 12-bit tables for long-range coulomb (src/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 = 34263 16000 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) = 13.5 | 13.5 | 13.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16690.019 0 -16690.019 -1268.9124 10 120.58553 -17767.489 0 -16689.521 -4063.8136 20 136.11736 -17882.538 0 -16665.724 -5124.6194 30 137.00764 -17872.302 0 -16647.529 -5337.1515 40 153.38867 -17999.256 0 -16628.046 -5213.5616 50 167.70342 -18103.046 0 -16603.87 -4460.6216 60 163.07134 -18034.842 0 -16577.074 -3284.9621 70 169.59286 -18064.622 0 -16548.556 -2606.3642 80 182.92892 -18153.485 0 -16518.202 -2385.4747 90 191.2793 -18195.343 0 -16485.411 -2235.3292 100 194.68587 -18192.446 0 -16452.061 -1948.3379 Loop time of 2.26946 on 4 procs for 100 steps with 4500 atoms Performance: 3.807 ns/day, 6.304 hours/ns, 44.063 timesteps/s 95.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4676 | 1.53 | 1.6054 | 4.5 | 67.42 Bond | 9.7752e-05 | 0.00012088 | 0.00013947 | 0.0 | 0.01 Kspace | 0.51974 | 0.59375 | 0.65496 | 7.2 | 26.16 Neigh | 0.075271 | 0.075279 | 0.075287 | 0.0 | 3.32 Comm | 0.028602 | 0.029937 | 0.031052 | 0.5 | 1.32 Output | 0.00035477 | 0.00062722 | 0.0014365 | 0.0 | 0.03 Modify | 0.03581 | 0.035956 | 0.036059 | 0.1 | 1.58 Other | | 0.003819 | | | 0.17 Nlocal: 1125 ave 1154 max 1092 min Histogram: 1 0 0 0 1 0 0 1 0 1 Nghost: 12256.2 ave 12296 max 12213 min Histogram: 1 0 1 0 0 0 0 0 1 1 Neighs: 650442 ave 678830 max 626373 min Histogram: 1 0 0 0 2 0 0 0 0 1 Total # of neighbors = 2601768 Ave neighs/atom = 578.171 Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 shell rm spce.table Total wall time: 0:00:02