LAMMPS (27 Jun 2024) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # demo for atom style template simulating a cyclohexane methane mixture # part 3: continuing from restart file # run the first part and write out restart include in.template-mix # 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: LAMMPS molecule file. Cyclohexane(UA) 1 molecules 0 fragments 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 6 6 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 -24 -24) to (24 24 24) 1 by 2 by 2 MPI processor grid create_atoms 0 box mol cychex 734594 Created 3072 atoms using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) create_atoms CPU = 0.001 seconds create_atoms 2 random 800 495437 box Created 800 atoms using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) 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 Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule 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 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 483.1464 -5653.8774 4952.4083 Loop time of 0.719475 on 4 procs for 204 steps with 3872 atoms 99.6% 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 -5648.75822666276 -5653.87742467986 Force two-norm initial, final = 8.7430661e+18 74.636836 Force max component initial, final = 4.1468626e+18 8.680078 Final line search alpha, max atom move = 0.0032186724 0.027938327 Iterations, force evaluations = 204 328 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59281 | 0.6027 | 0.60956 | 0.8 | 83.77 Bond | 0.018776 | 0.020785 | 0.026388 | 2.2 | 2.89 Neigh | 0.054209 | 0.054242 | 0.054273 | 0.0 | 7.54 Comm | 0.018189 | 0.03064 | 0.042206 | 4.9 | 4.26 Output | 3.3034e-05 | 3.5624e-05 | 4.3263e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01107 | | | 1.54 Nlocal: 968 ave 980 max 954 min Histogram: 1 0 1 0 0 0 0 0 1 1 Nghost: 6630 ave 6644 max 6616 min Histogram: 1 0 1 0 0 0 0 1 0 1 Neighs: 193550 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 Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 4.22 | 4.507 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 100 -6137.0238 483.1464 -4500.0059 5429.3515 100 107.18608 -5623.5468 925.13787 -3461.6193 5640.5922 200 119.37771 -5671.054 1050.9081 -3242.6804 7494.8576 300 127.21216 -5646.3171 1053.2825 -3125.1696 5661.5841 400 133.87894 -5674.4359 1139.3079 -2990.337 7202.7 500 138.76354 -5679.3297 1234.4508 -2843.7258 6745.1519 600 150.51628 -5665.2143 1210.3078 -2718.142 6301.1312 700 152.13291 -5680.6166 979.71444 -2945.4837 8424.0062 800 161.60449 -5579.521 1209.1388 -2505.674 5226.3319 900 177.80597 -5626.7406 1125.8767 -2449.2113 9035.9218 1000 181.98782 -5509.1736 924.24027 -2485.0276 5775.8317 1100 189.93412 -5534.8176 1169.5911 -2173.6307 8072.3434 1200 194.04459 -5508.0919 1169.0571 -2100.0095 7766.2625 1300 203.40621 -5400.0439 1229.5897 -1823.4077 6533.8169 1400 211.36099 -5362.2808 1318.5794 -1604.867 9789.8496 1500 221.24251 -5263.1861 1410.6972 -1299.6344 6407.5052 1600 234.83277 -5316.3854 1299.4287 -1307.2882 10199.28 1700 233.61193 -5187.0022 1246.0158 -1245.4048 7482.5096 1800 247.00713 -5193.2051 1451.1363 -891.92372 9836.6864 1900 250.10386 -5165.7314 1259.876 -1019.978 8648.7513 2000 257.7022 -5083.7142 1486.9813 -623.18058 9076.3674 2100 273.9293 -5061.7945 1463.3978 -437.60445 10039.49 2200 276.40166 -4948.9281 1538.5962 -221.01165 9013.3961 2300 287.28669 -5039.6841 1535.7768 -188.98782 10739.853 2400 290.35344 -4947.2095 1615.8983 18.994602 8326.4501 2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135 Loop time of 4.32742 on 4 procs for 2500 steps with 3872 atoms Performance: 49.914 ns/day, 0.481 hours/ns, 577.711 timesteps/s, 2.237 Matom-step/s 99.