forked from lijiext/lammps
175 lines
7.5 KiB
Groff
175 lines
7.5 KiB
Groff
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LAMMPS (22 Oct 2020)
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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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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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1 molecules
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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 = 6.0000000 6.0000000 6.0000000
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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 = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
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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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create_atoms CPU = 0.003 seconds
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create_atoms 2 random 800 495437 box
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Created 800 atoms
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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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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
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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/newton
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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 -6191.8175 457.61209 -5734.2054 4365.373
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Loop time of 3.46057 on 1 procs for 190 steps with 3872 atoms
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99.7% 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 -5729.17187196146 -5734.20542785978
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Force two-norm initial, final = 1.1080994e+15 72.746805
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Force max component initial, final = 4.6607099e+14 17.394645
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Final line search alpha, max atom move = 0.0041634525 0.072421779
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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 | 3.0573 | 3.0573 | 3.0573 | 0.0 | 88.35
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Bond | 0.10271 | 0.10271 | 0.10271 | 0.0 | 2.97
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Neigh | 0.26654 | 0.26654 | 0.26654 | 0.0 | 7.70
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Comm | 0.013532 | 0.013532 | 0.013532 | 0.0 | 0.39
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Output | 3.3796e-05 | 3.3796e-05 | 3.3796e-05 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.02041 | | | 0.59
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Nlocal: 3872.00 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: 12122.0 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: 774375.0 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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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 -6191.8175 457.61209 -4580.3339 4842.3161
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100 106.81295 -5670.2783 921.20332 -3516.5907 5959.5039
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200 119.22024 -5701.0103 1040.0336 -3285.3283 6755.0994
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300 127.23574 -5706.7587 1023.9882 -3214.6335 6081.4162
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400 133.7471 -5734.1781 1113.1696 -3077.7387 6569.8751
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500 138.72092 -5756.3282 1191.5668 -2964.1003 6433.1441
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600 149.02612 -5731.7291 1205.3124 -2806.8466 6366.853
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700 153.5469 -5670.5879 925.61956 -2973.2344 7677.5226
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800 163.38118 -5629.0757 1180.6507 -2563.216 5865.8079
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900 173.27279 -5639.6903 1160.2138 -2480.131 8168.7364
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1000 178.05354 -5579.0492 913.19337 -2611.3466 6220.8001
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1100 188.99752 -5551.4873 1178.9541 -2191.7446 7734.6527
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1200 196.9019 -5511.951 1121.4617 -2118.4942 7602.4591
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1300 202.98293 -5433.6794 1194.3592 -1897.1579 7067.1876
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1400 212.86876 -5411.3798 1276.3809 -1678.7668 8867.2713
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1500 221.26247 -5359.7405 1390.3889 -1416.2668 6939.8559
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1600 228.1783 -5288.5782 1375.3053 -1280.3883 9387.8277
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1700 234.74001 -5255.1136 1192.2292 -1354.2862 7400.1124
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1800 244.1285 -5282.2876 1386.5554 -1078.8029 9473.6491
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1900 253.62148 -5158.5569 1242.3041 -989.78669 8596.2722
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2000 260.24011 -5157.2005 1477.2039 -677.16002 9136.1769
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2100 263.80129 -5096.4397 1403.9977 -648.51387 9640.0807
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2200 278.10721 -5098.89 1545.7716 -344.11827 8509.7183
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2300 278.05084 -5053.818 1495.944 -349.52438 10299.97
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2400 287.92949 -5011.3524 1527.0261 -161.98978 8854.8877
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2500 302.37248 -4957.687 1700.6563 231.95939 10617.134
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Loop time of 18.6761 on 1 procs for 2500 steps with 3872 atoms
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Performance: 11.566 ns/day, 2.075 hours/ns, 133.861 timesteps/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 | 17.06 | 17.06 | 17.06 | 0.0 | 91.35
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Bond | 0.73068 | 0.73068 | 0.73068 | 0.0 | 3.91
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Neigh | 0.63671 | 0.63671 | 0.63671 | 0.0 | 3.41
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Comm | 0.10272 | 0.10272 | 0.10272 | 0.0 | 0.55
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Output | 0.00064976 | 0.00064976 | 0.00064976 | 0.0 | 0.00
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Modify | 0.098028 | 0.098028 | 0.098028 | 0.0 | 0.52
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Other | | 0.04742 | | | 0.25
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Nlocal: 3872.00 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: 11793.0 ave 11793 max 11793 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 770411.0 ave 770411 max 770411 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 770411
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Ave neighs/atom = 198.96978
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Ave special neighs/atom = 3.9669421
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Neighbor list builds = 33
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Dangerous builds = 0
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write_data molecular-mix.data
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System init for write_data ...
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Total wall time: 0:00:22
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