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Merge pull request #2418 from akohlmey/collected-small-changes 

Collected small changes and bugfixes for the stable release
This commit is contained in:
Axel Kohlmeyer 2020-10-14 17:45:10 -04:00 committed by GitHub
parent 28641bcbc7 61c33e5622
commit 89842fc7c4
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GPG Key ID: 4AEE18F83AFDEB23
116 changed files with 34330 additions and 33736 deletions
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1
bench/POTENTIALS/CH.rebo Symbolic link
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../../potentials/CH.rebo

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bench/POTENTIALS/data.eff
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bench/POTENTIALS/in.rebo
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@ -11,7 +11,7 @@ neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.airebo C H
pair_coeff * * CH.rebo C H
velocity all create 300.0 761341

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bench/POTENTIALS/log.16Mar18.airebo.1
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00154901 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139299.7 0 -138034.03 7998.7287
10 161.33916 -138711.85 0 -138031.17 33242.273
20 208.59505 -138911.77 0 -138031.73 -3199.2371
30 139.73485 -138617.76 0 -138028.23 10890.529
40 142.15332 -138628.03 0 -138028.3 14614.022
50 114.21945 -138509.87 0 -138027.98 24700.885
60 164.9432 -138725.08 0 -138029.19 35135.722
70 162.14928 -138714.86 0 -138030.77 5666.4609
80 157.17575 -138694.81 0 -138031.7 19838.161
90 196.16354 -138859.65 0 -138032.05 -7942.9718
100 178.30378 -138783.8 0 -138031.55 31012.15
Loop time of 60.9424 on 1 procs for 100 steps with 32640 atoms
Performance: 0.071 ns/day, 338.569 hours/ns, 1.641 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 55.299 | 55.299 | 55.299 | 0.0 | 90.74
Neigh | 5.5777 | 5.5777 | 5.5777 | 0.0 | 9.15
Comm | 0.027658 | 0.027658 | 0.027658 | 0.0 | 0.05
Output | 0.0011463 | 0.0011463 | 0.0011463 | 0.0 | 0.00
Modify | 0.024684 | 0.024684 | 0.024684 | 0.0 | 0.04
Other | | 0.012 | | | 0.02
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48190 ave 48190 max 48190 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.22179e+07 ave 2.22179e+07 max 2.22179e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22217870
Ave neighs/atom = 680.695
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:01:02

87
bench/POTENTIALS/log.16Mar18.airebo.4
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.00070262 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 29.37 | 29.75 | 30.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139299.7 0 -138034.03 7998.7287
10 161.33916 -138711.85 0 -138031.17 33242.273
20 208.59505 -138911.77 0 -138031.73 -3199.2371
30 139.73485 -138617.76 0 -138028.23 10890.529
40 142.15332 -138628.03 0 -138028.3 14614.022
50 114.21945 -138509.87 0 -138027.98 24700.885
60 164.9432 -138725.08 0 -138029.19 35135.722
70 162.14928 -138714.86 0 -138030.77 5666.4609
80 157.17575 -138694.81 0 -138031.7 19838.161
90 196.16354 -138859.65 0 -138032.05 -7942.9718
100 178.30378 -138783.8 0 -138031.55 31012.15
Loop time of 16.768 on 4 procs for 100 steps with 32640 atoms
Performance: 0.258 ns/day, 93.156 hours/ns, 5.964 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.538 | 14.589 | 14.654 | 1.3 | 87.00
Neigh | 1.8853 | 1.8992 | 1.9159 | 0.8 | 11.33
Comm | 0.18073 | 0.25896 | 0.31361 | 10.6 | 1.54
Output | 0.00050807 | 0.0040419 | 0.0077746 | 5.6 | 0.02
Modify | 0.0094635 | 0.0096973 | 0.0099616 | 0.2 | 0.06
Other | | 0.007481 | | | 0.04
Nlocal: 8160 ave 8174 max 8146 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 22614.5 ave 22629 max 22601 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5.55447e+06 ave 5.56557e+06 max 5.54193e+06 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 22217870
Ave neighs/atom = 680.695
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:17

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bench/POTENTIALS/log.16Mar18.reaxc.1
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
1 by 1 by 1 MPI processor grid
reading atoms ...
58 atoms
replicate 7 8 10
orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
1 by 1 by 1 MPI processor grid
32480 atoms
Time spent = 0.00162625 secs
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 1727 | 1727 | 1727 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5637 -3203096.6
10 299.37479 28983.59 -3232075.2 21746.778 -23987.41 7610.2967 -3203091.6
20 295.5855 28616.735 -3231710.1 18178.568 -10871.882 10603.247 -3203093.3
30 289.48845 28026.457 -3231123.2 12146.362 4985.5572 13364.455 -3203096.8
40 282.66404 27365.76 -3230467.5 4284.2794 18132.771 14133.719 -3203101.7
50 274.97005 26620.876 -3229730.4 -3719.11 25519.692 12551.708 -3203109.5
60 266.11301 25763.393 -3228883.8 -9271.4049 27307.216 9753.2509 -3203120.4
70 259.3263 25106.346 -3228237.2 -11150.726 24238.382 6578.5306 -3203130.8
80 260.33956 25204.444 -3228344.2 -9576.6006 16737.65 3454.5747 -3203139.7
90 269.90199 26130.219 -3229275.5 -5906.376 5246.1572 467.31789 -3203145.3
100 280.76717 27182.117 -3230330.6 -1363.8281 -8133.2509 -1689.7711 -3203148.5
Loop time of 437.886 on 1 procs for 100 steps with 32480 atoms
Performance: 0.002 ns/day, 12163.512 hours/ns, 0.228 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 350.29 | 350.29 | 350.29 | 0.0 | 80.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.026264 | 0.026264 | 0.026264 | 0.0 | 0.01
Output | 0.0024614 | 0.0024614 | 0.0024614 | 0.0 | 0.00
Modify | 87.55 | 87.55 | 87.55 | 0.0 | 19.99
Other | | 0.01296 | | | 0.00
Nlocal: 32480 ave 32480 max 32480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45128 ave 45128 max 45128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.27781e+07 ave 1.27781e+07 max 1.27781e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12778082
Ave neighs/atom = 393.414
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:07:24

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bench/POTENTIALS/log.16Mar18.reaxc.4
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
2 by 2 by 1 MPI processor grid
reading atoms ...
58 atoms
replicate 7 8 10
orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
1 by 2 by 2 MPI processor grid
32480 atoms
Time spent = 0.000803709 secs
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 647 | 647 | 647 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5638 -3203096.6
10 299.37479 28983.59 -3232075.2 21746.773 -23987.409 7610.2911 -3203091.6
20 295.58552 28616.737 -3231710.1 18178.576 -10871.874 10603.421 -3203093.3
30 289.48843 28026.455 -3231123.3 12146.158 4985.3436 13364.461 -3203096.8
40 282.66409 27365.764 -3230467.5 4284.5077 18133.151 14133.949 -3203101.7
50 274.97008 26620.879 -3229730.3 -3718.536 25520.328 12552.195 -3203109.5
60 266.11301 25763.393 -3228883.7 -9271.0381 27307.591 9753.5339 -3203120.4
70 259.32631 25106.348 -3228237.1 -11150.314 24238.962 6578.8636 -3203130.8
80 260.33966 25204.453 -3228344.1 -9575.5709 16738.467 3455.2525 -3203139.7
90 269.90213 26130.231 -3229275.5 -5906.0456 5246.2122 467.43473 -3203145.2
100 280.76727 27182.127 -3230330.6 -1363.1733 -8132.8726 -1689.3275 -3203148.4
Loop time of 128.275 on 4 procs for 100 steps with 32480 atoms
Performance: 0.007 ns/day, 3563.196 hours/ns, 0.780 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 92.314 | 97.932 | 103.53 | 44.1 | 76.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.039458 | 5.6409 | 11.263 | 184.0 | 4.40
Output | 0.00086117 | 0.0010868 | 0.0016167 | 0.9 | 0.00
Modify | 24.687 | 24.688 | 24.69 | 0.0 | 19.25
Other | | 0.01323 | | | 0.01
Nlocal: 8120 ave 8120 max 8120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 21992 ave 21992 max 21992 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3.48274e+06 ave 3.48274e+06 max 3.48274e+06 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13930976
Ave neighs/atom = 428.909
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:02:10

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bench/POTENTIALS/log.16Mar18.rebo.1
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00151849 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.48 0 -137176.8 2464.5258
10 179.38052 -137930.92 0 -137174.12 15656.95
20 206.87725 -138046.63 0 -137173.83 -24042.005
30 150.80048 -137807.07 0 -137170.86 -16524.069
40 173.25027 -137902 0 -137171.07 -5716.7297
50 151.80552 -137812.01 0 -137171.55 3481.1096
60 199.08762 -138013.46 0 -137173.53 17882.906
70 217.8592 -138093.51 0 -137174.38 -12269.648
80 202.37612 -138029.05 0 -137175.24 -7622.1573
90 194.905 -137996.68 0 -137174.4 -32267.297
100 185.17966 -137954.16 0 -137172.9 -6902.1493
Loop time of 5.17257 on 1 procs for 100 steps with 32640 atoms
Performance: 0.835 ns/day, 28.737 hours/ns, 19.333 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3427 | 3.3427 | 3.3427 | 0.0 | 64.62
Neigh | 1.7764 | 1.7764 | 1.7764 | 0.0 | 34.34
Comm | 0.017914 | 0.017914 | 0.017914 | 0.0 | 0.35
Output | 0.0011199 | 0.0011199 | 0.0011199 | 0.0 | 0.02
Modify | 0.024357 | 0.024357 | 0.024357 | 0.0 | 0.47
Other | | 0.01004 | | | 0.19
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26460 ave 26460 max 26460 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4902132
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:05

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bench/POTENTIALS/log.16Mar18.rebo.4
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.000838995 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.48 0 -137176.8 2464.5258
10 179.38052 -137930.92 0 -137174.12 15656.95
20 206.87725 -138046.63 0 -137173.83 -24042.005
30 150.80048 -137807.07 0 -137170.86 -16524.069
40 173.25027 -137902 0 -137171.07 -5716.7297
50 151.80552 -137812.01 0 -137171.55 3481.1096
60 199.08762 -138013.46 0 -137173.53 17882.906
70 217.8592 -138093.51 0 -137174.38 -12269.648
80 202.37612 -138029.05 0 -137175.24 -7622.1573
90 194.905 -137996.68 0 -137174.4 -32267.297
100 185.17966 -137954.16 0 -137172.9 -6902.1493
Loop time of 1.52214 on 4 procs for 100 steps with 32640 atoms
Performance: 2.838 ns/day, 8.456 hours/ns, 65.697 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.88531 | 0.90632 | 0.92546 | 1.6 | 59.54
Neigh | 0.53954 | 0.54258 | 0.54621 | 0.3 | 35.65
Comm | 0.035654 | 0.058364 | 0.079543 | 7.0 | 3.83
Output | 0.00048494 | 0.00065351 | 0.0011017 | 0.0 | 0.04
Modify | 0.0090034 | 0.0090633 | 0.0091114 | 0.0 | 0.60
Other | | 0.005168 | | | 0.34
Nlocal: 8160 ave 8163 max 8157 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11605.8 ave 11615 max 11593 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.22553e+06 ave 1.22734e+06 max 1.22455e+06 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 4902132
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:01

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bench/POTENTIALS/log.16Mar18.spce.1
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
1 by 1 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
replicate 2 4 1
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
1 by 1 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Time spent = 0.0105426 secs
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268801
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0331015
estimated relative force accuracy = 9.96841e-05
using double precision FFTs
3d grid and FFT values/proc = 91977 55296
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.8
ghost atom cutoff = 11.8
binsize = 5.9, bins = 13 25 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 105.1 | 105.1 | 105.1 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 516.17807
50 264.98553 -136986.74 0 -118030.61 -440.29256
100 274.45966 -136364.57 0 -116730.69 -128.61949
Loop time of 20.172 on 1 procs for 100 steps with 36000 atoms
Performance: 0.857 ns/day, 28.017 hours/ns, 4.957 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.818 | 15.818 | 15.818 | 0.0 | 78.41
Bond | 7.8201e-05 | 7.8201e-05 | 7.8201e-05 | 0.0 | 0.00
Kspace | 1.966 | 1.966 | 1.966 | 0.0 | 9.75
Neigh | 2.0639 | 2.0639 | 2.0639 | 0.0 | 10.23
Comm | 0.043918 | 0.043918 | 0.043918 | 0.0 | 0.22
Output | 0.00025153 | 0.00025153 | 0.00025153 | 0.0 | 0.00
Modify | 0.27056 | 0.27056 | 0.27056 | 0.0 | 1.34
Other | | 0.009522 | | | 0.05
Nlocal: 36000 ave 36000 max 36000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 56963 ave 56963 max 56963 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.24625e+07 ave 1.24625e+07 max 1.24625e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12462451
Ave neighs/atom = 346.179
Ave special neighs/atom = 2
Neighbor list builds = 9
Dangerous builds = 6
Total wall time: 0:00:20

132
bench/POTENTIALS/log.16Mar18.spce.4
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@ -1,132 +0,0 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
2 by 2 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
replicate 2 4 1
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
1 by 4 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Time spent = 0.00535488 secs
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268801
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0331015
estimated relative force accuracy = 9.96841e-05
using double precision FFTs
3d grid and FFT values/proc = 27993 13824
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.8
ghost atom cutoff = 11.8
binsize = 5.9, bins = 13 25 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 37.74 | 37.74 | 37.74 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 516.17807
50 264.98553 -136986.74 0 -118030.61 -440.29256
100 274.45966 -136364.57 0 -116730.69 -128.61949
Loop time of 5.43807 on 4 procs for 100 steps with 36000 atoms
Performance: 3.178 ns/day, 7.553 hours/ns, 18.389 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0016 | 4.0968 | 4.1706 | 3.3 | 75.34
Bond | 7.1049e-05 | 8.5771e-05 | 0.00010586 | 0.0 | 0.00
Kspace | 0.56386 | 0.63614 | 0.73036 | 8.3 | 11.70
Neigh | 0.52575 | 0.52587 | 0.52594 | 0.0 | 9.67
Comm | 0.045847 | 0.047308 | 0.048331 | 0.4 | 0.87
Output | 9.1314e-05 | 0.00012183 | 0.00021172 | 0.0 | 0.00
Modify | 0.12561 | 0.1258 | 0.12605 | 0.1 | 2.31
Other | | 0.005944 | | | 0.11
Nlocal: 9000 ave 9002 max 8998 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 24134.2 ave 24184 max 24062 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 3.11561e+06 ave 3.11676e+06 max 3.11446e+06 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 12462451
Ave neighs/atom = 346.179
Ave special neighs/atom = 2
Neighbor list builds = 9
Dangerous builds = 6
Total wall time: 0:00:05

38
bench/POTENTIALS/log.16Mar18.adp.1 → bench/POTENTIALS/log.9Oct20.adp.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in ADP
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00184107 secs
create_atoms CPU = 0.002 seconds
pair_style adp
pair_coeff * * Ni.adp Ni
Reading adp potential file Ni.adp with DATE: 2011-06-20
velocity all create 1600.0 376847 loop geom
@ -41,35 +41,35 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 27.56 | 27.56 | 27.56 Mbytes
Per MPI rank memory allocation (min/avg/max) = 27.57 | 27.57 | 27.57 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.105
100 793.05485 -139023.13 0 -135742.9 32175.694
Loop time of 11.9854 on 1 procs for 100 steps with 32000 atoms
Loop time of 11.0841 on 1 procs for 100 steps with 32000 atoms
Performance: 3.604 ns/day, 6.659 hours/ns, 8.344 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 3.897 ns/day, 6.158 hours/ns, 9.022 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.447 | 11.447 | 11.447 | 0.0 | 95.51
Neigh | 0.48465 | 0.48465 | 0.48465 | 0.0 | 4.04
Comm | 0.019317 | 0.019317 | 0.019317 | 0.0 | 0.16
Output | 0.00011063 | 0.00011063 | 0.00011063 | 0.0 | 0.00
Modify | 0.025319 | 0.025319 | 0.025319 | 0.0 | 0.21
Other | | 0.009125 | | | 0.08
Pair | 10.597 | 10.597 | 10.597 | 0.0 | 95.60
Neigh | 0.43765 | 0.43765 | 0.43765 | 0.0 | 3.95
Comm | 0.018561 | 0.018561 | 0.018561 | 0.0 | 0.17
Output | 0.0001123 | 0.0001123 | 0.0001123 | 0.0 | 0.00
Modify | 0.023261 | 0.023261 | 0.023261 | 0.0 | 0.21
Other | | 0.00792 | | | 0.07
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Nghost: 19911.0 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.33704e+06 ave 1.33704e+06 max 1.33704e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1337035
Ave neighs/atom = 41.7823
Ave neighs/atom = 41.782344
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:12
Total wall time: 0:00:11

36
bench/POTENTIALS/log.16Mar18.adp.4 → bench/POTENTIALS/log.9Oct20.adp.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in ADP
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000586033 secs
create_atoms CPU = 0.001 seconds
pair_style adp
pair_coeff * * Ni.adp Ni
Reading adp potential file Ni.adp with DATE: 2011-06-20
velocity all create 1600.0 376847 loop geom
@ -45,30 +45,30 @@ Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.105
100 793.05485 -139023.13 0 -135742.9 32175.694
Loop time of 3.49752 on 4 procs for 100 steps with 32000 atoms
Loop time of 3.54402 on 4 procs for 100 steps with 32000 atoms
Performance: 12.352 ns/day, 1.943 hours/ns, 28.592 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 12.190 ns/day, 1.969 hours/ns, 28.217 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3203 | 3.3261 | 3.3317 | 0.3 | 95.10
Neigh | 0.12544 | 0.12594 | 0.12634 | 0.1 | 3.60
Comm | 0.024059 | 0.03001 | 0.035574 | 2.9 | 0.86
Output | 4.8161e-05 | 6.8128e-05 | 0.00011802 | 0.0 | 0.00
Modify | 0.010666 | 0.010841 | 0.011109 | 0.2 | 0.31
Other | | 0.00457 | | | 0.13
Pair | 3.2768 | 3.3041 | 3.339 | 1.2 | 93.23
Neigh | 0.11542 | 0.11601 | 0.11661 | 0.1 | 3.27
Comm | 0.068218 | 0.10201 | 0.13103 | 7.0 | 2.88
Output | 4.4823e-05 | 8.0943e-05 | 0.000175 | 0.0 | 0.00
Modify | 0.010904 | 0.011064 | 0.011172 | 0.1 | 0.31
Other | | 0.01075 | | | 0.30
Nlocal: 8000 ave 8044 max 7960 min
Nlocal: 8000.00 ave 8044 max 7960 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 9131 ave 9171 max 9087 min
Nghost: 9131.00 ave 9171 max 9087 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 334259 ave 336108 max 332347 min
Neighs: 334259.0 ave 336108 max 332347 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 1337035
Ave neighs/atom = 41.7823
Ave neighs/atom = 41.782344
Neighbor list builds = 13
Dangerous builds = 0

90
bench/POTENTIALS/log.9Oct20.airebo.1 Normal file
View File

@ -0,0 +1,90 @@
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
Reading data file ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000 seconds
replicate 17 16 2
Replicating atoms ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
1 by 1 by 1 MPI processor grid
32640 atoms
replicate CPU = 0.002 seconds
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
Reading airebo potential file CH.airebo with DATE: 2011-10-25
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139300.72 0 -138035.04 7988.6646
10 161.34683 -138712.9 0 -138032.19 33228.921
20 208.59504 -138912.79 0 -138032.74 -3211.8806
30 139.7513 -138618.85 0 -138029.25 10878.143
40 142.14562 -138629.02 0 -138029.32 14601.302
50 114.23401 -138510.95 0 -138029 24691.124
60 164.92002 -138726 0 -138030.21 35125.541
70 162.15256 -138715.9 0 -138031.79 5658.7946
80 157.16184 -138695.77 0 -138032.72 19824.698
90 196.15907 -138860.65 0 -138033.07 -7950.8463
100 178.31875 -138784.89 0 -138032.57 30997.671
Loop time of 58.0757 on 1 procs for 100 steps with 32640 atoms
Performance: 0.074 ns/day, 322.643 hours/ns, 1.722 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 53.513 | 53.513 | 53.513 | 0.0 | 92.14
Neigh | 4.5013 | 4.5013 | 4.5013 | 0.0 | 7.75
Comm | 0.026609 | 0.026609 | 0.026609 | 0.0 | 0.05
Output | 0.0010192 | 0.0010192 | 0.0010192 | 0.0 | 0.00
Modify | 0.02275 | 0.02275 | 0.02275 | 0.0 | 0.04
Other | | 0.01074 | | | 0.02
Nlocal: 32640.0 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48190.0 ave 48190 max 48190 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.22178e+07 ave 2.22178e+07 max 2.22178e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22217840
Ave neighs/atom = 680.69363
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:59

90
bench/POTENTIALS/log.9Oct20.airebo.4 Normal file
View File

@ -0,0 +1,90 @@
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
Reading data file ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000 seconds
replicate 17 16 2
Replicating atoms ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
2 by 2 by 1 MPI processor grid
32640 atoms
replicate CPU = 0.001 seconds
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
Reading airebo potential file CH.airebo with DATE: 2011-10-25
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 29.43 | 29.81 | 30.19 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139300.72 0 -138035.04 7988.6646
10 161.34683 -138712.9 0 -138032.19 33228.921
20 208.59504 -138912.79 0 -138032.74 -3211.8806
30 139.7513 -138618.85 0 -138029.25 10878.143
40 142.14562 -138629.02 0 -138029.32 14601.302
50 114.23401 -138510.95 0 -138029 24691.124
60 164.92002 -138726 0 -138030.21 35125.541
70 162.15256 -138715.9 0 -138031.79 5658.7946
80 157.16184 -138695.77 0 -138032.72 19824.698
90 196.15907 -138860.65 0 -138033.07 -7950.8463
100 178.31875 -138784.89 0 -138032.57 30997.671
Loop time of 17.206 on 4 procs for 100 steps with 32640 atoms
Performance: 0.251 ns/day, 95.589 hours/ns, 5.812 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.655 | 14.727 | 14.848 | 1.9 | 85.59
Neigh | 1.5571 | 1.6135 | 1.6871 | 3.7 | 9.38
Comm | 0.7741 | 0.83422 | 0.90385 | 5.8 | 4.85
Output | 0.00047541 | 0.0027475 | 0.009517 | 7.5 | 0.02
Modify | 0.0091925 | 0.009367 | 0.0096078 | 0.2 | 0.05
Other | | 0.01908 | | | 0.11
Nlocal: 8160.00 ave 8174 max 8146 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 22614.5 ave 22629 max 22601 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5.55446e+06 ave 5.56556e+06 max 5.54192e+06 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 22217840
Ave neighs/atom = 680.69363
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:17