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7864 | 3.836 | 3.8948 | 2.2 | 88.64 Bond | 0.13058 | 0.13362 | 0.13735 | 0.8 | 3.09 Neigh | 0.13597 | 0.13601 | 0.13605 | 0.0 | 3.14 Comm | 0.12304 | 0.18542 | 0.23763 | 10.5 | 4.28 Output | 0.00033524 | 0.00036705 | 0.00045513 | 0.0 | 0.01 Modify | 0.027504 | 0.027917 | 0.028571 | 0.3 | 0.65 Other | | 0.008118 | | | 0.19 Nlocal: 968 ave 986 max 944 min Histogram: 1 0 0 1 0 0 0 0 0 2 Nghost: 6379.75 ave 6407 max 6352 min Histogram: 1 0 1 0 0 0 0 1 0 1 Neighs: 192584 ave 196718 max 188693 min Histogram: 1 1 0 0 0 0 0 1 0 1 Total # of neighbors = 770338 Ave neighs/atom = 198.95093 Ave special neighs/atom = 3.9669421 Neighbor list builds = 34 Dangerous builds = 0 #write_data template-mix.data #write_restart template-mix.restart write_restart template-mix.restart System init for write_restart ... Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule # now restart clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task molecule cychex cyclohexane.mol Read molecule template cychex: LAMMPS molecule file. Cyclohexane(UA) 1 molecules 0 fragments 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 read_restart template-mix.restart Reading restart file ... restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024 restoring atom style template from restart orthogonal box = (-24 -24 -24) to (24 24 24) 1 by 2 by 2 MPI processor grid restoring pair style lj/cut from restart restoring bond style harmonic from restart restoring angle style harmonic from restart restoring dihedral style harmonic from restart 3872 atoms 3072 template bonds 3072 template angles 3072 template dihedrals read_restart CPU = 0.001 seconds thermo 100 fix 1 all nvt temp 300.0 300.0 1.0 Resetting global fix info from restart file: fix style: nvt, fix ID: 1 # dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu run 2000 Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule All restart file global fix info was re-assigned 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 bin: standard Per MPI rank memory allocation (min/avg/max) = 4.192 | 4.288 | 4.574 Mbytes Step Temp E_pair E_mol TotEng Press 2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135 2600 296.63161 -4937.8377 1616.2295 101.13964 8654.8533 2700 303.79396 -4951.8442 1732.7298 286.27771 11140.127 2800 297.39677 -4879.1242 1642.1355 194.58806 8993.2494 2900 299.13542 -4888.1435 1660.1105 223.60558 10716.3 3000 298.07888 -4928.2353 1650.6616 161.87369 10088.459 3100 304.09536 -4901.4853 1614.3116 221.69625 9505.2057 3200 301.51357 -4930.5129 1628.4386 177.00496 11411.933 3300 297.45744 -4923.6217 1700.537 209.19205 8189.571 3400 298.52831 -5012.7313 1736.6929 168.59495 11673.119 3500 295.66767 -4947.4296 1700.0072 164.20283 8222.3067 3600 296.7267 -5112.3707 1727.4319 38.906285 10608.481 3700 302.92855 -4994.4012 1789.7274 290.73255 8829.4479 3800 296.77191 -5034.2589 1657.2635 47.371248 9968.3521 3900 299.86962 -4972.7385 1744.2808 231.65266 10076.37 4000 304.89527 -5011.2464 1664.6779 171.53137 8926.0386 4100 296.81738 -5013.2169 1727.5801 139.25455 10898.733 4200 300.67532 -4988.3547 1782.1574 263.20975 8164.1158 4300 297.74901 -5023.3433 1784.7361 197.03396 11344.862 4400 302.0571 -5033.3547 1723.2662 175.26243 8016.975 4500 305.31958 -5062.5597 1767.0048 227.44095 10827.294 Loop time of 3.5798 on 4 procs for 2000 steps with 3872 atoms Performance: 48.271 ns/day, 0.497 hours/ns, 558.691 timesteps/s, 2.163 Matom-step/s 99.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0514 | 3.1162 | 3.2058 | 3.3 | 87.05 Bond | 0.10377 | 0.10776 | 0.11194 | 1.0 | 3.01 Neigh | 0.14121 | 0.14125 | 0.1413 | 0.0 | 3.95 Comm | 0.092144 | 0.18542 | 0.25437 | 14.1 | 5.18 Output | 0.00025632 | 0.00028151 | 0.00035298 | 0.0 | 0.01 Modify | 0.02193 | 0.022227 | 0.022584 | 0.2 | 0.62 Other | | 0.006618 | | | 0.18 Nlocal: 968 ave 984 max 948 min Histogram: 1 0 0 1 0 0 0 0 1 1 Nghost: 6349.5 ave 6370 max 6330 min Histogram: 1 0 1 0 0 0 0 1 0 1 Neighs: 192457 ave 196654 max 187154 min Histogram: 1 0 0 0 1 0 0 0 1 1 Total # of neighbors = 769828 Ave neighs/atom = 198.81921 Ave special neighs/atom = 3.9669421 Neighbor list builds = 35 Dangerous builds = 0 # clean up shell rm template-mix.restart Total wall time: 0:00:08