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modified doc page, added examples

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Steve Plimpton
2024-05-06 16:44:45 -06:00
parent 25a9bf1ff6
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1
examples/README
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@ -104,6 +104,7 @@ prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: use of PYTHON package to invoke Python code from input script
qeq: use of QEQ package for charge equilibration
reaxff: RDX and TATB and several other models using ReaxFF
replicate: use of replicate command
rerun: use of rerun and read_dump commands
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void

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examples/replicate/README Normal file
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This directory has input scripts which demonstrate how to use the
replicate command both for systems with and without periodic bond
loops. A periodic bond loop is where a chain of bonds spans a
periodic dimension of the box and includes one or more bonds which
cross the periodic boundary to close the loop.
To run these scripts, LAMMPS should be built with the MOLECULE and
CLASS2 packages. The latter is only needed for the CNT example.
These scripts are tiny examples which illustrate both kinds of
systems. Each produces a series of images which can be visualized.
If the 3 lines for a dump movie command are uncommented, a MPG movie
is produced, assuming LAMMPS is build with FFMPEG support.
in.replicate.bond.x # linear chains in x direction, bond loop in x
in.replcate.bond.x.y # 2d grid of bonded atoms, bond loops in x and y
in.replicate.bond.xy # linear chains in diagonal direction, bond loop in x and y
in.replicate.bond.noloop # linear chains in x direction, no bond loop
This script is for a complex system of 3 orthogonal CNTs which has
periodic bond loops in all 3 dimensions xyz.
in.replicate.cnt

22
examples/replicate/data.bond.x Normal file
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# system with periodic bonds in x
3 atoms
3 bonds
1 atom types
1 bond types
0 3 xlo xhi
0 1 ylo yhi
Atoms
1 1 1 0.5 0.5 0
2 1 1 1.5 0.5 0
3 1 1 2.5 0.5 0
Bonds
1 1 1 2
2 1 2 3
3 1 3 1

21
examples/replicate/data.bond.x.noloop Normal file
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# system with non-periodic bonds in x
3 atoms
2 bonds
1 atom types
1 bond types
0 3 xlo xhi
0 1 ylo yhi
Atoms
1 1 1 0.5 0.5 0 0 0 0
2 1 1 1.5 0.5 0 0 0 0
3 1 1 2.5 0.5 0 -1 0 0
Bonds
1 1 1 2
2 1 3 1

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examples/replicate/data.bond.x.y Normal file
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# system with periodic bonds in both x and y
9 atoms
18 bonds
1 atom types
1 bond types
0 3 xlo xhi
0 3 ylo yhi
Atoms
1 1 1 0.5 0.5 0
2 1 1 1.5 0.5 0
3 1 1 2.5 0.5 0
4 1 1 0.5 1.5 0
5 1 1 1.5 1.5 0
6 1 1 2.5 1.5 0
7 1 1 0.5 2.5 0
8 1 1 1.5 2.5 0
9 1 1 2.5 2.5 0
Bonds
1 1 1 2
2 1 2 3
3 1 3 1
4 1 4 5
5 1 5 6
6 1 6 4
7 1 7 8
8 1 8 9
9 1 9 7
10 1 1 4
11 1 4 7
12 1 7 1
13 1 2 5
14 1 5 8
15 1 8 2
16 1 3 6
17 1 6 9
18 1 9 3

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examples/replicate/data.bond.xy Normal file
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# system with periodic bonds in xy direction
3 atoms
3 bonds
1 atom types
1 bond types
0 3 xlo xhi
0 3 ylo yhi
Atoms
1 1 1 0.5 0.5 0
2 1 1 1.5 1.5 0
3 1 1 2.5 2.5 0
Bonds
1 1 1 2
2 1 2 3
3 1 3 1

34
examples/replicate/in.replicate.bond.x Normal file
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# test of replicating system with periodic bonds in x
dimension 2
atom_style molecular
read_data data.bond.x
#replicate 3 3 1
replicate 3 3 1 bond/periodic
mass 1 1.0
velocity all create 0.02 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
bond_style harmonic
bond_coeff 1 50.0 1.0
special_bonds fene
fix 1 all nve
write_data tmp.data.x
dump 1 all image 100 tmp.image.x.*.ppm type type &
adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.x.mpg type type &
# adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000

