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Merge pull request #4614 from akohlmey/collected-small-fixes

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Collected small changes and fixes
This commit is contained in:
Axel Kohlmeyer
2025-06-12 23:59:06 -04:00
committed by GitHub
parent 66684deb9f 349def92d2
commit 949bac6b4a
22 changed files with 80 additions and 2009 deletions
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1
examples/PACKAGES/neighbor-swap/MoCoNiVFeAlCr_2nn.meam
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../../../potentials/MoCoNiVFeAlCr_2nn.meam

46
examples/PACKAGES/neighbor-swap/in.KMC_pulse_center
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# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
create_atoms 1 region whole
replicate 6 16 6
region puck block INF INF 7 9 INF INF
set region puck type 2
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124 loop geom
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
#write_data pulse_center.data

47
examples/PACKAGES/neighbor-swap/in.KMC_pulse_edge
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# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
create_atoms 1 region whole
replicate 6 16 6
region puck block INF INF INF 2 INF INF
set region puck type 2
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124 loop geom
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
#write_data pulse_end.data

1
examples/PACKAGES/neighbor-swap/library_2nn.meam
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../../../potentials/library_2nn.meam

154
examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_center.g++.1
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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
1 by 1 by 1 MPI processor grid
create_atoms 1 region whole
Created 4 atoms
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
create_atoms CPU = 0.000 seconds
replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
1 by 1 by 1 MPI processor grid
2304 atoms
replicate CPU = 0.000 seconds
region puck block INF INF 7 9 INF INF
set region puck type 2
Setting atom values ...
360 settings made for type
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 18 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -9674.3728 0 -9674.3728 -212400.94
Loop time of 1.202e-06 on 1 procs for 0 steps with 2304 atoms
0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.202e-06 | | |100.00
Nlocal: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4735 ave 4735 max 4735 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99072 ave 99072 max 99072 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 198144 ave 198144 max 198144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
0 2400 -187517.52 -187403.07 -187750.14 -187399.35 22.572 60.192 22.572 30667.534 -9674.3728 0 0
100 1664.9956 14000 14280.682 15095.077 12624.241 21.635315 57.726568 21.64791 27036.778 -9592.8978 24 22
200 1560.0093 -5452.2434 -5749.5816 -2957.4228 -7649.7258 21.734212 58.085959 21.724853 27426.596 -9562.8822 48 45
300 1586.4553 2030.9253 2776.4677 775.50538 2540.803 21.678654 58.101753 21.654423 27275.215 -9571.1308 72 66
400 1603.6896 -223.16773 156.17673 -478.47929 -347.20061 21.701021 58.098904 21.657752 27306.213 -9576.4456 96 90
500 1618.236 -925.51874 -1640.9078 451.6228 -1587.2713 21.718334 58.042685 21.666081 27312.054 -9581.2045 120 110
600 1581.9995 290.10126 1359.1314 1407.5434 -1896.371 21.679813 58.086147 21.692118 27316.815 -9570.4803 144 132
700 1568.3261 1387.3472 938.81523 2159.3686 1063.8577 21.685928 58.075626 21.67273 27295.153 -9566.2914 168 155
800 1607.1531 46.792964 -453.90265 -1533.3908 2127.6723 21.685188 58.202356 21.628338 27297.753 -9577.7848 192 177
900 1573.4747 -84.225488 548.90935 -1356.7479 555.16208 21.69634 58.150052 21.651847 27316.908 -9567.7039 216 196
1000 1609.2136 1215.0833 764.08936 3301.0811 -419.92053 21.683731 58.000401 21.68726 27275.31 -9578.2843 240 219
Loop time of 31.6263 on 1 procs for 1000 steps with 2304 atoms
Performance: 5.464 ns/day, 4.393 hours/ns, 31.619 timesteps/s, 72.851 katom-step/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 28.487 | 28.487 | 28.487 | 0.0 | 90.07
Neigh | 0.22789 | 0.22789 | 0.22789 | 0.0 | 0.72
Comm | 0.010808 | 0.010808 | 0.010808 | 0.0 | 0.03
Output | 0.00033526 | 0.00033526 | 0.00033526 | 0.0 | 0.00
Modify | 2.8963 | 2.8963 | 2.8963 | 0.0 | 9.16
Other | | 0.003905 | | | 0.01
Nlocal: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4750 ave 4750 max 4750 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 130023 ave 130023 max 130023 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 260046 ave 260046 max 260046 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 260046
Ave neighs/atom = 112.86719
Neighbor list builds = 65
Dangerous builds = 0
#write_data pulse_center.data
Total wall time: 0:00:31

