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 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 = 0.000 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) = 8.05 | 8.05 | 8.05 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 2.46574 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 -5729.17409504969 -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 | 2.1376 | 2.1376 | 2.1376 | 0.0 | 86.69 Bond | 0.068456 | 0.068456 | 0.068456 | 0.0 | 2.78 Neigh | 0.21212 | 0.21212 | 0.21212 | 0.0 | 8.60 Comm | 0.012436 | 0.012436 | 0.012436 | 0.0 | 0.50 Output | 2.9907e-05 | 2.9907e-05 | 2.9907e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03511 | | | 1.42 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) = 6.925 | 6.925 | 6.925 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 16.1773 on 1 procs for 2500 steps with 3872 atoms Performance: 13.352 ns/day, 1.797 hours/ns, 154.537 timesteps/s, 598.368 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 | 14.927 | 14.927 | 14.927 | 0.0 | 92.27 Bond | 0.52161 | 0.52161 | 0.52161 | 0.0 | 3.22 Neigh | 0.52299 | 0.52299 | 0.52299 | 0.0 | 3.23 Comm | 0.090871 | 0.090871 | 0.090871 | 0.0 | 0.56 Output | 0.00059782 | 0.00059782 | 0.00059782 | 0.0 | 0.00 Modify | 0.096104 | 0.096104 | 0.096104 | 0.0 | 0.59 Other | | 0.01791 | | | 0.11 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 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 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 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) = 6.88 | 6.88 | 6.88 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 13.2399 on 1 procs for 2000 steps with 3872 atoms Performance: 13.051 ns/day, 1.839 hours/ns, 151.058 timesteps/s, 584.898 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 | 12.13 | 12.13 | 12.13 | 0.0 | 91.61 Bond | 0.42044 | 0.42044 | 0.42044 | 0.0 | 3.18 Neigh | 0.52469 | 0.52469 | 0.52469 | 0.0 | 3.96 Comm | 0.072857 | 0.072857 | 0.072857 | 0.0 | 0.55 Output | 0.00053188 | 0.00053188 | 0.00053188 | 0.0 | 0.00 Modify | 0.076918 | 0.076918 | 0.076918 | 0.0 | 0.58 Other | | 0.0148 | | | 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 template-mix.restart Total wall time: 0:00:31