42
bench/POTENTIALS/log.16Mar18.bop.1 → bench/POTENTIALS/log.9Oct20.bop.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk CdTe via BOP
@ -7,19 +6,18 @@ units metal
atom_style atomic
lattice custom 6.82884 basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
Lattice spacing in x,y,z = 6.8288400 6.8288400 6.8288400
region box block 0 20 0 20 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (136.57680 136.57680 68.288400)
1 by 1 by 1 MPI processor grid
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
Created 32000 atoms
Time spent = 0.00191426 secs
create_atoms CPU = 0.002 seconds
pair_style bop
pair_coeff * * CdTe.bop.table Cd Te
Reading potential file CdTe.bop.table with DATE: 2012-06-25
Reading potential file CdTe.bop.table with DATE: 2012-06-25
Reading bop potential file CdTe.bop.table with DATE: 2012-06-25
mass 1 112.4
mass 2 127.6
@ -51,32 +49,32 @@ Per MPI rank memory allocation (min/avg/max) = 19.39 | 19.39 | 19.39 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -69539.487 0 -65403.292 3473.2595
100 572.16481 -67769.936 0 -65403.35 1838.6993
Loop time of 24.1696 on 1 procs for 100 steps with 32000 atoms
Loop time of 36.0284 on 1 procs for 100 steps with 32000 atoms
Performance: 0.357 ns/day, 67.138 hours/ns, 4.137 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.240 ns/day, 100.079 hours/ns, 2.776 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 23.355 | 23.355 | 23.355 | 0.0 | 96.63
Neigh | 0.7545 | 0.7545 | 0.7545 | 0.0 | 3.12
Comm | 0.026978 | 0.026978 | 0.026978 | 0.0 | 0.11
Output | 0.0001111 | 0.0001111 | 0.0001111 | 0.0 | 0.00
Modify | 0.024145 | 0.024145 | 0.024145 | 0.0 | 0.10
Other | | 0.009326 | | | 0.04
Pair | 35.306 | 35.306 | 35.306 | 0.0 | 97.99
Neigh | 0.66375 | 0.66375 | 0.66375 | 0.0 | 1.84
Comm | 0.027954 | 0.027954 | 0.027954 | 0.0 | 0.08
Output | 9.9182e-05 | 9.9182e-05 | 9.9182e-05 | 0.0 | 0.00
Modify | 0.022574 | 0.022574 | 0.022574 | 0.0 | 0.06
Other | | 0.008374 | | | 0.02
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 35071 ave 35071 max 35071 min
Nghost: 35071.0 ave 35071 max 35071 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 141288 ave 141288 max 141288 min
FullNghs: 141288.0 ave 141288 max 141288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 141288
Ave neighs/atom = 4.41525
Ave neighs/atom = 4.4152500
Neighbor list builds = 14
Dangerous builds = 0
Total wall time: 0:00:24
Total wall time: 0:00:36

44
bench/POTENTIALS/log.16Mar18.bop.4 → bench/POTENTIALS/log.9Oct20.bop.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk CdTe via BOP
@ -7,19 +6,18 @@ units metal
atom_style atomic
lattice custom 6.82884 basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
Lattice spacing in x,y,z = 6.8288400 6.8288400 6.8288400
region box block 0 20 0 20 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (136.57680 136.57680 68.288400)
2 by 2 by 1 MPI processor grid
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
Created 32000 atoms
Time spent = 0.000597477 secs
create_atoms CPU = 0.001 seconds
pair_style bop
pair_coeff * * CdTe.bop.table Cd Te
Reading potential file CdTe.bop.table with DATE: 2012-06-25
Reading potential file CdTe.bop.table with DATE: 2012-06-25
Reading bop potential file CdTe.bop.table with DATE: 2012-06-25
mass 1 112.4
mass 2 127.6
@ -47,36 +45,36 @@ Neighbor list info ...
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.497 | 8.497 | 8.497 Mbytes
Per MPI rank memory allocation (min/avg/max) = 8.495 | 8.495 | 8.495 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -69539.487 0 -65403.292 3473.2595
100 572.16481 -67769.936 0 -65403.35 1838.6993
Loop time of 6.50033 on 4 procs for 100 steps with 32000 atoms
Loop time of 10.2579 on 4 procs for 100 steps with 32000 atoms
Performance: 1.329 ns/day, 18.056 hours/ns, 15.384 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.842 ns/day, 28.494 hours/ns, 9.749 timesteps/s
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.7879 | 5.975 | 6.1607 | 5.4 | 91.92
Neigh | 0.27603 | 0.27621 | 0.27647 | 0.0 | 4.25
Comm | 0.049869 | 0.23531 | 0.42241 | 27.2 | 3.62
Output | 4.9829e-05 | 5.9724e-05 | 8.5592e-05 | 0.0 | 0.00
Modify | 0.0089927 | 0.0090921 | 0.0092406 | 0.1 | 0.14
Other | | 0.004665 | | | 0.07
Pair | 9.0899 | 9.3839 | 9.6808 | 6.9 | 91.48
Neigh | 0.24734 | 0.2533 | 0.25828 | 0.8 | 2.47
Comm | 0.30495 | 0.60685 | 0.89832 | 27.5 | 5.92
Output | 4.673e-05 | 7.695e-05 | 0.00016189 | 0.0 | 0.00
Modify | 0.0092409 | 0.00937 | 0.0094445 | 0.1 | 0.09
Other | | 0.004455 | | | 0.04
Nlocal: 8000 ave 8006 max 7994 min
Nlocal: 8000.00 ave 8006 max 7994 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 15171 ave 15177 max 15165 min
Nghost: 15171.0 ave 15177 max 15165 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 35322 ave 35412 max 35267 min
FullNghs: 35322.0 ave 35412 max 35267 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 141288
Ave neighs/atom = 4.41525
Ave neighs/atom = 4.4152500
Neighbor list builds = 14
Dangerous builds = 0
Total wall time: 0:00:06
Total wall time: 0:00:10

35
bench/POTENTIALS/log.16Mar18.comb.1 → bench/POTENTIALS/log.9Oct20.comb.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# SiO2 for COMB potential
@ -7,10 +6,12 @@ units metal
atom_style charge
read_data data.comb
triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (74.580000 74.580000 83.064000) with tilt (0.0000000 0.0000000 0.0000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
32400 atoms
read_data CPU = 0.022 seconds
mass 1 28.0855
group type1 type 1
@ -63,32 +64,32 @@ Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
80 272.98301 -6.803583 -6.8388677 4.6404093 -11.479277 2.8932784 -1.4466392 -9896.1704 462016.62
90 305.77651 -6.8036184 -6.8431419 4.6512736 -11.494415 2.8953109 -1.4476554 -15675.983 462016.62
100 331.58255 -6.8036753 -6.8465344 4.662727 -11.509261 2.897273 -1.4486365 -21675.515 462016.62
Loop time of 517.206 on 1 procs for 100 steps with 32400 atoms
Loop time of 426.185 on 1 procs for 100 steps with 32400 atoms
Performance: 0.003 ns/day, 7183.417 hours/ns, 0.193 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.004 ns/day, 5919.239 hours/ns, 0.235 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 114.18 | 114.18 | 114.18 | 0.0 | 22.08
Neigh | 0.47558 | 0.47558 | 0.47558 | 0.0 | 0.09
Comm | 0.030611 | 0.030611 | 0.030611 | 0.0 | 0.01
Output | 0.0024922 | 0.0024922 | 0.0024922 | 0.0 | 0.00
Modify | 402.51 | 402.51 | 402.51 | 0.0 | 77.82
Other | | 0.006137 | | | 0.00
Pair | 87.4 | 87.4 | 87.4 | 0.0 | 20.51
Neigh | 0.3908 | 0.3908 | 0.3908 | 0.0 | 0.09
Comm | 0.029936 | 0.029936 | 0.029936 | 0.0 | 0.01
Output | 0.0024605 | 0.0024605 | 0.0024605 | 0.0 | 0.00
Modify | 338.36 | 338.36 | 338.36 | 0.0 | 79.39
Other | | 0.005751 | | | 0.00
Nlocal: 32400 ave 32400 max 32400 min
Nlocal: 32400.0 ave 32400 max 32400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 42518 ave 42518 max 42518 min
Nghost: 42518.0 ave 42518 max 42518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.85317e+07 ave 1.85317e+07 max 1.85317e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18531740
Ave neighs/atom = 571.967
Ave neighs/atom = 571.96728
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:09:18
Total wall time: 0:07:40

37
bench/POTENTIALS/log.16Mar18.comb.4 → bench/POTENTIALS/log.9Oct20.comb.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# SiO2 for COMB potential
@ -7,10 +6,12 @@ units metal
atom_style charge
read_data data.comb
triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (74.580000 74.580000 83.064000) with tilt (0.0000000 0.0000000 0.0000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
32400 atoms
read_data CPU = 0.031 seconds
mass 1 28.0855
group type1 type 1
@ -50,7 +51,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 32.11 | 32.11 | 32.11 Mbytes
Per MPI rank memory allocation (min/avg/max) = 32.28 | 32.28 | 32.29 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
0 300 -6.8032038 -6.8419806 4.6274455 -11.469426 2.8875895 -1.4437947 13386.415 462016.62
10 273.21913 -6.8032489 -6.8385642 4.6221303 -11.460695 2.8872353 -1.4436176 13076.442 462016.62
@ -63,32 +64,32 @@ Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
80 272.98301 -6.803583 -6.8388677 4.6404093 -11.479277 2.8932784 -1.4466392 -9896.1704 462016.62
90 305.77651 -6.8036184 -6.8431419 4.6512736 -11.494415 2.8953109 -1.4476554 -15675.983 462016.62
100 331.58255 -6.8036753 -6.8465344 4.662727 -11.509261 2.897273 -1.4486365 -21675.515 462016.62
Loop time of 131.437 on 4 procs for 100 steps with 32400 atoms
Loop time of 116.902 on 4 procs for 100 steps with 32400 atoms
Performance: 0.013 ns/day, 1825.518 hours/ns, 0.761 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.015 ns/day, 1623.637 hours/ns, 0.855 timesteps/s
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 28.847 | 28.874 | 28.913 | 0.5 | 21.97
Neigh | 0.10981 | 0.11084 | 0.11145 | 0.2 | 0.08
Comm | 0.28924 | 0.32866 | 0.3556 | 4.5 | 0.25
Output | 0.0010426 | 0.0011656 | 0.0015302 | 0.6 | 0.00
Modify | 102.12 | 102.12 | 102.12 | 0.0 | 77.69
Other | | 0.003455 | | | 0.00
Pair | 22.866 | 23.181 | 23.375 | 4.0 | 19.83
Neigh | 0.093812 | 0.094818 | 0.095301 | 0.2 | 0.08
Comm | 0.94054 | 1.1329 | 1.4505 | 18.1 | 0.97
Output | 0.0011141 | 0.001422 | 0.0023448 | 1.4 | 0.00
Modify | 92.485 | 92.488 | 92.494 | 0.0 | 79.12
Other | | 0.003673 | | | 0.00
Nlocal: 8100 ave 8110 max 8090 min
Nlocal: 8100.00 ave 8110 max 8090 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 20725.2 ave 20772 max 20694 min
Nghost: 20725.2 ave 20772 max 20694 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4.63294e+06 ave 4.63866e+06 max 4.62736e+06 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 18531740
Ave neighs/atom = 571.967
Ave neighs/atom = 571.96728
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:02:21
Total wall time: 0:02:06

37
bench/POTENTIALS/log.16Mar18.dpd.1 → bench/POTENTIALS/log.9Oct20.dpd.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# DPD benchmark
@ -8,14 +7,14 @@ atom_style atomic
comm_modify mode single vel yes
lattice fcc 3.0
Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (22.012848 22.012848 22.012848)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.0018332 secs
create_atoms CPU = 0.002 seconds
mass 1 1.0
velocity all create 1.0 87287 loop geom
@ -46,30 +45,30 @@ Per MPI rank memory allocation (min/avg/max) = 11.32 | 11.32 | 11.32 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 3.6872574 0 5.1872105 28.880274
100 1.0246036 4.5727353 0 6.1095927 23.859969
Loop time of 3.09286 on 1 procs for 100 steps with 32000 atoms
Loop time of 2.63541 on 1 procs for 100 steps with 32000 atoms
Performance: 111741.340 tau/day, 32.333 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 131137.146 tau/day, 37.945 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5326 | 1.5326 | 1.5326 | 0.0 | 49.55
Neigh | 1.4771 | 1.4771 | 1.4771 | 0.0 | 47.76
Comm | 0.044292 | 0.044292 | 0.044292 | 0.0 | 1.43
Output | 0.00011039 | 0.00011039 | 0.00011039 | 0.0 | 0.00
Modify | 0.022322 | 0.022322 | 0.022322 | 0.0 | 0.72
Other | | 0.01648 | | | 0.53
Pair | 1.1841 | 1.1841 | 1.1841 | 0.0 | 44.93
Neigh | 1.3737 | 1.3737 | 1.3737 | 0.0 | 52.12
Comm | 0.04266 | 0.04266 | 0.04266 | 0.0 | 1.62
Output | 9.5844e-05 | 9.5844e-05 | 9.5844e-05 | 0.0 | 0.00
Modify | 0.020128 | 0.020128 | 0.020128 | 0.0 | 0.76
Other | | 0.01468 | | | 0.56
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14981 ave 14981 max 14981 min
Nghost: 14981.0 ave 14981 max 14981 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 660587 ave 660587 max 660587 min
Neighs: 660587.0 ave 660587 max 660587 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 660587
Ave neighs/atom = 20.6433
Ave neighs/atom = 20.643344
Neighbor list builds = 50
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:02

37
bench/POTENTIALS/log.16Mar18.dpd.4 → bench/POTENTIALS/log.9Oct20.dpd.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# DPD benchmark
@ -8,14 +7,14 @@ atom_style atomic
comm_modify mode single vel yes
lattice fcc 3.0
Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (22.012848 22.012848 22.012848)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000589132 secs
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.0 87287 loop geom
@ -42,34 +41,34 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.874 | 3.874 | 3.874 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.875 | 3.875 | 3.875 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 3.6872574 0 5.1872105 28.911346
100 1.0219182 4.5817845 0 6.1146139 23.803115
Loop time of 0.83904 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.882096 on 4 procs for 100 steps with 32000 atoms
Performance: 411899.440 tau/day, 119.184 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 391793.935 tau/day, 113.366 timesteps/s
93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.39605 | 0.40101 | 0.40702 | 0.6 | 47.79
Neigh | 0.38186 | 0.38494 | 0.38738 | 0.4 | 45.88
Comm | 0.032073 | 0.039688 | 0.045953 | 2.9 | 4.73
Output | 4.4823e-05 | 5.4002e-05 | 7.844e-05 | 0.0 | 0.01
Modify | 0.0056572 | 0.0056887 | 0.0057547 | 0.1 | 0.68
Other | | 0.007655 | | | 0.91
Pair | 0.31428 | 0.33654 | 0.37754 | 4.4 | 38.15
Neigh | 0.36308 | 0.3849 | 0.41542 | 3.1 | 43.63
Comm | 0.07276 | 0.14322 | 0.1842 | 11.3 | 16.24
Output | 4.22e-05 | 5.2989e-05 | 8.2493e-05 | 0.0 | 0.01
Modify | 0.0057678 | 0.0060433 | 0.0065472 | 0.4 | 0.69
Other | | 0.01134 | | | 1.29
Nlocal: 8000 ave 8014 max 7986 min
Nlocal: 8000.00 ave 8014 max 7986 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 6744 ave 6764 max 6726 min
Nghost: 6744.00 ave 6764 max 6726 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 165107 ave 166433 max 163419 min
Neighs: 165107.0 ave 166433 max 163419 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 660428
Ave neighs/atom = 20.6384
Ave neighs/atom = 20.638375
Neighbor list builds = 50
Dangerous builds = 0
Total wall time: 0:00:00

34
bench/POTENTIALS/log.16Mar18.eam.1 → bench/POTENTIALS/log.9Oct20.eam.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Cu in EAM
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
Lattice spacing in x,y,z = 3.6150000 3.6150000 3.6150000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (72.300000 72.300000 72.300000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00185037 secs
create_atoms CPU = 0.002 seconds
pair_style eam
pair_coeff 1 1 Cu_u3.eam
Reading eam potential file Cu_u3.eam with DATE: 2007-06-11
velocity all create 1600.0 376847 loop geom
@ -45,30 +45,30 @@ Per MPI rank memory allocation (min/avg/max) = 16.83 | 16.83 | 16.83 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 3.92295 on 1 procs for 100 steps with 32000 atoms
Loop time of 3.70399 on 1 procs for 100 steps with 32000 atoms
Performance: 11.012 ns/day, 2.179 hours/ns, 25.491 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 11.663 ns/day, 2.058 hours/ns, 26.998 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3913 | 3.3913 | 3.3913 | 0.0 | 86.45
Neigh | 0.48107 | 0.48107 | 0.48107 | 0.0 | 12.26
Comm | 0.01729 | 0.01729 | 0.01729 | 0.0 | 0.44
Output | 0.00011253 | 0.00011253 | 0.00011253 | 0.0 | 0.00
Modify | 0.024349 | 0.024349 | 0.024349 | 0.0 | 0.62
Other | | 0.008847 | | | 0.23
Pair | 3.2216 | 3.2216 | 3.2216 | 0.0 | 86.98
Neigh | 0.43766 | 0.43766 | 0.43766 | 0.0 | 11.82
Comm | 0.015404 | 0.015404 | 0.015404 | 0.0 | 0.42
Output | 0.000103 | 0.000103 | 0.000103 | 0.0 | 0.00
Modify | 0.021604 | 0.021604 | 0.021604 | 0.0 | 0.58
Other | | 0.007627 | | | 0.21
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19909 ave 19909 max 19909 min
Nghost: 19909.0 ave 19909 max 19909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Ave neighs/atom = 37.743250
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:03

38
bench/POTENTIALS/log.16Mar18.eam.4 → bench/POTENTIALS/log.9Oct20.eam.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Cu in EAM
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
Lattice spacing in x,y,z = 3.6150000 3.6150000 3.6150000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (72.300000 72.300000 72.300000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000595331 secs
create_atoms CPU = 0.001 seconds
pair_style eam
pair_coeff 1 1 Cu_u3.eam
Reading eam potential file Cu_u3.eam with DATE: 2007-06-11
velocity all create 1600.0 376847 loop geom
@ -41,34 +41,34 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.381 | 7.381 | 7.381 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.382 | 7.382 | 7.382 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 1.04497 on 4 procs for 100 steps with 32000 atoms
Loop time of 1.01466 on 4 procs for 100 steps with 32000 atoms
Performance: 41.341 ns/day, 0.581 hours/ns, 95.697 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 42.576 ns/day, 0.564 hours/ns, 98.555 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.88513 | 0.88724 | 0.89191 | 0.3 | 84.91
Neigh | 0.12418 | 0.12458 | 0.12511 | 0.1 | 11.92
Comm | 0.015654 | 0.020543 | 0.022984 | 2.0 | 1.97
Output | 4.8637e-05 | 5.8711e-05 | 8.6546e-05 | 0.0 | 0.01
Modify | 0.0085199 | 0.0085896 | 0.0086446 | 0.1 | 0.82
Other | | 0.003959 | | | 0.38
Pair | 0.86683 | 0.86797 | 0.86877 | 0.1 | 85.54
Neigh | 0.11567 | 0.11681 | 0.11992 | 0.5 | 11.51
Comm | 0.015399 | 0.017346 | 0.018526 | 0.9 | 1.71
Output | 4.6253e-05 | 8.1241e-05 | 0.00017262 | 0.0 | 0.01
Modify | 0.0085337 | 0.0085824 | 0.0086181 | 0.0 | 0.85
Other | | 0.003876 | | | 0.38
Nlocal: 8000 ave 8008 max 7993 min
Nlocal: 8000.00 ave 8008 max 7993 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 9130.25 ave 9138 max 9122 min
Nghost: 9130.25 ave 9138 max 9122 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 301946 ave 302392 max 301360 min
Neighs: 301946.0 ave 302392 max 301360 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Ave neighs/atom = 37.743250
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:01

33
bench/POTENTIALS/log.16Mar18.eff.1 → bench/POTENTIALS/log.9Oct20.eff.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# eFF benchmark of H plasma
@ -7,12 +6,14 @@ units electron
atom_style electron
read_data data.eff
orthogonal box = (0 0 0) to (41.9118 41.9118 41.9118)
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (41.911791 41.911791 41.911791)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.040 seconds
pair_style eff/cut 12
pair_coeff * *
@ -42,7 +43,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 370.9 | 370.9 | 370.9 Mbytes
Per MPI rank memory allocation (min/avg/max) = 371.5 | 371.5 | 371.5 Mbytes
Step TotEng PotEng KinEng Temp Press
0 4046.5854 796.63785 3249.9475 42763.133 4.4764483e+12
5 4046.5854 796.95799 3249.6274 42758.92 4.4728546e+12
@ -65,33 +66,33 @@ Step TotEng PotEng KinEng Temp Press
90 4046.5857 864.14162 3182.4441 41874.916 4.3868277e+12
95 4046.5857 871.30234 3175.2834 41780.695 4.3805068e+12
100 4046.5858 878.76023 3167.8255 41682.563 4.3740731e+12
Loop time of 323.031 on 1 procs for 100 steps with 32000 atoms
Loop time of 344.943 on 1 procs for 100 steps with 32000 atoms
Performance: 26.747 fs/day, 0.897 hours/fs, 0.310 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 25.048 fs/day, 0.958 hours/fs, 0.290 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 322.78 | 322.78 | 322.78 | 0.0 | 99.92
Pair | 344.71 | 344.71 | 344.71 | 0.0 | 99.93
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.1876 | 0.1876 | 0.1876 | 0.0 | 0.06
Output | 0.0027025 | 0.0027025 | 0.0027025 | 0.0 | 0.00
Modify | 0.032475 | 0.032475 | 0.032475 | 0.0 | 0.01
Other | | 0.02538 | | | 0.01
Comm | 0.1763 | 0.1763 | 0.1763 | 0.0 | 0.05
Output | 0.0024362 | 0.0024362 | 0.0024362 | 0.0 | 0.00
Modify | 0.030869 | 0.030869 | 0.030869 | 0.0 | 0.01
Other | | 0.02272 | | | 0.01
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 114349 ave 114349 max 114349 min
Nghost: 114349.0 ave 114349 max 114349 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8.10572e+07 ave 8.10572e+07 max 8.10572e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 81057159
Ave neighs/atom = 2533.04
Ave neighs/atom = 2533.0362
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:05:27
Total wall time: 0:05:49