154
examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_center.g++.4
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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
1 by 2 by 2 MPI processor grid
create_atoms 1 region whole
Created 4 atoms
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
create_atoms CPU = 0.000 seconds
replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
1 by 4 by 1 MPI processor grid
2304 atoms
replicate CPU = 0.000 seconds
region puck block INF INF 7 9 INF INF
set region puck type 2
Setting atom values ...
360 settings made for type
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 18 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -9674.3728 0 -9674.3728 -212400.94
Loop time of 1.422e-06 on 4 procs for 0 steps with 2304 atoms
35.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.422e-06 | | |100.00
Nlocal: 576 ave 576 max 576 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2131 ave 2131 max 2131 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 24768 ave 24768 max 24768 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 49536 ave 49536 max 49536 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
0 2400 -187517.52 -187403.09 -187750.05 -187399.42 22.572 60.192 22.572 30667.534 -9674.3728 0 0
100 1668.8754 13300.763 12419.304 15568.772 11914.212 21.636248 57.724775 21.647685 27036.823 -9594.7526 24 23
200 1584.9699 -5686.0414 -4741.8496 -5914.7681 -6401.5064 21.729384 58.060532 21.730736 27415.923 -9571.0639 48 46
300 1582.0473 2806.2983 3413.4122 2716.0124 2289.4702 21.6679 58.033587 21.694744 27280.402 -9570.5549 72 69
400 1582.5825 845.29268 -849.61221 2123.5339 1261.9563 21.676298 58.14253 21.656418 27293.905 -9570.7948 96 93
500 1591.7285 -501.17955 1151.9743 -1719.3712 -936.14174 21.696367 58.157211 21.648308 27315.839 -9573.5089 120 116
600 1610.708 -821.74669 -1002.4957 291.88502 -1754.6294 21.730338 58.008213 21.661226 27304.8 -9579.5573 144 138
700 1598.5176 -590.00633 -1844.42 408.97706 -334.57602 21.712908 57.96131 21.698129 27307.281 -9575.8973 168 162
800 1584.3478 330.16711 666.88818 74.698331 248.91482 21.650908 58.045055 21.719838 27295.933 -9571.9268 192 186
900 1557.9946 1471.1207 2124.6512 1526.9937 761.71731 21.645578 58.156083 21.681637 27293.323 -9564.4385 216 207
1000 1582.5312 379.57005 -602.96446 2696.737 -955.06238 21.655418 58.231248 21.649581 27300.598 -9571.9879 240 227
Loop time of 9.1632 on 4 procs for 1000 steps with 2304 atoms
Performance: 18.858 ns/day, 1.273 hours/ns, 109.132 timesteps/s, 251.440 katom-step/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.867 | 7.9923 | 8.1311 | 4.3 | 87.22
Neigh | 0.054997 | 0.057518 | 0.060145 | 1.0 | 0.63
Comm | 0.017529 | 0.14801 | 0.27408 | 29.5 | 1.62
Output | 0.00015963 | 0.00017216 | 0.00020869 | 0.0 | 0.00
Modify | 0.95227 | 0.96325 | 0.9917 | 1.7 | 10.51
Other | | 0.001983 | | | 0.02
Nlocal: 576 ave 609 max 540 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2161.5 ave 2173 max 2151 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 32450.2 ave 35422 max 29271 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 64900.5 ave 70800 max 58684 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 259602
Ave neighs/atom = 112.67448
Neighbor list builds = 62
Dangerous builds = 0
#write_data pulse_center.data
Total wall time: 0:00:09

155
examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_edge.g++.1
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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
1 by 1 by 1 MPI processor grid
create_atoms 1 region whole
Created 4 atoms
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
create_atoms CPU = 0.000 seconds
replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
1 by 1 by 1 MPI processor grid
2304 atoms
replicate CPU = 0.000 seconds
region puck block INF INF INF 2 INF INF
set region puck type 2
Setting atom values ...
360 settings made for type
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 18 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -9674.3728 0 -9674.3728 -212400.94
Loop time of 1.232e-06 on 1 procs for 0 steps with 2304 atoms
81.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.232e-06 | | |100.00
Nlocal: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4735 ave 4735 max 4735 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99072 ave 99072 max 99072 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 198144 ave 198144 max 198144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124 loop geom
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
0 2400 -187517.52 -187464.47 -188202.62 -186885.48 22.572 60.192 22.572 30667.534 -9674.3728 0 0
100 1665.6154 14281.316 14426.547 14555.867 13861.534 21.637238 57.719793 21.637281 27022.733 -9594.4303 24 24
200 1603.3309 -7325.7341 -8878.1524 -5333.0485 -7766.0015 21.710246 58.122827 21.725933 27415.106 -9577.4545 48 48
300 1603.2974 207.19165 1983.4565 -1841.9518 480.07024 21.678227 58.079126 21.674033 27288.745 -9577.6391 72 69
400 1600.1515 810.95054 1087.969 802.04946 542.83316 21.683731 58.045848 21.678505 27285.662 -9576.6508 96 92
500 1629.8313 -2808.1005 -3197.9357 310.89931 -5537.265 21.683924 58.090375 21.697076 27330.229 -9585.5435 120 113
600 1598.8232 -67.845623 -1573.0718 -1526.7607 2896.2957 21.70213 58.12191 21.653853 27313.504 -9576.4147 144 137
700 1607.2185 154.66718 -1777.2469 2566.4705 -325.22208 21.712408 57.971553 21.678708 27287.033 -9579.1772 168 158
800 1582.559 -891.23631 -632.46037 -636.88203 -1404.3665 21.671936 58.127004 21.678224 27308.594 -9571.6663 192 180
900 1586.7172 -617.17083 -2495.5378 -2302.8766 2946.9018 21.658489 58.181921 21.668968 27305.771 -9572.9641 216 204
1000 1607.563 -389.8113 810.4908 298.84287 -2278.7676 21.624573 58.076745 21.724272 27283.183 -9579.5034 240 227
Loop time of 31.7733 on 1 procs for 1000 steps with 2304 atoms
Performance: 5.439 ns/day, 4.413 hours/ns, 31.473 timesteps/s, 72.514 katom-step/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 28.604 | 28.604 | 28.604 | 0.0 | 90.02
Neigh | 0.21293 | 0.21293 | 0.21293 | 0.0 | 0.67
Comm | 0.010645 | 0.010645 | 0.010645 | 0.0 | 0.03
Output | 0.00033194 | 0.00033194 | 0.00033194 | 0.0 | 0.00
Modify | 2.9411 | 2.9411 | 2.9411 | 0.0 | 9.26
Other | | 0.00448 | | | 0.01
Nlocal: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4748 ave 4748 max 4748 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 130301 ave 130301 max 130301 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 260602 ave 260602 max 260602 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 260602
Ave neighs/atom = 113.10851
Neighbor list builds = 62
Dangerous builds = 0
#write_data pulse_end.data
Total wall time: 0:00:31

