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Merge pull request #2625 from yafshar/kim_citation

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Updating the kim citation report to lammps conventions
This commit is contained in:
Axel Kohlmeyer
2021-02-26 20:38:28 -05:00
committed by GitHub
parent ad7f14936e 335a6308d0
commit 1521c7a370
23 changed files with 597 additions and 260 deletions
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40
examples/kim/log.10Feb21.in.kim-ex.melt.clang.1
View File

@ -44,8 +44,8 @@ Created 32000 atoms
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LennardJones_Ar
WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1139)
WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1145)
WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1153)
WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1159)
pair_coeff * * Ar
#=== END kim interactions ====================================
@ -60,6 +60,26 @@ fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -76,20 +96,20 @@ Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 145069.63 0 164146.22 128015.94
100 95.179703 154939.42 0 164017.94 131602.75
Loop time of 2.8463 on 1 procs for 100 steps with 32000 atoms
Loop time of 2.85673 on 1 procs for 100 steps with 32000 atoms
Performance: 3.036 ns/day, 7.906 hours/ns, 35.133 timesteps/s
Performance: 3.024 ns/day, 7.935 hours/ns, 35.005 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5046 | 2.5046 | 2.5046 | 0.0 | 88.00
Neigh | 0.29437 | 0.29437 | 0.29437 | 0.0 | 10.34
Comm | 0.01182 | 0.01182 | 0.01182 | 0.0 | 0.42
Output | 7e-05 | 7e-05 | 7e-05 | 0.0 | 0.00
Modify | 0.024522 | 0.024522 | 0.024522 | 0.0 | 0.86
Other | | 0.01091 | | | 0.38
Pair | 2.4805 | 2.4805 | 2.4805 | 0.0 | 86.83
Neigh | 0.32948 | 0.32948 | 0.32948 | 0.0 | 11.53
Comm | 0.012038 | 0.012038 | 0.012038 | 0.0 | 0.42
Output | 7.4e-05 | 7.4e-05 | 7.4e-05 | 0.0 | 0.00
Modify | 0.023745 | 0.023745 | 0.023745 | 0.0 | 0.83
Other | | 0.01084 | | | 0.38
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

42
examples/kim/log.10Feb21.in.kim-ex.melt.clang.4
View File

@ -44,8 +44,8 @@ Created 32000 atoms
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LennardJones_Ar
WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1139)
WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1145)
WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1153)
WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1159)
pair_coeff * * Ar
#=== END kim interactions ====================================
@ -60,6 +60,26 @@ fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -76,20 +96,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.791 | 9.791 | 9.791 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 145069.63 0 164146.22 128015.94
100 95.179703 154939.42 0 164017.94 131602.75
Loop time of 0.857614 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.843382 on 4 procs for 100 steps with 32000 atoms
Performance: 10.074 ns/day, 2.382 hours/ns, 116.603 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 10.244 ns/day, 2.343 hours/ns, 118.570 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.73048 | 0.73398 | 0.73855 | 0.3 | 85.58
Neigh | 0.083739 | 0.083964 | 0.084335 | 0.1 | 9.79
Comm | 0.017996 | 0.022912 | 0.026515 | 2.1 | 2.67
Output | 2.7e-05 | 3.5e-05 | 4.5e-05 | 0.0 | 0.00
Modify | 0.010073 | 0.010158 | 0.010271 | 0.1 | 1.18
Other | | 0.006571 | | | 0.77
Pair | 0.71505 | 0.71942 | 0.72345 | 0.4 | 85.30
Neigh | 0.089886 | 0.090153 | 0.090611 | 0.1 | 10.69
Comm | 0.016342 | 0.020141 | 0.024546 | 2.5 | 2.39
Output | 2.4e-05 | 2.625e-05 | 3.2e-05 | 0.0 | 0.00
Modify | 0.008197 | 0.0083267 | 0.008504 | 0.1 | 0.99
Other | | 0.005318 | | | 0.63
Nlocal: 8000.00 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2

23
examples/kim/log.10Feb21.in.kim-pm-property.clang.1
View File

@ -96,7 +96,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_126566794224_004#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
@ -175,9 +190,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 3.119 | 3.119 | 3.119 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -0.34602203 0 -0.34602203 0.00061471244
Loop time of 0 on 1 procs for 0 steps with 4 atoms
Loop time of 3e-05 on 1 procs for 0 steps with 4 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
3.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -187,7 +202,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0 | | | 0.00
Other | | 3e-05 | | |100.00
Nlocal: 4.00000 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0

19
examples/kim/log.10Feb21.in.kim-pm-property.clang.4
View File

@ -78,7 +78,7 @@ Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.2485091 5.2485091
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4 atoms
create_atoms CPU = 0.000 seconds
create_atoms CPU = 0.001 seconds
mass 1 39.948
# Specify the KIM interactions
@ -96,7 +96,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_126566794224_004#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}

46
examples/kim/log.10Feb21.in.kim-pm-query.melt.clang.1
View File

@ -90,7 +90,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
@ -161,6 +176,19 @@ This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_0
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011},
}
- OpenKIM query: https://doi.org/10.1063/5.0014267
@Article{karls:bierbaum:2020,
author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott and J. P. Sethna and E. B. Tadmor},
title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic material property computation engine},
journal = {{T}he {J}ournal of {C}hemical {P}hysics},
year = 2020,
volume = 153,
number = 6,
pages = {064104},
doi = {10.1063/5.0014267}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
@ -179,20 +207,20 @@ Per MPI rank memory allocation (min/avg/max) = 10.36 | 10.36 | 10.36 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -126084.25 0 -107007.66 1528.8768
100 94.450495 -116016.03 0 -107007.07 2282.2685
Loop time of 18.2886 on 1 procs for 100 steps with 32000 atoms
Loop time of 18.2008 on 1 procs for 100 steps with 32000 atoms
Performance: 0.472 ns/day, 50.802 hours/ns, 5.468 timesteps/s
Performance: 0.475 ns/day, 50.558 hours/ns, 5.494 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.155 | 18.155 | 18.155 | 0.0 | 99.27
Neigh | 0.087194 | 0.087194 | 0.087194 | 0.0 | 0.48
Comm | 0.009477 | 0.009477 | 0.009477 | 0.0 | 0.05
Output | 6.7e-05 | 6.7e-05 | 6.7e-05 | 0.0 | 0.00
Modify | 0.02616 | 0.02616 | 0.02616 | 0.0 | 0.14
Other | | 0.0111 | | | 0.06
Pair | 18.058 | 18.058 | 18.058 | 0.0 | 99.21
Neigh | 0.097367 | 0.097367 | 0.097367 | 0.0 | 0.53
Comm | 0.009271 | 0.009271 | 0.009271 | 0.0 | 0.05
Output | 6.1e-05 | 6.1e-05 | 6.1e-05 | 0.0 | 0.00
Modify | 0.025469 | 0.025469 | 0.025469 | 0.0 | 0.14
Other | | 0.01084 | | | 0.06
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

