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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
Download Patch File Download Diff File Expand all files Collapse all files

40
examples/kim/log.10Feb21.in.kim-ex.melt.clang.1
View File

@ -44,8 +44,8 @@ Created 32000 atoms
kim interactions Ar kim interactions Ar
#=== BEGIN kim interactions ================================== #=== BEGIN kim interactions ==================================
pair_style kim LennardJones_Ar 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 '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:1145) WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1159)
pair_coeff * * Ar pair_coeff * * Ar
#=== END kim interactions ==================================== #=== 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 #fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100 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 ... Neighbor list info ...
update every 1 steps, delay 0 steps, check yes update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000 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 Step Temp E_pair E_mol TotEng Press
0 200 145069.63 0 164146.22 128015.94 0 200 145069.63 0 164146.22 128015.94
100 95.179703 154939.42 0 164017.94 131602.75 100 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 99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 2.5046 | 2.5046 | 2.5046 | 0.0 | 88.00 Pair | 2.4805 | 2.4805 | 2.4805 | 0.0 | 86.83
Neigh | 0.29437 | 0.29437 | 0.29437 | 0.0 | 10.34 Neigh | 0.32948 | 0.32948 | 0.32948 | 0.0 | 11.53
Comm | 0.01182 | 0.01182 | 0.01182 | 0.0 | 0.42 Comm | 0.012038 | 0.012038 | 0.012038 | 0.0 | 0.42
Output | 7e-05 | 7e-05 | 7e-05 | 0.0 | 0.00 Output | 7.4e-05 | 7.4e-05 | 7.4e-05 | 0.0 | 0.00
Modify | 0.024522 | 0.024522 | 0.024522 | 0.0 | 0.86 Modify | 0.023745 | 0.023745 | 0.023745 | 0.0 | 0.83
Other | | 0.01091 | | | 0.38 Other | | 0.01084 | | | 0.38
Nlocal: 32000.0 ave 32000 max 32000 min Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 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 kim interactions Ar
#=== BEGIN kim interactions ================================== #=== BEGIN kim interactions ==================================
pair_style kim LennardJones_Ar 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 '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:1145) WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1159)
pair_coeff * * Ar pair_coeff * * Ar
#=== END kim interactions ==================================== #=== 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 #fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100 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 ... Neighbor list info ...
update every 1 steps, delay 0 steps, check yes update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000 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 Step Temp E_pair E_mol TotEng Press
0 200 145069.63 0 164146.22 128015.94 0 200 145069.63 0 164146.22 128015.94
100 95.179703 154939.42 0 164017.94 131602.75 100 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 Performance: 10.244 ns/day, 2.343 hours/ns, 118.570 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads 99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.73048 | 0.73398 | 0.73855 | 0.3 | 85.58 Pair | 0.71505 | 0.71942 | 0.72345 | 0.4 | 85.30
Neigh | 0.083739 | 0.083964 | 0.084335 | 0.1 | 9.79 Neigh | 0.089886 | 0.090153 | 0.090611 | 0.1 | 10.69
Comm | 0.017996 | 0.022912 | 0.026515 | 2.1 | 2.67 Comm | 0.016342 | 0.020141 | 0.024546 | 2.5 | 2.39
Output | 2.7e-05 | 3.5e-05 | 4.5e-05 | 0.0 | 0.00 Output | 2.4e-05 | 2.625e-05 | 3.2e-05 | 0.0 | 0.00
Modify | 0.010073 | 0.010158 | 0.010271 | 0.1 | 1.18 Modify | 0.008197 | 0.0083267 | 0.008504 | 0.1 | 0.99
Other | | 0.006571 | | | 0.77 Other | | 0.005318 | | | 0.63
Nlocal: 8000.00 ave 8018 max 7967 min Nlocal: 8000.00 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2 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: 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} \documentclass{article}
\usepackage{url} \usepackage{url}
@ -175,9 +190,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 3.119 | 3.119 | 3.119 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.119 | 3.119 | 3.119 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -0.34602203 0 -0.34602203 0.00061471244 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: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total 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 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 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 Nlocal: 4.00000 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0 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 1 by 2 by 2 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4 atoms Created 4 atoms
