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.molecular-mix # demo for atom style template simulating a cyclohexane methane mixture 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 molecular 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 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2 Created orthogonal box = (-24 -24 -24) to (24 24 24) 1 by 1 by 1 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 = 0.004 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) = 12.28 | 12.28 | 12.28 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 -6191.8196 457.61266 -5734.2069 4365.4279 Loop time of 2.5667 on 1 procs for 190 steps with 3872 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 43897850768892.8 -5729.17409504969 -5734.20694761353 Force two-norm initial, final = 1.1080994e+15 72.745546 Force max component initial, final = 4.6607099e+14 17.390179 Final line search alpha, max atom move = 0.0041638487 0.072410076 Iterations, force evaluations = 190 297 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2379 | 2.2379 | 2.2379 | 0.0 | 87.19 Bond | 0.070658 | 0.070658 | 0.070658 | 0.0 | 2.75 Neigh | 0.21093 | 0.21093 | 0.21093 | 0.0 | 8.22 Comm | 0.012111 | 0.012111 | 0.012111 | 0.0 | 0.47 Output | 3.0458e-05 | 3.0458e-05 | 3.0458e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03504 | | | 1.37 Nlocal: 3872 ave 3872 max 3872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12122 ave 12122 max 12122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 774375 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 Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes Step Temp E_pair E_mol TotEng Press 0 100 -6191.8196 457.61266 -4580.3354 4842.371 100 106.81292 -5670.2785 921.2043 -3516.5903 5959.4321 200 119.24063 -5701.0127 1040.0231 -3285.1059 6755.2619 300 127.28216 -5706.3887 1026.2838 -3211.4322 6076.6123 400 133.79038 -5734.0279 1113.6088 -3076.65 6583.9393 500 138.77685 -5756.2532 1192.1349 -2962.8117 6436.3524 600 149.39857 -5730.563 1206.6372 -2800.0582 6357.5889 700 155.5825 -5671.0161 929.50406 -2946.2899 7697.5164 800 161.24677 -5628.3833 1186.5533 -2581.2493 5840.6503 900 172.81747 -5638.6453 1148.683 -2495.8707 8169.3352 1000 182.2048 -5579.5767 909.90783 -2567.2594 6270.7354 1100 188.95766 -5548.999 1183.6644 -2185.0058 7711.9244 1200 195.22147 -5511.6798 1111.3361 -2147.7386 7656.4439 1300 205.15867 -5431.6966 1195.8143 -1868.6148 7021.8716 1400 211.44641 -5410.5687 1299.0501 -1671.6986 8903.0061 1500 223.70124 -5359.4567 1388.4189 -1389.8128 6919.2408 1600 231.75318 -5288.3343 1348.829 -1265.3712 9409.2728 1700 229.61746 -5259.4318 1194.5663 -1415.375 7387.4923 1800 245.62483 -5281.0755 1389.3362 -1057.5441 9421.7241 1900 250.69445 -5158.7006 1236.5167 -1029.4919 8649.4835 2000 259.50657 -5148.4153 1485.1392 -668.90355 9130.4701 2100 270.77108 -5092.6634 1418.7937 -549.51913 9666.5632 2200 272.30152 -5079.7585 1514.5708 -423.17779 8568.2546 2300 285.20945 -5085.6197 1492.5671 -302.10191 10281.574 2400 286.95799 -4979.8608 1544.6159 -124.11819 8797.7435 2500 296.10218 -4928.5152 1698.282 186.40572 10946.864 Loop time of 17.2353 on 1 procs for 2500 steps with 3872 atoms Performance: 12.532 ns/day, 1.915 hours/ns, 145.052 timesteps/s, 561.639 katom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.936 | 15.936 | 15.936 | 0.0 | 92.46 Bond | 0.5636 | 0.5636 | 0.5636 | 0.0 | 3.27 Neigh | 