102 lines
4.4 KiB
Groff
102 lines
4.4 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 3: continuing from restart file
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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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read_restart template-mix.restart
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Reading restart file ...
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restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
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restoring atom style template from restart
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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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restoring pair style lj/cut from restart
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restoring bond style harmonic from restart
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restoring angle style harmonic from restart
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restoring dihedral style harmonic from restart
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3872 atoms
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3072 template bonds
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3072 template angles
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3072 template dihedrals
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read_restart CPU = 0.006 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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Resetting global fix info from restart file:
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fix style: nvt, fix ID: 1
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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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All restart file global fix info was re-assigned
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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) = 4.193 | 4.289 | 4.575 Mbytes
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Step Temp E_pair E_mol TotEng Press
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2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
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2600 303.6986 -4872.1658 1620.5986 252.72458 8824.1501
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2700 296.80713 -4884.3012 1753.5243 293.99628 11523.482
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2800 298.88856 -4849.1995 1639.5709 239.1615 9214.1261
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2900 297.12578 -4949.9958 1657.7582 136.2123 10727.69
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3000 298.19234 -4984.9797 1618.0356 73.812582 9576.9074
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3100 301.54182 -4999.9775 1588.997 68.424766 9225.9502
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3200 294.07259 -4962.8351 1646.3012 76.686125 11080.923
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3300 303.55697 -4900.0696 1721.4077 323.99573 8433.7992
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3400 297.80636 -5036.3758 1735.0734 135.00054 11440.101
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3500 303.96121 -4882.4297 1757.4268 382.31908 8497.7685
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3600 298.21153 -5006.6599 1759.9584 194.27658 11184.938
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3700 300.77921 -4941.495 1688.3988 217.50964 8820.5666
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3800 294.33206 -5011.7746 1653.7511 38.190478 10418.208
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3900 304.38175 -5004.4071 1719.9139 227.68132 9632.0557
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4000 302.44152 -5029.0544 1610.1577 70.889929 9237.6379
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4100 298.82638 -4971.4109 1755.8272 232.48883 10814.056
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4200 297.77273 -5040.0028 1718.5112 114.42322 8287.605
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4300 300.50984 -5082.4128 1742.354 127.43881 11003.298
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4400 310.02885 -4971.4191 1749.1209 355.03646 8502.7004
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4500 302.62639 -5033.3284 1753.488 212.07956 11150.514
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Loop time of 4.39645 on 4 procs for 2000 steps with 3872 atoms
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Performance: 39.304 ns/day, 0.611 hours/ns, 454.913 timesteps/s
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98.2% 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 | 3.6185 | 3.6709 | 3.7028 | 1.7 | 83.50
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Bond | 0.14772 | 0.15338 | 0.1621 | 1.5 | 3.49
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Neigh | 0.17739 | 0.17747 | 0.17756 | 0.0 | 4.04
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Comm | 0.29637 | 0.33265 | 0.39131 | 6.7 | 7.57
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Output | 0.00034028 | 0.0006627 | 0.0016284 | 0.0 | 0.02
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Modify | 0.039076 | 0.041988 | 0.043469 | 0.9 | 0.96
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Other | | 0.01937 | | | 0.44
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Nlocal: 968.000 ave 977 max 956 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Nghost: 6322.75 ave 6345 max 6308 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Neighs: 192555.0 ave 195249 max 188636 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Total # of neighbors = 770221
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Ave neighs/atom = 198.92071
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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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Total wall time: 0:00:04
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