add example for bondlist option validation
This commit is contained in:
jrgissing
32
examples/replicate/in.replicate
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32
examples/replicate/in.replicate
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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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replicate 2 2 2 bondlist
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fix 1 all nve
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run 100
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# write_restart replicate.restart
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# write_data replicate.data
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132
examples/replicate/log.7Jan22.replicate.g++.1
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132
examples/replicate/log.7Jan22.replicate.g++.1
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LAMMPS (7 Jan 2022)
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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 1 by 1 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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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 = 0.003 seconds
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read_data CPU = 0.115 seconds
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replicate 2 2 2 bondlist
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Replicating atoms ...
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orthogonal box = (0 0 0) to (161.92 161.92 161.92)
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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 = 1.62 MB
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average # of replicas added to proc = 8.00 out of 8 (100.00%)
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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 = 0.021 seconds
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replicate CPU = 0.052 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 geometric mixing rule
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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 = 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:814)
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Per MPI rank memory allocation (min/avg/max) = 51.87 | 51.87 | 51.87 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 15.0972 on 1 procs for 100 steps with 25344 atoms
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Performance: 0.572 ns/day, 41.937 hours/ns, 6.624 timesteps/s
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100.0% 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 | 3.7175 | 3.7175 | 3.7175 | 0.0 | 24.62
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Bond | 11.222 | 11.222 | 11.222 | 0.0 | 74.33
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Neigh | 0.1032 | 0.1032 | 0.1032 | 0.0 | 0.68
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Comm | 0.014487 | 0.014487 | 0.014487 | 0.0 | 0.10
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Output | 0.00010894 | 0.00010894 | 0.00010894 | 0.0 | 0.00
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Modify | 0.027112 | 0.027112 | 0.027112 | 0.0 | 0.18
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Other | | 0.01274 | | | 0.08
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Nlocal: 25344 ave 25344 max 25344 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 22737 ave 22737 max 22737 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2.89358e+06 ave 2.89358e+06 max 2.89358e+06 min
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Histogram: 1 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: 0:00:15
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132
examples/replicate/log.7Jan22.replicate.g++.4
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132
examples/replicate/log.7Jan22.replicate.g++.4
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@ -0,0 +1,132 @@
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LAMMPS (7 Jan 2022)
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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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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 = 0.315 seconds
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replicate 2 2 2 bondlist
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Replicating atoms ...
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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 = 0.007 seconds
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replicate CPU = 0.020 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 geometric mixing rule
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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 = 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:814)
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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 4.13195 on 4 procs for 100 steps with 25344 atoms
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Performance: 2.091 ns/day, 11.478 hours/ns, 24.202 timesteps/s
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100.0% 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 | 0.99372 | 1.014 | 1.0672 | 3.1 | 24.54
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Bond | 2.9449 | 2.9795 | 3.0136 | 2.0 | 72.11
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Neigh | 0.026695 | 0.026706 | 0.026716 | 0.0 | 0.65
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Comm | 0.012404 | 0.099546 | 0.15425 | 18.7 | 2.41
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Output | 4.3822e-05 | 5.0693e-05 | 7.0516e-05 | 0.0 | 0.00
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Modify | 0.0074219 | 0.0074887 | 0.0075411 | 0.1 | 0.18
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Other | | 0.004616 | | | 0.11
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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: 0:00:04
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BIN
examples/replicate/three_periodic_CNTs.data.gz
Normal file
BIN
examples/replicate/three_periodic_CNTs.data.gz
Normal file
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