LAMMPS (23 Jun 2022 - Update 1) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Rhodopsin model units real neigh_modify delay 5 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8.0 10.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data data.rhodo Reading data file ... orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 2 by 4 by 2 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 32000 velocities scanning bonds ... 4 = max bonds/atom scanning angles ... 8 = max angles/atom scanning dihedrals ... 18 = max dihedrals/atom scanning impropers ... 2 = max impropers/atom reading bonds ... 27723 bonds reading angles ... 40467 angles reading dihedrals ... 56829 dihedrals reading impropers ... 1034 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors special bonds CPU = 0.001 seconds read_data CPU = 0.299 seconds fix 1 all shake 0.0001 5 0 m 1.0 a 232 1617 = # of size 2 clusters 3633 = # of size 3 clusters 747 = # of size 4 clusters 4233 = # of frozen angles find clusters CPU = 0.001 seconds fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.24883488 grid = 25 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.035547797 estimated relative force accuracy = 0.00010705113 using double precision KISS FFT 3d grid and FFT values/proc = 4914 1664 Generated 2278 of 2278 mixed pair_coeff terms from arithmetic mixing rule Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 10 13 13 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/charmm/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 21.49 | 21.59 | 22.08 Mbytes ------------ Step 0 ----- CPU = 0 (sec) ------------- TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397 PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301 Volume = 307995.0335 ------------ Step 50 ----- CPU = 0.7261542 (sec) ------------- TotEng = -25330.0317 KinEng = 21501.0005 Temp = 299.8229 PotEng = -46831.0321 E_bond = 2471.7035 E_angle = 10836.5102 E_dihed = 5239.6319 E_impro = 227.1218 E_vdwl = -1993.2873 E_coul = 206797.6802 E_long = -270410.3926 Press = 237.6571 Volume = 308031.6762 ------------ Step 100 ----- CPU = 1.44903 (sec) ------------- TotEng = -25290.7303 KinEng = 21591.9085 Temp = 301.0906 PotEng = -46882.6388 E_bond = 2567.9807 E_angle = 10781.9571 E_dihed = 5198.7492 E_impro = 216.7864 E_vdwl = -1902.6618 E_coul = 206659.5225 E_long = -270404.9730 Press = 6.7406 Volume = 308134.2285 Loop time of 1.44908 on 16 procs for 100 steps with 32000 atoms Performance: 11.925 ns/day, 2.013 hours/ns, 69.009 timesteps/s 98.3% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8604 | 0.91598 | 0.96576 | 2.5 | 63.21 Bond | 0.029593 | 0.033928 | 0.038589 | 1.6 | 2.34 Kspace | 0.13133 | 0.18375 | 0.23385 | 5.7 | 12.68 Neigh | 0.2034 | 0.2036 | 0.20455 | 0.1 | 14.05 Comm | 0.038302 | 0.043743 | 0.045954 | 1.0 | 3.02 Output | 9.9512e-05 | 0.00010172 | 0.00012244 | 0.0 | 0.01 Modify | 0.058698 | 0.060619 | 0.061732 | 0.3 | 4.18 Other | | 0.007364 | | | 0.51 Nlocal: 2000 ave 2075 max 1940 min Histogram: 2 1 1 2 5 2 0 2 0 1 Nghost: 11843.2 ave 11929 max 11761 min Histogram: 3 0 2 1 3 0 2 3 1 1 Neighs: 751756 ave 797548 max 712805 min Histogram: 2 0 1 4 3 2 2 1 0 1 Total # of neighbors = 12028093 Ave neighs/atom = 375.87791 Ave special neighs/atom = 7.431875 Neighbor list builds = 11 Dangerous builds = 0 Total wall time: 0:00:01