create_atoms CPU = 0.000 seconds create_atoms CPU = 0.001 seconds
mass 1 39.948 mass 1 39.948
# Specify the KIM interactions # 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: 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} \documentclass{article}
\usepackage{url} \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: 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} \documentclass{article}
\usepackage{url} \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}, title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011}, 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 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ... 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 Step Temp E_pair E_mol TotEng Press
0 200 -126084.25 0 -107007.66 1528.8768 0 200 -126084.25 0 -107007.66 1528.8768
100 94.450495 -116016.03 0 -107007.07 2282.2685 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 99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 18.155 | 18.155 | 18.155 | 0.0 | 99.27 Pair | 18.058 | 18.058 | 18.058 | 0.0 | 99.21
Neigh | 0.087194 | 0.087194 | 0.087194 | 0.0 | 0.48 Neigh | 0.097367 | 0.097367 | 0.097367 | 0.0 | 0.53
Comm | 0.009477 | 0.009477 | 0.009477 | 0.0 | 0.05 Comm | 0.009271 | 0.009271 | 0.009271 | 0.0 | 0.05
Output | 6.7e-05 | 6.7e-05 | 6.7e-05 | 0.0 | 0.00 Output | 6.1e-05 | 6.1e-05 | 6.1e-05 | 0.0 | 0.00
Modify | 0.02616 | 0.02616 | 0.02616 | 0.0 | 0.14 Modify | 0.025469 | 0.025469 | 0.025469 | 0.0 | 0.14
Other | | 0.0111 | | | 0.06 Other | | 0.01084 | | | 0.06
Nlocal: 32000.0 ave 32000 max 32000 min Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 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: 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} \documentclass{article}
\usepackage{url} \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}, title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011}, 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 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ... 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 Step Temp E_pair E_mol TotEng Press
0 200 -126084.25 0 -107007.66 1528.8768 0 200 -126084.25 0 -107007.66 1528.8768
100 94.450495 -116016.03 0 -107007.07 2282.2685 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 Performance: 1.618 ns/day, 14.830 hours/ns, 18.731 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads 99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 4.9281 | 4.9366 | 4.9447 | 0.3 | 98.65 Pair | 5.244 | 5.2604 | 5.2753 | 0.5 | 98.53
Neigh | 0.02399 | 0.024135 | 0.024318 | 0.1 | 0.48 Neigh | 0.027617 | 0.027767 | 0.027955 | 0.1 | 0.52
Comm | 0.020646 | 0.029014 | 0.037515 | 4.3 | 0.58 Comm | 0.017101 | 0.031947 | 0.04856 | 6.3 | 0.60
Output | 2.9e-05 | 3.325e-05 | 4.2e-05 | 0.0 | 0.00 Output | 3.4e-05 | 4.525e-05 | 5.6e-05 | 0.0 | 0.00
Modify | 0.008808 | 0.0088445 | 0.00888 | 0.0 | 0.18 Modify | 0.011577 | 0.01165 | 0.011709 | 0.0 | 0.22
Other | | 0.005691 | | | 0.11 Other | | 0.0069 | | | 0.13
Nlocal: 8000.00 ave 8029 max 7968 min Nlocal: 8000.00 ave 8029 max 7968 min
Histogram: 1 1 0 0 0 0 0 0 0 2 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 1 by 1 by 1 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 32000 atoms Created 32000 atoms
create_atoms CPU = 0.002 seconds create_atoms CPU = 0.003 seconds
kim interactions Si kim interactions Si
#=== BEGIN kim interactions ================================== #=== 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: 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} \documentclass{article}
\usepackage{url} \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 Step Temp E_pair E_mol TotEng Press
0 200 -85249.847 0 -66173.259 -33302.387 0 200 -85249.847 0 -66173.259 -33302.387
100 253.43357 -90346.68 0 -66173.441 -14888.698 100 253.43357 -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 99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 17.64 | 17.64 | 17.64 | 0.0 | 99.41 Pair | 17.553 | 17.553 | 17.553 | 0.0 | 99.37
Neigh | 0.060149 | 0.060149 | 0.060149 | 0.0 | 0.34 Neigh | 0.063346 | 0.063346 | 0.063346 | 0.0 | 0.36
Comm | 0.008585 | 0.008585 | 0.008585 | 0.0 | 0.05 Comm | 0.009667 | 0.009667 | 0.009667 | 0.0 | 0.05
Output | 6.3e-05 | 6.3e-05 | 6.3e-05 | 0.0 | 0.00 Output | 6.6e-05 | 6.6e-05 | 6.6e-05 | 0.0 | 0.00