33
bench/POTENTIALS/log.16Mar18.eff.4 → bench/POTENTIALS/log.9Oct20.eff.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# eFF benchmark of H plasma
@ -7,12 +6,14 @@ units electron
atom_style electron
read_data data.eff
orthogonal box = (0 0 0) to (41.9118 41.9118 41.9118)
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (41.911791 41.911791 41.911791)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.064 seconds
pair_style eff/cut 12
pair_coeff * *
@ -42,7 +43,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 101.4 | 104.8 | 108.3 Mbytes
Per MPI rank memory allocation (min/avg/max) = 102.1 | 105.5 | 109.0 Mbytes
Step TotEng PotEng KinEng Temp Press
0 4046.5854 796.63785 3249.9475 42763.133 4.4764483e+12
5 4046.5854 796.95799 3249.6274 42758.92 4.4728546e+12
@ -65,33 +66,33 @@ Step TotEng PotEng KinEng Temp Press
90 4046.5857 864.14162 3182.4441 41874.916 4.3868277e+12
95 4046.5857 871.30234 3175.2834 41780.695 4.3805068e+12
100 4046.5858 878.76023 3167.8255 41682.563 4.3740731e+12
Loop time of 90.1636 on 4 procs for 100 steps with 32000 atoms
Loop time of 100.431 on 4 procs for 100 steps with 32000 atoms
Performance: 95.826 fs/day, 0.250 hours/fs, 1.109 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 86.029 fs/day, 0.279 hours/fs, 0.996 timesteps/s
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 83.772 | 86.516 | 89.593 | 29.5 | 95.95
Pair | 89.149 | 93.787 | 97.971 | 41.9 | 93.38
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.51677 | 3.5934 | 6.3368 | 144.6 | 3.99
Output | 0.0012872 | 0.0018208 | 0.0024981 | 1.0 | 0.00
Modify | 0.017231 | 0.018405 | 0.01983 | 0.8 | 0.02
Other | | 0.03431 | | | 0.04
Comm | 2.4073 | 6.5821 | 11.21 | 157.8 | 6.55
Output | 0.0014203 | 0.0094504 | 0.019111 | 8.3 | 0.01
Modify | 0.016678 | 0.016999 | 0.017425 | 0.2 | 0.02
Other | | 0.03524 | | | 0.04
Nlocal: 8000 ave 8112 max 7875 min
Nlocal: 8000.00 ave 8112 max 7875 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 65589 ave 66004 max 65177 min
Nghost: 65589.0 ave 66004 max 65177 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 2.02643e+07 ave 2.11126e+07 max 1.94058e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 81057159
Ave neighs/atom = 2533.04
Ave neighs/atom = 2533.0362
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:31
Total wall time: 0:01:42

41
bench/POTENTIALS/log.16Mar18.eim.1 → bench/POTENTIALS/log.9Oct20.eim.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# EIM benchmark
# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
@ -9,12 +8,14 @@ units metal
atom_style atomic
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
Reading data file ...
orthogonal box = (-0.5 -0.5 -0.5) to (71.580002 143.66000 71.580002)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.024 seconds
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
@ -44,34 +45,34 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.72 | 17.72 | 17.72 Mbytes
Per MPI rank memory allocation (min/avg/max) = 17.74 | 17.74 | 17.74 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -90567.58 -117883.6 -118039.81 -117894.07 1400
100 -91997.012 -4104.7052 -4138.276 -4145.8936 944.10136
Loop time of 11.4536 on 1 procs for 100 steps with 32000 atoms
100 -91997.39 -4127.237 -4160.9799 -4169.0581 944.09785
Loop time of 10.3731 on 1 procs for 100 steps with 32000 atoms
Performance: 0.377 ns/day, 63.631 hours/ns, 8.731 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.416 ns/day, 57.628 hours/ns, 9.640 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.8277 | 9.8277 | 9.8277 | 0.0 | 85.80
Neigh | 1.484 | 1.484 | 1.484 | 0.0 | 12.96
Comm | 0.028584 | 0.028584 | 0.028584 | 0.0 | 0.25
Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00
Modify | 0.09791 | 0.09791 | 0.09791 | 0.0 | 0.85
Other | | 0.0152 | | | 0.13
Pair | 8.8937 | 8.8937 | 8.8937 | 0.0 | 85.74
Neigh | 1.344 | 1.344 | 1.344 | 0.0 | 12.96
Comm | 0.028207 | 0.028207 | 0.028207 | 0.0 | 0.27
Output | 0.00020099 | 0.00020099 | 0.00020099 | 0.0 | 0.00
Modify | 0.093584 | 0.093584 | 0.093584 | 0.0 | 0.90
Other | | 0.0134 | | | 0.13
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21505 ave 21505 max 21505 min
Nghost: 21505.0 ave 21505 max 21505 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.5839e+06 ave 1.5839e+06 max 1.5839e+06 min
Neighs: 1.58387e+06 ave 1.58387e+06 max 1.58387e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1583901
Ave neighs/atom = 49.4969
Total # of neighbors = 1583871
Ave neighs/atom = 49.495969
Neighbor list builds = 37
Dangerous builds = 12
Total wall time: 0:00:11
Total wall time: 0:00:10

39
bench/POTENTIALS/log.16Mar18.eim.4 → bench/POTENTIALS/log.9Oct20.eim.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# EIM benchmark
# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
@ -9,12 +8,14 @@ units metal
atom_style atomic
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
Reading data file ...
orthogonal box = (-0.5 -0.5 -0.5) to (71.580002 143.66000 71.580002)
1 by 4 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.023 seconds
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
@ -44,34 +45,34 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.285 | 7.285 | 7.285 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.460 | 7.460 | 7.460 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -90567.58 -117883.6 -118039.81 -117894.07 1400
100 -91997.012 -4104.7052 -4138.276 -4145.8936 944.10136
Loop time of 3.12061 on 4 procs for 100 steps with 32000 atoms
100 -91997.39 -4127.237 -4160.9799 -4169.0581 944.09785
Loop time of 3.14457 on 4 procs for 100 steps with 32000 atoms
Performance: 1.384 ns/day, 17.337 hours/ns, 32.045 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 1.374 ns/day, 17.470 hours/ns, 31.801 timesteps/s
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6504 | 2.6583 | 2.6685 | 0.5 | 85.18
Neigh | 0.36996 | 0.37847 | 0.39396 | 1.5 | 12.13
Comm | 0.037041 | 0.040586 | 0.04504 | 1.4 | 1.30
Output | 7.081e-05 | 8.75e-05 | 0.00012994 | 0.0 | 0.00
Modify | 0.029286 | 0.035978 | 0.047942 | 3.9 | 1.15
Other | | 0.007206 | | | 0.23
Pair | 2.6017 | 2.6264 | 2.6758 | 1.8 | 83.52
Neigh | 0.34384 | 0.35308 | 0.36784 | 1.6 | 11.23
Comm | 0.039635 | 0.099661 | 0.15326 | 15.0 | 3.17
Output | 6.485e-05 | 9.656e-05 | 0.0001905 | 0.0 | 0.00
Modify | 0.035666 | 0.055446 | 0.098401 | 10.6 | 1.76
Other | | 0.009939 | | | 0.32
Nlocal: 8000 ave 8000 max 8000 min
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 9460.25 ave 9469 max 9449 min
Nghost: 9460.25 ave 9469 max 9449 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 395975 ave 397239 max 394616 min
Neighs: 395968.0 ave 397233 max 394606 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1583901
Ave neighs/atom = 49.4969
Total # of neighbors = 1583871
Ave neighs/atom = 49.495969
Neighbor list builds = 37
Dangerous builds = 12
Total wall time: 0:00:03

48
bench/POTENTIALS/log.16Mar18.fene.1 → bench/POTENTIALS/log.9Oct20.fene.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# FENE beadspring benchmark
@ -8,7 +7,8 @@ atom_style bond
special_bonds fene
read_data data.fene
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
Reading data file ...
orthogonal box = (-16.796000 -16.796000 -16.796000) to (16.796000 16.796000 16.796000)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
@ -18,8 +18,13 @@ read_data data.fene
1 = max bonds/atom
reading bonds ...
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 1.0 1.0
special bond factors coul: 0.0 1.0 1.0
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.003 seconds
read_data CPU = 0.054 seconds
neighbor 0.4 bin
neigh_modify delay 5 every 1
@ -49,36 +54,37 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.18 | 13.18 | 13.18 Mbytes
WARNING: Communication cutoff 1.52 is shorter than a bond length based estimate of 1.855. This may lead to errors. (src/comm.cpp:667)
Per MPI rank memory allocation (min/avg/max) = 13.20 | 13.20 | 13.20 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9729966 0.4361122 20.507698 22.40326 4.6548819
Loop time of 0.66285 on 1 procs for 100 steps with 32000 atoms
Loop time of 0.648089 on 1 procs for 100 steps with 32000 atoms
Performance: 156415.445 tau/day, 150.864 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 159978.044 tau/day, 154.300 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13075 | 0.13075 | 0.13075 | 0.0 | 19.73
Bond | 0.046363 | 0.046363 | 0.046363 | 0.0 | 6.99
Neigh | 0.3172 | 0.3172 | 0.3172 | 0.0 | 47.85
Comm | 0.016553 | 0.016553 | 0.016553 | 0.0 | 2.50
Output | 0.00010395 | 0.00010395 | 0.00010395 | 0.0 | 0.02
Modify | 0.14515 | 0.14515 | 0.14515 | 0.0 | 21.90
Other | | 0.006728 | | | 1.02
Pair | 0.12174 | 0.12174 | 0.12174 | 0.0 | 18.78
Bond | 0.050688 | 0.050688 | 0.050688 | 0.0 | 7.82
Neigh | 0.33136 | 0.33136 | 0.33136 | 0.0 | 51.13
Comm | 0.014753 | 0.014753 | 0.014753 | 0.0 | 2.28
Output | 9.8467e-05 | 9.8467e-05 | 9.8467e-05 | 0.0 | 0.02
Modify | 0.12378 | 0.12378 | 0.12378 | 0.0 | 19.10
Other | | 0.005668 | | | 0.87
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9493 ave 9493 max 9493 min
Nghost: 9493.00 ave 9493 max 9493 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 155873 ave 155873 max 155873 min
Neighs: 155873.0 ave 155873 max 155873 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 155873
Ave neighs/atom = 4.87103
Ave special neighs/atom = 1.98
Ave neighs/atom = 4.8710312
Ave special neighs/atom = 1.9800000
Neighbor list builds = 20
Dangerous builds = 20
Total wall time: 0:00:00

48
bench/POTENTIALS/log.16Mar18.fene.4 → bench/POTENTIALS/log.9Oct20.fene.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# FENE beadspring benchmark
@ -8,7 +7,8 @@ atom_style bond
special_bonds fene
read_data data.fene
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
Reading data file ...
orthogonal box = (-16.796000 -16.796000 -16.796000) to (16.796000 16.796000 16.796000)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
@ -18,8 +18,13 @@ read_data data.fene
1 = max bonds/atom
reading bonds ...
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 1.0 1.0
special bond factors coul: 0.0 1.0 1.0
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.048 seconds
neighbor 0.4 bin
neigh_modify delay 5 every 1
@ -49,36 +54,37 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.605 | 4.605 | 4.606 Mbytes
WARNING: Communication cutoff 1.52 is shorter than a bond length based estimate of 1.855. This may lead to errors. (src/comm.cpp:667)
Per MPI rank memory allocation (min/avg/max) = 4.779 | 4.780 | 4.780 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9736748 0.44378481 20.502389 22.40664 4.7809557
Loop time of 0.184782 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.179123 on 4 procs for 100 steps with 32000 atoms
Performance: 561093.346 tau/day, 541.178 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 578819.228 tau/day, 558.275 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.033747 | 0.034391 | 0.035036 | 0.3 | 18.61
Bond | 0.012475 | 0.012579 | 0.012812 | 0.1 | 6.81
Neigh | 0.083916 | 0.083953 | 0.084022 | 0.0 | 45.43
Comm | 0.012409 | 0.01363 | 0.014534 | 0.7 | 7.38
Output | 4.1246e-05 | 5.9545e-05 | 0.00010443 | 0.0 | 0.03
Modify | 0.036675 | 0.037876 | 0.038357 | 0.4 | 20.50
Other | | 0.002294 | | | 1.24
Pair | 0.031898 | 0.032311 | 0.032864 | 0.2 | 18.04
Bond | 0.01335 | 0.013471 | 0.013588 | 0.1 | 7.52
Neigh | 0.087105 | 0.087195 | 0.087282 | 0.0 | 48.68
Comm | 0.010541 | 0.011533 | 0.012463 | 0.7 | 6.44
Output | 3.8624e-05 | 5.6028e-05 | 0.00010157 | 0.0 | 0.03
Modify | 0.031766 | 0.03233 | 0.033015 | 0.3 | 18.05
Other | | 0.002227 | | | 1.24
Nlocal: 8000 ave 8023 max 7978 min
Nlocal: 8000.00 ave 8023 max 7978 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 4158.75 ave 4175 max 4145 min
Nghost: 4158.75 ave 4175 max 4145 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 38940 ave 39184 max 38640 min
Neighs: 38940.0 ave 39184 max 38640 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 155760
Ave neighs/atom = 4.8675
Ave special neighs/atom = 1.98
Ave neighs/atom = 4.8675000
Ave special neighs/atom = 1.9800000
Neighbor list builds = 20
Dangerous builds = 20
Total wall time: 0:00:00

47
bench/POTENTIALS/log.16Mar18.gb.1 → bench/POTENTIALS/log.9Oct20.gb.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Gay-Berne benchmark
# biaxial ellipsoid mesogens in isotropic phase
@ -18,13 +17,15 @@ atom_style ellipsoid
#set group all quat/random 982381
read_data data.gb
orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
Reading data file ...
orthogonal box = (2.1957493 2.1957493 2.1957493) to (50.812373 50.812373 50.812373)
1 by 1 by 1 MPI processor grid
reading atoms ...
32768 atoms
reading velocities ...
32768 velocities
32768 ellipsoids
read_data CPU = 0.097 seconds
compute rot all temp/asphere
group spheroid type 1
@ -63,41 +64,41 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 28.91 | 28.91 | 28.91 Mbytes
Per MPI rank memory allocation (min/avg/max) = 28.98 | 28.98 | 28.98 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.4 0.50438568 0 4.1042758 6.7818168 114909.09
20 2.7357818 0.26045557 0 4.364003 6.8299368 111715.16
40 2.9201296 0.22570735 0 4.605768 7.0767907 109473.23
60 2.9820039 0.19733812 0 4.6702075 7.1507065 108393.77
80 3.0148529 0.15114819 0 4.6732895 7.1699502 107672.24
100 3.0206703 0.10567623 0 4.6365433 7.154345 107184.83
Loop time of 43.7894 on 1 procs for 100 steps with 32768 atoms
20 2.7357797 0.26044978 0 4.363994 6.8299173 111715.2
40 2.9201268 0.2257049 0 4.6057615 7.0767796 109473.26
60 2.9820022 0.19733756 0 4.6702044 7.1507023 108393.79
80 3.014852 0.15114765 0 4.6732876 7.1699472 107672.25
100 3.0206698 0.105676 0 4.6365424 7.1543436 107184.84
Loop time of 57.1053 on 1 procs for 100 steps with 32768 atoms
Performance: 394.616 tau/day, 2.284 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 302.599 tau/day, 1.751 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 42.881 | 42.881 | 42.881 | 0.0 | 97.93
Neigh | 0.35071 | 0.35071 | 0.35071 | 0.0 | 0.80
Comm | 0.065153 | 0.065153 | 0.065153 | 0.0 | 0.15
Output | 0.00054383 | 0.00054383 | 0.00054383 | 0.0 | 0.00
Modify | 0.47852 | 0.47852 | 0.47852 | 0.0 | 1.09
Other | | 0.01337 | | | 0.03
Pair | 56.246 | 56.246 | 56.246 | 0.0 | 98.50
Neigh | 0.31058 | 0.31058 | 0.31058 | 0.0 | 0.54
Comm | 0.066039 | 0.066039 | 0.066039 | 0.0 | 0.12
Output | 0.00048757 | 0.00048757 | 0.00048757 | 0.0 | 0.00
Modify | 0.46972 | 0.46972 | 0.46972 | 0.0 | 0.82
Other | | 0.01198 | | | 0.02
Nlocal: 32768 ave 32768 max 32768 min
Nlocal: 32768.0 ave 32768 max 32768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 25669 ave 25669 max 25669 min
Nghost: 25669.0 ave 25669 max 25669 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.30433e+06 ave 2.30433e+06 max 2.30433e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2304332
Ave neighs/atom = 70.3226
Total # of neighbors = 2304331
Ave neighs/atom = 70.322601
Neighbor list builds = 6
Dangerous builds = 3
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:44
Total wall time: 0:00:57

49
bench/POTENTIALS/log.16Mar18.gb.4 → bench/POTENTIALS/log.9Oct20.gb.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Gay-Berne benchmark
# biaxial ellipsoid mesogens in isotropic phase
@ -18,13 +17,15 @@ atom_style ellipsoid
#set group all quat/random 982381
read_data data.gb
orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
Reading data file ...
orthogonal box = (2.1957493 2.1957493 2.1957493) to (50.812373 50.812373 50.812373)
1 by 2 by 2 MPI processor grid
reading atoms ...
32768 atoms
reading velocities ...
32768 velocities
32768 ellipsoids
read_data CPU = 0.079 seconds
compute rot all temp/asphere
group spheroid type 1
@ -63,41 +64,41 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes
Per MPI rank memory allocation (min/avg/max) = 11.99 | 11.99 | 12.00 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.4 0.50438568 0 4.1042758 6.7818168 114909.09
20 2.7357818 0.26045557 0 4.364003 6.8299368 111715.16
40 2.9201296 0.22570735 0 4.605768 7.0767907 109473.23
60 2.9820039 0.19733812 0 4.6702075 7.1507065 108393.77
80 3.0148529 0.15114819 0 4.6732895 7.1699502 107672.24
100 3.0206703 0.10567623 0 4.6365433 7.154345 107184.83
Loop time of 11.3124 on 4 procs for 100 steps with 32768 atoms
20 2.7357797 0.26044978 0 4.363994 6.8299173 111715.2
40 2.9201268 0.2257049 0 4.6057615 7.0767796 109473.26
60 2.9820022 0.19733756 0 4.6702044 7.1507023 108393.79
80 3.014852 0.15114765 0 4.6732876 7.1699472 107672.25
100 3.0206698 0.105676 0 4.6365424 7.1543436 107184.84
Loop time of 14.9338 on 4 procs for 100 steps with 32768 atoms
Performance: 1527.522 tau/day, 8.840 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 1157.109 tau/day, 6.696 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.778 | 10.849 | 10.934 | 2.0 | 95.90
Neigh | 0.088265 | 0.08871 | 0.089238 | 0.1 | 0.78
Comm | 0.1384 | 0.22518 | 0.29662 | 14.1 | 1.99
Output | 0.00020599 | 0.00024837 | 0.00036836 | 0.0 | 0.00
Modify | 0.13828 | 0.13899 | 0.13984 | 0.2 | 1.23
Other | | 0.01053 | | | 0.09
Pair | 14.317 | 14.457 | 14.545 | 2.5 | 96.81
Neigh | 0.080048 | 0.080928 | 0.082009 | 0.3 | 0.54
Comm | 0.15948 | 0.24734 | 0.38914 | 18.9 | 1.66
Output | 0.00018859 | 0.00034791 | 0.00082254 | 0.0 | 0.00
Modify | 0.137 | 0.13804 | 0.13981 | 0.3 | 0.92
Other | | 0.01041 | | | 0.07
Nlocal: 8192 ave 8215 max 8166 min
Nlocal: 8192.00 ave 8215 max 8166 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 11972.5 ave 11984 max 11959 min
Nghost: 11972.5 ave 11984 max 11959 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 576083 ave 579616 max 572161 min
Neighs: 576083.0 ave 579616 max 572161 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 2304332
Ave neighs/atom = 70.3226
Total # of neighbors = 2304331
Ave neighs/atom = 70.322601
Neighbor list builds = 6
Dangerous builds = 3
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:11
Total wall time: 0:00:15

