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 1 by 1 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) = 8.050 | 8.050 | 8.050 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14 100 0 -4351.8383 516.49891 -3835.3394 11635.037 190 0 -6191.8175 457.61209 -5734.2054 4365.373 Loop time of 3.4619 on 1 procs for 190 steps with 3872 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 43897850768892.8 -5729.17187196146 -5734.20542785978 Force two-norm initial, final = 1.1080994e+15 72.746805 Force max component initial, final = 4.6607099e+14 17.394645 Final line search alpha, max atom move = 0.0041634525 0.072421779 Iterations, force evaluations = 190 297 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0549 | 3.0549 | 3.0549 | 0.0 | 88.24 Bond | 0.10344 | 0.10344 | 0.10344 | 0.0 | 2.99 Neigh | 0.2695 | 0.2695 | 0.2695 | 0.0 | 7.78 Comm | 0.013772 | 0.013772 | 0.013772 | 0.0 | 0.40 Output | 3.3707e-05 | 3.3707e-05 | 3.3707e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02027 | | | 0.59 Nlocal: 3872.00 ave 3872 max 3872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12122.0 ave 12122 max 12122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 774375.0 ave 774375 max 774375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774375 Ave neighs/atom = 199.99354 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) = 6.925 | 6.925 | 6.925 Mbytes Step Temp E_pair E_mol TotEng Press 0 100 -6191.8175 457.61209 -4580.3339 4842.3161 100 106.81295 -5670.2783 921.20332 -3516.5907 5959.5039 200 119.22024 -5701.0103 1040.0336 -3285.3283 6755.0994 300 127.23574 -5706.7587 1023.9882 -3214.6335 6081.4162 400 133.7471 -5734.1781 1113.1696 -3077.7387 6569.8751 500 138.72092 -5756.3282 1191.5668 -2964.1003 6433.1441 600 149.02612 -5731.7291 1205.3124 -2806.8466 6366.853 700 153.5469 -5670.5879 925.61956 -2973.2344 7677.5226 800 163.38118 -5629.0757 1180.6507 -2563.216 5865.8079 900 173.27279 -5639.6903 1160.2138 -2480.131 8168.7364 1000 178.05354 -5579.0492 913.19337 -2611.3466 6220.8001 1100 188.99752 -5551.4873 1178.9541 -2191.7446 7734.6527 1200 196.9019 -5511.951 1121.4617 -2118.4942 7602.4591 1300 202.98293 -5433.6794 1194.3592 -1897.1579 7067.1876 1400 212.86876 -5411.3798 1276.3809 -1678.7668 8867.2713 1500 221.26247 -5359.7405 1390.3889 -1416.2668 6939.8559 1600 228.1783 -5288.5782 1375.3053 -1280.3883 9387.8277 1700 234.74001 -5255.1136 1192.2292 -1354.2862 7400.1124 1800 244.1285 -5282.2876 1386.5554 -1078.8029 9473.6491 1900 253.62148 -5158.5569 1242.3041 -989.78669 8596.2722 2000 260.24011 -5157.2005 1477.2039 -677.16002 9136.1769 2100 263.80129 -5096.4397 1403.9977 -648.51387 9640.0807 2200 278.10721 -5098.89 1545.7716 -344.11827 8509.7183 2300 278.05084 -5053.818 1495.944 -349.52438 10299.97 2400 287.92949 -5011.3524 1527.0261 -161.98978 8854.8877 2500 302.37248 -4957.687 1700.6563 231.95939 10617.134 Loop time of 18.7845 on 1 procs for 2500 steps with 3872 atoms Performance: 11.499 ns/day, 2.087 hours/ns, 133.089 timesteps/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.14 | 17.14 | 17.14 | 0.0 | 91.25 Bond | 0.74217 | 0.74217 | 0.74217 | 0.0 | 3.95 Neigh | 0.65005 | 0.65005 | 0.65005 | 0.0 | 3.46 Comm | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.55 Output | 0.0006739 | 0.0006739 | 0.0006739 | 0.0 | 0.00 Modify | 0.099647 | 0.099647 | 0.099647 | 0.0 | 0.53 Other | | 0.04816 | | | 0.26 Nlocal: 3872.00 ave 3872 max 3872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11793.0 ave 11793 max 11793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 770411.0 ave 770411 max 770411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 770411 Ave neighs/atom = 198.96978 Ave special neighs/atom = 3.9669421 Neighbor list builds = 33 Dangerous builds = 0 write_data template-mix.data System init for write_data ... Total wall time: 0:00:22