48
examples/kim/log.10Feb21.in.kim-pm-query.melt.clang.4
View File

@ -90,7 +90,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
@ -161,6 +176,19 @@ This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_0
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011},
}
- OpenKIM query: https://doi.org/10.1063/5.0014267
@Article{karls:bierbaum:2020,
author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott and J. P. Sethna and E. B. Tadmor},
title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic material property computation engine},
journal = {{T}he {J}ournal of {C}hemical {P}hysics},
year = 2020,
volume = 153,
number = 6,
pages = {064104},
doi = {10.1063/5.0014267}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
@ -179,20 +207,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.489 | 3.489 | 3.489 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -126084.25 0 -107007.66 1528.8768
100 94.450495 -116016.03 0 -107007.07 2282.2685
Loop time of 5.00432 on 4 procs for 100 steps with 32000 atoms
Loop time of 5.33871 on 4 procs for 100 steps with 32000 atoms
Performance: 1.727 ns/day, 13.901 hours/ns, 19.983 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 1.618 ns/day, 14.830 hours/ns, 18.731 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.9281 | 4.9366 | 4.9447 | 0.3 | 98.65
Neigh | 0.02399 | 0.024135 | 0.024318 | 0.1 | 0.48
Comm | 0.020646 | 0.029014 | 0.037515 | 4.3 | 0.58
Output | 2.9e-05 | 3.325e-05 | 4.2e-05 | 0.0 | 0.00
Modify | 0.008808 | 0.0088445 | 0.00888 | 0.0 | 0.18
Other | | 0.005691 | | | 0.11
Pair | 5.244 | 5.2604 | 5.2753 | 0.5 | 98.53
Neigh | 0.027617 | 0.027767 | 0.027955 | 0.1 | 0.52
Comm | 0.017101 | 0.031947 | 0.04856 | 6.3 | 0.60
Output | 3.4e-05 | 4.525e-05 | 5.6e-05 | 0.0 | 0.00
Modify | 0.011577 | 0.01165 | 0.011709 | 0.0 | 0.22
Other | | 0.0069 | | | 0.13
Nlocal: 8000.00 ave 8029 max 7968 min
Histogram: 1 1 0 0 0 0 0 0 0 2

35
examples/kim/log.10Feb21.in.kim-pm.melt.clang.1
View File

@ -60,7 +60,7 @@ Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.002 seconds
create_atoms CPU = 0.003 seconds
kim interactions Si
#=== BEGIN kim interactions ==================================
@ -84,7 +84,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
@ -173,20 +188,20 @@ Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -85249.847 0 -66173.259 -33302.387
100 253.43357 -90346.68 0 -66173.441 -14888.698
Loop time of 17.7449 on 1 procs for 100 steps with 32000 atoms
Loop time of 17.6645 on 1 procs for 100 steps with 32000 atoms
Performance: 0.487 ns/day, 49.291 hours/ns, 5.635 timesteps/s
Performance: 0.489 ns/day, 49.068 hours/ns, 5.661 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 17.64 | 17.64 | 17.64 | 0.0 | 99.41
Neigh | 0.060149 | 0.060149 | 0.060149 | 0.0 | 0.34
Comm | 0.008585 | 0.008585 | 0.008585 | 0.0 | 0.05
Output | 6.3e-05 | 6.3e-05 | 6.3e-05 | 0.0 | 0.00
Modify | 0.025324 | 0.025324 | 0.025324 | 0.0 | 0.14
Other | | 0.01057 | | | 0.06
Pair | 17.553 | 17.553 | 17.553 | 0.0 | 99.37
Neigh | 0.063346 | 0.063346 | 0.063346 | 0.0 | 0.36
Comm | 0.009667 | 0.009667 | 0.009667 | 0.0 | 0.05
Output | 6.6e-05 | 6.6e-05 | 6.6e-05 | 0.0 | 0.00
Modify | 0.02711 | 0.02711 | 0.02711 | 0.0 | 0.15
Other | | 0.01088 | | | 0.06
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

35
examples/kim/log.10Feb21.in.kim-pm.melt.clang.4
View File

@ -84,7 +84,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
@ -173,20 +188,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.517 | 3.517 | 3.517 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -85249.847 0 -66173.259 -33302.387
100 253.43357 -90346.68 0 -66173.441 -14888.698
Loop time of 4.87378 on 4 procs for 100 steps with 32000 atoms
Loop time of 4.88034 on 4 procs for 100 steps with 32000 atoms
Performance: 1.773 ns/day, 13.538 hours/ns, 20.518 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 1.770 ns/day, 13.556 hours/ns, 20.490 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8075 | 4.816 | 4.8244 | 0.3 | 98.81
Neigh | 0.015902 | 0.015996 | 0.016077 | 0.1 | 0.33
Comm | 0.018078 | 0.026375 | 0.034752 | 4.2 | 0.54
Output | 3e-05 | 3.5e-05 | 4.4e-05 | 0.0 | 0.00
Modify | 0.009331 | 0.0094922 | 0.009588 | 0.1 | 0.19
Other | | 0.005919 | | | 0.12
Pair | 4.8131 | 4.8235 | 4.8347 | 0.4 | 98.84
Neigh | 0.017627 | 0.017731 | 0.017825 | 0.1 | 0.36
Comm | 0.013892 | 0.025022 | 0.03536 | 5.0 | 0.51
Output | 3.4e-05 | 4.025e-05 | 4.7e-05 | 0.0 | 0.00
Modify | 0.008725 | 0.0087775 | 0.008862 | 0.1 | 0.18
Other | | 0.005278 | | | 0.11
Nlocal: 8000.00 ave 8014 max 7988 min
Histogram: 1 1 0 0 0 0 1 0 0 1

36
examples/kim/log.10Feb21.in.kim-query.clang.1
View File

@ -528,7 +528,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_123629422045_005#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
@ -589,7 +604,22 @@ This Model originally published in \cite{MO_123629422045_005a} is archived in Op
volume = {26},
year = {1994},
}
- @Comment
- OpenKIM query: https://doi.org/10.1063/5.0014267
@Article{karls:bierbaum:2020,
author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott and J. P. Sethna and E. B. Tadmor},
title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic material property computation engine},
journal = {{T}he {J}ournal of {C}hemical {P}hysics},
year = 2020,
volume = 153,
number = 6,
pages = {064104},
doi = {10.1063/5.0014267}
}
- OpenKIM potential: https://openkim.org/cite/MO_004835508849_000#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
@ -652,4 +682,4 @@ This Model originally published in \cite{MO_004835508849_000a} is archived in Op
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Total wall time: 0:01:58
Total wall time: 0:01:59