Modify | 0.025324 | 0.025324 | 0.025324 | 0.0 | 0.14 Modify | 0.02711 | 0.02711 | 0.02711 | 0.0 | 0.15
Other | | 0.01057 | | | 0.06 Other | | 0.01088 | | | 0.06
Nlocal: 32000.0 ave 32000 max 32000 min Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 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: 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} \documentclass{article}
\usepackage{url} \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 Step Temp E_pair E_mol TotEng Press
0 200 -85249.847 0 -66173.259 -33302.387 0 200 -85249.847 0 -66173.259 -33302.387
100 253.43357 -90346.68 0 -66173.441 -14888.698 100 253.43357 -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 Performance: 1.770 ns/day, 13.556 hours/ns, 20.490 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads 99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 4.8075 | 4.816 | 4.8244 | 0.3 | 98.81 Pair | 4.8131 | 4.8235 | 4.8347 | 0.4 | 98.84
Neigh | 0.015902 | 0.015996 | 0.016077 | 0.1 | 0.33 Neigh | 0.017627 | 0.017731 | 0.017825 | 0.1 | 0.36
Comm | 0.018078 | 0.026375 | 0.034752 | 4.2 | 0.54 Comm | 0.013892 | 0.025022 | 0.03536 | 5.0 | 0.51
Output | 3e-05 | 3.5e-05 | 4.4e-05 | 0.0 | 0.00 Output | 3.4e-05 | 4.025e-05 | 4.7e-05 | 0.0 | 0.00
Modify | 0.009331 | 0.0094922 | 0.009588 | 0.1 | 0.19 Modify | 0.008725 | 0.0087775 | 0.008862 | 0.1 | 0.18
Other | | 0.005919 | | | 0.12 Other | | 0.005278 | | | 0.11
Nlocal: 8000.00 ave 8014 max 7988 min Nlocal: 8000.00 ave 8014 max 7988 min
Histogram: 1 1 0 0 0 0 1 0 0 1 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: 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} \documentclass{article}
\usepackage{url} \usepackage{url}
@ -589,7 +604,22 @@ This Model originally published in \cite{MO_123629422045_005a} is archived in Op
volume = {26}, volume = {26},
year = {1994}, 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} \documentclass{article}
\usepackage{url} \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 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 kim interactions O
#=== BEGIN kim interactions ================================== #=== BEGIN kim interactions ==================================
variable kim_periodic equal 1 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_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-pgBW45WFK0TI/ffield.reax.rdx O 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-pgBW45WFK0TI/ffield.reax.rdx with DATE: 2010-02-19 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-pgBW45WFK0TI/param.qeq 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 ==================================== #=== 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: 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} \documentclass{article}
\usepackage{url} \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 Step Temp E_pair E_mol TotEng Press
0 200 -39091.147 0 -20014.559 19501.107 0 200 -39091.147 0 -20014.559 19501.107
100 63.198252 -26042.062 0 -20014.027 21497.661 100 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 99.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 24.364 | 24.364 | 24.364 | 0.0 | 60.52 Pair | 23.493 | 23.493 | 23.493 | 0.0 | 60.78
Neigh | 0.4185 | 0.4185 | 0.4185 | 0.0 | 1.04 Neigh | 0.4498 | 0.4498 | 0.4498 | 0.0 | 1.16
Comm | 0.022045 | 0.022045 | 0.022045 | 0.0 | 0.05 Comm | 0.020568 | 0.020568 | 0.020568 | 0.0 | 0.05
Output | 6.6e-05 | 6.6e-05 | 6.6e-05 | 0.0 | 0.00 Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00
Modify | 15.438 | 15.438 | 15.438 | 0.0 | 38.35 Modify | 14.677 | 14.677 | 14.677 | 0.0 | 37.97
Other | | 0.01285 | | | 0.03 Other | | 0.01223 | | | 0.03
Nlocal: 32000.0 ave 32000 max 32000 min Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -205,4 +220,4 @@ Total # of neighbors = 3739236
Ave neighs/atom = 116.85112 Ave neighs/atom = 116.85112
Neighbor list builds = 3 Neighbor list builds = 3
Dangerous builds = 0 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 kim interactions O
#=== BEGIN kim interactions ================================== #=== BEGIN kim interactions ==================================
variable kim_periodic equal 1 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_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-zYQfH0ms5WSw/ffield.reax.rdx O 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-zYQfH0ms5WSw/ffield.reax.rdx with DATE: 2010-02-19 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-zYQfH0ms5WSw/param.qeq 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 ==================================== #=== 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: 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} \documentclass{article}
