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 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 = 0.014 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) = 10.74 | 10.74 | 10.74 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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100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304
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200 296.49886 -4884.3039 1747.4798 284.39198 11537.322
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300 295.24937 -4850.2788 1642.4584 198.97822 9160.666
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400 297.73321 -4952.9967 1660.6439 143.10604 10751.859
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500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826
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600 299.50756 -4999.965 1588.0327 44.000269 9233.8621
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700 295.64728 -4958.2253 1646.2011 99.365838 11089.418
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800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685
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900 300.80754 -5033.4853 1727.4591 164.90648 11497.526
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1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551
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1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28
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1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201
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1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762
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1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178
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1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337
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1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415
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1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882
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1800 301.9386 -5068.1221 1755.577 171.43863 11229.315
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1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348
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2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209
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Loop time of 15.6807 on 1 procs for 2000 steps with 3872 atoms
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Performance: 11.020 ns/day, 2.178 hours/ns, 127.545 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 | 14.196 | 14.196 | 14.196 | 0.0 | 90.53
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Bond | 0.58712 | 0.58712 | 0.58712 | 0.0 | 3.74
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Neigh | 0.6978 | 0.6978 | 0.6978 | 0.0 | 4.45
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Comm | 0.082724 | 0.082724 | 0.082724 | 0.0 | 0.53
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Output | 0.00052338 | 0.00052338 | 0.00052338 | 0.0 | 0.00
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Modify | 0.078892 | 0.078892 | 0.078892 | 0.0 | 0.50
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Other | | 0.0374 | | | 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: 11633.0 ave 11633 max 11633 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 770365.0 ave 770365 max 770365 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 770365
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Ave neighs/atom = 198.95790
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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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