43
examples/kim/log.10Feb21.in.kim-sm.melt.clang.1
View File

@ -58,10 +58,10 @@ Created 32000 atoms
kim interactions O
#=== BEGIN kim interactions ==================================
variable kim_periodic equal 1
pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-pgBW45WFK0TI/lmp_control safezone 2.0 mincap 100
pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-pgBW45WFK0TI/ffield.reax.rdx O
Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-pgBW45WFK0TI/ffield.reax.rdx with DATE: 2010-02-19
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-pgBW45WFK0TI/param.qeq
pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/lmp_control safezone 2.0 mincap 100
pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/ffield.reax.rdx O
Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/ffield.reax.rdx with DATE: 2010-02-19
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/param.qeq
#=== END kim interactions ====================================
@ -80,7 +80,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/SM_107643900657_000#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
@ -179,20 +194,20 @@ Per MPI rank memory allocation (min/avg/max) = 1803.0 | 1803.0 | 1803.0 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -39091.147 0 -20014.559 19501.107
100 63.198252 -26042.062 0 -20014.027 21497.661
Loop time of 40.2545 on 1 procs for 100 steps with 32000 atoms
Loop time of 38.6526 on 1 procs for 100 steps with 32000 atoms
Performance: 0.215 ns/day, 111.818 hours/ns, 2.484 timesteps/s
Performance: 0.224 ns/day, 107.368 hours/ns, 2.587 timesteps/s
99.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 24.364 | 24.364 | 24.364 | 0.0 | 60.52
Neigh | 0.4185 | 0.4185 | 0.4185 | 0.0 | 1.04
Comm | 0.022045 | 0.022045 | 0.022045 | 0.0 | 0.05
Output | 6.6e-05 | 6.6e-05 | 6.6e-05 | 0.0 | 0.00
Modify | 15.438 | 15.438 | 15.438 | 0.0 | 38.35
Other | | 0.01285 | | | 0.03
Pair | 23.493 | 23.493 | 23.493 | 0.0 | 60.78
Neigh | 0.4498 | 0.4498 | 0.4498 | 0.0 | 1.16
Comm | 0.020568 | 0.020568 | 0.020568 | 0.0 | 0.05
Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00
Modify | 14.677 | 14.677 | 14.677 | 0.0 | 37.97
Other | | 0.01223 | | | 0.03
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -205,4 +220,4 @@ Total # of neighbors = 3739236
Ave neighs/atom = 116.85112
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:41
Total wall time: 0:00:39

45
examples/kim/log.10Feb21.in.kim-sm.melt.clang.4
View File

@ -58,10 +58,10 @@ Created 32000 atoms
kim interactions O
#=== BEGIN kim interactions ==================================
variable kim_periodic equal 1
pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-zYQfH0ms5WSw/lmp_control safezone 2.0 mincap 100
pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-zYQfH0ms5WSw/ffield.reax.rdx O
Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-zYQfH0ms5WSw/ffield.reax.rdx with DATE: 2010-02-19
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-zYQfH0ms5WSw/param.qeq
pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/lmp_control safezone 2.0 mincap 100
pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/ffield.reax.rdx O
Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/ffield.reax.rdx with DATE: 2010-02-19
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/param.qeq
#=== END kim interactions ====================================
@ -80,7 +80,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/SM_107643900657_000#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
@ -179,20 +194,20 @@ Per MPI rank memory allocation (min/avg/max) = 630.2 | 630.2 | 630.2 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -39091.147 0 -20014.559 19501.107
100 63.198252 -26042.062 0 -20014.027 21497.661
Loop time of 15.049 on 4 procs for 100 steps with 32000 atoms
Loop time of 14.1676 on 4 procs for 100 steps with 32000 atoms
Performance: 0.574 ns/day, 41.803 hours/ns, 6.645 timesteps/s
99.0% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.610 ns/day, 39.355 hours/ns, 7.058 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.8158 | 9.8159 | 9.8161 | 0.0 | 65.23
Neigh | 0.17685 | 0.17759 | 0.17832 | 0.1 | 1.18
Comm | 0.028692 | 0.028847 | 0.028942 | 0.1 | 0.19
Output | 2.5e-05 | 3.575e-05 | 4.6e-05 | 0.0 | 0.00
Modify | 5.0171 | 5.0179 | 5.0186 | 0.0 | 33.34
Other | | 0.008715 | | | 0.06
Pair | 9.3935 | 9.3935 | 9.3936 | 0.0 | 66.30
Neigh | 0.15786 | 0.15879 | 0.16003 | 0.2 | 1.12
Comm | 0.025777 | 0.025906 | 0.025992 | 0.1 | 0.18
Output | 2.8e-05 | 3.35e-05 | 4.6e-05 | 0.0 | 0.00
Modify | 4.5801 | 4.5814 | 4.5823 | 0.0 | 32.34
Other | | 0.00801 | | | 0.06
Nlocal: 8000.00 ave 8010 max 7993 min
Histogram: 2 0 0 0 0 1 0 0 0 1
@ -205,4 +220,4 @@ Total # of neighbors = 4003876
Ave neighs/atom = 125.12113
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:15
Total wall time: 0:00:14

18
examples/kim/log.10Feb21.in.lammps.melt.clang.1
View File

@ -59,20 +59,20 @@ Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 25367.408 6750.7421
100 98.747096 15900.676 0 25319.465 10184.453
Loop time of 1.92822 on 1 procs for 100 steps with 32000 atoms
Loop time of 1.87123 on 1 procs for 100 steps with 32000 atoms
Performance: 4.481 ns/day, 5.356 hours/ns, 51.861 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 4.617 ns/day, 5.198 hours/ns, 53.441 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7377 | 1.7377 | 1.7377 | 0.0 | 90.12
Neigh | 0.14234 | 0.14234 | 0.14234 | 0.0 | 7.38
Comm | 0.011694 | 0.011694 | 0.011694 | 0.0 | 0.61
Output | 6.7e-05 | 6.7e-05 | 6.7e-05 | 0.0 | 0.00
Modify | 0.02476 | 0.02476 | 0.02476 | 0.0 | 1.28
Other | | 0.01163 | | | 0.60
Pair | 1.686 | 1.686 | 1.686 | 0.0 | 90.10
Neigh | 0.14211 | 0.14211 | 0.14211 | 0.0 | 7.59
Comm | 0.01013 | 0.01013 | 0.01013 | 0.0 | 0.54
Output | 6.3e-05 | 6.3e-05 | 6.3e-05 | 0.0 | 0.00
Modify | 0.022686 | 0.022686 | 0.022686 | 0.0 | 1.21
Other | | 0.0102 | | | 0.55
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

