modified doc page, added examples
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Steve Plimpton
135
examples/replicate/log.6May24.replicate.cnt.g++.4
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examples/replicate/log.6May24.replicate.cnt.g++.4
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LAMMPS (17 Apr 2024)
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WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
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# three orthogonal periodic CNTs
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# demo for replicating triply looped system
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# infinite loops in x, y, z
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# includes bonded interactions across box corners
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# includes bonds, angles, dihedrals, impropers (class2)
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units real
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boundary p p p
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atom_style full
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pair_style lj/class2 10
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angle_style class2
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bond_style class2
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dihedral_style class2
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improper_style class2
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read_data three_periodic_CNTs.data.gz
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Reading data file ...
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orthogonal box = (0 0 0) to (80.96 80.96 80.96)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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3168 atoms
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reading velocities ...
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3168 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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3 = max angles/atom
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scanning dihedrals ...
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12 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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orthogonal box = (0 0 0) to (80.96 80.96 80.96)
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1 by 2 by 2 MPI processor grid
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reading bonds ...
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4752 bonds
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reading angles ...
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9504 angles
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reading dihedrals ...
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19008 dihedrals
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reading impropers ...
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3168 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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3 = max # of 1-2 neighbors
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6 = max # of 1-3 neighbors
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18 = max # of 1-4 neighbors
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18 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.064 seconds
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replicate 2 2 2 bond/periodic
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Replication is creating a 2x2x2 = 8 times larger system...
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orthogonal box = (0 0 0) to (161.92 161.92 161.92)
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1 by 2 by 2 MPI processor grid
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bounding box image = (0 0 0) to (0 0 0)
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bounding box extra memory = 1.62 MB
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average # of replicas added to proc = 4.50 out of 8 (56.25%)
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25344 atoms
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38016 bonds
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76032 angles
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152064 dihedrals
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25344 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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3 = max # of 1-2 neighbors
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6 = max # of 1-3 neighbors
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18 = max # of 1-4 neighbors
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18 = max # of special neighbors
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special bonds CPU = 0.004 seconds
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replicate CPU = 0.012 seconds
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fix 1 all nve
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run 100
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Generated 0 of 0 mixed pair_coeff terms from sixthpower/geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 27 27 27
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/class2, 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
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bin: standard
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WARNING: Inconsistent image flags (../domain.cpp:1051)
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Per MPI rank memory allocation (min/avg/max) = 28.69 | 28.69 | 28.69 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -14266.189 1466925.5 1452659.3 -29908.753
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100 2155.9128 -17224.188 1306769.8 1452409 1985.2082
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Loop time of 1.3667 on 4 procs for 100 steps with 25344 atoms
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Performance: 6.322 ns/day, 3.796 hours/ns, 73.169 timesteps/s, 1.854 Matom-step/s
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99.8% CPU use with 4 MPI tasks x no 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 | 0.43424 | 0.43539 | 0.43741 | 0.2 | 31.86
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Bond | 0.88613 | 0.89013 | 0.90094 | 0.7 | 65.13
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Neigh | 0.013198 | 0.013199 | 0.013201 | 0.0 | 0.97
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Comm | 0.010742 | 0.020522 | 0.02546 | 4.1 | 1.50
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Output | 3.2788e-05 | 3.6302e-05 | 4.4556e-05 | 0.0 | 0.00
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Modify | 0.0042029 | 0.0042366 | 0.004267 | 0.0 | 0.31
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Other | | 0.003188 | | | 0.23
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Nlocal: 6336 ave 6336 max 6336 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 10558 ave 10558 max 10558 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 723394 ave 723394 max 723394 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2893576
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Ave neighs/atom = 114.17203
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Ave special neighs/atom = 18
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Neighbor list builds = 1
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Dangerous builds = 0
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# write_restart replicate.restart
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# write_data replicate.data
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Total wall time: 0:00:01
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