176 lines
7.6 KiB
Groff
176 lines
7.6 KiB
Groff
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 2 by 2 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 = 0.011 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) = 9.623 | 9.719 | 10.01 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
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100 0 -3410.6986 572.28283 -2838.4158 14603.831
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200 0 -6109.2306 483.67771 -5625.5529 5069.1821
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204 0 -6137.0238 483.14639 -5653.8774 4952.4081
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Loop time of 1.10481 on 4 procs for 204 steps with 3872 atoms
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98.2% CPU use with 4 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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7.54300441078755e+16 -5648.75822692028 -5653.87742448419
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Force two-norm initial, final = 8.7430661e+18 74.636845
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Force max component initial, final = 4.1468626e+18 8.6800755
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Final line search alpha, max atom move = 0.0032186736 0.02793833
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Iterations, force evaluations = 204 328
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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 | 0.89902 | 0.90561 | 0.90821 | 0.4 | 81.97
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Bond | 0.029749 | 0.030411 | 0.031345 | 0.4 | 2.75
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Neigh | 0.088655 | 0.088662 | 0.088666 | 0.0 | 8.03
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Comm | 0.063187 | 0.068096 | 0.070678 | 1.1 | 6.16
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Output | 4.8304e-05 | 0.00011426 | 0.00031124 | 0.0 | 0.01
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.01191 | | | 1.08
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Nlocal: 968.000 ave 980 max 954 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Nghost: 6630.00 ave 6644 max 6616 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 193550.0 ave 195957 max 191376 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Total # of neighbors = 774200
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Ave neighs/atom = 199.94835
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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) = 8.498 | 8.785 | 8.881 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 100 -6137.0238 483.14639 -4500.0059 5429.3513
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100 107.18608 -5623.5468 925.13786 -3461.6193 5640.5924
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200 119.37927 -5671.054 1050.9079 -3242.6626 7494.8637
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300 127.21276 -5646.2809 1053.2662 -3125.143 5661.4525
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400 133.89893 -5674.1417 1139.7 -2989.42 7206.4877
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500 138.74889 -5679.3757 1234.644 -2843.7477 6741.4965
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600 150.20403 -5665.0258 1211.9245 -2719.9398 6299.2406
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700 156.0507 -5681.5445 978.62091 -2902.2989 8429.7188
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800 160.67293 -5579.9146 1214.6749 -2511.2805 5217.5425
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900 172.06808 -5627.6903 1118.4786 -2523.767 8995.6018
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1000 179.82813 -5508.1617 925.22393 -2507.9521 5760.9688
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1100 190.36338 -5536.6687 1176.6794 -2163.4405 8079.5754
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1200 195.57864 -5508.64 1163.8098 -2088.1038 7738.58
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1300 204.05249 -5401.8527 1219.9794 -1827.3697 6562.2311
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1400 211.74944 -5365.2571 1326.2667 -1595.6738 9772.2773
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1500 222.08023 -5265.4213 1418.3572 -1284.5435 6395.1161
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1600 225.86408 -5316.5874 1288.1407 -1422.2653 10163.26
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1700 232.35057 -5192.56 1254.0031 -1257.5297 7437.3606
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1800 238.16652 -5199.008 1457.8824 -992.98993 9783.4089
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1900 250.86418 -5166.917 1256.4887 -1015.7777 8635.027
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2000 262.41293 -5088.5573 1494.6069 -566.04218 9100.8833
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2100 268.55207 -5057.9273 1459.8499 -499.33144 10002.961
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2200 279.96891 -4963.9376 1526.8577 -206.59825 8943.2443
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2300 286.55635 -5047.2961 1538.5334 -202.27038 10711.176
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2400 292.56468 -4910.7083 1625.6283 90.740663 8482.6522
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2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
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Loop time of 5.954 on 4 procs for 2500 steps with 3872 atoms
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Performance: 36.278 ns/day, 0.662 hours/ns, 419.886 timesteps/s
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95.5% CPU use with 4 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 | 4.4642 | 4.6298 | 4.8946 | 7.5 | 77.76
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Bond | 0.18992 | 0.19849 | 0.20566 | 1.3 | 3.33
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Neigh | 0.18926 | 0.18928 | 0.18929 | 0.0 | 3.18
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Comm | 0.56456 | 0.82727 | 1.0096 | 17.9 | 13.89
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Output | 0.00044023 | 0.00092791 | 0.0020343 | 0.0 | 0.02
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Modify | 0.077974 | 0.080378 | 0.082874 | 0.8 | 1.35
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Other | | 0.02782 | | | 0.47
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Nlocal: 968.000 ave 989 max 944 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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Nghost: 6381.50 ave 6416 max 6351 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Neighs: 192557.0 ave 197456 max 188754 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Total # of neighbors = 770229
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Ave neighs/atom = 198.92278
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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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System init for write_data ...
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Total wall time: 0:00:07
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