18
examples/kim/log.10Feb21.in.lammps.melt.clang.4
View File

@ -59,20 +59,20 @@ Per MPI rank memory allocation (min/avg/max) = 7.633 | 7.633 | 7.633 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 25367.408 6750.7421
100 98.747096 15900.676 0 25319.465 10184.453
Loop time of 0.561006 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.532082 on 4 procs for 100 steps with 32000 atoms
Performance: 15.401 ns/day, 1.558 hours/ns, 178.251 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 16.238 ns/day, 1.478 hours/ns, 187.941 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.48486 | 0.48676 | 0.48817 | 0.2 | 86.77
Neigh | 0.040698 | 0.04091 | 0.041066 | 0.1 | 7.29
Comm | 0.016616 | 0.01811 | 0.0202 | 1.1 | 3.23
Output | 3e-05 | 3.575e-05 | 4.7e-05 | 0.0 | 0.01
Modify | 0.008934 | 0.009025 | 0.009142 | 0.1 | 1.61
Other | | 0.006161 | | | 1.10
Pair | 0.46077 | 0.46347 | 0.46621 | 0.3 | 87.10
Neigh | 0.038499 | 0.038599 | 0.038759 | 0.0 | 7.25
Comm | 0.01395 | 0.016623 | 0.019377 | 1.7 | 3.12
Output | 3.1e-05 | 3.675e-05 | 4.7e-05 | 0.0 | 0.01
Modify | 0.00787 | 0.007971 | 0.008083 | 0.1 | 1.50
Other | | 0.005382 | | | 1.01
Nlocal: 8000.00 ave 8012 max 7989 min
Histogram: 1 0 0 0 2 0 0 0 0 1

28
src/KIM/fix_store_kim.cpp
View File

@ -13,7 +13,8 @@
/* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (UMN)
Ryan S. Elliott (UMN),
Yaser Afshar (UMN)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
@ -55,11 +56,12 @@
------------------------------------------------------------------------- */
#include "fix_store_kim.h"
#include <cstring>
#include "error.h"
extern "C" {
#include "KIM_SimulatorModel.h"
}
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -114,27 +116,27 @@ int FixStoreKIM::setmask()
/* ---------------------------------------------------------------------- */
void FixStoreKIM::setptr(const char *name, void *ptr)
void FixStoreKIM::setptr(const std::string &name, void *ptr)
{
if (strcmp(name,"simulator_model") == 0) {
if (name == "simulator_model") {
if (simulator_model) {
KIM_SimulatorModel *sm = (KIM_SimulatorModel *)simulator_model;
KIM_SimulatorModel_Destroy(&sm);
}
simulator_model = ptr;
} else if (strcmp(name,"model_name") == 0) {
} else if (name == "model_name") {
if (model_name) {
char *mn = (char *)model_name;
delete[] mn;
}
model_name = ptr;
} else if (strcmp(name,"model_units") == 0) {
} else if (name == "model_units") {
if (model_units) {
char *mu = (char *)model_units;
delete[] mu;
}
model_units = ptr;
} else if (strcmp(name,"user_units") == 0) {
} else if (name == "user_units") {
if (user_units) {
char *uu = (char *)user_units;
delete[] uu;
@ -145,11 +147,11 @@ void FixStoreKIM::setptr(const char *name, void *ptr)
/* ---------------------------------------------------------------------- */
void *FixStoreKIM::getptr(const char *name)
void *FixStoreKIM::getptr(const std::string &name)
{
if (strcmp(name,"simulator_model") == 0) return simulator_model;
else if (strcmp(name,"model_name") == 0) return model_name;
else if (strcmp(name,"model_units") == 0) return model_units;
else if (strcmp(name,"user_units") == 0) return user_units;
if (name == "simulator_model") return simulator_model;
else if (name == "model_name") return model_name;
else if (name == "model_units") return model_units;
else if (name == "user_units") return user_units;
else return nullptr;
}

7
src/KIM/fix_store_kim.h
View File

@ -13,7 +13,8 @@
/* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (UMN)
Ryan S. Elliott (UMN),
Yaser Afshar (UMN)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
@ -73,8 +74,8 @@ class FixStoreKIM : public Fix {
~FixStoreKIM();
int setmask();
void setptr(const char *, void *);
void *getptr(const char *);
void setptr(const std::string &, void *);
void *getptr(const std::string &);
private:
void *simulator_model; // pointer to KIM simulator model class

51
src/KIM/kim_command.cpp
View File

@ -56,6 +56,7 @@
#include "kim_command.h"
#include "citeme.h"
#include "error.h"
// include KIM sub-command headers here
@ -65,10 +66,38 @@
#include "kim_property.h"
#include "kim_query.h"
#include <memory>
using namespace LAMMPS_NS;
static constexpr const char *const cite_openkim =
"OpenKIM: https://doi.org/10.1007/s11837-011-0102-6\n\n"
"@Article{tadmor:elliott:2011,\n"
" author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller "
"and C. A. Becker},\n"
" title = {The potential of atomistic simulations and the {K}nowledgebase of "
"{I}nteratomic {M}odels},\n"
" journal = {{JOM}},\n"
" year = 2011,\n"
" volume = 63,\n"
" number = 17,\n"
" pages = {17},\n"
" doi = {10.1007/s11837-011-0102-6}\n"
"}\n\n";
static constexpr const char *const cite_openkim_query =
"OpenKIM query: https://doi.org/10.1063/5.0014267\n\n"
"@Article{karls:bierbaum:2020,\n"
" author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott "
"and J. P. Sethna and E. B. Tadmor},\n"
" title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic "
"material property computation engine},\n"
" journal = {{T}he {J}ournal of {C}hemical {P}hysics},\n"
" year = 2020,\n"
" volume = 153,\n"
" number = 6,\n"
" pages = {064104},\n"
" doi = {10.1063/5.0014267}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
void KimCommand::command(int narg, char **arg)
@ -79,20 +108,28 @@ void KimCommand::command(int narg, char **arg)
narg--;
arg++;
if (lmp->citeme) lmp->citeme->add(cite_openkim);
if (subcmd == "init") {
std::unique_ptr<KimInit> cmd(new KimInit(lmp));
KimInit *cmd = new KimInit(lmp);
cmd->command(narg, arg);
delete cmd;
} else if (subcmd == "interactions") {
std::unique_ptr<KimInteractions> cmd(new KimInteractions(lmp));
KimInteractions *cmd = new KimInteractions(lmp);
cmd->command(narg, arg);
delete cmd;
} else if (subcmd == "param") {
std::unique_ptr<KimParam> cmd(new KimParam(lmp));
KimParam *cmd = new KimParam(lmp);
cmd->command(narg, arg);
delete cmd;
} else if (subcmd == "property") {
std::unique_ptr<KimProperty> cmd(new KimProperty(lmp));
KimProperty *cmd = new KimProperty(lmp);
cmd->command(narg, arg);
delete cmd;
} else if (subcmd == "query") {
std::unique_ptr<KimQuery> cmd(new KimQuery(lmp));
if (lmp->citeme) lmp->citeme->add(cite_openkim_query);
KimQuery *cmd = new KimQuery(lmp);
cmd->command(narg, arg);
delete cmd;
} else error->all(FLERR, fmt::format("Unknown kim subcommand {}", subcmd));
}