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examples/replicate/in.replicate.bond.x.noloop Normal file
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# test of replicating system with periodic bonds in x
dimension 2
atom_style molecular
read_data data.bond.x.noloop
replicate 3 3 1
#replicate 3 3 1 bond/periodic
mass 1 1.0
velocity all create 0.001 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
bond_style harmonic
bond_coeff 1 50.0 1.0
special_bonds fene
fix 1 all nve
write_data tmp.data.x.non
dump 1 all image 100 tmp.image.x.non.*.ppm type type &
adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.x.non.mpg type type &
# adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000

34
examples/replicate/in.replicate.bond.x.y Normal file
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# test of replicating system with periodic bonds in both x and y
dimension 2
atom_style molecular
read_data data.bond.x.y
#replicate 3 3 1
replicate 3 3 1 bond/periodic
mass 1 1.0
velocity all create 0.02 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
bond_style harmonic
bond_coeff 1 50.0 1.0
special_bonds fene
fix 1 all nve
write_data tmp.data.x.y
dump 1 all image 100 tmp.image.x.y.*.ppm type type &
adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.x.y.mpg type type &
# adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000

34
examples/replicate/in.replicate.bond.xy Normal file
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# test of replicating system with periodic bonds in xy diagonal direction
dimension 2
atom_style molecular
read_data data.bond.xy
#replicate 3 3 1
replicate 3 3 1 bond/periodic
mass 1 1.0
velocity all create 0.02 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.5
bond_style harmonic
bond_coeff 1 50.0 1.414
special_bonds fene
fix 1 all nve
write_data tmp.data.xy
dump 1 all image 100 tmp.image.xy.*.ppm type type &
adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.xy.mpg type type &
# adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000

2
examples/replicate/in.replicate → examples/replicate/in.replicate.cnt
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@ -22,7 +22,7 @@ improper_style class2
read_data three_periodic_CNTs.data.gz
replicate 2 2 2 bondlist
replicate 2 2 2 bond/periodic
fix 1 all nve

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examples/replicate/log.6May24.replicate.bond.x.g++.1 Normal file
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LAMMPS (17 Apr 2024)
# test of replicating system with periodic bonds in x
dimension 2
atom_style molecular
read_data data.bond.x
Reading data file ...
orthogonal box = (0 0 -0.5) to (3 1 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
3 atoms
scanning bonds ...
1 = max bonds/atom
orthogonal box = (0 0 -0.5) to (3 1 0.5)
1 by 1 by 1 MPI processor grid
reading bonds ...
3 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
#replicate 3 3 1
replicate 3 3 1 bond/periodic
Replication is creating a 3x3x1 = 9 times larger system...
orthogonal box = (0 0 -0.5) to (9 3 0.5)
1 by 1 by 1 MPI processor grid
bounding box image = (0 0 0) to (0 0 0)
bounding box extra memory = 0.00 MB
average # of replicas added to proc = 9.00 out of 9 (100.00%)
27 atoms
27 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
replicate CPU = 0.001 seconds
mass 1 1.0
velocity all create 0.02 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
bond_style harmonic
bond_coeff 1 50.0 1.0
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
fix 1 all nve
write_data tmp.data.x
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 3 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
dump 1 all image 100 tmp.image.x.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.x.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Inconsistent image flags (../domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 6.302 | 6.302 | 6.302 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.02 -1.1250229 0 -1.1057636 9.028122
5000 0.54111971 -1.9054641 0.29066874 -1.0937172 3.4346743
Loop time of 0.0764878 on 1 procs for 5000 steps with 27 atoms
Performance: 28239805.842 tau/day, 65369.921 timesteps/s, 1.765 Matom-step/s
66.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0048837 | 0.0048837 | 0.0048837 | 0.0 | 6.38
Bond | 0.00065879 | 0.00065879 | 0.00065879 | 0.0 | 0.86
Neigh | 0.0019897 | 0.0019897 | 0.0019897 | 0.0 | 2.60
Comm | 0.0012815 | 0.0012815 | 0.0012815 | 0.0 | 1.68
Output | 0.066351 | 0.066351 | 0.066351 | 0.0 | 86.75
Modify | 0.00069789 | 0.00069789 | 0.00069789 | 0.0 | 0.91
Other | | 0.0006247 | | | 0.82
Nlocal: 27 ave 27 max 27 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 284 ave 284 max 284 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 284
Ave neighs/atom = 10.518519
Ave special neighs/atom = 2
Neighbor list builds = 287
Dangerous builds = 0
Total wall time: 0:00:00