0.51213 | 0.51213 | 0.51213 | 0.0 | 2.97 Comm | 0.098127 | 0.098127 | 0.098127 | 0.0 | 0.57 Output | 0.00072478 | 0.00072478 | 0.00072478 | 0.0 | 0.00 Modify | 0.10177 | 0.10177 | 0.10177 | 0.0 | 0.59 Other | | 0.02248 | | | 0.13 Nlocal: 3872 ave 3872 max 3872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11821 ave 11821 max 11821 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 770416 ave 770416 max 770416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 770416 Ave neighs/atom = 198.97107 Ave special neighs/atom = 3.9669421 Neighbor list builds = 34 Dangerous builds = 0 #write_data molecular-mix.data #write_restart molecular-mix.restart write_restart molecular-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 molecular-mix.restart Reading restart file ... restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024 restoring atom style molecular from restart orthogonal box = (-24 -24 -24) to (24 24 24) 1 by 1 by 1 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 bonds 3072 angles 3072 dihedrals Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 7 = max # of special neighbors special bonds CPU = 0.001 seconds read_restart CPU = 0.003 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) = 11.12 | 11.12 | 11.12 Mbytes Step Temp E_pair E_mol TotEng Press 2500 296.10218 -4928.5152 1698.282 186.40572 10946.864 2600 302.98473 -4910.6997 1585.9276 171.28257 9066.357 2700 300.75989 -4935.1005 1723.6514 258.9337 10755.67 2800 294.26086 -4904.3072 1594.9394 86.02469 9420.9997 2900 296.15059 -4961.5041 1594.1004 49.793724 10129.823 3000 296.65334 -4934.6622 1596.9704 85.306731 10112.636 3100 301.62361 -4975.5261 1671.8512 176.67422 9500.7576 3200 297.34385 -5017.986 1603.4388 16.419054 10451.2 3300 297.01108 -4882.1137 1651.6426 196.65525 9124.096 3400 298.13642 -4983.4532 1742.3589 199.01715 10808.599 3500 315.91146 -4952.209 1651.2231 344.22669 8677.2632 3600 295.12433 -4950.6158 1721.3273 176.06725 10904.222 3700 300.65909 -4967.4001 1770.4243 272.244 9230.4292 3800 302.15034 -4991.9549 1644.8366 139.30847 10154.524 3900 302.16277 -5017.0117 1672.2353 141.79397 9705.6697 4000 303.1458 -4946.2517 1679.8498 231.51137 9527.8793 4100 303.54737 -5003.8276 1639.7221 138.44129 10406.442 4200 291.62491 -5009.3438 1707.6 63.233087 8645.4116 4300 306.17115 -5084.7139 1727.9528 176.0607 10563.216 4400 302.65581 -5004.4302 1747.5309 235.36003 8717.1253 4500 296.42334 -5014.9791 1723.2084 128.57389 10492.246 Loop time of 13.288 on 1 procs for 2000 steps with 3872 atoms Performance: 13.004 ns/day, 1.846 hours/ns, 150.512 timesteps/s, 582.781 katom-step/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 | 12.191 | 12.191 | 12.191 | 0.0 | 91.74 Bond | 0.4224 | 0.4224 | 0.4224 | 0.0 | 3.18 Neigh | 0.50894 | 0.50894 | 0.50894 | 0.0 | 3.83 Comm | 0.07309 | 0.07309 | 0.07309 | 0.0 | 0.55 Output | 0.00057158 | 0.00057158 | 0.00057158 | 0.0 | 0.00 Modify | 0.077778 | 0.077778 | 0.077778 | 0.0 | 0.59 Other | | 0.01451 | | | 0.11 Nlocal: 3872 ave 3872 max 3872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11685 ave 11685 max 11685 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 770346 ave 770346 max 770346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 770346 Ave neighs/atom = 198.953 Ave special neighs/atom = 3.9669421 Neighbor list builds = 34 Dangerous builds = 0 # clean up shell rm molecular-mix.restart Total wall time: 0:00:33