119
src/KIM/kim_init.cpp
View File

@ -86,10 +86,12 @@ void KimInit::command(int narg, char **arg)
if (domain->box_exist)
error->all(FLERR, "Must use 'kim init' command before "
"simulation box is defined");
char *model_name = utils::strdup(arg[0]);
char *user_units = utils::strdup(arg[1]);
if (narg == 3) {
if (strcmp(arg[2], "unit_conversion_mode")==0) unit_conversion_mode = true;
auto arg_str = std::string(arg[2]);
if (arg_str == "unit_conversion_mode") unit_conversion_mode = true;
else {
error->all(FLERR, fmt::format("Illegal 'kim init' command.\nThe argument "
"followed by unit_style {} is an optional "
@ -123,41 +125,42 @@ void get_kim_unit_names(
KIM_TimeUnit & timeUnit,
Error * error)
{
if (strcmp(system, "real") == 0) {
const std::string system_str(system);
if (system_str == "real") {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if (strcmp(system, "metal") == 0) {
} else if (system_str == "metal") {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps;
} else if (strcmp(system, "si") == 0) {
} else if (system_str == "si") {
lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if (strcmp(system, "cgs") == 0) {
} else if (system_str == "cgs") {
lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if (strcmp(system, "electron") == 0) {
} else if (system_str == "electron") {
lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if (strcmp(system, "lj") == 0 ||
strcmp(system, "micro") ==0 ||
strcmp(system, "nano")==0) {
} else if ((system_str == "lj") ||
(system_str == "micro") ||
(system_str == "nano")) {
error->all(FLERR, fmt::format("LAMMPS unit_style {} not supported "
"by KIM models", system));
"by KIM models", system_str));
} else {
error->all(FLERR, "Unknown unit_style");
}
@ -255,15 +258,16 @@ void KimInit::determine_model_type_and_units(char * model_name,
int sim_fields;
int sim_lines;
char const * sim_field;
char const * sim_value;
char const *sim_field;
char const *sim_value;
KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields);
KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
for (int i=0; i < sim_fields; ++i) {
for (int i = 0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel, i, &sim_lines, &sim_field);
if (0 == strcmp(sim_field, "units")) {
const std::string sim_field_str(sim_field);
if (sim_field_str == "units") {
KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel, i, 0, &sim_value);
*model_units = utils::strdup(sim_value);
@ -272,9 +276,11 @@ void KimInit::determine_model_type_and_units(char * model_name,
}
KIM_SimulatorModel_Destroy(&simulatorModel);
if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) {
const std::string model_units_str(*model_units);
const std::string user_units_str(user_units);
if ((!unit_conversion_mode) && (model_units_str != user_units_str)) {
error->all(FLERR, fmt::format("Incompatible units for KIM Simulator Model"
", required units = {}", *model_units));
", required units = {}", model_units_str));
}
}
}
@ -300,12 +306,10 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units,
input->write_echo("#=== BEGIN kim init ==================================="
"=======\n");
KIM_SimulatorModel * simulatorModel;
KIM_SimulatorModel *simulatorModel;
if (model_type == SM) {
int kim_error =
KIM_SimulatorModel_Create(model_name, &simulatorModel);
if (kim_error)
error->all(FLERR, "Unable to load KIM Simulator Model");
int kim_error = KIM_SimulatorModel_Create(model_name, &simulatorModel);
if (kim_error) error->all(FLERR, "Unable to load KIM Simulator Model");
auto logID = fmt::format("{}_SimulatorModel", comm->me);
KIM_SimulatorModel_SetLogID(simulatorModel, logID.c_str());
@ -314,20 +318,15 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units,
KIM_SimulatorModel_GetSimulatorNameAndVersion(
simulatorModel, &sim_name, &sim_version);
if (0 != strcmp(sim_name, "LAMMPS"))
const std::string sim_name_str(sim_name);
if (sim_name_str != "LAMMPS")
error->all(FLERR, "Incompatible KIM Simulator Model");
if (comm->me == 0) {
std::string mesg("# Using KIM Simulator Model : ");
mesg += model_name;
mesg += "\n";
mesg += "# For Simulator : ";
mesg += std::string(sim_name) + " " + sim_version + "\n";
mesg += "# Running on : LAMMPS ";
mesg += lmp->version;
mesg += "\n";
mesg += "#\n";
auto mesg = fmt::format("# Using KIM Simulator Model : {}\n"
"# For Simulator : {} {}\n"
"# Running on : LAMMPS {}\n#\n", model_name,
sim_name_str, sim_version, lmp->version);
utils::logmesg(lmp, mesg);
}
@ -343,24 +342,24 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units,
// set units
std::string cmd("units ");
cmd += model_units;
const std::string model_units_str(model_units);
auto cmd = fmt::format("units {}", model_units_str);
input->one(cmd);
// Set the skin and timestep default values as
// 2.0 Angstroms and 1.0 femtosecond
std::string skin_cmd =
(strcmp(model_units, "real") == 0) ? "neighbor 2.0 bin # Angstroms":
(strcmp(model_units, "metal") == 0) ? "neighbor 2.0 bin # Angstroms":
(strcmp(model_units, "si") == 0) ? "neighbor 2e-10 bin # meters":
(strcmp(model_units, "cgs") == 0) ? "neighbor 2e-8 bin # centimeters":
const std::string skin_cmd =
(model_units_str == "real") ? "neighbor 2.0 bin # Angstroms":
(model_units_str == "metal") ? "neighbor 2.0 bin # Angstroms":
(model_units_str == "si") ? "neighbor 2e-10 bin # meters":
(model_units_str == "cgs") ? "neighbor 2e-8 bin # centimeters":
"neighbor 3.77945224 bin # Bohr";
std::string step_cmd =
(strcmp(model_units, "real") == 0) ? "timestep 1.0 # femtoseconds":
(strcmp(model_units, "metal") == 0) ? "timestep 1.0e-3 # picoseconds":
(strcmp(model_units, "si") == 0) ? "timestep 1e-15 # seconds":
(strcmp(model_units, "cgs") == 0) ? "timestep 1e-15 # seconds":
const std::string step_cmd =
(model_units_str == "real") ? "timestep 1.0 # femtoseconds":
(model_units_str == "metal") ? "timestep 1.0e-3 # picoseconds":
(model_units_str == "si") ? "timestep 1e-15 # seconds":
(model_units_str == "cgs") ? "timestep 1e-15 # seconds":
"timestep 1.0 # femtoseconds";
input->one(skin_cmd);
input->one(step_cmd);
@ -372,11 +371,13 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units,
// init model
for (int i=0; i < sim_fields; ++i) {
for (int i = 0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel, i, &sim_lines, &sim_field);
if (0 == strcmp(sim_field, "model-init")) {
for (int j=0; j < sim_lines; ++j) {
const std::string sim_field_str(sim_field);
if (sim_field_str == "model-init") {
for (int j = 0; j < sim_lines; ++j) {
KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel, i, j, &sim_value);
input->one(sim_value);
@ -489,7 +490,15 @@ void KimInit::do_variables(const std::string &from, const std::string &to)
void KimInit::write_log_cite(char *model_name)
{
KIM_Collections * collections;
if (!lmp->citeme) return;
std::string model_name_str(model_name);
std::string re = "[MS][OM]_\\d\\d\\d\\d\\d\\d\\d\\d\\d\\d\\d\\d_\\d\\d\\d";
std::string kim_id = utils::strfind(model_name_str, re);
if (kim_id.empty()) return;
KIM_Collections *collections;
int err = KIM_Collections_Create(&collections);
if (err) return;
@ -514,19 +523,23 @@ void KimInit::write_log_cite(char *model_name)
return;
}
auto cite_id = fmt::format("OpenKIM potential: https://openkim.org/cite/"
"{}#item-citation\n\n",kim_id);
for (int i = 0; i < extent; ++i) {
char const * fileName;
char const *fileName;
int availableAsString;
char const * fileString;
char const *fileString;
err = KIM_Collections_GetItemMetadataFile(
collections, i, &fileName, nullptr, nullptr,
&availableAsString, &fileString);
if (err) continue;
if (0 == strncmp("kimcite", fileName, 7)) {
if ((lmp->citeme) && (availableAsString)) lmp->citeme->add(fileString);
}
if (utils::strmatch(fileName, "^kimcite") && availableAsString)
cite_id += fileString;
}
lmp->citeme->add(cite_id);
KIM_Collections_Destroy(&collections);
}