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examples/replicate/log.6May24.replicate.bond.x.g++.4 Normal file
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LAMMPS (17 Apr 2024)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
# test of replicating system with periodic bonds in x
dimension 2
atom_style molecular
read_data data.bond.x
Reading data file ...
orthogonal box = (0 0 -0.5) to (3 1 0.5)
4 by 1 by 1 MPI processor grid
reading atoms ...
3 atoms
scanning bonds ...
1 = max bonds/atom
orthogonal box = (0 0 -0.5) to (3 1 0.5)
4 by 1 by 1 MPI processor grid
reading bonds ...
3 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
#replicate 3 3 1
replicate 3 3 1 bond/periodic
Replication is creating a 3x3x1 = 9 times larger system...
orthogonal box = (0 0 -0.5) to (9 3 0.5)
4 by 1 by 1 MPI processor grid
bounding box image = (0 0 0) to (0 0 0)
bounding box extra memory = 0.00 MB
average # of replicas added to proc = 5.25 out of 9 (58.33%)
27 atoms
27 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
replicate CPU = 0.002 seconds
mass 1 1.0
velocity all create 0.02 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
bond_style harmonic
bond_coeff 1 50.0 1.0
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
fix 1 all nve
write_data tmp.data.x
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 3 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
dump 1 all image 100 tmp.image.x.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.x.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Inconsistent image flags (../domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 6.309 | 6.309 | 6.309 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.02 -1.1250229 0 -1.1057636 9.028122
5000 0.50911963 -1.7968226 0.21209852 -1.0944607 4.1676488
Loop time of 0.21682 on 4 procs for 5000 steps with 27 atoms
Performance: 9962160.612 tau/day, 23060.557 timesteps/s, 622.635 katom-step/s
93.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.001787 | 0.0021247 | 0.0028772 | 1.0 | 0.98
Bond | 0.00039682 | 0.00045617 | 0.00059887 | 0.0 | 0.21
Neigh | 0.0013626 | 0.0014006 | 0.0014798 | 0.1 | 0.65
Comm | 0.017009 | 0.01791 | 0.018656 | 0.5 | 8.26
Output | 0.06892 | 0.12188 | 0.18918 | 13.7 | 56.21
Modify | 0.00060336 | 0.00072159 | 0.00088047 | 0.0 | 0.33
Other | | 0.07233 | | | 33.36
Nlocal: 6.75 ave 7 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 64.5 ave 65 max 63 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 70.25 ave 77 max 60 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 281
Ave neighs/atom = 10.407407
Ave special neighs/atom = 2
Neighbor list builds = 287
Dangerous builds = 0
Total wall time: 0:00:00

