forked from lijiext/lammps
123 lines
4.7 KiB
Groff
123 lines
4.7 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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# part 2: continuing from data file
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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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read_data molecular-mix.data
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Reading data file ...
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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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reading atoms ...
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3872 atoms
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reading velocities ...
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3872 velocities
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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scanning dihedrals ...
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2 = max dihedrals/atom
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reading bonds ...
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3072 bonds
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reading angles ...
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3072 angles
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reading dihedrals ...
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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 0.0 0.0
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special bond factors coul: 0.0 0.0 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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5 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.039 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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# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
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run 2000
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Neighbor list info ...
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update every 1 steps, delay 10 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) = 8.101 | 8.197 | 8.483 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
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100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
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200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
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300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
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400 302 -4951.4895 1664.5419 197.74463 10784.638
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500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
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600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
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700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
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800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
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900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
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1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
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1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
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1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
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1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
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1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
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1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
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1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
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1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
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1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
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1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
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2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
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Loop time of 4.33662 on 4 procs for 2000 steps with 3872 atoms
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Performance: 39.847 ns/day, 0.602 hours/ns, 461.188 timesteps/s
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98.8% 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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---------------------------------------------------------------
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Pair | 3.6239 | 3.6669 | 3.7143 | 1.8 | 84.56
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Bond | 0.14954 | 0.15355 | 0.15614 | 0.7 | 3.54
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Neigh | 0.17931 | 0.17933 | 0.17934 | 0.0 | 4.14
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Comm | 0.23604 | 0.28181 | 0.32663 | 6.5 | 6.50
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Output | 0.00034802 | 0.00069388 | 0.0017292 | 0.0 | 0.02
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Modify | 0.029915 | 0.036141 | 0.039601 | 1.9 | 0.83
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Other | | 0.01821 | | | 0.42
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Nlocal: 968.000 ave 979 max 948 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Nghost: 6321.25 ave 6336 max 6309 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Neighs: 192540.0 ave 195406 max 187182 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Total # of neighbors = 770161
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Ave neighs/atom = 198.90522
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Ave special neighs/atom = 3.9669421
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Neighbor list builds = 35
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Dangerous builds = 0
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Total wall time: 0:00:04
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