25
src/KIM/kim_interactions.cpp
View File

@ -97,7 +97,8 @@ void KimInteractions::command(int narg, char **arg)
void KimInteractions::do_setup(int narg, char **arg)
{
bool fixed_types;
if ((narg == 1) && (0 == strcmp("fixed_types", arg[0]))) {
const std::string arg_str(arg[0]);
if ((narg == 1) && (arg_str == "fixed_types")) {
fixed_types = true;
} else if (narg != atom->ntypes) {
error->all(FLERR, fmt::format("Illegal 'kim interactions' command.\nThe "
@ -178,11 +179,15 @@ void KimInteractions::do_setup(int narg, char **arg)
KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel, i, &sim_lines, &sim_field);
if (strcmp(sim_field, "units") == 0) {
const std::string sim_field_str(sim_field);
if (sim_field_str == "units") {
KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel, i, 0, &sim_value);
if (strcmp(sim_value, update->unit_style) != 0)
error->all(FLERR,"Incompatible units for KIM Simulator Model");
const std::string sim_value_str(sim_value);
const std::string unit_style_str(update->unit_style);
if (sim_value_str != unit_style_str)
error->all(FLERR, "Incompatible units for KIM Simulator Model");
}
}
@ -190,13 +195,15 @@ void KimInteractions::do_setup(int narg, char **arg)
for (int i = 0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel, i, &sim_lines, &sim_field);
if (strcmp(sim_field, "model-defn") == 0) {
if (domain->periodicity[0]&&
domain->periodicity[1]&&
const std::string sim_field_str(sim_field);
if (sim_field_str == "model-defn") {
if (domain->periodicity[0] &&
domain->periodicity[1] &&
domain->periodicity[2])
input->one("variable kim_periodic equal 1");
else if (domain->periodicity[0]&&
domain->periodicity[1]&&
else if (domain->periodicity[0] &&
domain->periodicity[1] &&
!domain->periodicity[2])
input->one("variable kim_periodic equal 2");
else input->one("variable kim_periodic equal 0");