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examples/replicate/log.6May24.replicate.bond.x.noloop.g++.1 Normal file
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LAMMPS (17 Apr 2024)
# test of replicating system with periodic bonds in x
dimension 2
atom_style molecular
read_data data.bond.x.non
Reading data file ...
orthogonal box = (0 0 -0.5) to (3 1 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
3 atoms
scanning bonds ...
1 = max bonds/atom
orthogonal box = (0 0 -0.5) to (3 1 0.5)
1 by 1 by 1 MPI processor grid
reading bonds ...
2 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
replicate 3 3 1
Replication is creating a 3x3x1 = 9 times larger system...
orthogonal box = (0 0 -0.5) to (9 3 0.5)
1 by 1 by 1 MPI processor grid
27 atoms
18 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
replicate CPU = 0.001 seconds
#replicate 3 3 1 bond/periodic
mass 1 1.0
velocity all create 0.001 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
bond_style harmonic
bond_coeff 1 50.0 1.0
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
fix 1 all nve
write_data tmp.data.x.non
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 3 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
dump 1 all image 100 tmp.image.x.non.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.x.non.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.052 | 6.052 | 6.052 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.001 -1.1250229 0 -1.1240599 13.009826
5000 0.62003692 -2.0147214 0.30861545 -1.1090334 8.0279226
Loop time of 0.0734456 on 1 procs for 5000 steps with 27 atoms
Performance: 29409520.548 tau/day, 68077.594 timesteps/s, 1.838 Matom-step/s
94.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0051444 | 0.0051444 | 0.0051444 | 0.0 | 7.00
Bond | 0.00048789 | 0.00048789 | 0.00048789 | 0.0 | 0.66
Neigh | 0.0019333 | 0.0019333 | 0.0019333 | 0.0 | 2.63
Comm | 0.001332 | 0.001332 | 0.001332 | 0.0 | 1.81
Output | 0.063139 | 0.063139 | 0.063139 | 0.0 | 85.97
Modify | 0.00077014 | 0.00077014 | 0.00077014 | 0.0 | 1.05
Other | | 0.0006387 | | | 0.87
Nlocal: 27 ave 27 max 27 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 101 ave 101 max 101 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 288
Ave neighs/atom = 10.666667
Ave special neighs/atom = 1.3333333
Neighbor list builds = 322
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (17 Apr 2024)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
# test of replicating system with periodic bonds in x
dimension 2
atom_style molecular
read_data data.bond.x.non
Reading data file ...
orthogonal box = (0 0 -0.5) to (3 1 0.5)
4 by 1 by 1 MPI processor grid
reading atoms ...
3 atoms
scanning bonds ...
1 = max bonds/atom
orthogonal box = (0 0 -0.5) to (3 1 0.5)
4 by 1 by 1 MPI processor grid
reading bonds ...
2 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
replicate 3 3 1
Replication is creating a 3x3x1 = 9 times larger system...
orthogonal box = (0 0 -0.5) to (9 3 0.5)
4 by 1 by 1 MPI processor grid
27 atoms
18 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
replicate CPU = 0.002 seconds
#replicate 3 3 1 bond/periodic
mass 1 1.0
velocity all create 0.001 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
bond_style harmonic
bond_coeff 1 50.0 1.0
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
fix 1 all nve
write_data tmp.data.x.non
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 3 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
dump 1 all image 100 tmp.image.x.non.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.x.non.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.059 | 6.059 | 6.059 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.001 -1.1250229 0 -1.1240599 13.009826
5000 0.74931971 -2.233724 0.40158766 -1.1105692 5.6354701
Loop time of 0.197835 on 4 procs for 5000 steps with 27 atoms
Performance: 10918214.594 tau/day, 25273.645 timesteps/s, 682.388 katom-step/s
88.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0018771 | 0.0021131 | 0.0027188 | 0.8 | 1.07
Bond | 0.00032659 | 0.00038248 | 0.00049555 | 0.0 | 0.19
Neigh | 0.001385 | 0.0014211 | 0.0014704 | 0.1 | 0.72
Comm | 0.017163 | 0.017405 | 0.017805 | 0.2 | 8.80
Output | 0.070971 | 0.11052 | 0.17112 | 12.1 | 55.87
Modify | 0.00058993 | 0.00067708 | 0.00075608 | 0.0 | 0.34
Other | | 0.06532 | | | 33.02
Nlocal: 6.75 ave 7 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 59.75 ave 60 max 59 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 72 ave 79 max 63 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Total # of neighbors = 288
Ave neighs/atom = 10.666667
Ave special neighs/atom = 1.3333333
Neighbor list builds = 323
Dangerous builds = 0
Total wall time: 0:00:00

