LAMMPS (22 Oct 2020) using 1 OpenMP thread(s) per MPI task # demo for atom style template simulating a cyclohexane methane mixture # part 1: creating system with create_atoms 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 template cychex pair_style lj/cut 12.0 pair_modify mix geometric tail yes bond_style harmonic angle_style harmonic dihedral_style harmonic lattice sc 6.0 Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000 variable boxlen index 4.0 region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000) 1 by 2 by 2 MPI processor grid create_atoms 0 box mol cychex 734594 Created 3072 atoms create_atoms CPU = 0.001 seconds create_atoms 2 random 800 495437 box Created 800 atoms create_atoms CPU = 0.000 seconds mass 1 14.027 mass 2 16.043 pair_coeff 1 1 0.1180 3.905 pair_coeff 2 2 0.2940 3.730 bond_coeff 1 260.00 1.5260 angle_coeff 1 63.0 112.40 dihedral_coeff 1 2.0 1 3 thermo 100 minimize 0.001 0.001 500 1000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Neighbor list info ... update every 1 steps, delay 0 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) = 5.345 | 5.441 | 5.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17 100 0 -3410.6986 572.28283 -2838.4158 14603.831 200 0 -6109.2306 483.67771 -5625.5529 5069.1821 204 0 -6137.0238 483.14639 -5653.8774 4952.4081 Loop time of 1.08919 on 4 procs for 204 steps with 3872 atoms 97.9% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 7.54300441078755e+16 -5648.75822692028 -5653.87742448419 Force two-norm initial, final = 8.7430661e+18 74.636845 Force max component initial, final = 4.1468626e+18 8.6800755 Final line search alpha, max atom move = 0.0032186736 0.02793833 Iterations, force evaluations = 204 328 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8748 | 0.88765 | 0.9004 | 1.2 | 81.50 Bond | 0.029354 | 0.029865 | 0.030434 | 0.2 | 2.74 Neigh | 0.07699 | 0.077483 | 0.077966 | 0.2 | 7.11 Comm | 0.072926 | 0.084481 | 0.097433 | 3.8 | 7.76 Output | 4.7316e-05 | 0.00010999 | 0.00029778 | 0.0 | 0.01 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009602 | | | 0.88 Nlocal: 968.000 ave 980 max 954 min Histogram: 1 0 1 0 0 0 0 0 1 1 Nghost: 6630.00 ave 6644 max 6616 min Histogram: 1 0 1 0 0 0 0 1 0 1 Neighs: 193550.0 ave 195957 max 191376 min Histogram: 2 0 0 0 0 0 0 0 1 1 Total # of neighbors = 774200 Ave neighs/atom = 199.94835 Ave special neighs/atom = 3.9669421 Neighbor list builds = 14 Dangerous builds = 0 reset_timestep 0 velocity all create 100.0 6234235 fix 1 all nvt temp 100.0 300.0 1.0 # dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu run 2500 Per MPI rank memory allocation (min/avg/max) = 4.220 | 4.507 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 100 -6137.0238 483.14639 -4500.0059 5429.3513 100 107.18608 -5623.5468 925.13786 -3461.6193 5640.5924 200 119.37927 -5671.054 1050.9079 -3242.6626 7494.8637 300 127.21276 -5646.2809 1053.2662 -3125.143 5661.4525 400 133.89893 -5674.1417 1139.7 -2989.42 7206.4877 500 138.74889 -5679.3757 1234.644 -2843.7477 6741.4965 600 150.20403 -5665.0258 1211.9245 -2719.9398 6299.2406 700 156.0507 -5681.5445 978.62091 -2902.2989 8429.7188 800 160.67293 -5579.9146 1214.6749 -2511.2805 5217.5425 900 172.06808 -5627.6903 1118.4786 -2523.767 8995.6018 1000 179.82813 -5508.1617 925.22393 -2507.9521 5760.9688 1100 190.36338 -5536.6687 1176.6794 -2163.4405 8079.5754 1200 195.57864 -5508.64 1163.8098 -2088.1038 7738.58 1300 204.05249 -5401.8527 1219.9794 -1827.3697 6562.2311 1400 211.74944 -5365.2571 1326.2667 -1595.6738 9772.2773 1500 222.08023 -5265.4213 1418.3572 -1284.5435 6395.1161 1600 225.86408 -5316.5874 1288.1407 -1422.2653 10163.26 1700 232.35057 -5192.56 1254.0031 -1257.5297 7437.3606 1800 238.16652 -5199.008 1457.8824 -992.98993 9783.4089 1900 250.86418 -5166.917 1256.4887 -1015.7777 8635.027 2000 262.41293 -5088.5573 1494.6069 -566.04218 9100.8833 2100 268.55207 -5057.9273 1459.8499 -499.33144 10002.961 2200 279.96891 -4963.9376 1526.8577 -206.59825 8943.2443 2300 286.55635 -5047.2961 1538.5334 -202.27038 10711.176 2400 292.56468 -4910.7083 1625.6283 90.740663 8482.6522 2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089 Loop time of 5.70106 on 4 procs for 2500 steps with 3872 atoms Performance: 37.888 ns/day, 0.633 hours/ns, 438.515 timesteps/s 96.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4476 | 4.5874 | 4.9593 | 10.1 | 80.47 Bond | 0.18485 | 0.19038 | 0.19543 | 0.9 | 3.34 Neigh | 0.18057 | 0.18059 | 0.18062 | 0.0 | 3.17 Comm | 0.30256 | 0.67081 | 0.81456 | 26.1 | 11.77 Output | 0.00042399 | 0.00053327 | 0.00085633 | 0.0 | 0.01 Modify | 0.035251 | 0.043755 | 0.052209 | 4.0 | 0.77 Other | | 0.02758 | | | 0.48 Nlocal: 968.000 ave 989 max 944 min Histogram: 1 0 1 0 0 0 0 0 0 2 Nghost: 6381.50 ave 6416 max 6351 min Histogram: 1 0 0 1 0 1 0 0 0 1 Neighs: 192557.0 ave 197456 max 188754 min Histogram: 2 0 0 0 0 0 0 1 0 1 Total # of neighbors = 770229 Ave neighs/atom = 198.92278 Ave special neighs/atom = 3.9669421 Neighbor list builds = 34 Dangerous builds = 0 write_data template-mix.data System init for write_data ... Total wall time: 0:00:06