\usepackage{url} \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 Step Temp E_pair E_mol TotEng Press
0 200 -39091.147 0 -20014.559 19501.107 0 200 -39091.147 0 -20014.559 19501.107
100 63.198252 -26042.062 0 -20014.027 21497.661 100 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 Performance: 0.610 ns/day, 39.355 hours/ns, 7.058 timesteps/s
99.0% CPU use with 4 MPI tasks x no OpenMP threads 99.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 9.8158 | 9.8159 | 9.8161 | 0.0 | 65.23 Pair | 9.3935 | 9.3935 | 9.3936 | 0.0 | 66.30
Neigh | 0.17685 | 0.17759 | 0.17832 | 0.1 | 1.18 Neigh | 0.15786 | 0.15879 | 0.16003 | 0.2 | 1.12
Comm | 0.028692 | 0.028847 | 0.028942 | 0.1 | 0.19 Comm | 0.025777 | 0.025906 | 0.025992 | 0.1 | 0.18
Output | 2.5e-05 | 3.575e-05 | 4.6e-05 | 0.0 | 0.00 Output | 2.8e-05 | 3.35e-05 | 4.6e-05 | 0.0 | 0.00
Modify | 5.0171 | 5.0179 | 5.0186 | 0.0 | 33.34 Modify | 4.5801 | 4.5814 | 4.5823 | 0.0 | 32.34
Other | | 0.008715 | | | 0.06 Other | | 0.00801 | | | 0.06
Nlocal: 8000.00 ave 8010 max 7993 min Nlocal: 8000.00 ave 8010 max 7993 min
Histogram: 2 0 0 0 0 1 0 0 0 1 Histogram: 2 0 0 0 0 1 0 0 0 1
@ -205,4 +220,4 @@ Total # of neighbors = 4003876
Ave neighs/atom = 125.12113 Ave neighs/atom = 125.12113
Neighbor list builds = 3 Neighbor list builds = 3
Dangerous builds = 0 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 Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 25367.408 6750.7421 0 200 6290.8194 0 25367.408 6750.7421
100 98.747096 15900.676 0 25319.465 10184.453 100 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 Performance: 4.617 ns/day, 5.198 hours/ns, 53.441 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads 99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 1.7377 | 1.7377 | 1.7377 | 0.0 | 90.12 Pair | 1.686 | 1.686 | 1.686 | 0.0 | 90.10
Neigh | 0.14234 | 0.14234 | 0.14234 | 0.0 | 7.38 Neigh | 0.14211 | 0.14211 | 0.14211 | 0.0 | 7.59
Comm | 0.011694 | 0.011694 | 0.011694 | 0.0 | 0.61 Comm | 0.01013 | 0.01013 | 0.01013 | 0.0 | 0.54
Output | 6.7e-05 | 6.7e-05 | 6.7e-05 | 0.0 | 0.00 Output | 6.3e-05 | 6.3e-05 | 6.3e-05 | 0.0 | 0.00
Modify | 0.02476 | 0.02476 | 0.02476 | 0.0 | 1.28 Modify | 0.022686 | 0.022686 | 0.022686 | 0.0 | 1.21
Other | | 0.01163 | | | 0.60 Other | | 0.0102 | | | 0.55
Nlocal: 32000.0 ave 32000 max 32000 min Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 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 Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 25367.408 6750.7421 0 200 6290.8194 0 25367.408 6750.7421
100 98.747096 15900.676 0 25319.465 10184.453 100 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 Performance: 16.238 ns/day, 1.478 hours/ns, 187.941 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads 99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.48486 | 0.48676 | 0.48817 | 0.2 | 86.77 Pair | 0.46077 | 0.46347 | 0.46621 | 0.3 | 87.10
Neigh | 0.040698 | 0.04091 | 0.041066 | 0.1 | 7.29 Neigh | 0.038499 | 0.038599 | 0.038759 | 0.0 | 7.25
Comm | 0.016616 | 0.01811 | 0.0202 | 1.1 | 3.23 Comm | 0.01395 | 0.016623 | 0.019377 | 1.7 | 3.12
Output | 3e-05 | 3.575e-05 | 4.7e-05 | 0.0 | 0.01 Output | 3.1e-05 | 3.675e-05 | 4.7e-05 | 0.0 | 0.01
Modify | 0.008934 | 0.009025 | 0.009142 | 0.1 | 1.61 Modify | 0.00787 | 0.007971 | 0.008083 | 0.1 | 1.50
Other | | 0.006161 | | | 1.10 Other | | 0.005382 | | | 1.01
Nlocal: 8000.00 ave 8012 max 7989 min Nlocal: 8000.00 ave 8012 max 7989 min
Histogram: 1 0 0 0 2 0 0 0 0 1 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), 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 "fix_store_kim.h"
#include <cstring>
#include "error.h"
extern "C" { extern "C" {
#include "KIM_SimulatorModel.h" #include "KIM_SimulatorModel.h"
} }
#include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; 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) { if (simulator_model) {
KIM_SimulatorModel *sm = (KIM_SimulatorModel *)simulator_model; KIM_SimulatorModel *sm = (KIM_SimulatorModel *)simulator_model;
KIM_SimulatorModel_Destroy(&sm); KIM_SimulatorModel_Destroy(&sm);
} }
simulator_model = ptr; simulator_model = ptr;
} else if (strcmp(name,"model_name") == 0) { } else if (name == "model_name") {
if (model_name) { if (model_name) {
char *mn = (char *)model_name; char *mn = (char *)model_name;
delete[] mn; delete[] mn;
} }
model_name = ptr; model_name = ptr;
} else if (strcmp(name,"model_units") == 0) { } else if (name == "model_units") {