125
examples/replicate/log.6May24.replicate.bond.x.y.g++.1 Normal file
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LAMMPS (17 Apr 2024)
# test of replicating system with periodic bonds in both x and y
dimension 2
atom_style molecular
read_data data.bond.x.y
Reading data file ...
orthogonal box = (0 0 -0.5) to (3 3 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
9 atoms
scanning bonds ...
2 = max bonds/atom
orthogonal box = (0 0 -0.5) to (3 3 0.5)
1 by 1 by 1 MPI processor grid
reading bonds ...
18 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
48 = max # of 1-4 neighbors
8 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
#replicate 3 3 1
replicate 3 3 1 bond/periodic
Replication is creating a 3x3x1 = 9 times larger system...
orthogonal box = (0 0 -0.5) to (9 9 0.5)
1 by 1 by 1 MPI processor grid
bounding box image = (0 0 0) to (0 0 0)
bounding box extra memory = 0.00 MB
average # of replicas added to proc = 9.00 out of 9 (100.00%)
81 atoms
162 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
48 = max # of 1-4 neighbors
24 = max # of special neighbors
special bonds CPU = 0.000 seconds
replicate CPU = 0.001 seconds
mass 1 1.0
velocity all create 0.02 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
bond_style harmonic
bond_coeff 1 50.0 1.0
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
4 = max # of 1-2 neighbors
24 = max # of special neighbors
special bonds CPU = 0.000 seconds
fix 1 all nve
write_data tmp.data.x.y
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
dump 1 all image 100 tmp.image.x.y.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.x.y.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Inconsistent image flags (../domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 7.555 | 7.555 | 7.555 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.02 -1.1250229 0 -1.1052698 -2.9713842
5000 0.046175679 -1.2280388 0.080003864 -1.1024293 -4.1097897
Loop time of 0.212344 on 1 procs for 5000 steps with 81 atoms
Performance: 10172161.526 tau/day, 23546.670 timesteps/s, 1.907 Matom-step/s
93.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.01283 | 0.01283 | 0.01283 | 0.0 | 6.04
Bond | 0.0032785 | 0.0032785 | 0.0032785 | 0.0 | 1.54
Neigh | 0.0018379 | 0.0018379 | 0.0018379 | 0.0 | 0.87
Comm | 0.0016247 | 0.0016247 | 0.0016247 | 0.0 | 0.77
Output | 0.18991 | 0.18991 | 0.18991 | 0.0 | 89.44
Modify | 0.0018198 | 0.0018198 | 0.0018198 | 0.0 | 0.86
Other | | 0.001039 | | | 0.49
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 144 ave 144 max 144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 714 ave 714 max 714 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 714
Ave neighs/atom = 8.8148148
Ave special neighs/atom = 4
Neighbor list builds = 72
Dangerous builds = 0
Total wall time: 0:00:00

126
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LAMMPS (17 Apr 2024)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
# test of replicating system with periodic bonds in both x and y
dimension 2
atom_style molecular
read_data data.bond.x.y
Reading data file ...
orthogonal box = (0 0 -0.5) to (3 3 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
9 atoms
scanning bonds ...
2 = max bonds/atom
orthogonal box = (0 0 -0.5) to (3 3 0.5)
2 by 2 by 1 MPI processor grid
reading bonds ...
18 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
48 = max # of 1-4 neighbors
8 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
#replicate 3 3 1
replicate 3 3 1 bond/periodic
Replication is creating a 3x3x1 = 9 times larger system...
orthogonal box = (0 0 -0.5) to (9 9 0.5)
2 by 2 by 1 MPI processor grid
bounding box image = (0 0 0) to (0 0 0)
bounding box extra memory = 0.00 MB
average # of replicas added to proc = 6.25 out of 9 (69.44%)
81 atoms
162 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
48 = max # of 1-4 neighbors
24 = max # of special neighbors
special bonds CPU = 0.000 seconds
replicate CPU = 0.001 seconds
mass 1 1.0
velocity all create 0.02 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
bond_style harmonic
bond_coeff 1 50.0 1.0
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
4 = max # of 1-2 neighbors
24 = max # of special neighbors
special bonds CPU = 0.000 seconds
fix 1 all nve
write_data tmp.data.x.y
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
dump 1 all image 100 tmp.image.x.y.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.x.y.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Inconsistent image flags (../domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 7.552 | 7.552 | 7.552 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.02 -1.1250229 0 -1.1052698 -2.9713842
5000 0.046175679 -1.2280388 0.080003864 -1.1024293 -4.1097897
Loop time of 0.273847 on 4 procs for 5000 steps with 81 atoms
Performance: 7887622.810 tau/day, 18258.386 timesteps/s, 1.479 Matom-step/s
92.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0039465 | 0.0042593 | 0.0046129 | 0.4 | 1.56
Bond | 0.0011489 | 0.001207 | 0.0012757 | 0.2 | 0.44
Neigh | 0.00079819 | 0.0008044 | 0.00081324 | 0.0 | 0.29
Comm | 0.024107 | 0.024703 | 0.025269 | 0.3 | 9.02
Output | 0.14406 | 0.18123 | 0.23779 | 8.7 | 66.18
Modify | 0.00089401 | 0.00095321 | 0.0010422 | 0.0 | 0.35
Other | | 0.06069 | | | 22.16
Nlocal: 20.25 ave 22 max 19 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 81.5 ave 82 max 80 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 178.5 ave 195 max 165 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 714
Ave neighs/atom = 8.8148148
Ave special neighs/atom = 4
Neighbor list builds = 72
Dangerous builds = 0
Total wall time: 0:00:00

