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/long 12.0 python 12.0 kspace_style pppm 1.0e-6 pair_coeff * * coul/long 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 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 python, perpetual, skip from (1) attributes: half, newton on pair build: skip stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 14.64 | 14.64 | 14.64 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16692.369 0 -16692.369 -1289.222 10 120.56861 -17769.719 0 -16691.902 -4082.7098 20 136.08014 -17884.591 0 -16668.109 -5140.7824 30 136.97316 -17874.351 0 -16649.887 -5351.3571 40 153.37285 -18001.493 0 -16630.424 -5227.0601 50 167.70414 -18105.435 0 -16606.252 -4473.2089 60 163.08253 -18037.29 0 -16579.422 -3295.8963 70 169.60395 -18067.078 0 -16550.912 -2615.7026 80 182.94811 -18155.978 0 -16520.523 -2393.3156 90 191.29902 -18197.887 0 -16487.779 -2242.7104 100 194.70949 -18195.021 0 -16454.425 -1955.2916 Loop time of 4.36104 on 4 procs for 100 steps with 4500 atoms Performance: 1.981 ns/day, 12.114 hours/ns, 22.930 timesteps/s 97.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5019 | 3.6105 | 3.738 | 4.4 | 82.79 Bond | 0.00010133 | 0.00013196 | 0.00017118 | 0.0 | 0.00 Kspace | 0.47082 | 0.59641 | 0.70417 | 10.8 | 13.68 Neigh | 0.081036 | 0.081042 | 0.081047 | 0.0 | 1.86 Comm | 0.030113 | 0.03092 | 0.03135 | 0.3 | 0.71 Output | 0.00034952 | 0.00064117 | 0.001514 | 0.0 | 0.01 Modify | 0.036583 | 0.037553 | 0.038021 | 0.3 | 0.86 Other | | 0.00388 | | | 0.09 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: 650440 ave 678828 max 626375 min Histogram: 1 0 0 0 2 0 0 0 0 1 Total # of neighbors = 2601762 Ave neighs/atom = 578.169 Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 Total wall time: 0:00:04