if (model_units) { if (model_units) {
char *mu = (char *)model_units; char *mu = (char *)model_units;
delete[] mu; delete[] mu;
} }
model_units = ptr; model_units = ptr;
} else if (strcmp(name,"user_units") == 0) { } else if (name == "user_units") {
if (user_units) { if (user_units) {
char *uu = (char *)user_units; char *uu = (char *)user_units;
delete[] uu; 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; if (name == "simulator_model") return simulator_model;
else if (strcmp(name,"model_name") == 0) return model_name; else if (name == "model_name") return model_name;
else if (strcmp(name,"model_units") == 0) return model_units; else if (name == "model_units") return model_units;
else if (strcmp(name,"user_units") == 0) return user_units; else if (name == "user_units") return user_units;
else return nullptr; else return nullptr;
} }

7
src/KIM/fix_store_kim.h
View File

@ -13,7 +13,8 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U), 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(); ~FixStoreKIM();
int setmask(); int setmask();
void setptr(const char *, void *); void setptr(const std::string &, void *);
void *getptr(const char *); void *getptr(const std::string &);
private: private:
void *simulator_model; // pointer to KIM simulator model class 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 "kim_command.h"
#include "citeme.h"
#include "error.h" #include "error.h"
// include KIM sub-command headers here // include KIM sub-command headers here
@ -65,10 +66,38 @@
#include "kim_property.h" #include "kim_property.h"
#include "kim_query.h" #include "kim_query.h"
#include <memory>
using namespace LAMMPS_NS; 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) void KimCommand::command(int narg, char **arg)
@ -79,20 +108,28 @@ void KimCommand::command(int narg, char **arg)
narg--; narg--;
arg++; arg++;
if (lmp->citeme) lmp->citeme->add(cite_openkim);
if (subcmd == "init") { if (subcmd == "init") {
std::unique_ptr<KimInit> cmd(new KimInit(lmp)); KimInit *cmd = new KimInit(lmp);
cmd->command(narg, arg); cmd->command(narg, arg);
delete cmd;
} else if (subcmd == "interactions") { } else if (subcmd == "interactions") {
std::unique_ptr<KimInteractions> cmd(new KimInteractions(lmp)); KimInteractions *cmd = new KimInteractions(lmp);
cmd->command(narg, arg); cmd->command(narg, arg);
delete cmd;
} else if (subcmd == "param") { } else if (subcmd == "param") {
std::unique_ptr<KimParam> cmd(new KimParam(lmp)); KimParam *cmd = new KimParam(lmp);
cmd->command(narg, arg); cmd->command(narg, arg);
delete cmd;
} else if (subcmd == "property") { } else if (subcmd == "property") {
std::unique_ptr<KimProperty> cmd(new KimProperty(lmp)); KimProperty *cmd = new KimProperty(lmp);
cmd->command(narg, arg); cmd->command(narg, arg);
delete cmd;
} else if (subcmd == "query") { } 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); cmd->command(narg, arg);
delete cmd;
} else error->all(FLERR, fmt::format("Unknown kim subcommand {}", subcmd)); } else error->all(FLERR, fmt::format("Unknown kim subcommand {}", subcmd));
} }

129
src/KIM/kim_init.cpp
View File

@ -86,10 +86,12 @@ void KimInit::command(int narg, char **arg)
if (domain->box_exist) if (domain->box_exist)
error->all(FLERR, "Must use 'kim init' command before " error->all(FLERR, "Must use 'kim init' command before "
"simulation box is defined"); "simulation box is defined");
char *model_name = utils::strdup(arg[0]); char *model_name = utils::strdup(arg[0]);
char *user_units = utils::strdup(arg[1]); char *user_units = utils::strdup(arg[1]);
if (narg == 3) { 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 { else {
error->all(FLERR, fmt::format("Illegal 'kim init' command.\nThe argument " error->all(FLERR, fmt::format("Illegal 'kim init' command.\nThe argument "
"followed by unit_style {} is an optional " "followed by unit_style {} is an optional "
@ -123,41 +125,42 @@ void get_kim_unit_names(
KIM_TimeUnit & timeUnit, KIM_TimeUnit & timeUnit,
Error * error) Error * error)
{ {
if (strcmp(system, "real") == 0) { const std::string system_str(system);
if (system_str == "real") {
lengthUnit = KIM_LENGTH_UNIT_A; lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol; energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if (strcmp(system, "metal") == 0) { } else if (system_str == "metal") {
lengthUnit = KIM_LENGTH_UNIT_A; lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV; energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps; timeUnit = KIM_TIME_UNIT_ps;
} else if (strcmp(system, "si") == 0) { } else if (system_str == "si") {
