126 lines
4.4 KiB
Groff
126 lines
4.4 KiB
Groff
LAMMPS (17 Apr 2024)
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# test of replicating system with periodic bonds in xy diagonal direction
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dimension 2
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atom_style molecular
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read_data data.bond.xy
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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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1 by 1 by 1 MPI processor grid
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reading atoms ...
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3 atoms
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scanning bonds ...
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1 = max bonds/atom
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orthogonal box = (0 0 -0.5) to (3 3 0.5)
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1 by 1 by 1 MPI processor grid
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reading bonds ...
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3 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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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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2 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.004 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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1 by 1 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 = 9.00 out of 9 (100.00%)
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27 atoms
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27 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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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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6 = 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 1.5
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bond_style harmonic
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bond_coeff 1 50.0 1.414
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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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2 = max # of 1-2 neighbors
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6 = 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.xy
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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.xy.*.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.xy.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) = 6.302 | 6.302 | 6.302 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.02 -0.66256987 2.2804444e-06 -0.64330834 -0.59475371
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5000 0.43110862 -1.1484506 0.16888799 -0.56442095 -0.3683968
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Loop time of 0.124095 on 1 procs for 5000 steps with 27 atoms
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Performance: 17406010.885 tau/day, 40291.692 timesteps/s, 1.088 Matom-step/s
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82.3% CPU use with 1 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 | 0.0013734 | 0.0013734 | 0.0013734 | 0.0 | 1.11
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Bond | 0.00064058 | 0.00064058 | 0.00064058 | 0.0 | 0.52
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Neigh | 0.00090424 | 0.00090424 | 0.00090424 | 0.0 | 0.73
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Comm | 0.00081732 | 0.00081732 | 0.00081732 | 0.0 | 0.66
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Output | 0.11905 | 0.11905 | 0.11905 | 0.0 | 95.93
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Modify | 0.0007252 | 0.0007252 | 0.0007252 | 0.0 | 0.58
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Other | | 0.0005888 | | | 0.47
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Nlocal: 27 ave 27 max 27 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 45 ave 45 max 45 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 66 ave 66 max 66 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 66
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Ave neighs/atom = 2.4444444
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Ave special neighs/atom = 2
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Neighbor list builds = 244
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Dangerous builds = 0
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Total wall time: 0:00:00
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