125
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LAMMPS (17 Apr 2024)
# test of replicating system with periodic bonds in xy diagonal direction
dimension 2
atom_style molecular
read_data data.bond.xy
Reading data file ...
orthogonal box = (0 0 -0.5) to (3 3 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
3 atoms
scanning bonds ...
1 = max bonds/atom
orthogonal box = (0 0 -0.5) to (3 3 0.5)
1 by 1 by 1 MPI processor grid
reading bonds ...
3 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
#replicate 3 3 1
replicate 3 3 1 bond/periodic
Replication is creating a 3x3x1 = 9 times larger system...
orthogonal box = (0 0 -0.5) to (9 9 0.5)
1 by 1 by 1 MPI processor grid
bounding box image = (0 0 0) to (0 0 0)
bounding box extra memory = 0.00 MB
average # of replicas added to proc = 9.00 out of 9 (100.00%)
27 atoms
27 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
replicate CPU = 0.001 seconds
mass 1 1.0
velocity all create 0.02 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.5
bond_style harmonic
bond_coeff 1 50.0 1.414
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
fix 1 all nve
write_data tmp.data.xy
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
dump 1 all image 100 tmp.image.xy.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.xy.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Inconsistent image flags (../domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 6.302 | 6.302 | 6.302 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.02 -0.66256987 2.2804444e-06 -0.64330834 -0.59475371
5000 0.43110862 -1.1484506 0.16888799 -0.56442095 -0.3683968
Loop time of 0.124095 on 1 procs for 5000 steps with 27 atoms
Performance: 17406010.885 tau/day, 40291.692 timesteps/s, 1.088 Matom-step/s
82.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0013734 | 0.0013734 | 0.0013734 | 0.0 | 1.11
Bond | 0.00064058 | 0.00064058 | 0.00064058 | 0.0 | 0.52
Neigh | 0.00090424 | 0.00090424 | 0.00090424 | 0.0 | 0.73
Comm | 0.00081732 | 0.00081732 | 0.00081732 | 0.0 | 0.66
Output | 0.11905 | 0.11905 | 0.11905 | 0.0 | 95.93
Modify | 0.0007252 | 0.0007252 | 0.0007252 | 0.0 | 0.58
Other | | 0.0005888 | | | 0.47
Nlocal: 27 ave 27 max 27 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 66 ave 66 max 66 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 66
Ave neighs/atom = 2.4444444
Ave special neighs/atom = 2
Neighbor list builds = 244
Dangerous builds = 0
Total wall time: 0:00:00

126
examples/replicate/log.6May24.replicate.bond.xy.g++.4 Normal file
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LAMMPS (17 Apr 2024)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
# test of replicating system with periodic bonds in xy diagonal direction
dimension 2
atom_style molecular
read_data data.bond.xy
Reading data file ...
orthogonal box = (0 0 -0.5) to (3 3 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
3 atoms
scanning bonds ...
1 = max bonds/atom
orthogonal box = (0 0 -0.5) to (3 3 0.5)
2 by 2 by 1 MPI processor grid
reading bonds ...
3 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
#replicate 3 3 1
replicate 3 3 1 bond/periodic
Replication is creating a 3x3x1 = 9 times larger system...
orthogonal box = (0 0 -0.5) to (9 9 0.5)
2 by 2 by 1 MPI processor grid
bounding box image = (0 0 0) to (0 0 0)
bounding box extra memory = 0.00 MB
average # of replicas added to proc = 6.25 out of 9 (69.44%)
27 atoms
27 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
replicate CPU = 0.001 seconds
mass 1 1.0
velocity all create 0.02 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.5
bond_style harmonic
bond_coeff 1 50.0 1.414
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
fix 1 all nve
write_data tmp.data.xy
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
dump 1 all image 100 tmp.image.xy.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6
dump_modify 1 pad 5
#dump 2 all movie 100 tmp.movie.xy.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify 2 pad 5
run 5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Inconsistent image flags (../domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 6.301 | 6.301 | 6.301 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.02 -0.66256988 2.2804444e-06 -0.64330834 -0.59475371
5000 0.43110877 -1.1484507 0.168888 -0.56442093 -0.36839692
Loop time of 0.286423 on 4 procs for 5000 steps with 27 atoms
Performance: 7541285.935 tau/day, 17456.680 timesteps/s, 471.330 katom-step/s
92.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00054941 | 0.00084836 | 0.0013689 | 0.0 | 0.30
Bond | 0.00034068 | 0.00045816 | 0.00068461 | 0.0 | 0.16
Neigh | 0.00092076 | 0.00098494 | 0.0010463 | 0.0 | 0.34
Comm | 0.018151 | 0.018737 | 0.019531 | 0.4 | 6.54
Output | 0.13261 | 0.19363 | 0.2596 | 10.7 | 67.60
Modify | 0.00053153 | 0.00071381 | 0.0010268 | 0.0 | 0.25
Other | | 0.07105 | | | 24.81
Nlocal: 6.75 ave 9 max 5 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 26.25 ave 28 max 25 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 16.5 ave 23 max 10 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 66
Ave neighs/atom = 2.4444444
Ave special neighs/atom = 2
Neighbor list builds = 244
Dangerous builds = 0
Total wall time: 0:00:00