lengthUnit = KIM_LENGTH_UNIT_m; lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J; energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C; chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s; timeUnit = KIM_TIME_UNIT_s;
} else if (strcmp(system, "cgs") == 0) { } else if (system_str == "cgs") {
lengthUnit = KIM_LENGTH_UNIT_cm; lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg; energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC; chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s; timeUnit = KIM_TIME_UNIT_s;
} else if (strcmp(system, "electron") == 0) { } else if (system_str == "electron") {
lengthUnit = KIM_LENGTH_UNIT_Bohr; lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree; energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if (strcmp(system, "lj") == 0 || } else if ((system_str == "lj") ||
strcmp(system, "micro") ==0 || (system_str == "micro") ||
strcmp(system, "nano")==0) { (system_str == "nano")) {
error->all(FLERR, fmt::format("LAMMPS unit_style {} not supported " error->all(FLERR, fmt::format("LAMMPS unit_style {} not supported "
"by KIM models", system)); "by KIM models", system_str));
} else { } else {
error->all(FLERR, "Unknown unit_style"); 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_fields;
int sim_lines; int sim_lines;
char const * sim_field; char const *sim_field;
char const * sim_value; char const *sim_value;
KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields); KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields);
KIM_SimulatorModel_CloseTemplateMap(simulatorModel); KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
for (int i=0; i < sim_fields; ++i) { for (int i = 0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata( KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel, i, &sim_lines, &sim_field); 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( KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel, i, 0, &sim_value); simulatorModel, i, 0, &sim_value);
*model_units = utils::strdup(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); 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" 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 ===================================" input->write_echo("#=== BEGIN kim init ==================================="
"=======\n"); "=======\n");
KIM_SimulatorModel * simulatorModel; KIM_SimulatorModel *simulatorModel;
if (model_type == SM) { if (model_type == SM) {
int kim_error = int kim_error = KIM_SimulatorModel_Create(model_name, &simulatorModel);
KIM_SimulatorModel_Create(model_name, &simulatorModel); if (kim_error) error->all(FLERR, "Unable to load KIM Simulator Model");
if (kim_error)
error->all(FLERR, "Unable to load KIM Simulator Model");
auto logID = fmt::format("{}_SimulatorModel", comm->me); auto logID = fmt::format("{}_SimulatorModel", comm->me);
KIM_SimulatorModel_SetLogID(simulatorModel, logID.c_str()); 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( KIM_SimulatorModel_GetSimulatorNameAndVersion(
simulatorModel, &sim_name, &sim_version); 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"); error->all(FLERR, "Incompatible KIM Simulator Model");
if (comm->me == 0) { if (comm->me == 0) {
std::string mesg("# Using KIM Simulator Model : "); auto mesg = fmt::format("# Using KIM Simulator Model : {}\n"
mesg += model_name; "# For Simulator : {} {}\n"
mesg += "\n"; "# Running on : LAMMPS {}\n#\n", model_name,
mesg += "# For Simulator : "; sim_name_str, sim_version, lmp->version);
mesg += std::string(sim_name) + " " + sim_version + "\n";
mesg += "# Running on : LAMMPS ";
mesg += lmp->version;
mesg += "\n";
mesg += "#\n";
utils::logmesg(lmp, mesg); utils::logmesg(lmp, mesg);
} }
@ -343,24 +342,24 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units,
// set units // set units
std::string cmd("units "); const std::string model_units_str(model_units);
cmd += model_units; auto cmd = fmt::format("units {}", model_units_str);
input->one(cmd); input->one(cmd);
// Set the skin and timestep default values as // Set the skin and timestep default values as
// 2.0 Angstroms and 1.0 femtosecond // 2.0 Angstroms and 1.0 femtosecond
std::string skin_cmd = const std::string skin_cmd =
(strcmp(model_units, "real") == 0) ? "neighbor 2.0 bin # Angstroms": (model_units_str == "real") ? "neighbor 2.0 bin # Angstroms":
(strcmp(model_units, "metal") == 0) ? "neighbor 2.0 bin # Angstroms": (model_units_str == "metal") ? "neighbor 2.0 bin # Angstroms":
(strcmp(model_units, "si") == 0) ? "neighbor 2e-10 bin # meters": (model_units_str == "si") ? "neighbor 2e-10 bin # meters":
