LAMMPS (22 Oct 2020) using 1 OpenMP thread(s) per MPI task # demo for atom style template simulating a cyclohexane methane mixture # part 2: continuing from data file units real boundary p p p molecule cychex cyclohexane.mol Read molecule template cychex: 1 molecules 6 atoms with max type 1 6 bonds with max type 1 6 angles with max type 1 6 dihedrals with max type 1 0 impropers with max type 0 atom_style molecular pair_style lj/cut 12.0 pair_modify mix geometric tail yes bond_style harmonic angle_style harmonic dihedral_style harmonic read_data molecular-mix.data Reading data file ... orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000) 1 by 1 by 1 MPI processor grid reading atoms ... 3872 atoms reading velocities ... 3872 velocities scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom scanning dihedrals ... 2 = max dihedrals/atom reading bonds ... 3072 bonds reading angles ... 3072 angles reading dihedrals ... 3072 dihedrals Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0.0 0.0 0.0 special bond factors coul: 0.0 0.0 0.0 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 5 = max # of special neighbors special bonds CPU = 0.001 seconds read_data CPU = 0.014 seconds thermo 100 fix 1 all nvt temp 300.0 300.0 1.0 # dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu run 2000 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 = 7 7 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, 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) = 10.74 | 10.74 | 10.74 Mbytes Step Temp E_pair E_mol TotEng Press 0 297.79426 -4928.7403 1686.5107 193.93377 11481.089 100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304 200 296.49886 -4884.3039 1747.4798 284.39198 11537.322 300 295.24937 -4850.2788 1642.4584 198.97822 9160.666 400 297.73321 -4952.9967 1660.6439 143.10604 10751.859 500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826 600 299.50756 -4999.965 1588.0327 44.000269 9233.8621 700 295.64728 -4958.2253 1646.2011 99.365838 11089.418 800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685 900 300.80754 -5033.4853 1727.4591 164.90648 11497.526 1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551 1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28 1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201 1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762 1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178 1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337 1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415 1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882 1800 301.9386 -5068.1221 1755.577 171.43863 11229.315 1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348 2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209 Loop time of 15.6807 on 1 procs for 2000 steps with 3872 atoms Performance: 11.020 ns/day, 2.178 hours/ns, 127.545 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.196 | 14.196 | 14.196 | 0.0 | 90.53 Bond | 0.58712 | 0.58712 | 0.58712 | 0.0 | 3.74 Neigh | 0.6978 | 0.6978 | 0.6978 | 0.0 | 4.45 Comm | 0.082724 | 0.082724 | 0.082724 | 0.0 | 0.53 Output | 0.00052338 | 0.00052338 | 0.00052338 | 0.0 | 0.00 Modify | 0.078892 | 0.078892 | 0.078892 | 0.0 | 0.50 Other | | 0.0374 | | | 0.24 Nlocal: 3872.00 ave 3872 max 3872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11633.0 ave 11633 max 11633 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 770365.0 ave 770365 max 770365 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 770365 Ave neighs/atom = 198.95790 Ave special neighs/atom = 3.9669421 Neighbor list builds = 35 Dangerous builds = 0 Total wall time: 0:00:15