48
examples/replicate/log.7Jan22.replicate.g++.1 → examples/replicate/log.6May24.replicate.cnt.g++.1
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@ -1,4 +1,4 @@
LAMMPS (7 Jan 2022)
LAMMPS (17 Apr 2024)
# three orthogonal periodic CNTs
# demo for replicating triply looped system
# infinite loops in x, y, z
@ -37,6 +37,8 @@ Reading data file ...
12 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (0 0 0) to (80.96 80.96 80.96)
1 by 1 by 1 MPI processor grid
reading bonds ...
4752 bonds
reading angles ...
@ -52,11 +54,11 @@ Finding 1-2 1-3 1-4 neighbors ...
6 = max # of 1-3 neighbors
18 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.003 seconds
read_data CPU = 0.115 seconds
special bonds CPU = 0.002 seconds
read_data CPU = 0.056 seconds
replicate 2 2 2 bondlist
Replicating atoms ...
replicate 2 2 2 bond/periodic
Replication is creating a 2x2x2 = 8 times larger system...
orthogonal box = (0 0 0) to (161.92 161.92 161.92)
1 by 1 by 1 MPI processor grid
bounding box image = (0 0 0) to (0 0 0)
@ -74,15 +76,15 @@ Finding 1-2 1-3 1-4 neighbors ...
6 = max # of 1-3 neighbors
18 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.021 seconds
replicate CPU = 0.052 seconds
special bonds CPU = 0.012 seconds
replicate CPU = 0.027 seconds
fix 1 all nve
run 100
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 0 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
@ -93,26 +95,26 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Inconsistent image flags (../domain.cpp:814)
WARNING: Inconsistent image flags (../domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 51.87 | 51.87 | 51.87 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -14266.189 1466925.5 1452659.3 -29908.753
100 2155.9128 -17224.188 1306769.8 1452409 1985.2082
Loop time of 15.0972 on 1 procs for 100 steps with 25344 atoms
Step Temp E_pair E_mol TotEng Press
0 0 -14266.189 1466925.5 1452659.3 -29908.753
100 2155.9128 -17224.188 1306769.8 1452409 1985.2082
Loop time of 5.0155 on 1 procs for 100 steps with 25344 atoms
Performance: 0.572 ns/day, 41.937 hours/ns, 6.624 timesteps/s
Performance: 1.723 ns/day, 13.932 hours/ns, 19.938 timesteps/s, 505.314 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.7175 | 3.7175 | 3.7175 | 0.0 | 24.62
Bond | 11.222 | 11.222 | 11.222 | 0.0 | 74.33
Neigh | 0.1032 | 0.1032 | 0.1032 | 0.0 | 0.68
Comm | 0.014487 | 0.014487 | 0.014487 | 0.0 | 0.10
Output | 0.00010894 | 0.00010894 | 0.00010894 | 0.0 | 0.00
Modify | 0.027112 | 0.027112 | 0.027112 | 0.0 | 0.18
Other | | 0.01274 | | | 0.08
Pair | 1.6557 | 1.6557 | 1.6557 | 0.0 | 33.01
Bond | 3.2813 | 3.2813 | 3.2813 | 0.0 | 65.42
Neigh | 0.047025 | 0.047025 | 0.047025 | 0.0 | 0.94
Comm | 0.0085317 | 0.0085317 | 0.0085317 | 0.0 | 0.17
Output | 7.8551e-05 | 7.8551e-05 | 7.8551e-05 | 0.0 | 0.00
Modify | 0.014635 | 0.014635 | 0.014635 | 0.0 | 0.29
Other | | 0.008159 | | | 0.16
Nlocal: 25344 ave 25344 max 25344 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -129,4 +131,4 @@ Dangerous builds = 0
# write_restart replicate.restart
# write_data replicate.data
Total wall time: 0:00:15
Total wall time: 0:00:05

