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 1 by 1 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 = 0.028 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) = 10.75 | 10.75 | 10.75 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 302.37248 -4957.687 1700.6563 231.95939 10617.134
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100 305.85975 -4885.1313 1589.9657 234.06312 9178.0262
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200 296.72843 -4951.5636 1681.209 153.51039 10767.695
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300 308.16536 -4956.3355 1604.2261 203.72314 9266.9134
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400 297.43236 -4959.7758 1596.8717 69.083277 10221.765
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500 304.09059 -5004.7041 1531.3818 35.492587 9778.2126
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600 301.19423 -4974.2139 1694.3778 195.55858 9597.0895
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700 297.83153 -4993.867 1671.6871 114.41347 10360.771
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800 301.50873 -5038.4606 1671.0584 111.62133 8730.9918
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900 298.13466 -5056.328 1719.8923 103.65538 10561.792
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1000 297.16177 -4951.3098 1655.784 133.33949 8784.2239
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1100 303.33432 -4972.3579 1696.3014 224.03195 10764.88
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1200 307.51509 -4909.5175 1773.9263 412.73795 9220.984
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1300 305.02405 -4974.013 1714.5967 260.16943 10357.602
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1400 293.6948 -4998.3679 1683.6803 74.173172 9499.7569
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1500 300.79313 -4978.7126 1719.2548 211.30869 9602.7975
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1600 302.62922 -4924.5134 1709.726 277.16506 10649.017
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1700 301.27221 -4935.4932 1744.1182 284.9194 9169.4275
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1800 296.72398 -5019.7387 1712.9372 117.0122 10540.894
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1900 301.63962 -4971.0508 1757.1132 266.59621 8983.2539
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2000 304.05902 -5013.5663 1752.1581 247.04237 10422.56
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Loop time of 15.6283 on 1 procs for 2000 steps with 3872 atoms
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Performance: 11.057 ns/day, 2.171 hours/ns, 127.973 timesteps/s
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99.5% 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 | 14.126 | 14.126 | 14.126 | 0.0 | 90.39
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Bond | 0.60335 | 0.60335 | 0.60335 | 0.0 | 3.86
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Neigh | 0.69884 | 0.69884 | 0.69884 | 0.0 | 4.47
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Comm | 0.083166 | 0.083166 | 0.083166 | 0.0 | 0.53
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Output | 0.00054701 | 0.00054701 | 0.00054701 | 0.0 | 0.00
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Modify | 0.079684 | 0.079684 | 0.079684 | 0.0 | 0.51
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Other | | 0.03683 | | | 0.24
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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: 11716.0 ave 11716 max 11716 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 769907.0 ave 769907 max 769907 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 769907
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Ave neighs/atom = 198.83962
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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: 0:00:15
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