103 lines
4.5 KiB
Groff
103 lines
4.5 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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WARNING: Restart file used different # of processors: 4 vs. 1 (src/read_restart.cpp:697)
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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 1 by 1 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 = 0.002 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) = 6.879 | 6.879 | 6.879 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 303.69861 -4872.1658 1620.5986 252.72467 8824.1501
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2700 304.64827 -4885.5903 1747.1956 376.85504 11560.748
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2800 298.79617 -4851.2752 1644.5913 241.04014 9198.1133
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2900 302.323 -4949.4247 1661.0637 200.05824 10788.039
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3000 302.8192 -4983.7441 1617.1412 127.5418 9606.2027
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3100 305.27495 -4999.5335 1589.7081 112.65547 9258.8096
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3200 294.9932 -4960.8253 1650.5396 93.556955 11103.25
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3300 299.8705 -4896.6757 1711.6029 275.0477 8404.2758
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3400 308.43113 -5035.583 1732.7837 256.09989 11520.651
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3500 302.54 -4887.2016 1770.4336 374.15506 8359.8351
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3600 294.00064 -5011.409 1768.0298 149.01058 11257.53
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3700 303.26654 -4942.0636 1690.4493 247.69209 8749.4281
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3800 294.7064 -5009.5839 1638.6276 29.577045 10460.396
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3900 300.34826 -5011.778 1699.4384 153.29355 9558.3891
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4000 298.76709 -5014.8089 1613.1902 45.769836 9254.1067
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4100 297.77294 -4978.3228 1736.8967 194.49122 10810.757
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4200 302.14768 -5049.4356 1713.0187 149.97929 8258.5093
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4300 295.1467 -5094.2287 1757.8215 69.206733 11022.023
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4400 305.24677 -4967.1951 1762.3252 317.28577 8423.2256
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4500 305.53119 -5047.7285 1775.2795 252.98852 11178.338
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Loop time of 15.3536 on 1 procs for 2000 steps with 3872 atoms
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Performance: 11.255 ns/day, 2.132 hours/ns, 130.263 timesteps/s
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99.6% 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 | 13.88 | 13.88 | 13.88 | 0.0 | 90.40
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Bond | 0.58065 | 0.58065 | 0.58065 | 0.0 | 3.78
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Neigh | 0.69518 | 0.69518 | 0.69518 | 0.0 | 4.53
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Comm | 0.0826 | 0.0826 | 0.0826 | 0.0 | 0.54
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Output | 0.00053438 | 0.00053438 | 0.00053438 | 0.0 | 0.00
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Modify | 0.07779 | 0.07779 | 0.07779 | 0.0 | 0.51
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Other | | 0.03687 | | | 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: 11670.0 ave 11670 max 11670 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 770032.0 ave 770032 max 770032 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 770032
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Ave neighs/atom = 198.87190
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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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