LAMMPS (4 Jan 2019) using 1 OpenMP thread(s) per MPI task Reading data file ... orthogonal box = (-11.9781 -12.1246 -12.5483) to (12.6781 12.6246 12.2183) 2 by 2 by 4 MPI processor grid reading atoms ... 1432 atoms reading velocities ... 1432 velocities scanning bonds ... 7 = max bonds/atom scanning angles ... 22 = max angles/atom scanning dihedrals ... 90 = max dihedrals/atom scanning impropers ... 7 = max impropers/atom reading bonds ... 1484 bonds reading angles ... 2628 angles reading dihedrals ... 5360 dihedrals reading impropers ... 264 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 7 = max # of 1-3 neighbors 15 = max # of 1-4 neighbors 21 = max # of special neighbors Read molecule mol1: 27 atoms with max type 7 26 bonds with max type 13 47 angles with max type 23 112 dihedrals with max type 28 0 impropers with max type 0 Read molecule mol2: 27 atoms with max type 8 26 bonds with max type 14 47 angles with max type 28 168 dihedrals with max type 47 0 impropers with max type 0 Read molecule mol3: 21 atoms with max type 7 20 bonds with max type 13 35 angles with max type 23 68 dihedrals with max type 28 0 impropers with max type 0 Read molecule mol4: 21 atoms with max type 8 20 bonds with max type 14 35 angles with max type 28 124 dihedrals with max type 47 0 impropers with max type 0 Read molecule mol5: 28 atoms with max type 8 27 bonds with max type 14 48 angles with max type 28 118 dihedrals with max type 47 0 impropers with max type 0 Read molecule mol6: 28 atoms with max type 8 27 bonds with max type 14 48 angles with max type 28 174 dihedrals with max type 47 0 impropers with max type 0 dynamic group bond_react_MASTER_group defined dynamic group nonreactgroup_REACT defined PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.298204 grid = 12 12 12 stencil order = 5 estimated absolute RMS force accuracy = 0.0253142 estimated relative force accuracy = 7.62329e-05 using single precision FFTs 3d grid and FFT values/proc = 968 108 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 10000, page size: 100000 master list distance cutoff = 9.4 ghost atom cutoff = 9.4 binsize = 4.7, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/charmm/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) fix bond/react, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 45.94 | 45.97 | 46.14 Mbytes Step Temp TotEng Density f_rxns[1] f_rxns[2] f_rxns[3] 0 302.31754 21782.385 1.0504016 0 0 0 10 370.23233 41438.512 1.0534582 2 4 0 20 407.19516 32075.867 1.0626232 2 4 0 30 433.95436 34221.573 1.0750613 2 5 0 40 442.15381 28905.652 1.0888843 2 5 0 50 438.47749 25582.683 1.1020805 2 5 0 60 446.87791 23863.61 1.1131515 2 5 0 70 484.6618 23251.176 1.1214249 2 5 0 80 518.70862 27595.905 1.127912 2 6 0 90 525.64164 25347.866 1.1340633 2 6 0 100 531.85932 30722.152 1.1399257 2 7 0 110 540.86769 27425.008 1.1465723 2 7 0 120 566.43798 26950.132 1.1535094 3 7 0 130 594.01996 27192.728 1.160211 3 8 0 140 628.25657 24724.781 1.1662404 3 8 0 150 651.53993 23633.862 1.1710456 3 8 0 160 652.7888 23291.304 1.174019 3 8 0 170 663.74718 30888.479 1.1753109 4 9 0 180 678.9227 32711.833 1.1776511 4 10 0 190 672.99558 28034.254 1.181777 4 10 0 200 692.60872 25399.957 1.1858069 4 10 0 210 679.82851 24213.658 1.188612 4 10 0 220 668.68035 23685.544 1.1897915 4 10 0 230 689.42484 30979.338 1.1892149 4 11 0 240 696.58317 28262.767 1.1887802 4 11 0 250 723.59428 28376.118 1.1881823 5 11 0 260 728.41353 25819.108 1.187287 5 11 0 270 743.96236 24397.572 1.1850406 5 11 0 280 716.12023 23720.309 1.1809629 5 11 0 290 727.93166 26575.286 1.1751965 5 12 0 300 756.88393 24774.094 1.1685749 5 12 0 310 762.1068 23881.875 1.1614975 5 12 0 320 766.20285 23515.292 1.1539283 5 12 0 330 750.74524 23375.436 1.1461722 5 12 0 340 750.38601 26187.881 1.1383343 5 13 0 350 738.74424 24524.117 1.1306068 5 13 0 360 716.85606 23741.448 1.1233544 5 13 0 370 739.55441 34886.951 1.1171549 5 14 0 380 731.23841 31457.924 1.1136983 5 14 0 390 727.33183 28787.421 1.1115694 5 14 0 400 751.38555 26820.597 1.1098243 5 14 0 410 729.12453 25377.017 1.1077345 5 14 0 420 751.31962 33851.535 1.1050782 5 15 1 430 855.74538 29940.731 1.1036021 5 15 1 440 767.32426 27469.106 1.1028685 5 15 1 450 896.67046 33875.121 1.1020514 5 16 1 460 905.94724 29786.309 1.101565 5 16 1 470 865.22586 27066.428 1.1016191 5 16 1 480 884.04356 36318.333 1.1016214 5 16 2 490 953.09863 32233.727 1.1032226 5 16 2 500 928.20814 29338.914 1.1055637 5 16 2 WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:903) Loop time of 1.67638 on 16 procs for 500 steps with 1432 atoms Performance: 25.770 ns/day, 0.931 hours/ns, 298.261 timesteps/s 97.4% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29349 | 0.33051 | 0.37179 | 4.3 | 19.72 Bond | 0.035872 | 0.048629 | 0.067894 | 3.9 | 2.90 Kspace | 0.10994 | 0.15489 | 0.20429 | 7.8 | 9.24 Neigh | 0.51435 | 0.51525 | 0.51703 | 0.1 | 30.74 Comm | 0.12946 | 0.13102 | 0.13208 | 0.2 | 7.82 Output | 0.033123 | 0.033421 | 0.034112 | 0.1 | 1.99 Modify | 0.45469 | 0.45721 | 0.4592 | 0.2 | 27.27 Other | | 0.00546 | | | 0.33 Nlocal: 89.5 ave 108 max 79 min Histogram: 2 3 2 3 2 1 2 0 0 1 Nghost: 2287.19 ave 2322 max 2253 min Histogram: 2 0 2 1 3 3 2 0 2 1 Neighs: 15470.8 ave 19104 max 13012 min Histogram: 2 3 1 3 2 1 1 2 0 1 Total # of neighbors = 247533 Ave neighs/atom = 172.858 Ave special neighs/atom = 10.2779 Neighbor list builds = 500 Dangerous builds = 0 System init for write_data ... PPPM initialization ... WARNING: System is not charge neutral, net charge = 2.185 (../kspace.cpp:302) using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.300143 grid = 12 12 12 stencil order = 5 estimated absolute RMS force accuracy = 0.0259935 estimated relative force accuracy = 7.82786e-05 using single precision FFTs 3d grid and FFT values/proc = 968 108 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:02