35
bench/POTENTIALS/log.16Mar18.granular.1 → bench/POTENTIALS/log.9Oct20.granular.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# granular chute flow
@ -10,12 +9,14 @@ newton off
comm_modify vel yes
read_data data.granular
orthogonal box = (0 0 0) to (40 20 37.2886)
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.000000 20.000000 37.288600)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.050 seconds
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
@ -52,34 +53,34 @@ Neighbor list info ...
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 23.36 | 23.36 | 23.36 Mbytes
Per MPI rank memory allocation (min/avg/max) = 23.37 | 23.37 | 23.37 Mbytes
Step Atoms KinEng c_1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
Loop time of 0.292816 on 1 procs for 100 steps with 32000 atoms
Loop time of 0.274779 on 1 procs for 100 steps with 32000 atoms
Performance: 2950.657 tau/day, 341.511 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 3144.341 tau/day, 363.928 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17449 | 0.17449 | 0.17449 | 0.0 | 59.59
Neigh | 0.031927 | 0.031927 | 0.031927 | 0.0 | 10.90
Comm | 0.010195 | 0.010195 | 0.010195 | 0.0 | 3.48
Output | 0.00019121 | 0.00019121 | 0.00019121 | 0.0 | 0.07
Modify | 0.064463 | 0.064463 | 0.064463 | 0.0 | 22.01
Other | | 0.01155 | | | 3.94
Pair | 0.16956 | 0.16956 | 0.16956 | 0.0 | 61.71
Neigh | 0.027646 | 0.027646 | 0.027646 | 0.0 | 10.06
Comm | 0.010068 | 0.010068 | 0.010068 | 0.0 | 3.66
Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.06
Modify | 0.056372 | 0.056372 | 0.056372 | 0.0 | 20.52
Other | | 0.01096 | | | 3.99
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5463 ave 5463 max 5463 min
Nghost: 5463.00 ave 5463 max 5463 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 115133 ave 115133 max 115133 min
Neighs: 115133.0 ave 115133 max 115133 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 115133
Ave neighs/atom = 3.59791
Ave neighs/atom = 3.5979062
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:00

35
bench/POTENTIALS/log.16Mar18.granular.4 → bench/POTENTIALS/log.9Oct20.granular.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# granular chute flow
@ -10,12 +9,14 @@ newton off
comm_modify vel yes
read_data data.granular
orthogonal box = (0 0 0) to (40 20 37.2886)
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.000000 20.000000 37.288600)
2 by 1 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.052 seconds
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
@ -52,34 +53,34 @@ Neighbor list info ...
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.41 | 10.42 | 10.42 Mbytes
Per MPI rank memory allocation (min/avg/max) = 10.59 | 10.59 | 10.60 Mbytes
Step Atoms KinEng c_1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
Loop time of 0.0903978 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.0952788 on 4 procs for 100 steps with 32000 atoms
Performance: 9557.751 tau/day, 1106.221 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 9068.124 tau/day, 1049.551 timesteps/s
95.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.046331 | 0.049088 | 0.052195 | 1.2 | 54.30
Neigh | 0.0090401 | 0.0091327 | 0.0091863 | 0.1 | 10.10
Comm | 0.0073855 | 0.0080023 | 0.0086699 | 0.6 | 8.85
Output | 7.1049e-05 | 0.00010067 | 0.00012088 | 0.0 | 0.11
Modify | 0.017226 | 0.017449 | 0.01803 | 0.3 | 19.30
Other | | 0.006625 | | | 7.33
Pair | 0.044316 | 0.047274 | 0.049681 | 1.0 | 49.62
Neigh | 0.0079038 | 0.0079354 | 0.0079608 | 0.0 | 8.33
Comm | 0.0082569 | 0.0089372 | 0.0094819 | 0.5 | 9.38
Output | 6.9857e-05 | 9.3222e-05 | 0.00010514 | 0.0 | 0.10
Modify | 0.015689 | 0.016034 | 0.016789 | 0.4 | 16.83
Other | | 0.015 | | | 15.75
Nlocal: 8000 ave 8008 max 7992 min
Nlocal: 8000.00 ave 8008 max 7992 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2439 ave 2450 max 2428 min
Nghost: 2439.00 ave 2450 max 2428 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 29500.5 ave 30488 max 28513 min
Neighs: 29500.5 ave 30488 max 28513 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 118002
Ave neighs/atom = 3.68756
Ave neighs/atom = 3.6875625
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:00

33
bench/POTENTIALS/log.16Mar18.lj.1 → bench/POTENTIALS/log.9Oct20.lj.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
@ -7,14 +6,14 @@ units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (33.591924 33.591924 33.591924)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00183916 secs
create_atoms CPU = 0.002 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
@ -44,30 +43,30 @@ Per MPI rank memory allocation (min/avg/max) = 15.82 | 15.82 | 15.82 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.75745998 -5.7584998 0 -4.6223453 0.20729996
Loop time of 1.721 on 1 procs for 100 steps with 32000 atoms
Loop time of 1.59245 on 1 procs for 100 steps with 32000 atoms
Performance: 25101.720 tau/day, 58.106 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 27127.959 tau/day, 62.796 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2551 | 1.2551 | 1.2551 | 0.0 | 72.93
Neigh | 0.41825 | 0.41825 | 0.41825 | 0.0 | 24.30
Comm | 0.015347 | 0.015347 | 0.015347 | 0.0 | 0.89
Output | 0.00010729 | 0.00010729 | 0.00010729 | 0.0 | 0.01
Modify | 0.023436 | 0.023436 | 0.023436 | 0.0 | 1.36
Other | | 0.008766 | | | 0.51
Pair | 1.1654 | 1.1654 | 1.1654 | 0.0 | 73.18
Neigh | 0.38321 | 0.38321 | 0.38321 | 0.0 | 24.06
Comm | 0.014476 | 0.014476 | 0.014476 | 0.0 | 0.91
Output | 9.5844e-05 | 9.5844e-05 | 9.5844e-05 | 0.0 | 0.01
Modify | 0.021453 | 0.021453 | 0.021453 | 0.0 | 1.35
Other | | 0.007799 | | | 0.49
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19669 ave 19669 max 19669 min
Nghost: 19669.0 ave 19669 max 19669 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20318e+06 ave 1.20318e+06 max 1.20318e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1203176
Ave neighs/atom = 37.5992
Ave neighs/atom = 37.599250
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:01

37
bench/POTENTIALS/log.16Mar18.lj.4 → bench/POTENTIALS/log.9Oct20.lj.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
@ -7,14 +6,14 @@ units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (33.591924 33.591924 33.591924)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000587225 secs
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
@ -40,34 +39,34 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.88 | 6.88 | 6.88 Mbytes
Per MPI rank memory allocation (min/avg/max) = 6.881 | 6.881 | 6.881 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.75745998 -5.7584998 0 -4.6223453 0.20729996
Loop time of 0.469936 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.452443 on 4 procs for 100 steps with 32000 atoms
Performance: 91927.316 tau/day, 212.795 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 95481.741 tau/day, 221.023 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.32713 | 0.32917 | 0.33317 | 0.4 | 70.05
Neigh | 0.10836 | 0.10931 | 0.11007 | 0.2 | 23.26
Comm | 0.015526 | 0.020355 | 0.022399 | 2.0 | 4.33
Output | 4.2439e-05 | 5.8353e-05 | 0.00010061 | 0.0 | 0.01
Modify | 0.0071156 | 0.0072448 | 0.007309 | 0.1 | 1.54
Other | | 0.003793 | | | 0.81
Pair | 0.31149 | 0.3132 | 0.31493 | 0.2 | 69.22
Neigh | 0.1006 | 0.10164 | 0.10385 | 0.4 | 22.47
Comm | 0.02195 | 0.025904 | 0.028603 | 1.6 | 5.73
Output | 4.3631e-05 | 7.534e-05 | 0.00015879 | 0.0 | 0.02
Modify | 0.0067751 | 0.0073788 | 0.0088398 | 1.0 | 1.63
Other | | 0.004243 | | | 0.94
Nlocal: 8000 ave 8041 max 7958 min
Nlocal: 8000.00 ave 8041 max 7958 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 9011 ave 9065 max 8961 min
Nghost: 9011.00 ave 9065 max 8961 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 300794 ave 304843 max 297317 min
Neighs: 300794.0 ave 304843 max 297317 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 1203176
Ave neighs/atom = 37.5992
Ave neighs/atom = 37.599250
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:00

41
bench/POTENTIALS/log.16Mar18.meamc.1 → bench/POTENTIALS/log.9Oct20.meamc.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
@ -7,17 +6,19 @@ units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00184226 secs
create_atoms CPU = 0.002 seconds
pair_style meam/c
pair_coeff * * library.meam Ni4 Ni.meam Ni4
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam with DATE: 2007-06-11
velocity all create 1600.0 376847 loop geom
@ -47,37 +48,37 @@ Neighbor list info ...
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 55.91 | 55.91 | 55.91 Mbytes
Per MPI rank memory allocation (min/avg/max) = 55.92 | 55.92 | 55.92 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.431
100 895.50973 -139454.3 0 -135750.3 31804.185
Loop time of 22.9343 on 1 procs for 100 steps with 32000 atoms
Loop time of 21.655 on 1 procs for 100 steps with 32000 atoms
Performance: 1.884 ns/day, 12.741 hours/ns, 4.360 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 1.995 ns/day, 12.031 hours/ns, 4.618 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.397 | 22.397 | 22.397 | 0.0 | 97.66
Neigh | 0.48781 | 0.48781 | 0.48781 | 0.0 | 2.13
Comm | 0.013967 | 0.013967 | 0.013967 | 0.0 | 0.06
Output | 0.00022793 | 0.00022793 | 0.00022793 | 0.0 | 0.00
Modify | 0.025412 | 0.025412 | 0.025412 | 0.0 | 0.11
Other | | 0.009448 | | | 0.04
Pair | 21.181 | 21.181 | 21.181 | 0.0 | 97.81
Neigh | 0.42787 | 0.42787 | 0.42787 | 0.0 | 1.98
Comm | 0.013557 | 0.013557 | 0.013557 | 0.0 | 0.06
Output | 0.00020766 | 0.00020766 | 0.00020766 | 0.0 | 0.00
Modify | 0.023456 | 0.023456 | 0.023456 | 0.0 | 0.11
Other | | 0.008504 | | | 0.04
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13576 ave 13576 max 13576 min
Nghost: 13576.0 ave 13576 max 13576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 780360 ave 780360 max 780360 min
Neighs: 780360.0 ave 780360 max 780360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Ave neighs/atom = 48.772500
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:23
Total wall time: 0:00:21

39
bench/POTENTIALS/log.16Mar18.meamc.4 → bench/POTENTIALS/log.9Oct20.meamc.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
@ -7,17 +6,19 @@ units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00058651 secs
create_atoms CPU = 0.001 seconds
pair_style meam/c
pair_coeff * * library.meam Ni4 Ni.meam Ni4
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam with DATE: 2007-06-11
velocity all create 1600.0 376847 loop geom
@ -47,37 +48,37 @@ Neighbor list info ...
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.41 | 17.41 | 17.41 Mbytes
Per MPI rank memory allocation (min/avg/max) = 17.42 | 17.42 | 17.42 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.431
100 895.50973 -139454.3 0 -135750.3 31804.185
Loop time of 6.45947 on 4 procs for 100 steps with 32000 atoms
Loop time of 6.34746 on 4 procs for 100 steps with 32000 atoms
Performance: 6.688 ns/day, 3.589 hours/ns, 15.481 timesteps/s
Performance: 6.806 ns/day, 3.526 hours/ns, 15.754 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.22 | 6.2385 | 6.265 | 0.7 | 96.58
Neigh | 0.12657 | 0.12691 | 0.12721 | 0.1 | 1.96
Comm | 0.052339 | 0.07915 | 0.097897 | 5.9 | 1.23
Output | 9.7752e-05 | 0.0001151 | 0.00016594 | 0.0 | 0.00
Modify | 0.010194 | 0.010291 | 0.010442 | 0.1 | 0.16
Other | | 0.004529 | | | 0.07
Pair | 6.0585 | 6.1109 | 6.1535 | 1.4 | 96.27
Neigh | 0.11286 | 0.11651 | 0.12455 | 1.4 | 1.84
Comm | 0.058046 | 0.099641 | 0.15569 | 11.7 | 1.57
Output | 9.0122e-05 | 0.00016046 | 0.0003624 | 0.0 | 0.00
Modify | 0.010822 | 0.011674 | 0.014224 | 1.4 | 0.18
Other | | 0.008601 | | | 0.14
Nlocal: 8000 ave 8045 max 7947 min
Nlocal: 8000.00 ave 8045 max 7947 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 6066.75 ave 6120 max 6021 min
Nghost: 6066.75 ave 6120 max 6021 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 195090 ave 196403 max 193697 min
Neighs: 195090.0 ave 196403 max 193697 min
Histogram: 1 0 0 1 0 0 0 1 0 1
FullNghs: 390180 ave 392616 max 387490 min
FullNghs: 390180.0 ave 392616 max 387490 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Ave neighs/atom = 48.772500
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:06

33
bench/POTENTIALS/log.16Mar18.peri.1 → bench/POTENTIALS/log.9Oct20.peri.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Crack growth in notched 3D Peridynamic block
@ -58,11 +57,11 @@ region plate block 0 0.01975 0 0.01575 ${myzmin} ${myzmax} units bo
region plate block 0 0.01975 0 0.01575 0 ${myzmax} units box
region plate block 0 0.01975 0 0.01575 0 0.01225 units box
create_box 3 plate
Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (0.01975 0.01575 0.01225)
1 by 1 by 1 MPI processor grid
create_atoms 1 region plate
Created 32000 atoms
Time spent = 0.00362897 secs
create_atoms CPU = 0.004 seconds
pair_style peri/pmb
@ -101,8 +100,10 @@ region topright block 0.009875 0.01975 0.01075 0.01575 ${myzmin} ${myzmax}
region topright block 0.009875 0.01975 0.01075 0.01575 0 ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 0.01575 0 0.01225 units box
set region topleft type 2
Setting atom values ...
5000 settings made for type
set region topright type 3
Setting atom values ...
5000 settings made for type
pair_coeff 1 1 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
@ -129,11 +130,13 @@ pair_coeff 1 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 1 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
set group all density ${mydensity}
set group all density 2440
Setting atom values ...
32000 settings made for density
variable myvolume equal ($h)^3
variable myvolume equal (0.0005)^3
set group all volume ${myvolume}
set group all volume 1.25e-10
Setting atom values ...
32000 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
@ -184,23 +187,23 @@ Step Temp E_pair E_mol TotEng Press Volume
60 9.8975313e+26 5.7284448e+08 0 1.2287455e+09 1.2048543e+14 3.6292128e-06
80 9.3888573e+26 4.0928092e+08 0 1.0314725e+09 1.1429321e+14 3.6292128e-06
100 8.3930314e+26 3.8522361e+08 0 9.4142265e+08 1.0217075e+14 3.6292128e-06
Loop time of 11.0398 on 1 procs for 100 steps with 32000 atoms
Loop time of 10.1036 on 1 procs for 100 steps with 32000 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.005 | 11.005 | 11.005 | 0.0 | 99.68
Pair | 10.07 | 10.07 | 10.07 | 0.0 | 99.67
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.6042e-05 | 6.6042e-05 | 6.6042e-05 | 0.0 | 0.00
Output | 0.00057292 | 0.00057292 | 0.00057292 | 0.0 | 0.01
Modify | 0.0256 | 0.0256 | 0.0256 | 0.0 | 0.23
Other | | 0.008592 | | | 0.08
Comm | 6.6519e-05 | 6.6519e-05 | 6.6519e-05 | 0.0 | 0.00
Output | 0.00051737 | 0.00051737 | 0.00051737 | 0.0 | 0.01
Modify | 0.024288 | 0.024288 | 0.024288 | 0.0 | 0.24
Other | | 0.008486 | | | 0.08
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.74442e+06 ave 6.74442e+06 max 6.74442e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -208,10 +211,10 @@ FullNghs: 1.34888e+07 ave 1.34888e+07 max 1.34888e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13488836
Ave neighs/atom = 421.526
Ave neighs/atom = 421.52612
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:11
Total wall time: 0:00:10

39
bench/POTENTIALS/log.16Mar18.peri.4 → bench/POTENTIALS/log.9Oct20.peri.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Crack growth in notched 3D Peridynamic block
@ -58,11 +57,11 @@ region plate block 0 0.01975 0 0.01575 ${myzmin} ${myzmax} units bo
region plate block 0 0.01975 0 0.01575 0 ${myzmax} units box
region plate block 0 0.01975 0 0.01575 0 0.01225 units box
create_box 3 plate
Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (0.01975 0.01575 0.01225)
2 by 2 by 1 MPI processor grid
create_atoms 1 region plate
Created 32000 atoms
Time spent = 0.0011344 secs
create_atoms CPU = 0.001 seconds
pair_style peri/pmb
@ -101,8 +100,10 @@ region topright block 0.009875 0.01975 0.01075 0.01575 ${myzmin} ${myzmax}
region topright block 0.009875 0.01975 0.01075 0.01575 0 ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 0.01575 0 0.01225 units box
set region topleft type 2
Setting atom values ...
5000 settings made for type
set region topright type 3
Setting atom values ...
5000 settings made for type
pair_coeff 1 1 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
@ -129,11 +130,13 @@ pair_coeff 1 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 1 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
set group all density ${mydensity}
set group all density 2440
Setting atom values ...
32000 settings made for density
variable myvolume equal ($h)^3
variable myvolume equal (0.0005)^3
set group all volume ${myvolume}
set group all volume 1.25e-10
Setting atom values ...
32000 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
@ -176,7 +179,7 @@ Neighbor list info ...
Peridynamic bonds:
total # of bonds = 3457032
bonds/atom = 108.032
Per MPI rank memory allocation (min/avg/max) = 47.63 | 48.11 | 48.78 Mbytes
Per MPI rank memory allocation (min/avg/max) = 47.70 | 48.18 | 48.85 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.0134233e+27 0 0 1.3342785e+09 2.4509971e+14 3.6292128e-06
20 1.7695805e+27 1.6163291e+08 0 1.3343188e+09 2.1541601e+14 3.6292128e-06
@ -184,34 +187,34 @@ Step Temp E_pair E_mol TotEng Press Volume
60 9.8975313e+26 5.7284448e+08 0 1.2287455e+09 1.2048543e+14 3.6292128e-06
80 9.3888573e+26 4.0928092e+08 0 1.0314725e+09 1.1429321e+14 3.6292128e-06
100 8.3930314e+26 3.8522361e+08 0 9.4142265e+08 1.0217075e+14 3.6292128e-06
Loop time of 2.8928 on 4 procs for 100 steps with 32000 atoms
Loop time of 2.82804 on 4 procs for 100 steps with 32000 atoms
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7472 | 2.7951 | 2.8585 | 2.9 | 96.62
Pair | 2.6021 | 2.6599 | 2.7081 | 2.4 | 94.05
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019592 | 0.083156 | 0.13278 | 17.0 | 2.87
Output | 0.00022125 | 0.00034326 | 0.00058961 | 0.0 | 0.01
Modify | 0.0083542 | 0.0089623 | 0.0095983 | 0.5 | 0.31
Other | | 0.005276 | | | 0.18
Comm | 0.10341 | 0.15313 | 0.21057 | 10.3 | 5.41
Output | 0.00020409 | 0.00041658 | 0.00093699 | 0.0 | 0.01
Modify | 0.008944 | 0.0092288 | 0.0095088 | 0.3 | 0.33
Other | | 0.005395 | | | 0.19
Nlocal: 8000 ave 8000 max 8000 min
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5125 ave 5125 max 5125 min
Nghost: 5125.00 ave 5125 max 5125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 1.6861e+06 ave 1.77502e+06 max 1.60625e+06 min
Neighs: 1.68610e+06 ave 1.77502e+06 max 1.60625e+06 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 3.37221e+06 ave 3.41832e+06 max 3.3261e+06 min
FullNghs: 3.37221e+06 ave 3.41832e+06 max 3.3261e+06 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 13488836
Ave neighs/atom = 421.526
Ave neighs/atom = 421.52612
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03
Total wall time: 0:00:02

86
bench/POTENTIALS/log.16Mar18.protein.1 → bench/POTENTIALS/log.9Oct20.protein.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Rhodopsin model
@ -17,7 +16,8 @@ pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.protein
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
Reading data file ...
orthogonal box = (-27.500000 -38.500000 -36.364600) to (27.500000 38.500000 36.361500)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
@ -39,16 +39,22 @@ read_data data.protein
56829 dihedrals
reading impropers ...
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
special bonds CPU = 0.011 seconds
read_data CPU = 0.125 seconds
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
find clusters CPU = 0.006 seconds
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
@ -58,13 +64,13 @@ timestep 2.0
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.248835
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.24883488
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.0355478
estimated relative force accuracy = 0.000107051
using double precision FFTs
estimated absolute RMS force accuracy = 0.035547797
estimated relative force accuracy = 0.00010705113
using double precision KISS FFT
3d grid and FFT values/proc = 41070 25600
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
@ -78,46 +84,46 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 140 | 140 | 140 Mbytes
Per MPI rank memory allocation (min/avg/max) = 140.0 | 140.0 | 140.0 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
Volume = 307995.0335
---------------- Step 100 ----- CPU = 23.7567 (sec) ----------------
TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
PotEng = -46882.6482 E_bond = 2567.9789 E_angle = 10781.9556
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
Volume = 308133.9933
Loop time of 23.7568 on 1 procs for 100 steps with 32000 atoms
---------------- Step 100 ----- CPU = 20.0022 (sec) ----------------
TotEng = -25290.7304 KinEng = 21591.9084 Temp = 301.0906
PotEng = -46882.6388 E_bond = 2567.9807 E_angle = 10781.9571
E_dihed = 5198.7492 E_impro = 216.7864 E_vdwl = -1902.6618
E_coul = 206659.5226 E_long = -270404.9730 Press = 6.7406
Volume = 308134.2285
Loop time of 20.0022 on 1 procs for 100 steps with 32000 atoms
Performance: 0.727 ns/day, 32.995 hours/ns, 4.209 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.864 ns/day, 27.781 hours/ns, 4.999 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 17.905 | 17.905 | 17.905 | 0.0 | 75.37
Bond | 0.73417 | 0.73417 | 0.73417 | 0.0 | 3.09
Kspace | 1.4676 | 1.4676 | 1.4676 | 0.0 | 6.18
Neigh | 2.9907 | 2.9907 | 2.9907 | 0.0 | 12.59
Comm | 0.037427 | 0.037427 | 0.037427 | 0.0 | 0.16
Output | 0.00011754 | 0.00011754 | 0.00011754 | 0.0 | 0.00
Modify | 0.60985 | 0.60985 | 0.60985 | 0.0 | 2.57
Other | | 0.01201 | | | 0.05
Pair | 15 | 15 | 15 | 0.0 | 74.99
Bond | 0.65091 | 0.65091 | 0.65091 | 0.0 | 3.25
Kspace | 1.2144 | 1.2144 | 1.2144 | 0.0 | 6.07
Neigh | 2.6096 | 2.6096 | 2.6096 | 0.0 | 13.05
Comm | 0.035203 | 0.035203 | 0.035203 | 0.0 | 0.18
Output | 0.00010848 | 0.00010848 | 0.00010848 | 0.0 | 0.00
Modify | 0.48116 | 0.48116 | 0.48116 | 0.0 | 2.41
Other | | 0.01032 | | | 0.05
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 47958 ave 47958 max 47958 min
Nghost: 47958.0 ave 47958 max 47958 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Total # of neighbors = 12028093
Ave neighs/atom = 375.87791
Ave special neighs/atom = 7.4318750
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:24
Total wall time: 0:00:20