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examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_edge.g++.4
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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
1 by 2 by 2 MPI processor grid
create_atoms 1 region whole
Created 4 atoms
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
create_atoms CPU = 0.000 seconds
replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
1 by 4 by 1 MPI processor grid
2304 atoms
replicate CPU = 0.000 seconds
region puck block INF INF INF 2 INF INF
set region puck type 2
Setting atom values ...
360 settings made for type
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 18 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -9674.3728 0 -9674.3728 -212400.94
Loop time of 1.53e-06 on 4 procs for 0 steps with 2304 atoms
65.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.53e-06 | | |100.00
Nlocal: 576 ave 576 max 576 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2131 ave 2131 max 2131 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 24768 ave 24768 max 24768 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 49536 ave 49536 max 49536 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124 loop geom
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
0 2400 -187517.52 -187464.47 -188202.62 -186885.48 22.572 60.192 22.572 30667.534 -9674.3728 0 0
100 1665.569 14271.813 14638.855 14316.569 13860.016 21.63675 57.721065 21.637799 27023.366 -9594.291 24 24
200 1598.6479 -6990.8349 -8574.1986 -5033.6147 -7364.6916 21.708963 58.123129 21.724821 27412.223 -9575.7322 48 47
300 1604.388 456.43285 1926.408 -1214.1721 657.0626 21.673369 58.090421 21.671716 27285.018 -9577.698 72 70
400 1601.1591 1303.6721 703.88473 1137.6607 2069.471 21.684004 58.049595 21.671161 27278.522 -9576.4811 96 94
500 1623.6044 -2243.2478 -2084.532 320.87709 -4966.0885 21.686171 58.097101 21.695911 27334.758 -9583.1878 120 118
600 1587.2041 421.60034 190.88741 -328.76599 1402.6796 21.712439 58.086039 21.655927 27312.229 -9572.559 144 141
700 1591.2923 32.327829 -2893.2353 1839.7574 1150.4614 21.719102 57.999862 21.666164 27292.974 -9573.9009 168 165
800 1580.8587 -105.51079 654.26389 -160.04168 -810.75457 21.670225 58.109245 21.684683 27306.229 -9570.6482 192 186
900 1570.7648 1290.088 1252.3689 255.62548 2362.2695 21.68101 58.100507 21.658755 27283.051 -9567.9864 216 209
1000 1598.1483 -125.35291 -3626.5479 3404.789 -154.29983 21.720146 57.952942 21.686111 27297.313 -9576.2975 240 231
Loop time of 9.17241 on 4 procs for 1000 steps with 2304 atoms
Performance: 18.839 ns/day, 1.274 hours/ns, 109.023 timesteps/s, 251.188 katom-step/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7477 | 8.0143 | 8.1344 | 5.5 | 87.37
Neigh | 0.050543 | 0.056882 | 0.05986 | 1.6 | 0.62
Comm | 0.069784 | 0.16898 | 0.40996 | 34.2 | 1.84
Output | 0.00015612 | 0.0001707 | 0.00021249 | 0.0 | 0.00
Modify | 0.90628 | 0.93003 | 0.96157 | 2.2 | 10.14
Other | | 0.002053 | | | 0.02
Nlocal: 576 ave 614 max 505 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2165.75 ave 2204 max 2132 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Neighs: 32430.8 ave 35552 max 26564 min
Histogram: 1 0 0 0 0 0 1 0 0 2
FullNghs: 64861.5 ave 71111 max 53164 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 259446
Ave neighs/atom = 112.60677
Neighbor list builds = 62
Dangerous builds = 0
#write_data pulse_end.data
Total wall time: 0:00:09