(strcmp(model_units, "cgs") == 0) ? "neighbor 2e-8 bin # centimeters": (model_units_str == "cgs") ? "neighbor 2e-8 bin # centimeters":
"neighbor 3.77945224 bin # Bohr"; "neighbor 3.77945224 bin # Bohr";
std::string step_cmd = const std::string step_cmd =
(strcmp(model_units, "real") == 0) ? "timestep 1.0 # femtoseconds": (model_units_str == "real") ? "timestep 1.0 # femtoseconds":
(strcmp(model_units, "metal") == 0) ? "timestep 1.0e-3 # picoseconds": (model_units_str == "metal") ? "timestep 1.0e-3 # picoseconds":
(strcmp(model_units, "si") == 0) ? "timestep 1e-15 # seconds": (model_units_str == "si") ? "timestep 1e-15 # seconds":
(strcmp(model_units, "cgs") == 0) ? "timestep 1e-15 # seconds": (model_units_str == "cgs") ? "timestep 1e-15 # seconds":
"timestep 1.0 # femtoseconds"; "timestep 1.0 # femtoseconds";
input->one(skin_cmd); input->one(skin_cmd);
input->one(step_cmd); input->one(step_cmd);
@ -372,13 +371,15 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units,
// init model // init model
for (int i=0; i < sim_fields; ++i) { for (int i = 0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata( KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel, i, &sim_lines, &sim_field); 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( KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel, i, j, &sim_value); simulatorModel, i, j, &sim_value);
input->one(sim_value); input->one(sim_value);
} }
break; break;
@ -489,7 +490,15 @@ void KimInit::do_variables(const std::string &from, const std::string &to)
void KimInit::write_log_cite(char *model_name) 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); int err = KIM_Collections_Create(&collections);
if (err) return; if (err) return;
@ -514,19 +523,23 @@ void KimInit::write_log_cite(char *model_name)
return; 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) { for (int i = 0; i < extent; ++i) {
char const * fileName; char const *fileName;
int availableAsString; int availableAsString;
char const * fileString; char const *fileString;
err = KIM_Collections_GetItemMetadataFile( err = KIM_Collections_GetItemMetadataFile(
collections, i, &fileName, nullptr, nullptr, collections, i, &fileName, nullptr, nullptr,
&availableAsString, &fileString); &availableAsString, &fileString);
if (err) continue; if (err) continue;
if (0 == strncmp("kimcite", fileName, 7)) { if (utils::strmatch(fileName, "^kimcite") && availableAsString)
if ((lmp->citeme) && (availableAsString)) lmp->citeme->add(fileString); cite_id += fileString;
}
} }
lmp->citeme->add(cite_id);
KIM_Collections_Destroy(&collections); 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) void KimInteractions::do_setup(int narg, char **arg)
{ {
bool fixed_types; 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; fixed_types = true;
} else if (narg != atom->ntypes) { } else if (narg != atom->ntypes) {
error->all(FLERR, fmt::format("Illegal 'kim interactions' command.\nThe " 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( KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel, i, &sim_lines, &sim_field); 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( KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel, i, 0, &sim_value); 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) { for (int i = 0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata( KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel, i, &sim_lines, &sim_field); simulatorModel, i, &sim_lines, &sim_field);
if (strcmp(sim_field, "model-defn") == 0) {
if (domain->periodicity[0]&& const std::string sim_field_str(sim_field);
domain->periodicity[1]&& if (sim_field_str == "model-defn") {
if (domain->periodicity[0] &&
domain->periodicity[1] &&
domain->periodicity[2]) domain->periodicity[2])
input->one("variable kim_periodic equal 1"); input->one("variable kim_periodic equal 1");
else if (domain->periodicity[0]&& else if (domain->periodicity[0] &&
domain->periodicity[1]&& domain->periodicity[1] &&
!domain->periodicity[2]) !domain->periodicity[2])
input->one("variable kim_periodic equal 2"); input->one("variable kim_periodic equal 2");
else input->one("variable kim_periodic equal 0"); 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, KIM_TimeUnit &timeUnit,
Error *error) Error *error)
{ {
if ((strcmp(system, "real") == 0)) { const std::string system_str(system);
if (system_str == "real") {
lengthUnit = KIM_LENGTH_UNIT_A; lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol; energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if ((strcmp(system, "metal") == 0)) { } else if (system_str == "metal") {