88
bench/POTENTIALS/log.16Mar18.protein.4 → bench/POTENTIALS/log.9Oct20.protein.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Rhodopsin model
@ -17,7 +16,8 @@ pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.protein
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
Reading data file ...
orthogonal box = (-27.500000 -38.500000 -36.364600) to (27.500000 38.500000 36.361500)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
@ -39,16 +39,22 @@ read_data data.protein
56829 dihedrals
reading impropers ...
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
special bonds CPU = 0.005 seconds
read_data CPU = 0.210 seconds
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
find clusters CPU = 0.003 seconds
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
@ -58,13 +64,13 @@ timestep 2.0
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.248835
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.24883488
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.0355478
estimated relative force accuracy = 0.000107051
using double precision FFTs
estimated absolute RMS force accuracy = 0.035547797
estimated relative force accuracy = 0.00010705113
using double precision KISS FFT
3d grid and FFT values/proc = 13230 6400
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
@ -78,46 +84,46 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 49.07 | 49.17 | 49.46 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.25 | 49.35 | 49.64 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
Volume = 307995.0335
---------------- Step 100 ----- CPU = 6.3997 (sec) ----------------
TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
PotEng = -46882.6483 E_bond = 2567.9789 E_angle = 10781.9556
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
Volume = 308133.9933
Loop time of 6.39977 on 4 procs for 100 steps with 32000 atoms
---------------- Step 100 ----- CPU = 5.5375 (sec) ----------------
TotEng = -25290.7303 KinEng = 21591.9085 Temp = 301.0906
PotEng = -46882.6388 E_bond = 2567.9807 E_angle = 10781.9571
E_dihed = 5198.7492 E_impro = 216.7864 E_vdwl = -1902.6618
E_coul = 206659.5225 E_long = -270404.9730 Press = 6.7406
Volume = 308134.2285
Loop time of 5.53765 on 4 procs for 100 steps with 32000 atoms
Performance: 2.700 ns/day, 8.889 hours/ns, 15.626 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 3.120 ns/day, 7.691 hours/ns, 18.058 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4434 | 4.5321 | 4.6846 | 4.3 | 70.82
Bond | 0.17894 | 0.18568 | 0.19951 | 1.9 | 2.90
Kspace | 0.4651 | 0.61064 | 0.69123 | 11.1 | 9.54
Neigh | 0.7739 | 0.77394 | 0.774 | 0.0 | 12.09
Comm | 0.057676 | 0.069183 | 0.07901 | 3.0 | 1.08
Output | 5.6505e-05 | 6.6578e-05 | 9.4414e-05 | 0.0 | 0.00
Modify | 0.21444 | 0.21866 | 0.22524 | 0.9 | 3.42
Other | | 0.009451 | | | 0.15
Pair | 3.8921 | 3.9427 | 4.0762 | 3.9 | 71.20
Bond | 0.16218 | 0.16829 | 0.17972 | 1.7 | 3.04
Kspace | 0.35196 | 0.48475 | 0.53996 | 11.1 | 8.75
Neigh | 0.69975 | 0.69981 | 0.69988 | 0.0 | 12.64
Comm | 0.04908 | 0.049445 | 0.049767 | 0.1 | 0.89
Output | 5.1737e-05 | 8.5056e-05 | 0.00018382 | 0.0 | 0.00
Modify | 0.18393 | 0.18474 | 0.18528 | 0.1 | 3.34
Other | | 0.007858 | | | 0.14
Nlocal: 8000 ave 8143 max 7933 min
Nlocal: 8000.00 ave 8143 max 7933 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 22733.5 ave 22769 max 22693 min
Nghost: 22733.5 ave 22769 max 22693 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Total # of neighbors = 12028093
Ave neighs/atom = 375.87791
Ave special neighs/atom = 7.4318750
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:06
Total wall time: 0:00:05

96
bench/POTENTIALS/log.9Oct20.reaxc.1 Normal file
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LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4910650 9.4910650 6.9912300)
1 by 1 by 1 MPI processor grid
reading atoms ...
58 atoms
read_data CPU = 0.000 seconds
replicate 7 8 10
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (66.437455 75.928520 69.912300)
1 by 1 by 1 MPI processor grid
32480 atoms
replicate CPU = 0.002 seconds
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 1727.0 | 1727.0 | 1727.0 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5638 -3203096.6
10 299.37479 28983.59 -3232075.2 21746.783 -23987.396 7610.3039 -3203091.6
20 295.58549 28616.733 -3231710.1 18178.443 -10872.027 10603.19 -3203093.3
30 289.48845 28026.456 -3231123.3 12146.101 4985.2572 13364.258 -3203096.8
40 282.66408 27365.763 -3230467.5 4284.1187 18132.512 14133.51 -3203101.7
50 274.97007 26620.878 -3229730.4 -3718.933 25520.016 12551.903 -3203109.5
60 266.11301 25763.393 -3228883.8 -9271.3498 27307.451 9753.2362 -3203120.4
70 259.32635 25106.351 -3228237.2 -11150.623 24238.509 6578.531 -3203130.8
80 260.33969 25204.456 -3228344.2 -9576.4144 16737.758 3454.6426 -3203139.7
90 269.9021 26130.229 -3229275.5 -5905.8652 5246.3236 467.53439 -3203145.2
100 280.76723 27182.123 -3230330.6 -1363.6002 -8133.2093 -1689.6535 -3203148.5
Loop time of 213.234 on 1 procs for 100 steps with 32480 atoms
Performance: 0.004 ns/day, 5923.154 hours/ns, 0.469 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 157 | 157 | 157 | 0.0 | 73.63
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.024997 | 0.024997 | 0.024997 | 0.0 | 0.01
Output | 0.0022025 | 0.0022025 | 0.0022025 | 0.0 | 0.00
Modify | 56.19 | 56.19 | 56.19 | 0.0 | 26.35
Other | | 0.01211 | | | 0.01
Nlocal: 32480.0 ave 32480 max 32480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45128.0 ave 45128 max 45128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.27781e+07 ave 1.27781e+07 max 1.27781e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12778082
Ave neighs/atom = 393.41385
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:03:37

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bench/POTENTIALS/log.9Oct20.reaxc.4 Normal file
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@ -0,0 +1,96 @@
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4910650 9.4910650 6.9912300)
2 by 2 by 1 MPI processor grid
reading atoms ...
58 atoms
read_data CPU = 0.000 seconds
replicate 7 8 10
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (66.437455 75.928520 69.912300)
1 by 2 by 2 MPI processor grid
32480 atoms
replicate CPU = 0.001 seconds
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 647.0 | 647.0 | 647.0 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5638 -3203096.6
10 299.37479 28983.59 -3232075.2 21746.771 -23987.411 7610.2901 -3203091.6
20 295.58551 28616.736 -3231710.1 18178.439 -10871.954 10603.303 -3203093.3
30 289.48844 28026.456 -3231123.2 12146.289 4985.5678 13364.519 -3203096.8
40 282.66406 27365.762 -3230467.4 4284.8179 18133.406 14134.156 -3203101.7
50 274.97009 26620.88 -3229730.3 -3718.6796 25520.338 12552.205 -3203109.5
60 266.11302 25763.394 -3228883.8 -9271.5644 27307.146 9753.1034 -3203120.4
70 259.32636 25106.352 -3228237.1 -11150.66 24238.705 6578.7141 -3203130.8
80 260.33966 25204.454 -3228344.1 -9576.2474 16737.753 3454.7607 -3203139.7
90 269.90207 26130.226 -3229275.5 -5905.8809 5246.1687 467.42114 -3203145.2
100 280.76722 27182.122 -3230330.6 -1363.4752 -8133.2096 -1689.5922 -3203148.5
Loop time of 69.1187 on 4 procs for 100 steps with 32480 atoms
Performance: 0.013 ns/day, 1919.965 hours/ns, 1.447 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 45.964 | 48.533 | 51.423 | 29.3 | 70.22
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.19604 | 3.0913 | 5.6647 | 116.3 | 4.47
Output | 0.00074649 | 0.0011722 | 0.0023553 | 2.0 | 0.00
Modify | 17.48 | 17.485 | 17.489 | 0.1 | 25.30
Other | | 0.008528 | | | 0.01
Nlocal: 8120.00 ave 8120 max 8120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 21992.0 ave 21992 max 21992 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3.48274e+06 ave 3.48274e+06 max 3.48274e+06 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13930976
Ave neighs/atom = 428.90936
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:10

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LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
Reading data file ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000 seconds
replicate 17 16 2
Replicating atoms ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
1 by 1 by 1 MPI processor grid
32640 atoms
replicate CPU = 0.002 seconds
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.rebo C H
Reading rebo potential file CH.rebo with DATE: 2018-7-3
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.83 0 -137177.16 2463.0748
10 179.37985 -137931.27 0 -137174.48 15655.936
20 206.87654 -138046.99 0 -137174.19 -24042.627
30 150.80122 -137807.43 0 -137171.21 -16524.118
40 173.24945 -137902.35 0 -137171.42 -5716.9119
50 151.80455 -137812.36 0 -137171.91 3480.4584
60 199.08777 -138013.82 0 -137173.88 17881.372
70 217.85748 -138093.86 0 -137174.73 -12270.999
80 202.37482 -138029.39 0 -137175.59 -7622.7319
90 194.90628 -137997.05 0 -137174.75 -32267.471
100 185.17818 -137954.51 0 -137173.26 -6901.7499
Loop time of 4.83649 on 1 procs for 100 steps with 32640 atoms
Performance: 0.893 ns/day, 26.869 hours/ns, 20.676 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3248 | 3.3248 | 3.3248 | 0.0 | 68.74
Neigh | 1.4583 | 1.4583 | 1.4583 | 0.0 | 30.15
Comm | 0.01934 | 0.01934 | 0.01934 | 0.0 | 0.40
Output | 0.0011871 | 0.0011871 | 0.0011871 | 0.0 | 0.02
Modify | 0.023516 | 0.023516 | 0.023516 | 0.0 | 0.49
Other | | 0.009316 | | | 0.19
Nlocal: 32640.0 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26460.0 ave 26460 max 26460 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4902134
Ave neighs/atom = 150.18793
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:05

90
bench/POTENTIALS/log.9Oct20.rebo.4 Normal file
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@ -0,0 +1,90 @@
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
Reading data file ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000 seconds
replicate 17 16 2
Replicating atoms ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
2 by 2 by 1 MPI processor grid
32640 atoms
replicate CPU = 0.001 seconds
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.rebo C H
Reading rebo potential file CH.rebo with DATE: 2018-7-3
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.80 | 12.00 | 12.19 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.83 0 -137177.16 2463.0748
10 179.37985 -137931.27 0 -137174.48 15655.936
20 206.87654 -138046.99 0 -137174.19 -24042.627
30 150.80122 -137807.43 0 -137171.21 -16524.118
40 173.24945 -137902.35 0 -137171.42 -5716.9119
50 151.80455 -137812.36 0 -137171.91 3480.4584
60 199.08777 -138013.82 0 -137173.88 17881.372
70 217.85748 -138093.86 0 -137174.73 -12270.999
80 202.37482 -138029.39 0 -137175.59 -7622.7319
90 194.90628 -137997.05 0 -137174.75 -32267.471
100 185.17818 -137954.51 0 -137173.26 -6901.7499
Loop time of 1.74701 on 4 procs for 100 steps with 32640 atoms
Performance: 2.473 ns/day, 9.706 hours/ns, 57.241 timesteps/s
94.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.89836 | 0.96998 | 1.054 | 6.0 | 55.52
Neigh | 0.453 | 0.47091 | 0.50316 | 2.8 | 26.96
Comm | 0.15706 | 0.27291 | 0.36547 | 14.5 | 15.62
Output | 0.00047016 | 0.00073808 | 0.0015287 | 0.0 | 0.04
Modify | 0.0093558 | 0.010209 | 0.011958 | 1.0 | 0.58
Other | | 0.02227 | | | 1.27
Nlocal: 8160.00 ave 8163 max 8157 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11605.8 ave 11615 max 11593 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.22553e+06 ave 1.22735e+06 max 1.22455e+06 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 4902134
Ave neighs/atom = 150.18793
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:01

147
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LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
Reading data file ...
orthogonal box = (0.02645 0.02645 0.02641) to (35.532800 35.532800 35.473600)
1 by 1 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 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 = 0.001 seconds
read_data CPU = 0.009 seconds
replicate 2 4 1
Replicating atoms ...
orthogonal box = (0.02645 0.02645 0.02641) to (71.039150 142.05185 35.473600)
1 by 1 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 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 = 0.005 seconds
replicate CPU = 0.012 seconds
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.5
special bond factors coul: 0.0 0.0 0.5
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 = 0.005 seconds
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
find clusters CPU = 0.005 seconds
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.2688011
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.033101471
estimated relative force accuracy = 9.9684097e-05
using double precision KISS FFT
3d grid and FFT values/proc = 91977 55296
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.8
ghost atom cutoff = 11.8
binsize = 5.9, bins = 13 25 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 105.4 | 105.4 | 105.4 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 516.17807
50 264.98553 -136986.74 0 -118030.61 -440.29256
100 274.45966 -136364.57 0 -116730.69 -128.61948
Loop time of 18.5133 on 1 procs for 100 steps with 36000 atoms
Performance: 0.933 ns/day, 25.713 hours/ns, 5.402 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.557 | 14.557 | 14.557 | 0.0 | 78.63
Bond | 7.1764e-05 | 7.1764e-05 | 7.1764e-05 | 0.0 | 0.00
Kspace | 1.7651 | 1.7651 | 1.7651 | 0.0 | 9.53
Neigh | 1.8703 | 1.8703 | 1.8703 | 0.0 | 10.10
Comm | 0.042219 | 0.042219 | 0.042219 | 0.0 | 0.23
Output | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.00
Modify | 0.26983 | 0.26983 | 0.26983 | 0.0 | 1.46
Other | | 0.008397 | | | 0.05
Nlocal: 36000.0 ave 36000 max 36000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 56963.0 ave 56963 max 56963 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.24625e+07 ave 1.24625e+07 max 1.24625e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12462451
Ave neighs/atom = 346.17919
Ave special neighs/atom = 2.0000000
Neighbor list builds = 9
Dangerous builds = 6
Total wall time: 0:00:19

147
bench/POTENTIALS/log.9Oct20.spce.4 Normal file
View File

@ -0,0 +1,147 @@
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
Reading data file ...
orthogonal box = (0.02645 0.02645 0.02641) to (35.532800 35.532800 35.473600)
2 by 2 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 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 = 0.001 seconds
read_data CPU = 0.008 seconds
replicate 2 4 1
Replicating atoms ...
orthogonal box = (0.02645 0.02645 0.02641) to (71.039150 142.05185 35.473600)
1 by 4 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 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 = 0.002 seconds
replicate CPU = 0.005 seconds
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.5
special bond factors coul: 0.0 0.0 0.5
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 = 0.004 seconds
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
find clusters CPU = 0.003 seconds
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.2688011
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.033101471
estimated relative force accuracy = 9.9684097e-05
using double precision KISS FFT
3d grid and FFT values/proc = 27993 13824
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.8
ghost atom cutoff = 11.8
binsize = 5.9, bins = 13 25 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 37.90 | 37.90 | 37.90 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 516.17807
50 264.98553 -136986.74 0 -118030.61 -440.29255
100 274.45966 -136364.57 0 -116730.69 -128.61954
Loop time of 5.44355 on 4 procs for 100 steps with 36000 atoms
Performance: 3.174 ns/day, 7.560 hours/ns, 18.370 timesteps/s
95.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.82 | 3.8744 | 3.9155 | 1.8 | 71.17
Bond | 7.8917e-05 | 8.6784e-05 | 9.4891e-05 | 0.0 | 0.00
Kspace | 0.79192 | 0.83671 | 0.88328 | 3.5 | 15.37
Neigh | 0.51754 | 0.5178 | 0.51789 | 0.0 | 9.51
Comm | 0.069774 | 0.078783 | 0.088247 | 2.3 | 1.45
Output | 9.0361e-05 | 0.00015712 | 0.00035048 | 0.0 | 0.00
Modify | 0.12822 | 0.13016 | 0.13486 | 0.8 | 2.39
Other | | 0.005435 | | | 0.10
Nlocal: 9000.00 ave 9002 max 8998 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 24134.2 ave 24184 max 24062 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 3.11561e+06 ave 3.11676e+06 max 3.11446e+06 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 12462451
Ave neighs/atom = 346.17919
Ave special neighs/atom = 2.0000000
Neighbor list builds = 9
Dangerous builds = 6
Total wall time: 0:00:05

40
bench/POTENTIALS/log.16Mar18.sw.1 → bench/POTENTIALS/log.9Oct20.sw.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Stillinger-Weber
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00191712 secs
create_atoms CPU = 0.002 seconds
pair_style sw
pair_coeff * * Si.sw Si
Reading sw potential file Si.sw with DATE: 2007-06-11
mass 1 28.06
velocity all create 1000.0 376847 loop geom
@ -46,32 +46,32 @@ Per MPI rank memory allocation (min/avg/max) = 12.52 | 12.52 | 12.52 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -138771.2 0 -134635 6866.6499
100 508.80533 -136736.12 0 -134631.6 6361.7858
Loop time of 5.66634 on 1 procs for 100 steps with 32000 atoms
Loop time of 3.9309 on 1 procs for 100 steps with 32000 atoms
Performance: 1.525 ns/day, 15.740 hours/ns, 17.648 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 2.198 ns/day, 10.919 hours/ns, 25.439 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.5464 | 5.5464 | 5.5464 | 0.0 | 97.88
Neigh | 0.075834 | 0.075834 | 0.075834 | 0.0 | 1.34
Comm | 0.0092049 | 0.0092049 | 0.0092049 | 0.0 | 0.16
Output | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.00
Modify | 0.024666 | 0.024666 | 0.024666 | 0.0 | 0.44
Other | | 0.01014 | | | 0.18
Pair | 3.8206 | 3.8206 | 3.8206 | 0.0 | 97.19
Neigh | 0.067368 | 0.067368 | 0.067368 | 0.0 | 1.71
Comm | 0.0091503 | 0.0091503 | 0.0091503 | 0.0 | 0.23
Output | 0.0001049 | 0.0001049 | 0.0001049 | 0.0 | 0.00
Modify | 0.023839 | 0.023839 | 0.023839 | 0.0 | 0.61
Other | | 0.009882 | | | 0.25
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12495 ave 12495 max 12495 min
Nghost: 12495.0 ave 12495 max 12495 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 894818 ave 894818 max 894818 min
FullNghs: 894818.0 ave 894818 max 894818 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 894818
Ave neighs/atom = 27.9631
Ave neighs/atom = 27.963062
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:05
Total wall time: 0:00:03

38
bench/POTENTIALS/log.16Mar18.sw.4 → bench/POTENTIALS/log.9Oct20.sw.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Stillinger-Weber
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000604153 secs
create_atoms CPU = 0.001 seconds
pair_style sw
pair_coeff * * Si.sw Si
Reading sw potential file Si.sw with DATE: 2007-06-11
mass 1 28.06
velocity all create 1000.0 376847 loop geom
@ -46,32 +46,32 @@ Per MPI rank memory allocation (min/avg/max) = 4.104 | 4.104 | 4.104 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -138771.2 0 -134635 6866.6499
100 508.80533 -136736.12 0 -134631.6 6361.7858
Loop time of 1.47105 on 4 procs for 100 steps with 32000 atoms
Loop time of 1.04386 on 4 procs for 100 steps with 32000 atoms
Performance: 5.873 ns/day, 4.086 hours/ns, 67.978 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 8.277 ns/day, 2.900 hours/ns, 95.798 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3788 | 1.3929 | 1.4053 | 0.8 | 94.69
Neigh | 0.019134 | 0.019502 | 0.019816 | 0.2 | 1.33
Comm | 0.024183 | 0.035734 | 0.049122 | 4.7 | 2.43
Output | 5.1975e-05 | 6.6102e-05 | 0.00010204 | 0.0 | 0.00
Modify | 0.0063825 | 0.0064374 | 0.0064764 | 0.0 | 0.44
Other | | 0.01638 | | | 1.11
Pair | 0.96496 | 0.97632 | 0.9978 | 1.3 | 93.53
Neigh | 0.01732 | 0.017998 | 0.019718 | 0.7 | 1.72
Comm | 0.012035 | 0.036398 | 0.049588 | 7.7 | 3.49
Output | 4.5061e-05 | 5.5015e-05 | 7.7248e-05 | 0.0 | 0.01
Modify | 0.0070148 | 0.0070775 | 0.0071096 | 0.0 | 0.68
Other | | 0.006012 | | | 0.58
Nlocal: 8000 ave 8015 max 7978 min
Nlocal: 8000.00 ave 8015 max 7978 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 4995 ave 5017 max 4980 min
Nghost: 4995.00 ave 5017 max 4980 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 223704 ave 224108 max 223131 min
FullNghs: 223704.0 ave 224108 max 223131 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 894818
Ave neighs/atom = 27.9631
Ave neighs/atom = 27.963062
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:01

