303 lines
14 KiB
Groff
303 lines
14 KiB
Groff
LAMMPS (27 Jun 2024)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# demo for atom style template simulating a cyclohexane methane mixture
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# part 3: continuing from restart file
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# run the first part and write out restart
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include in.molecular-mix
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# demo for atom style template simulating a cyclohexane methane mixture
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units real
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boundary p p p
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molecule cychex cyclohexane.mol
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Read molecule template cychex:
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LAMMPS molecule file. Cyclohexane(UA)
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1 molecules
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0 fragments
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6 atoms with max type 1
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6 bonds with max type 1
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6 angles with max type 1
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6 dihedrals with max type 1
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0 impropers with max type 0
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atom_style molecular
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pair_style lj/cut 12.0
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pair_modify mix geometric tail yes
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bond_style harmonic
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angle_style harmonic
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dihedral_style harmonic
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lattice sc 6.0
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Lattice spacing in x,y,z = 6 6 6
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variable boxlen index 4.0
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region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
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region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
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region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
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region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
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region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
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region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
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region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
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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
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Created orthogonal box = (-24 -24 -24) to (24 24 24)
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1 by 1 by 1 MPI processor grid
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create_atoms 0 box mol cychex 734594
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Created 3072 atoms
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using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
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create_atoms CPU = 0.004 seconds
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create_atoms 2 random 800 495437 box
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Created 800 atoms
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using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
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create_atoms CPU = 0.000 seconds
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mass 1 14.027
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mass 2 16.043
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pair_coeff 1 1 0.1180 3.905
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pair_coeff 2 2 0.2940 3.730
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bond_coeff 1 260.00 1.5260
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angle_coeff 1 63.0 112.40
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dihedral_coeff 1 2.0 1 3
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thermo 100
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minimize 0.001 0.001 500 1000
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Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 12.28 | 12.28 | 12.28 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
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100 0 -4351.8383 516.49891 -3835.3394 11635.037
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190 0 -6191.8196 457.61266 -5734.2069 4365.4279
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Loop time of 2.5667 on 1 procs for 190 steps with 3872 atoms
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99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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43897850768892.8 -5729.17409504969 -5734.20694761353
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Force two-norm initial, final = 1.1080994e+15 72.745546
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Force max component initial, final = 4.6607099e+14 17.390179
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Final line search alpha, max atom move = 0.0041638487 0.072410076
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Iterations, force evaluations = 190 297
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.2379 | 2.2379 | 2.2379 | 0.0 | 87.19
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Bond | 0.070658 | 0.070658 | 0.070658 | 0.0 | 2.75
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Neigh | 0.21093 | 0.21093 | 0.21093 | 0.0 | 8.22
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Comm | 0.012111 | 0.012111 | 0.012111 | 0.0 | 0.47
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Output | 3.0458e-05 | 3.0458e-05 | 3.0458e-05 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.03504 | | | 1.37
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Nlocal: 3872 ave 3872 max 3872 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 12122 ave 12122 max 12122 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 774375 ave 774375 max 774375 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 774375
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Ave neighs/atom = 199.99354
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Ave special neighs/atom = 3.9669421
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Neighbor list builds = 14
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Dangerous builds = 0
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reset_timestep 0
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velocity all create 100.0 6234235
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fix 1 all nvt temp 100.0 300.0 1.0
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# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
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run 2500
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Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 100 -6191.8196 457.61266 -4580.3354 4842.371
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100 106.81292 -5670.2785 921.2043 -3516.5903 5959.4321
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200 119.24063 -5701.0127 1040.0231 -3285.1059 6755.2619
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300 127.28216 -5706.3887 1026.2838 -3211.4322 6076.6123
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400 133.79038 -5734.0279 1113.6088 -3076.65 6583.9393
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500 138.77685 -5756.2532 1192.1349 -2962.8117 6436.3524
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600 149.39857 -5730.563 1206.6372 -2800.0582 6357.5889
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700 155.5825 -5671.0161 929.50406 -2946.2899 7697.5164
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800 161.24677 -5628.3833 1186.5533 -2581.2493 5840.6503
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900 172.81747 -5638.6453 1148.683 -2495.8707 8169.3352
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1000 182.2048 -5579.5767 909.90783 -2567.2594 6270.7354
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1100 188.95766 -5548.999 1183.6644 -2185.0058 7711.9244
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1200 195.22147 -5511.6798 1111.3361 -2147.7386 7656.4439
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1300 205.15867 -5431.6966 1195.8143 -1868.6148 7021.8716
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1400 211.44641 -5410.5687 1299.0501 -1671.6986 8903.0061
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1500 223.70124 -5359.4567 1388.4189 -1389.8128 6919.2408
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1600 231.75318 -5288.3343 1348.829 -1265.3712 9409.2728
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1700 229.61746 -5259.4318 1194.5663 -1415.375 7387.4923
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1800 245.62483 -5281.0755 1389.3362 -1057.5441 9421.7241
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1900 250.69445 -5158.7006 1236.5167 -1029.4919 8649.4835
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2000 259.50657 -5148.4153 1485.1392 -668.90355 9130.4701
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2100 270.77108 -5092.6634 1418.7937 -549.51913 9666.5632
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2200 272.30152 -5079.7585 1514.5708 -423.17779 8568.2546
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2300 285.20945 -5085.6197 1492.5671 -302.10191 10281.574
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2400 286.95799 -4979.8608 1544.6159 -124.11819 8797.7435
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2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
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Loop time of 17.2353 on 1 procs for 2500 steps with 3872 atoms
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Performance: 12.532 ns/day, 1.915 hours/ns, 145.052 timesteps/s, 561.639 katom-step/s
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99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 15.936 | 15.936 | 15.936 | 0.0 | 92.46
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Bond | 0.5636 | 0.5636 | 0.5636 | 0.0 | 3.27
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Neigh | 0.51213 | 0.51213 | 0.51213 | 0.0 | 2.97
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Comm | 0.098127 | 0.098127 | 0.098127 | 0.0 | 0.57
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Output | 0.00072478 | 0.00072478 | 0.00072478 | 0.0 | 0.00
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Modify | 0.10177 | 0.10177 | 0.10177 | 0.0 | 0.59
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Other | | 0.02248 | | | 0.13
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Nlocal: 3872 ave 3872 max 3872 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11821 ave 11821 max 11821 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 770416 ave 770416 max 770416 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 770416
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Ave neighs/atom = 198.97107
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Ave special neighs/atom = 3.9669421
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Neighbor list builds = 34
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Dangerous builds = 0
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#write_data molecular-mix.data
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#write_restart molecular-mix.restart
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write_restart molecular-mix.restart
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System init for write_restart ...