52
src/KIM/kim_param.cpp
View File

@ -90,43 +90,45 @@ void get_kim_unit_names(
KIM_TimeUnit &timeUnit,
Error *error)
{
if ((strcmp(system, "real") == 0)) {
const std::string system_str(system);
if (system_str == "real") {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if ((strcmp(system, "metal") == 0)) {
} else if (system_str == "metal") {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps;
} else if ((strcmp(system, "si") == 0)) {
} else if (system_str == "si") {
lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if ((strcmp(system, "cgs") == 0)) {
} else if (system_str == "cgs") {
lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if ((strcmp(system, "electron") == 0)) {
} else if (system_str == "electron") {
lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if (strcmp(system, "lj") == 0 ||
strcmp(system, "micro") ==0 ||
strcmp(system, "nano")==0) {
} else if ((system_str == "lj") ||
(system_str == "micro") ||
(system_str == "nano")) {
error->all(FLERR, fmt::format("LAMMPS unit_style {} not supported "
"by KIM models", system));
} else
"by KIM models", system_str));
} else {
error->all(FLERR, "Unknown unit_style");
}
}
} // namespace
@ -213,7 +215,7 @@ void KimParam::command(int narg, char **arg)
if (kim_param_get_set == "get") {
int kim_error;
// Parameter name
char *paramname = nullptr;
std::string paramname;
// Variable name
std::string varname;
@ -221,7 +223,7 @@ void KimParam::command(int narg, char **arg)
for (int i = 1; i < narg;) {
// Parameter name
if (i < narg)
paramname = arg[i++];
paramname = std::string(arg[i++]);
else
break;
@ -239,7 +241,8 @@ void KimParam::command(int narg, char **arg)
if (kim_error)
error->all(FLERR, "KIM GetParameterMetadata returned error");
if (strcmp(paramname, str_name) == 0) break;
const std::string str_name_str(str_name);
if (paramname == str_name_str) break;
}
if (param_index >= numberOfParameters) {
@ -302,8 +305,10 @@ void KimParam::command(int narg, char **arg)
if (i < narg) {
// Get the variable/variable_base name
varname = arg[i++];
if (varname == "split" || varname == "list" || varname == "explicit")
varname = std::string(arg[i++]);
if ((varname == "split") ||
(varname == "list") ||
(varname == "explicit"))
error->all(FLERR, "Illegal variable name in 'kim param get'");
} else {
std::string msg("Wrong number of arguments in 'kim param get' ");
@ -316,13 +321,14 @@ void KimParam::command(int narg, char **arg)
if (nvars > 1) {
if (i < narg) {
if (strcmp(arg[i], "split") == 0) {
std::string formatarg(arg[i]);
if (formatarg == "split") {
varsname.resize(nvars);
for (int j = 0, k = nlbound; j < nvars; ++j, ++k) {
varsname[j] = fmt::format("{}_{}", varname, k);
}
++i;
} else if (strcmp(arg[i], "list") == 0) {
} else if (formatarg == "list") {
list_requested = true;
varsname.resize(1);
varsname[0] = varname;
@ -332,13 +338,14 @@ void KimParam::command(int narg, char **arg)
varsname.resize(nvars);
--i;
for (int j = 0; j < nvars; ++j, ++i) {
varsname[j] = arg[i];
varsname[j] = std::string(arg[i]);
if (varsname[j] == "split" || varsname[j] == "list" ||
varsname[j] == "explicit")
error->all(FLERR, "Illegal variable name in 'kim param get'");
}
if (i < narg) {
if (strcmp(arg[i], "explicit") == 0) ++i;
formatarg = std::string(arg[i]);
if (formatarg == "explicit") ++i;
}
} else {
auto msg =
@ -357,13 +364,12 @@ void KimParam::command(int narg, char **arg)
} else {
varsname.resize(1);
if (i < narg) {
if (strcmp(arg[i], "split") == 0) {
const std::string formatarg(arg[i]);
if (formatarg == "split") {
varsname[0] = fmt::format("{}_{}", varname, nlbound);
++i;
} else {
if ((strcmp(arg[i], "list") == 0) ||
(strcmp(arg[i], "explicit") == 0)) ++i;
if (formatarg == "list" || formatarg == "explicit") ++i;
varsname[0] = varname;
}
} else {

19
src/KIM/kim_property.cpp
View File

@ -85,11 +85,10 @@ void KimProperty::command(int narg, char **arg)
#if LMP_PYTHON
#if PY_MAJOR_VERSION >= 3
if (narg < 2) error->all(FLERR, "Invalid 'kim property' command");
if (!(strcmp(arg[0], "create") == 0) &&
!(strcmp(arg[0], "destroy") == 0) &&
!(strcmp(arg[0], "modify") == 0) &&
!(strcmp(arg[0], "remove") == 0) &&
!(strcmp(arg[0], "dump") == 0)) {
const std::string subcmd(arg[0]);
if ((subcmd != "create") && (subcmd != "destroy") && (subcmd != "modify") &&
(subcmd != "remove") && (subcmd != "dump")) {
std::string msg("Incorrect arguments in 'kim property' command.\n");
msg += "'kim property create/destroy/modify/remove/dump' is mandatory";
error->all(FLERR, msg);
@ -130,7 +129,7 @@ void KimProperty::command(int narg, char **arg)
}
// kim_property create 1 cohesive-potential-energy-cubic-crystal
if (strcmp(arg[0], "create") == 0) {
if (subcmd == "create") {
if (narg != 3) {
PyGILState_Release(gstate);
error->all(FLERR, "Invalid 'kim property create' command");
@ -196,7 +195,7 @@ void KimProperty::command(int narg, char **arg)
Py_XDECREF(pArgs);
Py_XDECREF(pFunc);
Py_XDECREF(pValue);
} else if (strcmp(arg[0], "destroy") == 0) {
} else if (subcmd == "destroy") {
if (narg != 2) {
PyGILState_Release(gstate);
error->all(FLERR, "Invalid 'kim property destroy' command");
@ -256,7 +255,7 @@ void KimProperty::command(int narg, char **arg)
Py_XDECREF(pArgs);
Py_XDECREF(pFunc);
Py_XDECREF(pValue);
} else if (strcmp(arg[0], "modify") == 0) {
} else if (subcmd == "modify") {
if (narg < 6) {
PyGILState_Release(gstate);
error->all(FLERR, "Invalid 'kim property modify' command");
@ -321,7 +320,7 @@ void KimProperty::command(int narg, char **arg)
Py_XDECREF(pArgs);
Py_XDECREF(pFunc);
Py_XDECREF(pValue);
} else if (strcmp(arg[0], "remove") == 0) {
} else if (subcmd == "remove") {
if (narg < 4) {
PyGILState_Release(gstate);
error->all(FLERR, "Invalid 'kim property remove' command");
@ -386,7 +385,7 @@ void KimProperty::command(int narg, char **arg)
Py_XDECREF(pArgs);
Py_XDECREF(pFunc);
Py_XDECREF(pValue);
} else if (strcmp(arg[0], "dump") == 0) {
} else if (subcmd == "dump") {
if (narg != 2) {
PyGILState_Release(gstate);
error->all(FLERR, "Invalid 'kim property dump' command");

4
src/KIM/kim_query.cpp
View File

@ -130,7 +130,7 @@ void KimQuery::command(int narg, char **arg)
// check the query_args format (a series of keyword=value pairs)
for (int i = 2; i < narg; ++i) {
if (!strchr(arg[i], '=') || !strchr(arg[i], '[') || !strchr(arg[i], ']')) {
if (!utils::strmatch(arg[i], "[=][\\[].*[\\]]")) {
auto msg = fmt::format("Illegal query format.\nInput argument "
"of `{}` to 'kim query' is wrong. The query format is the "
"keyword=[value], where value is always an array of one or "
@ -142,7 +142,7 @@ void KimQuery::command(int narg, char **arg)
if (query_function != "get_available_models") {
for (int i = 2; i < narg; ++i) {
// check if the model is specified as an argument
if (strncmp("model=", arg[i], 6) == 0) {
if (utils::strmatch(arg[i], "^model=")) {
ValueTokenizer values(arg[i], "=[]");
std::string key = values.next_string();
model_name = values.next_string();