42
bench/POTENTIALS/log.16Mar18.tersoff.1 → bench/POTENTIALS/log.9Oct20.tersoff.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Tersoff
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.0019412 secs
create_atoms CPU = 0.002 seconds
pair_style tersoff
pair_coeff * * Si.tersoff Si
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
mass 1 28.06
velocity all create 1000.0 376847 loop geom
@ -42,36 +42,36 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.1 | 11.1 | 11.1 Mbytes
Per MPI rank memory allocation (min/avg/max) = 11.11 | 11.11 | 11.11 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -148173.19 0 -144036.99 7019.4434
100 430.57813 -145815.61 0 -144034.65 -14550.734
Loop time of 8.53088 on 1 procs for 100 steps with 32000 atoms
Loop time of 4.71424 on 1 procs for 100 steps with 32000 atoms
Performance: 1.013 ns/day, 23.697 hours/ns, 11.722 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 1.833 ns/day, 13.095 hours/ns, 21.212 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.4236 | 8.4236 | 8.4236 | 0.0 | 98.74
Neigh | 0.065852 | 0.065852 | 0.065852 | 0.0 | 0.77
Comm | 0.0078607 | 0.0078607 | 0.0078607 | 0.0 | 0.09
Output | 0.00010872 | 0.00010872 | 0.00010872 | 0.0 | 0.00
Modify | 0.023968 | 0.023968 | 0.023968 | 0.0 | 0.28
Other | | 0.009521 | | | 0.11
Pair | 4.612 | 4.612 | 4.612 | 0.0 | 97.83
Neigh | 0.060618 | 0.060618 | 0.060618 | 0.0 | 1.29
Comm | 0.008847 | 0.008847 | 0.008847 | 0.0 | 0.19
Output | 9.9659e-05 | 9.9659e-05 | 9.9659e-05 | 0.0 | 0.00
Modify | 0.023234 | 0.023234 | 0.023234 | 0.0 | 0.49
Other | | 0.00941 | | | 0.20
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11537 ave 11537 max 11537 min
Nghost: 11537.0 ave 11537 max 11537 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 530500 ave 530500 max 530500 min
FullNghs: 530500.0 ave 530500 max 530500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 530500
Ave neighs/atom = 16.5781
Ave neighs/atom = 16.578125
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:08
Total wall time: 0:00:04

42
bench/POTENTIALS/log.16Mar18.tersoff.4 → bench/POTENTIALS/log.9Oct20.tersoff.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Tersoff
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000605822 secs
create_atoms CPU = 0.001 seconds
pair_style tersoff
pair_coeff * * Si.tersoff Si
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
mass 1 28.06
velocity all create 1000.0 376847 loop geom
@ -42,36 +42,36 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.753 | 3.753 | 3.753 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.754 | 3.754 | 3.754 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -148173.19 0 -144036.99 7019.4434
100 430.57813 -145815.61 0 -144034.65 -14550.734
Loop time of 2.16161 on 4 procs for 100 steps with 32000 atoms
Loop time of 1.32053 on 4 procs for 100 steps with 32000 atoms
Performance: 3.997 ns/day, 6.004 hours/ns, 46.262 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 6.543 ns/day, 3.668 hours/ns, 75.727 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1122 | 2.1165 | 2.122 | 0.2 | 97.91
Neigh | 0.016894 | 0.016915 | 0.016955 | 0.0 | 0.78
Comm | 0.012348 | 0.017858 | 0.022105 | 2.7 | 0.83
Output | 4.7684e-05 | 6.2048e-05 | 9.9421e-05 | 0.0 | 0.00
Modify | 0.0064063 | 0.0064579 | 0.0065169 | 0.0 | 0.30
Other | | 0.003793 | | | 0.18
Pair | 1.1729 | 1.2118 | 1.2453 | 2.3 | 91.77
Neigh | 0.015989 | 0.016319 | 0.016708 | 0.3 | 1.24
Comm | 0.046884 | 0.078767 | 0.11602 | 8.9 | 5.96
Output | 3.9816e-05 | 7.0453e-05 | 0.00015831 | 0.0 | 0.01
Modify | 0.0070612 | 0.0071967 | 0.0073555 | 0.1 | 0.54
Other | | 0.006331 | | | 0.48
Nlocal: 8000 ave 8005 max 7993 min
Nlocal: 8000.00 ave 8005 max 7993 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 4580.25 ave 4593 max 4567 min
Nghost: 4580.25 ave 4593 max 4567 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 132625 ave 132785 max 132562 min
FullNghs: 132625.0 ave 132785 max 132562 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 530500
Ave neighs/atom = 16.5781
Ave neighs/atom = 16.578125
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:01

37
cmake/CMakeLists.txt
View File

@ -584,7 +584,7 @@ endif()
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
foreach(_HEADER ${LAMMPS_CXX_HEADERS})
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
@ -696,15 +696,6 @@ include(Testing)
include(CodeCoverage)
include(CodingStandard)
###############################################################################
# Print package summary
###############################################################################
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
if(PKG_${PKG})
message(STATUS "Building package: ${PKG}")
endif()
endforeach()
get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
include(FeatureSummary)
feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
@ -712,8 +703,24 @@ message(STATUS "<<< Build configuration >>>
Operating System: ${CMAKE_SYSTEM_NAME}
Build type: ${CMAKE_BUILD_TYPE}
Install path: ${CMAKE_INSTALL_PREFIX}
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}
-- <<< Compilers and Flags: >>>
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
###############################################################################
# Print package summary
###############################################################################
set(ENABLED_PACKAGES)
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
if(PKG_${PKG})
list(APPEND ENABLED_PACKAGES ${PKG})
endif()
endforeach()
if(ENABLED_PACKAGES)
list(SORT ENABLED_PACKAGES)
else()
set(ENABLED_PACKAGES "<None>")
endif()
message(STATUS "Enabled packages: ${ENABLED_PACKAGES}")
message(STATUS "<<< Compilers and Flags: >>>
-- C++ Compiler: ${CMAKE_CXX_COMPILER}
Type: ${CMAKE_CXX_COMPILER_ID}
Version: ${CMAKE_CXX_COMPILER_VERSION}
@ -815,3 +822,9 @@ endif()
if(BUILD_LAMMPS_SHELL)
message(STATUS "<<< Building LAMMPS Shell >>>")
endif()
if(ENABLE_TESTING)
message(STATUS "<<< Building Unit Tests >>>")
if(ENABLE_COVERAGE)
message(STATUS "Collecting code coverage data")
endif()
endif()

4
cmake/Modules/StyleHeaderUtils.cmake
View File

@ -59,7 +59,6 @@ function(CreateStyleHeader path filename)
set(temp "${temp}#include \"${FNAME}\"\n")
endforeach()
endif()
message(STATUS "Generating ${filename}...")
file(WRITE "${path}/${filename}.tmp" "${temp}" )
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
@ -142,6 +141,7 @@ function(RegisterStylesExt search_path extension sources)
endfunction(RegisterStylesExt)
function(GenerateStyleHeaders output_path)
message(STATUS "Generating style headers...")
GenerateStyleHeader(${output_path} ANGLE angle ) # force
GenerateStyleHeader(${output_path} ATOM_VEC atom ) # atom atom_vec_hybrid
GenerateStyleHeader(${output_path} BODY body ) # atom_vec_body
@ -232,7 +232,6 @@ function(CreatePackagesHeader path filename)
set(temp "${temp}#include \"${DNAME}/${FNAME}\"\n")
endforeach()
endif()
message(STATUS "Generating ${filename}...")
file(WRITE "${path}/${filename}.tmp" "${temp}" )
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
@ -244,6 +243,7 @@ function(GeneratePackagesHeader path property style)
endfunction(GeneratePackagesHeader)
function(GeneratePackagesHeaders output_path)
message(STATUS "Generating package headers...")
GeneratePackagesHeader(${output_path} PKGANGLE angle ) # force
GeneratePackagesHeader(${output_path} PKGATOM_VEC atom ) # atom atom_vec_hybrid
GeneratePackagesHeader(${output_path} PKGBODY body ) # atom_vec_body

4
cmake/presets/clang.cmake
View File

@ -2,7 +2,8 @@
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
@ -14,4 +15,3 @@ set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

17
cmake/presets/gcc.cmake Normal file
View File

@ -0,0 +1,17 @@
# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "g++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "gcc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)

4
cmake/presets/hip.cmake
View File

@ -2,11 +2,11 @@
set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

19
doc/documentation_conventions.md
View File

@ -41,11 +41,17 @@ The layout and formatting of added files should follow the example
of the existing files. Since those are directly derived from their
former .txt format versions and the manual has been maintained in
that format for many years, there is a large degree of consistency
already, so comparision with similar files should give you a good
already, so comparison with similar files should give you a good
idea what kind of information and sections are needed.
## Formatting conventions
For headlines we try to follow the conventions posted here:
https://documentation-style-guide-sphinx.readthedocs.io/en/latest/style-guide.html#headings
It seems to be sufficient to have this consistent only within
any single file and it is not (yet) enforced strictly, but making
this globally consistent makes it easier to move sections around.
Filenames, folders, paths, (shell) commands, definitions, makefile
settings and similar should be formatted as "literals" with
double backward quotes bracketing the item: \`\`path/to/some/file\`\`
@ -67,8 +73,19 @@ a `.. parsed-literal::` block can be used, which allows some
formatting directives, which means that related characters need
to be escaped with a preceding backslash: `\*`.
For more compact display of alternatives (e.g. compilation or
configuration directions for CMake versus GNU make) a `.. tabs::`
block can be used, followed by multiple `.. tab::` blocks, one
for each alternative. This is only used for HTML output. For other
outputs, the `.. tabs::` directive is transparently removed and
the individual `.. tab::` blocks will be replaced with an
`.. admonition::`` block. Thus in PDF and ePUB output those will
be realized as sequential and plain notes.
Special remarks can be highlighted with a `.. note::` block and
strong warnings can be put into a `.. warning::` block.
For notes with a title, use `.. admonition:: title text` followed
by ` :class: note`.
## Required steps when adding a custom style to LAMMPS

2
doc/src/Build.rst
View File

@ -1,5 +1,5 @@
Build LAMMPS
************
============
LAMMPS is built as a library and an executable from source code using
either traditional makefiles for use with GNU make (which may require

9
doc/src/Build_basics.rst
View File

@ -299,10 +299,11 @@ LAMMPS.
then you have either an unsupported (old) compiler or you have
to turn on C++11 mode. The latter applies to GCC 4.8.x shipped
with RHEL 7.x and CentOS 7.x. For those compilers, you need to
add the ``-std=c++11`` flag. Otherwise, you would have to
install a newer compiler that supports C++11; either as a
binary package or through compiling from source.
with RHEL 7.x and CentOS 7.x or GCC 5.4.x shipped with Ubuntu16.04.
For those compilers, you need to add the ``-std=c++11`` flag.
If there is no compiler that supports this flag (or equivalent),
you would have to install a newer compiler that supports C++11;
either as a binary package or through compiling from source.
If you build LAMMPS with any :doc:`Speed_packages` included,
there may be specific compiler or linker flags that are either

2
doc/src/Build_cmake.rst
View File

@ -1,5 +1,5 @@
Build LAMMPS with CMake
=======================
-----------------------
This page describes how to use `CMake <https://cmake.org>`_ in general
to build LAMMPS. Details for specific compile time settings and options

9
doc/src/Build_package.rst
View File

@ -158,6 +158,7 @@ one of them as a starting point and customize it to your needs.
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/gcc.cmake [OPTIONS] ../cmake # change settings to use the GNU compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages
@ -166,9 +167,11 @@ one of them as a starting point and customize it to your needs.
.. note::
Running cmake this way manipulates the CMake settings cache in your
current build directory. You can combine multiple presets and options
current build directory. You can combine multiple presets and options
in a single cmake run, or change settings incrementally by running
cmake with new flags.
cmake with new flags. If you use a present for selecting a set of
compilers, it will reset all settings from previous CMake runs.
Example
"""""""
@ -187,7 +190,7 @@ Example
# to reset the package selection from above to the default of no packages
# but leaving all other settings untouched. You can run:
cmake -C ../cmake/presets/no_all.cmake .
cmake -C ../cmake/presets/all_off.cmake .
----------

97
doc/src/Build_windows.rst
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@ -1,5 +1,5 @@
Notes for building LAMMPS on Windows
====================================
------------------------------------
* :ref:`General remarks <generic>`
* :ref:`Running Linux on Windows <linux>`
@ -11,59 +11,58 @@ Notes for building LAMMPS on Windows
.. _generic:
General remarks
-----------------------------
^^^^^^^^^^^^^^^
LAMMPS is developed and tested primarily on Linux machines. The vast
majority of HPC clusters and supercomputers today runs on Linux as well.
majority of HPC clusters and supercomputers today run on Linux as well.
While portability to other platforms is desired, it is not always achieved.
The LAMMPS developers strongly rely on LAMMPS users giving feedback and
providing assistance in resolving portability issues. This is particularly
The LAMMPS developers are dependent on LAMMPS users giving feedback and
providing assistance in resolving portability issues. This is particularly
true for compiling LAMMPS on Windows, since this platform has significant
differences with some low-level functionality.
differences in some low-level functionality.
.. _linux:
Running Linux on Windows
------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^
So before trying to build LAMMPS on Windows, please consider if using
the pre-compiled Windows binary packages are sufficient for your needs
(as an aside, those packages themselves are build on a Linux machine
using cross-compilers). If it is necessary for you to compile LAMMPS
on a Windows machine (e.g. because it is your main desktop), please also
consider using a virtual machine software and compile and run LAMMPS in
a Linux virtual machine, or - if you have a recently updated Windows 10
Before trying to build LAMMPS on Windows, please consider if the
pre-compiled Windows binary packages are sufficient for your needs. If
it is necessary for you to compile LAMMPS on a Windows machine
(e.g. because it is your main desktop), please also consider using a
virtual machine software and compile and run LAMMPS in a Linux virtual
machine, or - if you have a sufficiently up-to-date Windows 10
installation - consider using the Windows subsystem for Linux. This
optional Windows feature allows you to run the bash shell from Ubuntu
from within Windows and from there on, you can pretty much use that
shell like you are running on an Ubuntu Linux machine (e.g. installing
software via apt-get and more). For more details on that, please
see :doc:`this tutorial <Howto_wsl>`.
software via apt-get and more). For more details on that, please see
:doc:`this tutorial <Howto_wsl>`.
.. _gnu:
Using a GNU GCC ported to Windows
-----------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
One option for compiling LAMMPS on Windows natively, that has been known
One option for compiling LAMMPS on Windows natively that has been known
to work in the past is to install a bash shell, unix shell utilities,
perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
provides a unix/linux interface to low-level Windows functions, so LAMMPS
can be compiled on Windows. The necessary (minor) modifications to LAMMPS
are included, but may not always up-to-date for recently added functionality
and the corresponding new code. A machine makefile for using cygwin for
the old build system is provided. Using CMake for this mode of compilation
is untested and not likely to work.
perl, GNU make, and a GNU compiler ported to Windows. The Cygwin
package provides a unix/linux interface to low-level Windows functions,
so LAMMPS can be compiled on Windows. The necessary (minor)
modifications to LAMMPS are included, but may not always up-to-date for
recently added functionality and the corresponding new code. A machine
makefile for using cygwin for the old build system is provided. Using
CMake for this mode of compilation is untested and not likely to work.
When compiling for Windows do **not** set the -DLAMMPS_MEMALIGN define
in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
flags in LIB makefile variable. Try adding -static-libgcc or -static or
both to the linker flags when your resulting LAMMPS Windows executable
complains about missing .dll files. The CMake configuration should set
this up automatically, but is untested.
When compiling for Windows do **not** set the ``-DLAMMPS_MEMALIGN``
define in the LMP_INC makefile variable and add ``-lwsock32 -lpsapi`` to
the linker flags in LIB makefile variable. Try adding ``-static-libgcc``
or ``-static`` or both to the linker flags when your resulting LAMMPS
Windows executable complains about missing .dll files. The CMake
configuration should set this up automatically, but is untested.
In case of problems, you are recommended to contact somebody with
experience in using cygwin. If you do come across portability problems
experience in using Cygwin. If you do come across portability problems
requiring changes to the LAMMPS source code, or figure out corrections
yourself, please report them on the lammps-users mailing list, or file
them as an issue or pull request on the LAMMPS GitHub project.
@ -71,31 +70,23 @@ them as an issue or pull request on the LAMMPS GitHub project.
.. _cross:
Using a cross-compiler
----------------------------------
^^^^^^^^^^^^^^^^^^^^^^
If you need to provide custom LAMMPS binaries for Windows, but do not
need to do the compilation on Windows, please consider using a Linux
to Windows cross-compiler. This is how currently the Windows binary
packages are created by the LAMMPS developers. Because of that, this is
need to do the compilation on Windows, please consider using a Linux to
Windows cross-compiler. This is how currently the Windows binary
packages are created by the LAMMPS developers. Because of that, this is
probably the currently best tested and supported way to build LAMMPS
executables for Windows. There are makefiles provided for the
traditional build system, but CMake has also been successfully tested
using the mingw32-cmake and mingw64-cmake wrappers that are bundled
with the cross-compiler environment on Fedora machines. A CMake preset
selecting all packages compatible with this cross-compilation build
is provided. The GPU package can only be compiled with OpenCL support
and you need to download and install the pre-compiled
`OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
into your MinGW64 cross-compiler environment. With CMake this will be
done transparently. To compile with MPI support, a pre-compiled
library and the corresponding header files are required. There is
`one package for 32-bit Windows <https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz>`_
and `a second package for 64-bit Windows <https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz>`_.
When building with CMake, the matching package will be downloaded
automatically, but MPI support has to be explicitly enabled with ``-DBUILD_MPI=on``.
executables for Windows. A CMake preset selecting all packages
compatible with this cross-compilation build is provided. The GPU
package can only be compiled with OpenCL support. To compile with MPI
support, a pre-compiled library and the corresponding header files are
required. When building with CMake the matching package will be
downloaded automatically, but MPI support has to be explicitly enabled
with ``-DBUILD_MPI=on``.
Please keep in mind, though, that this only applies to **compiling** LAMMPS.
Whether the resulting binaries do work correctly is not tested by the
Whether the resulting binaries do work correctly is rarely tested by the
LAMMPS developers. We instead rely on the feedback of the users
of these pre-compiled LAMMPS packages for Windows. We will try to resolve
issues to the best of our abilities if we become aware of them. However
@ -104,7 +95,7 @@ this is subject to time constraints and focus on HPC platforms.
.. _native:
Native Visual C++ support
--------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^
Support for the Visual C++ compilers is currently not available. The
CMake build system is capable of creating suitable a Visual Studio

4
doc/src/Developer.rst
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@ -1,5 +1,5 @@
LAMMPS Developer Guide
**********************
Information for Developers
==========================
This section describes the internal structure and basic algorithms
of the LAMMPS code. This is a work in progress and additional

2
doc/src/Developer_flow.rst
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@ -1,5 +1,5 @@
How a timestep works
====================
--------------------
The first and most fundamental operation within LAMMPS to understand is
how a timestep is structured. Timestepping is performed by calling

4
doc/src/Developer_org.rst
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@ -1,5 +1,5 @@
LAMMPS source files
===================
-------------------
The source files of the LAMMPS code are found in two
directories of the distribution: ``src`` and ``lib``.
@ -47,7 +47,7 @@ A small number of C++ classes and utility functions are implemented with
only a ``.h`` file. Examples are the Pointer class or the MathVec functions.
LAMMPS class topology
=====================
---------------------
Though LAMMPS has a lot of source files and classes, its class topology
is relative flat, as outlined in the :ref:`class-topology` figure. Each

12
doc/src/Developer_utils.rst
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@ -1,6 +1,6 @@
LAMMPS utility functions
========================
------------------------
The ``utils`` sub-namespace inside the ``LAMMPS_NS`` namespace provides
a collection of convenience functions and utilities that perform common
@ -173,7 +173,7 @@ Customized standard functions
---------------------------
Communication buffer coding with *ubuf*
=========================================
---------------------------------------
LAMMPS uses communication buffers where it collects data from various
class instances and then exchanges the data with neighboring sub-domains.
@ -194,7 +194,7 @@ the communication buffers.
---------------------------
Tokenizer classes
=================
-----------------
The purpose of the tokenizer classes is to simplify the recurring task
of breaking lines of text down into words and/or numbers.
@ -308,7 +308,7 @@ This code example should produce the following output:
----------
File reader classes
====================
-------------------
The purpose of the file reader classes is to simplify the recurring task
of reading and parsing files. They can use the
@ -382,7 +382,7 @@ A file that would be parsed by the reader code fragment looks like this:
----------
Memory pool classes
===================
-------------------
The memory pool classes are used for cases where otherwise many
small memory allocations would be needed and where the data would
@ -446,7 +446,7 @@ its size is registered later with :cpp:func:`vgot()
----------
Eigensolver functions
=====================
---------------------
The ``MathEigen`` sub-namespace of the ``LAMMPS_NS`` namespace contains
functions and classes for eigensolvers. Currently only the

2
doc/src/Developer_write.rst
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@ -1,5 +1,5 @@
Writing LAMMPS styles
=====================
---------------------
The :doc:`Modify` section of the manual gives an overview of how LAMMPS can
be extended by writing new classes that derive from existing

12
doc/src/Howto_cmake.rst
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@ -401,11 +401,19 @@ It is also possible to do this incrementally.
cmake -C ../cmake/presets/minimal.cmake ../cmake
cmake -D PKG_MISC=on .
will achieve the same configuration like in the first example above. In
this scenario it is particularly convenient to do the second
will achieve the same final configuration as in the first example above.
In this scenario it is particularly convenient to do the second
configuration step using either the text mode or graphical user
interface (``ccmake`` or ``cmake-gui``).
.. note::
Using a preset to select a compiler package (``clang.cmake``,
``gcc.cmake``, or ``intel.cmake``) are an exception to the option
of updating the configuration incrementally, as they will trigger
a reset of cached internal CMake settings and thus reset them to
their default values.
Compilation and build targets
-----------------------------

2
doc/src/Install.rst
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@ -1,5 +1,5 @@
Install LAMMPS
**************
==============
You can download LAMMPS as an executable or as source code.

2
doc/src/Install_conda.rst
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@ -1,5 +1,5 @@
Download an executable for Linux or Mac via Conda
=================================================
-------------------------------------------------
Binaries are available for MacOS or Linux via `Conda <conda_>`_.