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Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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# now restart
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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molecule cychex cyclohexane.mol
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Read molecule template cychex:
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LAMMPS molecule file. Cyclohexane(UA)
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1 molecules
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0 fragments
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6 atoms with max type 1
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6 bonds with max type 1
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6 angles with max type 1
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6 dihedrals with max type 1
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0 impropers with max type 0
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read_restart molecular-mix.restart
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Reading restart file ...
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restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
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restoring atom style molecular from restart
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orthogonal box = (-24 -24 -24) to (24 24 24)
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1 by 1 by 1 MPI processor grid
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restoring pair style lj/cut from restart
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restoring bond style harmonic from restart
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restoring angle style harmonic from restart
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restoring dihedral style harmonic from restart
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3872 atoms
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3072 bonds
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3072 angles
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3072 dihedrals
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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7 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_restart CPU = 0.003 seconds
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thermo 100
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fix 1 all nvt temp 300.0 300.0 1.0
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Resetting global fix info from restart file:
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fix style: nvt, fix ID: 1
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# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
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run 2000
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Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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All restart file global fix info was re-assigned
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 11.12 | 11.12 | 11.12 Mbytes
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Step Temp E_pair E_mol TotEng Press
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2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
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2600 302.98473 -4910.6997 1585.9276 171.28257 9066.357
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2700 300.75989 -4935.1005 1723.6514 258.9337 10755.67
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2800 294.26086 -4904.3072 1594.9394 86.02469 9420.9997
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2900 296.15059 -4961.5041 1594.1004 49.793724 10129.823
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3000 296.65334 -4934.6622 1596.9704 85.306731 10112.636
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3100 301.62361 -4975.5261 1671.8512 176.67422 9500.7576
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3200 297.34385 -5017.986 1603.4388 16.419054 10451.2
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3300 297.01108 -4882.1137 1651.6426 196.65525 9124.096
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3400 298.13642 -4983.4532 1742.3589 199.01715 10808.599
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3500 315.91146 -4952.209 1651.2231 344.22669 8677.2632
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3600 295.12433 -4950.6158 1721.3273 176.06725 10904.222
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3700 300.65909 -4967.4001 1770.4243 272.244 9230.4292
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3800 302.15034 -4991.9549 1644.8366 139.30847 10154.524
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3900 302.16277 -5017.0117 1672.2353 141.79397 9705.6697
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4000 303.1458 -4946.2517 1679.8498 231.51137 9527.8793
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4100 303.54737 -5003.8276 1639.7221 138.44129 10406.442
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4200 291.62491 -5009.3438 1707.6 63.233087 8645.4116
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4300 306.17115 -5084.7139 1727.9528 176.0607 10563.216
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4400 302.65581 -5004.4302 1747.5309 235.36003 8717.1253
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4500 296.42334 -5014.9791 1723.2084 128.57389 10492.246
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Loop time of 13.288 on 1 procs for 2000 steps with 3872 atoms
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Performance: 13.004 ns/day, 1.846 hours/ns, 150.512 timesteps/s, 582.781 katom-step/s
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99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 12.191 | 12.191 | 12.191 | 0.0 | 91.74
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Bond | 0.4224 | 0.4224 | 0.4224 | 0.0 | 3.18
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Neigh | 0.50894 | 0.50894 | 0.50894 | 0.0 | 3.83
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Comm | 0.07309 | 0.07309 | 0.07309 | 0.0 | 0.55
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Output | 0.00057158 | 0.00057158 | 0.00057158 | 0.0 | 0.00
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Modify | 0.077778 | 0.077778 | 0.077778 | 0.0 | 0.59
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Other | | 0.01451 | | | 0.11
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Nlocal: 3872 ave 3872 max 3872 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11685 ave 11685 max 11685 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 770346 ave 770346 max 770346 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 770346
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Ave neighs/atom = 198.953
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Ave special neighs/atom = 3.9669421
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Neighbor list builds = 34
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Dangerous builds = 0
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# clean up
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shell rm molecular-mix.restart
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Total wall time: 0:00:33
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