127 lines
4.5 KiB
Groff
127 lines
4.5 KiB
Groff
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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# test of replicating system with periodic bonds in both x and y
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dimension 2
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atom_style molecular
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read_data data.bond.x.y
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Reading data file ...
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orthogonal box = (0 0 -0.5) to (3 3 0.5)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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9 atoms
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scanning bonds ...
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2 = max bonds/atom
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orthogonal box = (0 0 -0.5) to (3 3 0.5)
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2 by 2 by 1 MPI processor grid
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reading bonds ...
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18 bonds
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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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4 = max # of 1-2 neighbors
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12 = max # of 1-3 neighbors
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48 = max # of 1-4 neighbors
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8 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.003 seconds
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#replicate 3 3 1
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replicate 3 3 1 bond/periodic
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Replication is creating a 3x3x1 = 9 times larger system...
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orthogonal box = (0 0 -0.5) to (9 9 0.5)
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2 by 2 by 1 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 = 0.00 MB
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average # of replicas added to proc = 6.25 out of 9 (69.44%)
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81 atoms
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162 bonds
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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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4 = max # of 1-2 neighbors
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12 = max # of 1-3 neighbors
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48 = max # of 1-4 neighbors
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24 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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replicate CPU = 0.001 seconds
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mass 1 1.0
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velocity all create 0.02 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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bond_style harmonic
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bond_coeff 1 50.0 1.0
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special_bonds fene
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 1 1
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4 = max # of 1-2 neighbors
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24 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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fix 1 all nve
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write_data tmp.data.x.y
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System init for write_data ...
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Generated 0 of 0 mixed pair_coeff terms from 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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 7 7 1
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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/2d
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bin: standard
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dump 1 all image 100 tmp.image.x.y.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6
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dump_modify 1 pad 5
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#dump 2 all movie 100 tmp.movie.x.y.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6
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#dump_modify 2 pad 5
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run 5000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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WARNING: Inconsistent image flags (../domain.cpp:1051)
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Per MPI rank memory allocation (min/avg/max) = 7.552 | 7.552 | 7.552 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.02 -1.1250229 0 -1.1052698 -2.9713842
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5000 0.046175679 -1.2280388 0.080003864 -1.1024293 -4.1097897
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Loop time of 0.273847 on 4 procs for 5000 steps with 81 atoms
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Performance: 7887622.810 tau/day, 18258.386 timesteps/s, 1.479 Matom-step/s
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92.4% 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 | 0.0039465 | 0.0042593 | 0.0046129 | 0.4 | 1.56
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Bond | 0.0011489 | 0.001207 | 0.0012757 | 0.2 | 0.44
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Neigh | 0.00079819 | 0.0008044 | 0.00081324 | 0.0 | 0.29
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Comm | 0.024107 | 0.024703 | 0.025269 | 0.3 | 9.02
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Output | 0.14406 | 0.18123 | 0.23779 | 8.7 | 66.18
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Modify | 0.00089401 | 0.00095321 | 0.0010422 | 0.0 | 0.35
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Other | | 0.06069 | | | 22.16
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Nlocal: 20.25 ave 22 max 19 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Nghost: 81.5 ave 82 max 80 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Neighs: 178.5 ave 195 max 165 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Total # of neighbors = 714
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Ave neighs/atom = 8.8148148
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Ave special neighs/atom = 4
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Neighbor list builds = 72
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Dangerous builds = 0
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Total wall time: 0:00:00
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