2
doc/src/Install_git.rst
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@ -1,5 +1,5 @@
Download the LAMMPS source with git
===================================
-----------------------------------
All LAMMPS development is coordinated through the "LAMMPS GitHub
site". If you clone the LAMMPS repository onto your local machine, it

14
doc/src/Install_linux.rst
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@ -1,5 +1,5 @@
Download an executable for Linux
================================
--------------------------------
Binaries are available for different versions of Linux:
@ -16,7 +16,7 @@ Binaries are available for different versions of Linux:
.. _ubuntu:
Pre-built Ubuntu Linux executables
-----------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A pre-built LAMMPS executable suitable for running on the latest
Ubuntu Linux versions, can be downloaded as a Debian package. This
@ -108,7 +108,7 @@ Ubuntu package capability.
.. _fedora:
Pre-built Fedora Linux executables
-----------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Pre-built LAMMPS packages for stable releases are available
in the Fedora Linux distribution as of version 28. The packages
@ -162,7 +162,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
.. _epel:
Pre-built EPEL Linux executable
------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Pre-built LAMMPS (and KIM) packages for stable releases are available
in the `Extra Packages for Enterprise Linux (EPEL) repository <https://fedoraproject.org/wiki/EPEL>`_
@ -182,7 +182,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
.. _opensuse:
Pre-built OpenSuse Linux executable
--------------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A pre-built LAMMPS package for stable releases is available
in OpenSuse as of Leap 15.0. You can install the package with:
@ -217,7 +217,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
.. _gentoo:
Gentoo Linux executable
------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS is part of Gentoo's main package tree and can be installed by
typing:
@ -245,7 +245,7 @@ this Gentoo capability.
.. _arch:
Archlinux build-script
---------------------------------
^^^^^^^^^^^^^^^^^^^^^^
LAMMPS is available via Arch's unofficial Arch User repository (AUR).
There are three scripts available, named lammps, lammps-beta and lammps-git.

2
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@ -1,5 +1,5 @@
Download an executable for Mac
==============================
------------------------------
LAMMPS can be downloaded, built, and configured for OS X on a Mac with
`Homebrew <homebrew_>`_. (Alternatively, see the install instructions for

2
doc/src/Install_patch.rst
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@ -1,5 +1,5 @@
Applying patches
================
----------------
It is easy to stay current with the most recent LAMMPS patch releases
if you use git to track the LAMMPS development. Instructions for

2
doc/src/Install_tarball.rst
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@ -1,5 +1,5 @@
Download source and documentation as a tarball
==============================================
----------------------------------------------
You can download a current LAMMPS tarball from the `download page <download_>`_
of the `LAMMPS website <lws_>`_.

2
doc/src/Install_windows.rst
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@ -1,5 +1,5 @@
Download an executable for Windows
==================================
----------------------------------
Pre-compiled Windows installers which install LAMMPS executables on a
Windows system can be downloaded from this site:

2
doc/src/Intro.rst
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@ -1,5 +1,5 @@
Introduction
************
============
These pages provide a brief introduction to LAMMPS.

2
doc/src/Intro_authors.rst
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@ -1,5 +1,5 @@
Authors of LAMMPS
=================
-----------------
The primary LAMMPS developers are at Sandia National Labs and Temple
University:

2
doc/src/Intro_citing.rst
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@ -1,5 +1,5 @@
Citing LAMMPS
=============
-------------
Core Algorithms
^^^^^^^^^^^^^^^

36
doc/src/Intro_features.rst
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@ -1,5 +1,5 @@
LAMMPS features
===============
---------------
LAMMPS is a classical molecular dynamics (MD) code with these general
classes of functionality:
@ -21,7 +21,7 @@ classes of functionality:
.. _general:
General features
------------------------------
^^^^^^^^^^^^^^^^
* runs on a single processor or in parallel
* distributed-memory message-passing parallelism (MPI)
@ -41,9 +41,9 @@ General features
.. _particle:
Particle and model types
---------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^
(:doc:`atom style <atom_style>` command)
(See :doc:`atom style <atom_style>` command)
* atoms
* coarse-grained particles (e.g. bead-spring polymers)
@ -61,9 +61,9 @@ Particle and model types
.. _ff:
Interatomic potentials (force fields)
----------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
(:doc:`pair style <pair_style>`, :doc:`bond style <bond_style>`,
(See :doc:`pair style <pair_style>`, :doc:`bond style <bond_style>`,
:doc:`angle style <angle_style>`, :doc:`dihedral style <dihedral_style>`,
:doc:`improper style <improper_style>`, :doc:`kspace style <kspace_style>`
commands)
@ -92,9 +92,9 @@ commands)
.. _create:
Atom creation
--------------------------
^^^^^^^^^^^^^
(:doc:`read_data <read_data>`, :doc:`lattice <lattice>`,
(See :doc:`read_data <read_data>`, :doc:`lattice <lattice>`,
:doc:`create_atoms <create_atoms>`, :doc:`delete_atoms <delete_atoms>`,
:doc:`displace_atoms <displace_atoms>`, :doc:`replicate <replicate>` commands)
@ -107,9 +107,9 @@ Atom creation
.. _ensemble:
Ensembles, constraints, and boundary conditions
--------------------------------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
(:doc:`fix <fix>` command)
(See :doc:`fix <fix>` command)
* 2d or 3d systems
* orthogonal or non-orthogonal (triclinic symmetry) simulation domains
@ -129,9 +129,9 @@ Ensembles, constraints, and boundary conditions
.. _integrate:
Integrators
---------------------------
^^^^^^^^^^^
(:doc:`run <run>`, :doc:`run_style <run_style>`, :doc:`minimize <minimize>` commands)
(See :doc:`run <run>`, :doc:`run_style <run_style>`, :doc:`minimize <minimize>` commands)
* velocity-Verlet integrator
* Brownian dynamics
@ -143,14 +143,14 @@ Integrators
.. _diag:
Diagnostics
----------------------
^^^^^^^^^^^
* see various flavors of the :doc:`fix <fix>` and :doc:`compute <compute>` commands
.. _output:
Output
-------------------
^^^^^^
(:doc:`dump <dump>`, :doc:`restart <restart>` commands)
@ -167,7 +167,7 @@ Output
.. _replica1:
Multi-replica models
-----------------------------------
^^^^^^^^^^^^^^^^^^^^
* :doc:`nudged elastic band <neb>`
* :doc:`parallel replica dynamics <prd>`
@ -177,11 +177,11 @@ Multi-replica models
.. _prepost:
Pre- and post-processing
--------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^
* A handful of pre- and post-processing tools are packaged with LAMMPS,
some of which can convert input and output files to/from formats used
by other codes; see the :doc:`Tools <Tools>` doc page.
by other codes; see the :doc:`Tools <Tools>` page.
* Our group has also written and released a separate toolkit called
`Pizza.py <pizza_>`_ which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
@ -194,7 +194,7 @@ Pre- and post-processing
.. _special:
Specialized features
----------------------------------
^^^^^^^^^^^^^^^^^^^^
LAMMPS can be built with optional packages which implement a variety
of additional capabilities. See the :doc:`Optional Packages <Packages>`

2
doc/src/Intro_nonfeatures.rst
View File

@ -1,5 +1,5 @@
LAMMPS non-features
===================
-------------------
LAMMPS is designed to be a fast, parallel engine for molecular
dynamics (MD) simulations. It provides only a modest amount of

2
doc/src/Intro_opensource.rst
View File

@ -1,5 +1,5 @@
LAMMPS open-source license
==========================
--------------------------
LAMMPS is a freely-available open-source code, distributed under the
terms of the `GNU Public License <gnu_>`_, which means you can use or

2
doc/src/Intro_overview.rst
View File

@ -1,5 +1,5 @@
Overview of LAMMPS
==================
------------------
LAMMPS is a classical molecular dynamics (MD) code that models
ensembles of particles in a liquid, solid, or gaseous state. It can

2
doc/src/Intro_website.rst
View File

@ -1,5 +1,5 @@
Additional website links
========================
------------------------
The `LAMMPS website <lws_>`_ has a variety of additional info about
LAMMPS, beyond what is in this manual. Some other useful resources

31
doc/src/Manual.rst
View File

@ -1,3 +1,4 @@
######################################
LAMMPS version |version| Documentation
######################################
@ -12,10 +13,11 @@ funding for LAMMPS has come from the US Department of Energy (DOE).
LAMMPS is an open-source code, distributed freely under the terms of
the GNU Public License (GPL).
The `LAMMPS website <lws_>`_ has a variety of information about the code.
It includes links to an on-line version of this manual, a `mailing list <https://lammps.sandia.gov/mail.html>`_ where users can post
questions, and a `GitHub site <https://github.com/lammps/lammps>`_ where
all LAMMPS development is coordinated.
The `LAMMPS website <lws_>`_ has a variety of information about the
code. It includes links to an on-line version of this manual, a
`mailing list <https://lammps.sandia.gov/mail.html>`_ where users can
post questions, and a `GitHub site <https://github.com/lammps/lammps>`_
where all LAMMPS development is coordinated.
----------
@ -23,8 +25,8 @@ The content for this manual is part of the LAMMPS distribution. You can
build a local copy of the Manual as HTML pages or a PDF file, by
following the steps on the :doc:`Build_manual` page. The manual is
organized in two parts:
1) the :ref:`User documentation <user_documentation>` for how to install
and use LAMMPS and 2) the :ref:`Programmer documentation <programmer_documentation>`
1) the :ref:`User's Guide <user_documentation>` for how to install
and use LAMMPS and 2) the :ref:`Programmer's Guide <programmer_documentation>`
for how to write programs using the LAMMPS library from different
programming languages and how to modify and extend LAMMPS.
@ -38,14 +40,16 @@ programming languages and how to modify and extend LAMMPS.
----------
User Documentation
******************
************
User's Guide
************
.. _user_documentation:
.. toctree::
:maxdepth: 2
:numbered: 3
:caption: User Documentation
:caption: User's Guide
:name: userdoc
:includehidden:
@ -61,14 +65,16 @@ User Documentation
Tools
Errors
Programmer Documentation
************************
******************
Programmer's Guide
******************
.. _programmer_documentation:
.. toctree::
:maxdepth: 2
:numbered: 3
:caption: Programmer Documentation
:caption: Programmer's Guide
:name: progdoc
:includehidden:
@ -93,6 +99,7 @@ Programmer Documentation
fix_modify_atc_commands
Bibliography
******************
Indices and tables
******************

2
doc/src/Manual_version.rst
View File

@ -1,5 +1,5 @@
What does a LAMMPS version mean
===============================
-------------------------------
The LAMMPS "version" is the date when it was released, such as 1 May
2014. LAMMPS is updated continuously. Whenever we fix a bug or add a

80
doc/src/Packages_details.rst
View File

@ -10,10 +10,10 @@ scripts, and pictures/movies (if available) that illustrate use of the
package.
The majority of packages can be included in a LAMMPS build with a
single setting (-D PGK_NAME for CMake) or command ("make yes-name" for
make). See the :doc:`Build package <Build_package>` doc page for more
info. A few packages may require additional steps; this is indicated
in the descriptions below. The :doc:`Build extras <Build_extras>` doc
single setting (``-D PGK_<NAME>=on`` for CMake) or command
(``make yes-<name>`` for make). See the :doc:`Build package <Build_package>`
page for more info. A few packages may require additional steps;
this is indicated in the descriptions below. The :doc:`Build extras <Build_extras>`
page gives those details.
.. note::
@ -143,7 +143,7 @@ BODY package
Body-style particles with internal structure. Computes,
time-integration fixes, pair styles, as well as the body styles
themselves. See the :doc:`Howto body <Howto_body>` doc page for an
themselves. See the :doc:`Howto body <Howto_body>` page for an
overview.
**Supporting info:**
@ -225,7 +225,7 @@ available on your system.
**Install:**
This package has :ref:`specific installation instructions <compress>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <compress>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -249,7 +249,7 @@ CORESHELL package
Compute and pair styles that implement the adiabatic core/shell model
for polarizability. The pair styles augment Born, Buckingham, and
Lennard-Jones styles with core/shell capabilities. The :doc:`compute temp/cs <compute_temp_cs>` command calculates the temperature of a
system with core/shell particles. See the :doc:`Howto coreshell <Howto_coreshell>` doc page for an overview of how to use
system with core/shell particles. See the :doc:`Howto coreshell <Howto_coreshell>` page for an overview of how to use
this package.
**Author:** Hendrik Heenen (Technical U of Munich).
@ -312,7 +312,7 @@ Kuznetsov, Vladimir Stegailov, and Vsevolod Nikolskiy (HSE University).
**Install:**
This package has :ref:`specific installation instructions <gpu>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <gpu>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -410,7 +410,7 @@ Ryan Elliott.
**Install:**
This package has :ref:`specific installation instructions <kim>` on the
:doc:`Build extras <Build_extras>` doc page.
:doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -434,7 +434,7 @@ Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
styles adapted to compile using the Kokkos library which can convert
them to OpenMP or CUDA code so that they run efficiently on multicore
CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their
style name. The :doc:`KOKKOS package <Speed_kokkos>` doc page gives
style name. The :doc:`KOKKOS package <Speed_kokkos>` page gives
details of what hardware and software is required on your system, and
how to build and use this package. Its styles can be invoked at run
time via the "-sf kk" or "-suffix kk" :doc:`command-line switches <Run_options>`. Also see the :ref:`GPU <PKG-GPU>`, :ref:`OPT <PKG-OPT>`,
@ -457,7 +457,7 @@ lib/kokkos.
**Install:**
This package has :ref:`specific installation instructions <kokkos>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <kokkos>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -494,7 +494,7 @@ interactions. These include Ewald, particle-particle particle-mesh
Building with this package requires a 1d FFT library be present on
your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, third party libraries like FFTW, or a
vendor-supplied FFT library. See the :doc:`Build settings <Build_settings>` doc page for details on how to select
vendor-supplied FFT library. See the :doc:`Build settings <Build_settings>` page for details on how to select
different FFT options for your LAMPMS build.
**Supporting info:**
@ -535,7 +535,7 @@ Cawkwell, Anders Niklasson, and Christian Negre.
**Install:**
This package has :ref:`specific installation instructions <latte>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <latte>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -609,7 +609,7 @@ another application.
**Install:**
This package has :ref:`specific installation instructions <message>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <message>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -753,7 +753,7 @@ University of Chicago.
**Install:**
This package has :ref:`specific installation instructions <mscg>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <mscg>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -774,7 +774,7 @@ OPT package
A handful of pair styles which are optimized for improved CPU
performance on single or multiple cores. These include EAM, LJ,
CHARMM, and Morse potentials. The styles have an "opt" suffix in
their style name. The :doc:`OPT package <Speed_opt>` doc page gives
their style name. The :doc:`OPT package <Speed_opt>` page gives
details of how to build and use this package. Its styles can be
invoked at run time via the "-sf opt" or "-suffix opt" :doc:`command-line switches <Run_options>`. See also the :ref:`KOKKOS <PKG-KOKKOS>`,
:ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`USER-OMP <PKG-USER-OMP>` packages, which
@ -785,7 +785,7 @@ and Vincent Natoli (Stone Ridge Technology).
**Install:**
This package has :ref:`specific installation instructions <opt>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <opt>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -846,7 +846,7 @@ connections at hinge points.
**Install:**
This package has :ref:`specific installation instructions <poems>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <poems>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -867,8 +867,8 @@ PYTHON package
A :doc:`python <python>` command which allow you to execute Python code
from a LAMMPS input script. The code can be in a separate file or
embedded in the input script itself. See the :doc:`Python call <Python_call>` doc page for an overview of using Python from
LAMMPS in this manner and all the :doc:`Python <Python_head>` doc pages
embedded in the input script itself. See the :doc:`Python call <Python_call>` page for an overview of using Python from
LAMMPS in this manner and all the :doc:`Python <Python_head>` manual pages
for other ways to use LAMMPS and Python together.
.. note::
@ -880,7 +880,7 @@ for other ways to use LAMMPS and Python together.
**Install:**
This package has :ref:`specific installation instructions <python>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <python>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -919,7 +919,7 @@ REPLICA package
**Contents:**
A collection of multi-replica methods which can be used when running
multiple LAMMPS simulations (replicas). See the :doc:`Howto replica <Howto_replica>` doc page for an overview of how to run
multiple LAMMPS simulations (replicas). See the :doc:`Howto replica <Howto_replica>` page for an overview of how to run
multi-replica simulations in LAMMPS. Methods in the package include
nudged elastic band (NEB), parallel replica dynamics (PRD),
temperature accelerated dynamics (TAD), parallel tempering, and a
@ -1093,7 +1093,7 @@ and LBNL.
**Install:**
This package has :ref:`specific installation instructions <voronoi>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <voronoi>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -1121,7 +1121,7 @@ commands to write and read data using the ADIOS library.
**Install:**
This package has :ref:`specific installation instructions <user-adios>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-adios>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -1150,7 +1150,7 @@ atomic information to continuum fields.
**Install:**
This package has :ref:`specific installation instructions <user-atc>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-atc>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -1178,7 +1178,7 @@ model.
**Install:**
This package has :ref:`specific installation instructions <user-awpmd>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-awpmd>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -1297,7 +1297,7 @@ the NAMD MD code, but with portability in mind. Axel Kohlmeyer
**Install:**
This package has :ref:`specific installation instructions <user-colvars>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-colvars>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -1330,7 +1330,7 @@ Tribello.
**Install:**
This package has :ref:`specific installation instructions <user-plumed>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-plumed>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -1412,7 +1412,7 @@ USER-DRUDE package
**Contents:**
Fixes, pair styles, and a compute to simulate thermalized Drude
oscillators as a model of polarization. See the :doc:`Howto drude <Howto_drude>` and :doc:`Howto drude2 <Howto_drude2>` doc pages
oscillators as a model of polarization. See the :doc:`Howto drude <Howto_drude>` and :doc:`Howto drude2 <Howto_drude2>` pages
for an overview of how to use the package. There are auxiliary tools
for using this package in tools/drude.
@ -1522,7 +1522,7 @@ H5MD format.
**Install:**
This package has :ref:`specific installation instructions <user-h5md>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-h5md>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -1563,7 +1563,7 @@ supported, performance will be sub-optimal.
**Install:**
This package has :ref:`specific installation instructions <user-intel>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-intel>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -1650,7 +1650,7 @@ src/USER-MISC/README file.
* src/USER-MISC: filenames -> commands
* src/USER-MISC/README
* one doc page per individual command listed in src/USER-MISC/README
* one page per individual command listed in src/USER-MISC/README
* examples/USER/misc
----------
@ -1856,7 +1856,7 @@ at
**Install:**
This package has :ref:`specific installation instructions <user-molfile>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-molfile>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -1896,7 +1896,7 @@ tools:
**Install:**
This package has :ref:`specific installation instructions <user-netcdf>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-netcdf>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -1943,7 +1943,7 @@ install/un-install the package and build LAMMPS in the usual manner:
**Install:**
This package has :ref:`specific installation instructions <user-omp>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-omp>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -2043,7 +2043,7 @@ changes to LAMMPS itself.
**Install:**
This package has :ref:`specific installation instructions <user-qmmm>`
on the :doc:`Build extras <Build_extras>` doc page.
on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -2104,7 +2104,7 @@ on your system.
**Install:**
This package has :ref:`specific installation instructions <user-quip>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-quip>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -2194,7 +2194,7 @@ the Forschungszentrum Juelich.
**Install:**
This package has :ref:`specific installation instructions <user-scafacos>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-scafacos>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -2260,7 +2260,7 @@ Dynamics, Ernst Mach Institute, Germany).
**Install:**
This package has :ref:`specific installation instructions <user-smd>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-smd>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
@ -2399,7 +2399,7 @@ system.
**Install:**
This package has :ref:`specific installation instructions <user-vtk>` on the :doc:`Build extras <Build_extras>` doc page.
This package has :ref:`specific installation instructions <user-vtk>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**

22
doc/src/Speed_packages.rst
View File

@ -40,13 +40,13 @@ standard or user packages:
Inverting this list, LAMMPS currently has acceleration support for
three kinds of hardware, via the listed packages:
+----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Many-core CPUs | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`USER-OMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
+----------------+-----------------------------------------------------------------------------------------------------------------------------+
| NVIDIA GPUs | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Intel Phi | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+----------------+-----------------------------------------------------------------------------------------------------------------------------+
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Many-core CPUs | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`USER-OMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| NVIDIA/AMD GPUs | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Intel Phi/AVX | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
Which package is fastest for your hardware may depend on the size
problem you are running and what commands (accelerated and
@ -153,8 +153,8 @@ size and number of compute nodes, on different hardware platforms.
Here is a brief summary of what the various packages provide. Details
are in the individual accelerator sections.
* Styles with a "gpu" suffix are part of the GPU package, and can be run
on NVIDIA GPUs. The speed-up on a GPU depends on a variety of
* Styles with a "gpu" suffix are part of the GPU package and can be run
on NVIDIA or AMD GPUs. The speed-up on a GPU depends on a variety of
factors, discussed in the accelerator sections.
* Styles with an "intel" suffix are part of the USER-INTEL
package. These styles support vectorized single and mixed precision
@ -164,8 +164,8 @@ are in the individual accelerator sections.
co-processors. This can result in additional speedup over 2x depending
on the hardware configuration.
* Styles with a "kk" suffix are part of the KOKKOS package, and can be
run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
Xeon Phi in "native" mode. The speed-up depends on a variety of
run using OpenMP on multicore CPUs, on an NVIDIA or AMD GPU, or on an
Intel Xeon Phi in "native" mode. The speed-up depends on a variety of
factors, as discussed on the KOKKOS accelerator page.
* Styles with an "omp" suffix are part of the USER-OMP package and allow
a pair-style to be run in multi-threaded mode using OpenMP. This can

5
doc/src/fix_widom.rst
View File

@ -86,11 +86,6 @@ molecule file. See the :doc:`molecule <molecule>` command for details.
The only settings required to be in this file are the coordinates and
types of atoms in the molecule.
If you wish to insert molecules via the *mol* keyword, that will have
their bonds or angles constrained via SHAKE, use the *shake* keyword,
specifying as its value the ID of a separate :doc:`fix shake
<fix_shake>` command which also appears in your input script.
Note that fix widom does not use configurational bias MC or any other
kind of sampling of intramolecular degrees of freedom. Inserted
molecules can have different orientations, but they will all have the

17
doc/src/write_restart.rst
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@ -58,10 +58,21 @@ file via the MPI-IO library, which is part of the MPI standard for
versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g.
.. code-block:: bash
.. tabs::
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform
.. tab:: CMake build
.. code-block:: bash
cmake . -DPKG_MPIIO=on # enables the MPIIO package in the build folder
cmake --build . # recompiles LAMMPS with the package code included
.. tab:: Traditional make
.. code-block:: bash
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform
Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters.

