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 hybrid/overlay coul/long 12.0 python 12.0 kspace_style pppm 1.0e-6 pair_coeff * * coul/long pair_coeff * * python py_pot.LJCutSPCE OW NULL pair_modify table 0 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 PPPM initialization ... WARNING: Using polynomial approximation 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 = 0.000394206 estimated relative force accuracy = 1.18714e-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 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 PPPM initialization ... WARNING: Using polynomial approximation 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 = 0.000394206 estimated relative force accuracy = 1.18714e-06 using double precision FFTs 3d grid and FFT values/proc = 103823 64000 pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 PPPM initialization ... WARNING: Using polynomial approximation 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 = 0.000394206 estimated relative force accuracy = 1.18714e-06 using double precision FFTs 3d grid and FFT values/proc = 103823 64000 # 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 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 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) = 35.26 | 35.26 | 35.26 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -100272.97 0 -100272.97 -1282.0708 10 120.61568 -101350.63 0 -100272.39 -4077.5051 20 136.11379 -101465.43 0 -100248.65 -5136.5677 30 137.01602 -101455.3 0 -100230.46 -5347.8311 40 153.424 -101582.46 0 -100210.93 -5223.1676 50 167.73654 -101686.24 0 -100186.77 -4468.6687 60 163.11642 -101618.16 0 -100159.99 -3291.7815 70 169.64512 -101647.89 0 -100131.35 -2611.638 80 182.9979 -101737.01 0 -100101.11 -2390.6293 90 191.33873 -101778.71 0 -100068.24 -2239.386 100 194.7458 -101775.84 0 -100034.92 -1951.9128 Loop time of 7.63869 on 1 procs for 100 steps with 4500 atoms Performance: 1.131 ns/day, 21.219 hours/ns, 13.091 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 | 5.7777 | 5.7777 | 5.7777 | 0.0 | 75.64 Bond | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.00 Kspace | 1.5385 | 1.5385 | 1.5385 | 0.0 | 20.14 Neigh | 0.22962 | 0.22962 | 0.22962 | 0.0 | 3.01 Comm | 0.024123 | 0.024123 | 0.024123 | 0.0 | 0.32 Output | 0.00061131 | 0.00061131 | 0.00061131 | 0.0 | 0.01 Modify | 0.062444 | 0.062444 | 0.062444 | 0.0 | 0.82 Other | | 0.005466 | | | 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 = 2601766 Ave neighs/atom = 578.17 Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 shell rm spce.table Total wall time: 0:00:07