62
src/KIM/pair_kim.cpp
View File

@ -57,6 +57,7 @@
#include "pair_kim.h"
#include "atom.h"
#include "citeme.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
@ -73,6 +74,21 @@
using namespace LAMMPS_NS;
static constexpr const char *const cite_openkim =
"OpenKIM: https://doi.org/10.1007/s11837-011-0102-6\n\n"
"@Article{tadmor:elliott:2011,\n"
" author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller "
"and C. A. Becker},\n"
" title = {The potential of atomistic simulations and the {K}nowledgebase of "
"{I}nteratomic {M}odels},\n"
" journal = {{JOM}},\n"
" year = 2011,\n"
" volume = 63,\n"
" number = 17,\n"
" pages = {17},\n"
" doi = {10.1007/s11837-011-0102-6}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairKIM::PairKIM(LAMMPS *lmp) :
@ -120,6 +136,8 @@ PairKIM::PairKIM(LAMMPS *lmp) :
// (used by kim_free(), etc.)
kim_init_ok = false;
kim_particle_codes_ok = false;
if (lmp->citeme) lmp->citeme->add(cite_openkim);
// END
}
@ -291,10 +309,11 @@ void PairKIM::settings(int narg, char **arg)
init_style_call_count = 0;
if (narg != 1) {
if ((narg > 0) && ((0 == strcmp("KIMvirial", arg[0])) ||
(0 == strcmp("LAMMPSvirial", arg[0])))) {
error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not "
"supported with kim-api");
const std::string arg_str(arg[0]);
if ((narg > 0) &&
((arg_str == "KIMvirial") || (arg_str == "LAMMPSvirial"))) {
error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not supported "
"with kim-api");
} else error->all(FLERR,"Illegal pair_style command");
}
// arg[0] is the KIM Model name
@ -337,14 +356,16 @@ void PairKIM::coeff(int narg, char **arg)
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
const std::string arg_0_str(arg[0]);
const std::string arg_1_str(arg[1]);
if ((arg_0_str != "*") || (arg_1_str != "*"))
error->all(FLERR,"Incorrect args for pair coefficients.\nThe first two "
"arguments of pair_coeff command must be * * to span "
"all LAMMPS atom types");
int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
utils::bounds(FLERR,arg_0_str,1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg_1_str,1,atom->ntypes,jlo,jhi,error);
// read args that map atom species to KIM elements
// lmps_map_species_to_unique[i] =
@ -426,12 +447,12 @@ void PairKIM::coeff(int narg, char **arg)
int kimerror;
// Parameter name
char *paramname = nullptr;
std::string paramname;
for (int i = 2 + atom->ntypes; i < narg;) {
// Parameter name
if (i < narg)
paramname = arg[i++];
paramname = std::string(arg[i++]);
else
break;
@ -448,7 +469,8 @@ void PairKIM::coeff(int narg, char **arg)
if (kimerror)
error->all(FLERR,"KIM GetParameterMetadata returned error");
if (strcmp(paramname, str_name) == 0) break;
const std::string str_name_str(str_name);
if (paramname == str_name_str) break;
}
if (param_index >= numberOfParameters) {
@ -994,47 +1016,49 @@ void PairKIM::set_lmps_flags()
if (force->pair_match("hybrid",0))
error->all(FLERR,"pair_kim does not support hybrid");
const std::string unit_style_str(update->unit_style);
// determine unit system and set lmps_units flag
if (strcmp(update->unit_style,"real") == 0) {
if (unit_style_str == "real") {
lmps_units = REAL;
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if (strcmp(update->unit_style,"metal") == 0) {
} else if (unit_style_str == "metal") {
lmps_units = METAL;
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps;
} else if (strcmp(update->unit_style,"si") == 0) {
} else if (unit_style_str == "si") {
lmps_units = SI;
lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if (strcmp(update->unit_style,"cgs") == 0) {
} else if (unit_style_str == "cgs") {
lmps_units = CGS;
lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if (strcmp(update->unit_style,"electron") == 0) {
} else if (unit_style_str == "electron") {
lmps_units = ELECTRON;
lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if (strcmp(update->unit_style,"lj") == 0 ||
strcmp(update->unit_style,"micro") == 0 ||
strcmp(update->unit_style,"nano") == 0) {
} else if ((unit_style_str == "lj") ||
(unit_style_str == "micro") ||
(unit_style_str == "nano")) {
error->all(FLERR,fmt::format("LAMMPS unit_style {} not supported "
"by KIM models", update->unit_style));
"by KIM models", unit_style_str));
} else {
error->all(FLERR,"Unknown unit_style");
}

32
unittest/commands/test_kim_commands.cpp
View File

@ -570,6 +570,38 @@ TEST_F(KimCommandsTest, kim_query)
"one or more comma-separated items.*",
lmp->input->one(squery););
squery = "kim query a0 get_lattice_constant_cubic ";
squery += "crystal=[fcc] species=[Al,Ni, units=[angstrom]";
TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species="
"\\[Al,Ni,` to 'kim query' is wrong. The query format is "
"the keyword=\\[value\\], where value is always an array of "
"one or more comma-separated items.*",
lmp->input->one(squery););
squery = "kim query a0 get_lattice_constant_cubic ";
squery += "crystal=[fcc] species=Al,Ni], units=[angstrom]";
TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species="
"Al,Ni\\],` to 'kim query' is wrong. The query format is "
"the keyword=\\[value\\], where value is always an array of "
"one or more comma-separated items.*",
lmp->input->one(squery););
squery = "kim query a0 get_lattice_constant_cubic ";
squery += "crystal=[fcc] species=Al,\"Ni\"], units=[angstrom]";
TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species="
"Al,\"Ni\"\\],` to 'kim query' is wrong. The query format is "
"the keyword=\\[value\\], where value is always an array of "
"one or more comma-separated items.*",
lmp->input->one(squery););
squery = "kim query a0 get_lattice_constant_cubic ";
squery += "crystal=[fcc] species=\"Al\",Ni], units=[angstrom]";
TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species="
"\"Al\",Ni\\],` to 'kim query' is wrong. The query format is "
"the keyword=\\[value\\], where value is always an array of "
"one or more comma-separated items.*",
lmp->input->one(squery););
squery = "kim query a0 get_lattice_constant_cubic crystal=[\"fcc\"] "
"species=[\"Al\"]";
TEST_FAILURE(".*ERROR: Illegal query format.\nMust use 'kim init' before "