4
doc/utils/sphinx-config/_static/css/lammps.css
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@ -27,11 +27,11 @@ hr {
margin-bottom: 12px !important;
}
#user-documentation.section h2 {
#user-s-guide.section h2 {
display: none;
}
#programmer-documentation.section h2 {
#programmer-s-guide.section h2 {
display: none;
}

2
doc/utils/sphinx-config/false_positives.txt
View File

@ -2074,6 +2074,7 @@ ncorr
ncount
nd
ndihedrals
ndihedraltypes
Ndihedraltype
Ndirango
ndof
@ -2121,6 +2122,7 @@ Nicklas
Niklasson
Nikolskiy
nimpropers
nimpropertypes
Nimpropertype
Ninteger
Nissila

11
python/lammps.py
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@ -1114,7 +1114,7 @@ class lammps(object):
after the data is copied to a Python variable or list.
The variable must be either an equal-style (or equivalent)
variable or an atom-style variable. The variable type has to
provided as ``vartype`` parameter which may be two constants:
provided as ``vartype`` parameter which may be one of two constants:
``LMP_VAR_EQUAL`` or ``LMP_VAR_STRING``; it defaults to
equal-style variables.
The group parameter is only used for atom-style variables and
@ -1135,7 +1135,8 @@ class lammps(object):
if vartype == LMP_VAR_EQUAL:
self.lib.lammps_extract_variable.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
result = ptr[0]
if ptr: result = ptr[0]
else: return None
self.lib.lammps_free(ptr)
return result
elif vartype == LMP_VAR_ATOM:
@ -1143,8 +1144,10 @@ class lammps(object):
result = (c_double*nlocal)()
self.lib.lammps_extract_variable.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
for i in range(nlocal): result[i] = ptr[i]
self.lib.lammps_free(ptr)
if ptr:
for i in range(nlocal): result[i] = ptr[i]
self.lib.lammps_free(ptr)
else: return None
return result
return None

1
src/KSPACE/msm_cg.cpp
View File

@ -26,7 +26,6 @@
#include "force.h"
#include "neighbor.h"
#include "memory.h"
#include "utils.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;

4
src/create_bonds.cpp
View File

@ -298,8 +298,8 @@ void CreateBonds::many()
if (!newton_bond || tag[i] < tag[j]) {
if (num_bond[i] == atom->bond_per_atom)
error->one(FLERR,
"New bond exceeded bonds per atom in create_bonds");
error->one(FLERR,fmt::format("New bond exceeded bonds per atom limit "
" of {} in create_bonds",atom->bond_per_atom));
bond_type[i][num_bond[i]] = btype;
bond_atom[i][num_bond[i]] = tag[j];
num_bond[i]++;

32
src/dump_custom.cpp
View File

@ -157,12 +157,12 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
// setup format strings
vformat = new char*[size_one];
vformat = new char*[nfield];
format_default = new char[4*size_one+1];
format_default = new char[4*nfield+1];
format_default[0] = '\0';
for (int i = 0; i < size_one; i++) {
for (int i = 0; i < nfield; i++) {
if (vtype[i] == Dump::INT) strcat(format_default,"%d ");
else if (vtype[i] == Dump::DOUBLE) strcat(format_default,"%g ");
else if (vtype[i] == Dump::STRING) strcat(format_default,"%s ");
@ -170,8 +170,8 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
vformat[i] = nullptr;
}
format_column_user = new char*[size_one];
for (int i = 0; i < size_one; i++) format_column_user[i] = nullptr;
format_column_user = new char*[nfield];
for (int i = 0; i < nfield; i++) format_column_user[i] = nullptr;
// setup column string
@ -244,12 +244,12 @@ DumpCustom::~DumpCustom()
delete [] typenames;
if (vformat) {
for (int i = 0; i < size_one; i++) delete [] vformat[i];
for (int i = 0; i < nfield; i++) delete [] vformat[i];
delete [] vformat;
}
if (format_column_user) {
for (int i = 0; i < size_one; i++) delete [] format_column_user[i];
for (int i = 0; i < nfield; i++) delete [] format_column_user[i];
delete [] format_column_user;
}
@ -277,7 +277,7 @@ void DumpCustom::init_style()
// lo priority = line, medium priority = int/float, hi priority = column
char *ptr;
for (int i = 0; i < size_one; i++) {
for (int i = 0; i < nfield; i++) {
if (i == 0) ptr = strtok(format," \0");
else ptr = strtok(nullptr," \0");
if (ptr == nullptr) error->all(FLERR,"Dump_modify format line is too short");
@ -300,7 +300,7 @@ void DumpCustom::init_style()
strcpy(vformat[i],ptr);
}
if (i+1 < size_one) vformat[i] = strcat(vformat[i]," ");
if (i+1 < nfield) vformat[i] = strcat(vformat[i]," ");
}
// setup boundary string
@ -466,7 +466,7 @@ void DumpCustom::header_binary(bigint ndump)
fwrite(&boxyhi,sizeof(double),1,fp);
fwrite(&boxzlo,sizeof(double),1,fp);
fwrite(&boxzhi,sizeof(double),1,fp);
fwrite(&size_one,sizeof(int),1,fp);
fwrite(&nfield,sizeof(int),1,fp);
header_unit_style_binary();
header_time_binary();
@ -495,7 +495,7 @@ void DumpCustom::header_binary_triclinic(bigint ndump)
fwrite(&boxxy,sizeof(double),1,fp);
fwrite(&boxxz,sizeof(double),1,fp);
fwrite(&boxyz,sizeof(double),1,fp);
fwrite(&size_one,sizeof(int),1,fp);
fwrite(&nfield,sizeof(int),1,fp);
header_unit_style_binary();
header_time_binary();
@ -1178,13 +1178,13 @@ int DumpCustom::convert_string(int n, double *mybuf)
int offset = 0;
int m = 0;
for (i = 0; i < n; i++) {
if (offset + size_one*ONEFIELD > maxsbuf) {
if (offset + nfield*ONEFIELD > maxsbuf) {
if ((bigint) maxsbuf + DELTA > MAXSMALLINT) return -1;
maxsbuf += DELTA;
memory->grow(sbuf,maxsbuf,"dump:sbuf");
}
for (j = 0; j < size_one; j++) {
for (j = 0; j < nfield; j++) {
if (vtype[j] == Dump::INT)
offset += sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
else if (vtype[j] == Dump::DOUBLE)
@ -1233,7 +1233,7 @@ void DumpCustom::write_lines(int n, double *mybuf)
int m = 0;
for (i = 0; i < n; i++) {
for (j = 0; j < size_one; j++) {
for (j = 0; j < nfield; j++) {
if (vtype[j] == Dump::INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
else if (vtype[j] == Dump::DOUBLE) fprintf(fp,vformat[j],mybuf[m]);
else if (vtype[j] == Dump::STRING)
@ -1709,7 +1709,7 @@ int DumpCustom::modify_param(int narg, char **arg)
if (strcmp(arg[1],"none") == 0) {
// just clear format_column_user allocated by this dump child class
for (int i = 0; i < size_one; i++) {
for (int i = 0; i < nfield; i++) {
delete [] format_column_user[i];
format_column_user[i] = nullptr;
}
@ -1746,7 +1746,7 @@ int DumpCustom::modify_param(int narg, char **arg)
} else {
int i = utils::inumeric(FLERR,arg[1],false,lmp) - 1;
if (i < 0 || i >= size_one)
if (i < 0 || i >= nfield)
error->all(FLERR,"Illegal dump_modify command");
if (format_column_user[i]) delete [] format_column_user[i];
int n = strlen(arg[2]) + 1;

2
src/info.cpp
View File

@ -391,7 +391,7 @@ void Info::command(int narg, char **arg)
if (atom->molecular > 0) {
const char *msg;
msg = force->bond_style ? force->bond_style : "none";
fmt::print(out,"Bonds = {:12}, types = {:8}, style = {}\n",
fmt::print(out,"Bonds = {:12}, types = {:8}, style = {}\n",
atom->nbonds, atom->nbondtypes, msg);
msg = force->angle_style ? force->angle_style : "none";

206
src/library.cpp
View File

@ -867,8 +867,17 @@ void lammps_reset_box(void *handle, double *boxlo, double *boxhi,
This function will retrieve or compute global properties. In contrast to
:cpp:func:`lammps_get_thermo` this function returns an ``int``. The
following keywords are currently supported. If a keyword is not
recognized, the function returns -1.
following tables list the currently supported keyword. If a keyword is
not recognized, the function returns -1.
* :ref:`Integer sizes <extract_integer_sizes>`
* :ref:`System status <extract_system_status>`
* :ref:`System sizes <extract_system_sizes>`
* :ref:`Atom style flags <extract_atom_flags>`
.. _extract_integer_sizes:
**Integer sizes**
.. list-table::
:header-rows: 1
@ -885,6 +894,17 @@ recognized, the function returns -1.
* - imageint
- size of the ``imageint`` integer type, 4 or 8 bytes.
Set at :ref:`compile time <size>`.
.. _extract_system_status:
**System status**
.. list-table::
:header-rows: 1
:widths: auto
* - Keyword
- Description / Return value
* - dimension
- Number of dimensions: 2 or 3. See :doc:`dimension`.
* - box_exist
@ -893,6 +913,17 @@ recognized, the function returns -1.
* - triclinic
- 1 if the the simulation box is triclinic, 0 if orthogonal.
See :doc:`change_box`.
.. _extract_system_sizes:
**System sizes**
.. list-table::
:header-rows: 1
:widths: auto
* - Keyword
- Description / Return value
* - nlocal
- number of "owned" atoms of the current MPI rank.
* - nghost
@ -903,6 +934,25 @@ recognized, the function returns -1.
- maximum of nlocal+nghost across all MPI ranks (for per-atom data array size).
* - ntypes
- number of atom types
* - nbondtypes
- number of bond types
* - nangletypes
- number of angle types
* - ndihedraltypes
- number of dihedral types
* - nimpropertypes
- number of improper types
.. _extract_atom_flags:
**Atom style flags**
.. list-table::
:header-rows: 1
:widths: auto
* - Keyword
- Description / Return value
* - molecule_flag
- 1 if the atom style includes molecular topology data. See :doc:`atom_style`.
* - q_flag
@ -911,6 +961,18 @@ recognized, the function returns -1.
- 1 if the atom style includes point dipoles. See :doc:`atom_style`.
* - rmass_flag
- 1 if the atom style includes per-atom masses, 0 if there are per-type masses. See :doc:`atom_style`.
* - radius_flag
- 1 if the atom style includes a per-atom radius. See :doc:`atom_style`.
* - sphere_flag
- 1 if the atom style describes extended particles that can rotate. See :doc:`atom_style`.
* - ellipsoid_flag
- 1 if the atom style describes extended particles that may be ellipsoidal. See :doc:`atom_style`.
* - omega_flag
- 1 if the atom style can store per-atom rotational velocities. See :doc:`atom_style`.
* - torque_flag
- 1 if the atom style can store per-atom torques. See :doc:`atom_style`.
* - angmom_flag
- 1 if the atom style can store per-atom angular momentum. See :doc:`atom_style`.
*See also*
:cpp:func:`lammps_extract_global`
@ -939,11 +1001,22 @@ int lammps_extract_setting(void *handle, const char *keyword)
if (strcmp(keyword,"nall") == 0) return lmp->atom->nlocal+lmp->atom->nghost;
if (strcmp(keyword,"nmax") == 0) return lmp->atom->nmax;
if (strcmp(keyword,"ntypes") == 0) return lmp->atom->ntypes;
if (strcmp(keyword,"nbondtypes") == 0) return lmp->atom->nbondtypes;
if (strcmp(keyword,"nangletypes") == 0) return lmp->atom->nangletypes;
if (strcmp(keyword,"ndihedraltypes") == 0) return lmp->atom->ndihedraltypes;
if (strcmp(keyword,"nimpropertypes") == 0) return lmp->atom->nimpropertypes;
if (strcmp(keyword,"molecule_flag") == 0) return lmp->atom->molecule_flag;
if (strcmp(keyword,"q_flag") == 0) return lmp->atom->q_flag;
if (strcmp(keyword,"mu_flag") == 0) return lmp->atom->mu_flag;
if (strcmp(keyword,"rmass_flag") == 0) return lmp->atom->rmass_flag;
if (strcmp(keyword,"radius_flag") == 0) return lmp->atom->radius_flag;
if (strcmp(keyword,"sphere_flag") == 0) return lmp->atom->sphere_flag;
if (strcmp(keyword,"ellipsoid_flag") == 0) return lmp->atom->ellipsoid_flag;
if (strcmp(keyword,"omega_flag") == 0) return lmp->atom->omega_flag;
if (strcmp(keyword,"torque_flag") == 0) return lmp->atom->torque_flag;
if (strcmp(keyword,"angmom_flag") == 0) return lmp->atom->angmom_flag;
if (strcmp(keyword,"peri_flag") == 0) return lmp->atom->peri_flag;
return -1;
}
@ -976,11 +1049,24 @@ Please also see :cpp:func:`lammps_extract_setting`,
settings derived from such settings. Where possible a reference to
such a command or a relevant section of the manual is given below.
This table lists the supported names, their data types, length of the
data area, and a short description. The ``bigint`` type may be defined
to be either an ``int`` or an ``int64_t``. This is selected at
:ref:`compile time <size>` and can be queried through calling
The following tables list the supported names, their data types, length
of the data area, and a short description. The data type can also be
queried through calling :cpp:func:`lammps_extract_global_datatype`.
The ``bigint`` type may be defined to be either an ``int`` or an
``int64_t``. This is set at :ref:`compile time <size>` of the LAMMPS
library and can be queried through calling
:cpp:func:`lammps_extract_setting`.
The function :cpp:func:`lammps_extract_global_datatype` will directly
report the "native" data type. The following tables are provided:
* :ref:`Timestep settings <extract_timestep_settings>`
* :ref:`Simulation box settings <extract_box_settings>`
* :ref:`System property settings <extract_system_settings>`
* :ref:`Unit settings <extract_unit_settings>`
.. _extract_timestep_settings:
**Timestep settings**
.. list-table::
:header-rows: 1
@ -990,10 +1076,6 @@ to be either an ``int`` or an ``int64_t``. This is selected at
- Type
- Length
- Description
* - units
- char \*
- 1
- string with the current unit style. See :doc:`units`.
* - dt
- double
- 1
@ -1002,6 +1084,27 @@ to be either an ``int`` or an ``int64_t``. This is selected at
- bigint
- 1
- current time step number. See :doc:`reset_timestep`.
* - atime
- double
- 1
- accumulated simulation time in time units.
* - atimestep
- bigint
- 1
- the number of the timestep when "atime" was last updated.
.. _extract_box_settings:
**Simulation box settings**
.. list-table::
:header-rows: 1
:widths: auto
* - Name
- Type
- Length
- Description
* - boxlo
- double
- 3
@ -1056,10 +1159,23 @@ to be either an ``int`` or an ``int64_t``. This is selected at
- double
- 1
- triclinic tilt factor. See :doc:`Howto_triclinic`.
* - natoms
- bigint
.. _extract_system_settings:
**System property settings**
.. list-table::
:header-rows: 1
:widths: auto
* - Name
- Type
- Length
- Description
* - ntypes
- int
- 1
- total number of atoms in the simulation.
- number of atom types
* - nbonds
- bigint
- 1
@ -1076,6 +1192,10 @@ to be either an ``int`` or an ``int64_t``. This is selected at
- bigint
- 1
- total number of impropers in the simulation.
* - natoms
- bigint
- 1
- total number of atoms in the simulation.
* - nlocal
- int
- 1
@ -1088,22 +1208,27 @@ to be either an ``int`` or an ``int64_t``. This is selected at
- int
- 1
- maximum of nlocal+nghost across all MPI ranks (for per-atom data array size).
* - ntypes
- int
- 1
- number of atom types
* - q_flag
- int
- 1
- 1 if the atom style includes point charges. See :doc:`atom_style`.
* - atime
- double
- **deprecated**. Use :cpp:func:`lammps_extract_setting` instead.
.. _extract_unit_settings:
**Unit settings**
.. list-table::
:header-rows: 1
:widths: auto
* - Name
- Type
- Length
- Description
* - units
- char \*
- 1
- accumulated simulation time in time units.
* - atimestep
- bigint
- 1
- the number of the timestep when "atime" was last updated.
- string with the current unit style. See :doc:`units`.
* - boltz
- double
- 1
@ -1195,6 +1320,12 @@ void *lammps_extract_global(void *handle, const char *name)
if (strcmp(name,"units") == 0) return (void *) lmp->update->unit_style;
if (strcmp(name,"dt") == 0) return (void *) &lmp->update->dt;
if (strcmp(name,"ntimestep") == 0) return (void *) &lmp->update->ntimestep;
// update->atime can be referenced as a pointer
// thermo "timer" data cannot be, since it is computed on request
// lammps_get_thermo() can access all thermo keywords by value
if (strcmp(name,"atime") == 0) return (void *) &lmp->update->atime;
if (strcmp(name,"atimestep") == 0) return (void *) &lmp->update->atimestep;
if (strcmp(name,"boxlo") == 0) return (void *) lmp->domain->boxlo;
if (strcmp(name,"boxhi") == 0) return (void *) lmp->domain->boxhi;
if (strcmp(name,"boxxlo") == 0) return (void *) &lmp->domain->boxlo[0];
@ -1208,7 +1339,9 @@ void *lammps_extract_global(void *handle, const char *name)
if (strcmp(name,"xy") == 0) return (void *) &lmp->domain->xy;
if (strcmp(name,"xz") == 0) return (void *) &lmp->domain->xz;
if (strcmp(name,"yz") == 0) return (void *) &lmp->domain->yz;
if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms;
if (strcmp(name,"ntypes") == 0) return (void *) &lmp->atom->ntypes;
if (strcmp(name,"nbonds") == 0) return (void *) &lmp->atom->nbonds;
if (strcmp(name,"nangles") == 0) return (void *) &lmp->atom->nangles;
if (strcmp(name,"ndihedrals") == 0) return (void *) &lmp->atom->ndihedrals;
@ -1216,17 +1349,9 @@ void *lammps_extract_global(void *handle, const char *name)
if (strcmp(name,"nlocal") == 0) return (void *) &lmp->atom->nlocal;
if (strcmp(name,"nghost") == 0) return (void *) &lmp->atom->nghost;
if (strcmp(name,"nmax") == 0) return (void *) &lmp->atom->nmax;
if (strcmp(name,"ntypes") == 0) return (void *) &lmp->atom->ntypes;
if (strcmp(name,"q_flag") == 0) return (void *) &lmp->atom->q_flag;
// update->atime can be referenced as a pointer
// thermo "timer" data cannot be, since it is computed on request
// lammps_get_thermo() can access all thermo keywords by value
if (strcmp(name,"atime") == 0) return (void *) &lmp->update->atime;
if (strcmp(name,"atimestep") == 0) return (void *) &lmp->update->atimestep;
// global constants defined by units
if (strcmp(name,"boltz") == 0) return (void *) &lmp->force->boltz;
@ -1308,9 +1433,11 @@ to then decide how to cast the (void*) pointer and access the data.
int lammps_extract_global_datatype(void *, const char *name)
{
if (strcmp(name,"units") == 0) return LAMMPS_STRING;
if (strcmp(name,"dt") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"ntimestep") == 0) return LAMMPS_BIGINT;
if (strcmp(name,"atime") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"atimestep") == 0) return LAMMPS_BIGINT;
if (strcmp(name,"boxlo") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"boxhi") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"boxxlo") == 0) return LAMMPS_DOUBLE;
@ -1324,6 +1451,7 @@ int lammps_extract_global_datatype(void *, const char *name)
if (strcmp(name,"xy") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"xz") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"yz") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"natoms") == 0) return LAMMPS_BIGINT;
if (strcmp(name,"nbonds") == 0) return LAMMPS_BIGINT;
if (strcmp(name,"nangles") == 0) return LAMMPS_BIGINT;
@ -1336,15 +1464,7 @@ int lammps_extract_global_datatype(void *, const char *name)
if (strcmp(name,"q_flag") == 0) return LAMMPS_INT;
// update->atime can be referenced as a pointer
// thermo "timer" data cannot be, since it is computed on request
// lammps_get_thermo() can access all thermo keywords by value
if (strcmp(name,"atime") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"atimestep") == 0) return LAMMPS_BIGINT;
// global constants defined by units
if (strcmp(name,"units") == 0) return LAMMPS_STRING;
if (strcmp(name,"boltz") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"hplanck") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"mvv2e") == 0) return LAMMPS_DOUBLE;

1
src/min.cpp
View File

@ -70,6 +70,7 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp)
halfstepback_flag = 1;
delaystep_start_flag = 1;
max_vdotf_negatif = 2000;
alpha_final = 0.0;
elist_global = elist_atom = nullptr;
vlist_global = vlist_atom = cvlist_atom = nullptr;

11
src/read_data.cpp
View File

@ -917,6 +917,17 @@ void ReadData::header(int firstpass)
int n;
char *ptr;
// initialize type counts by the "extra" numbers so they get counted
// in case the corresponding "types" line is missing and thus the extra
// value will not be processed.
if (addflag == NONE) {
atom->ntypes = extra_atom_types;
atom->nbondtypes = extra_bond_types;
atom->nangletypes = extra_angle_types;
atom->ndihedraltypes = extra_dihedral_types;
atom->nimpropertypes = extra_improper_types;
}
// customize for new sections
const char *section_keywords[NSECTIONS] =

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