49
examples/replicate/log.7Jan22.replicate.g++.4 → examples/replicate/log.6May24.replicate.cnt.g++.4
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@ -1,4 +1,5 @@
LAMMPS (7 Jan 2022)
LAMMPS (17 Apr 2024)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
# three orthogonal periodic CNTs
# demo for replicating triply looped system
# infinite loops in x, y, z
@ -37,6 +38,8 @@ Reading data file ...
12 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (0 0 0) to (80.96 80.96 80.96)
1 by 2 by 2 MPI processor grid
reading bonds ...
4752 bonds
reading angles ...
@ -53,10 +56,10 @@ Finding 1-2 1-3 1-4 neighbors ...
18 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.315 seconds
read_data CPU = 0.064 seconds
replicate 2 2 2 bondlist
Replicating atoms ...
replicate 2 2 2 bond/periodic
Replication is creating a 2x2x2 = 8 times larger system...
orthogonal box = (0 0 0) to (161.92 161.92 161.92)
1 by 2 by 2 MPI processor grid
bounding box image = (0 0 0) to (0 0 0)
@ -74,15 +77,15 @@ Finding 1-2 1-3 1-4 neighbors ...
6 = max # of 1-3 neighbors
18 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.007 seconds
replicate CPU = 0.020 seconds
special bonds CPU = 0.004 seconds
replicate CPU = 0.012 seconds
fix 1 all nve
run 100
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 0 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
@ -93,26 +96,26 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Inconsistent image flags (../domain.cpp:814)
WARNING: Inconsistent image flags (../domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 28.69 | 28.69 | 28.69 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -14266.189 1466925.5 1452659.3 -29908.753
100 2155.9128 -17224.188 1306769.8 1452409 1985.2082
Loop time of 4.13195 on 4 procs for 100 steps with 25344 atoms
Step Temp E_pair E_mol TotEng Press
0 0 -14266.189 1466925.5 1452659.3 -29908.753
100 2155.9128 -17224.188 1306769.8 1452409 1985.2082
Loop time of 1.3667 on 4 procs for 100 steps with 25344 atoms
Performance: 2.091 ns/day, 11.478 hours/ns, 24.202 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 6.322 ns/day, 3.796 hours/ns, 73.169 timesteps/s, 1.854 Matom-step/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.99372 | 1.014 | 1.0672 | 3.1 | 24.54
Bond | 2.9449 | 2.9795 | 3.0136 | 2.0 | 72.11
Neigh | 0.026695 | 0.026706 | 0.026716 | 0.0 | 0.65
Comm | 0.012404 | 0.099546 | 0.15425 | 18.7 | 2.41
Output | 4.3822e-05 | 5.0693e-05 | 7.0516e-05 | 0.0 | 0.00
Modify | 0.0074219 | 0.0074887 | 0.0075411 | 0.1 | 0.18
Other | | 0.004616 | | | 0.11
Pair | 0.43424 | 0.43539 | 0.43741 | 0.2 | 31.86
Bond | 0.88613 | 0.89013 | 0.90094 | 0.7 | 65.13
Neigh | 0.013198 | 0.013199 | 0.013201 | 0.0 | 0.97
Comm | 0.010742 | 0.020522 | 0.02546 | 4.1 | 1.50
Output | 3.2788e-05 | 3.6302e-05 | 4.4556e-05 | 0.0 | 0.00
Modify | 0.0042029 | 0.0042366 | 0.004267 | 0.0 | 0.31
Other | | 0.003188 | | | 0.23
Nlocal: 6336 ave 6336 max 6336 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -129,4 +132,4 @@ Dangerous builds = 0
# write_restart replicate.restart
# write_data replicate.data
Total wall time: 0:00:04
Total wall time: 0:00:01