lengthUnit = KIM_LENGTH_UNIT_A; lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV; energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps; timeUnit = KIM_TIME_UNIT_ps;
} else if ((strcmp(system, "si") == 0)) { } else if (system_str == "si") {
lengthUnit = KIM_LENGTH_UNIT_m; lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J; energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C; chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s; timeUnit = KIM_TIME_UNIT_s;
} else if ((strcmp(system, "cgs") == 0)) { } else if (system_str == "cgs") {
lengthUnit = KIM_LENGTH_UNIT_cm; lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg; energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC; chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s; timeUnit = KIM_TIME_UNIT_s;
} else if ((strcmp(system, "electron") == 0)) { } else if (system_str == "electron") {
lengthUnit = KIM_LENGTH_UNIT_Bohr; lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree; energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if (strcmp(system, "lj") == 0 || } else if ((system_str == "lj") ||
strcmp(system, "micro") ==0 || (system_str == "micro") ||
strcmp(system, "nano")==0) { (system_str == "nano")) {
error->all(FLERR, fmt::format("LAMMPS unit_style {} not supported " error->all(FLERR, fmt::format("LAMMPS unit_style {} not supported "
"by KIM models", system)); "by KIM models", system_str));
} else } else {
error->all(FLERR, "Unknown unit_style"); error->all(FLERR, "Unknown unit_style");
}
} }
} // namespace } // namespace
@ -213,7 +215,7 @@ void KimParam::command(int narg, char **arg)
if (kim_param_get_set == "get") { if (kim_param_get_set == "get") {
int kim_error; int kim_error;
// Parameter name // Parameter name
char *paramname = nullptr; std::string paramname;
// Variable name // Variable name
std::string varname; std::string varname;
@ -221,7 +223,7 @@ void KimParam::command(int narg, char **arg)
for (int i = 1; i < narg;) { for (int i = 1; i < narg;) {
// Parameter name // Parameter name
if (i < narg) if (i < narg)
paramname = arg[i++]; paramname = std::string(arg[i++]);
else else
break; break;
@ -239,7 +241,8 @@ void KimParam::command(int narg, char **arg)
if (kim_error) if (kim_error)
error->all(FLERR, "KIM GetParameterMetadata returned 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) { if (param_index >= numberOfParameters) {
@ -302,8 +305,10 @@ void KimParam::command(int narg, char **arg)
if (i < narg) { if (i < narg) {
// Get the variable/variable_base name // Get the variable/variable_base name
varname = arg[i++]; varname = std::string(arg[i++]);
if (varname == "split" || varname == "list" || varname == "explicit") if ((varname == "split") ||
(varname == "list") ||
(varname == "explicit"))
error->all(FLERR, "Illegal variable name in 'kim param get'"); error->all(FLERR, "Illegal variable name in 'kim param get'");
} else { } else {
std::string msg("Wrong number of arguments in 'kim param get' "); 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 (nvars > 1) {
if (i < narg) { if (i < narg) {
if (strcmp(arg[i], "split") == 0) { std::string formatarg(arg[i]);
if (formatarg == "split") {
varsname.resize(nvars); varsname.resize(nvars);
for (int j = 0, k = nlbound; j < nvars; ++j, ++k) { for (int j = 0, k = nlbound; j < nvars; ++j, ++k) {
varsname[j] = fmt::format("{}_{}", varname, k); varsname[j] = fmt::format("{}_{}", varname, k);
} }
++i; ++i;
} else if (strcmp(arg[i], "list") == 0) { } else if (formatarg == "list") {
list_requested = true; list_requested = true;
varsname.resize(1); varsname.resize(1);
varsname[0] = varname; varsname[0] = varname;
@ -332,13 +338,14 @@ void KimParam::command(int narg, char **arg)
varsname.resize(nvars); varsname.resize(nvars);
--i; --i;
for (int j = 0; j < nvars; ++j, ++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" || if (varsname[j] == "split" || varsname[j] == "list" ||
varsname[j] == "explicit") varsname[j] == "explicit")
error->all(FLERR, "Illegal variable name in 'kim param get'"); error->all(FLERR, "Illegal variable name in 'kim param get'");
} }
if (i < narg) { if (i < narg) {
if (strcmp(arg[i], "explicit") == 0) ++i; formatarg = std::string(arg[i]);
if (formatarg == "explicit") ++i;
} }
} else { } else {
auto msg = auto msg =
@ -357,13 +364,12 @@ void KimParam::command(int narg, char **arg)
} else { } else {
varsname.resize(1); varsname.resize(1);
if (i < narg) { if (i < narg) {
if (strcmp(arg[i], "split") == 0) { const std::string formatarg(arg[i]);
if (formatarg == "split") {
varsname[0] = fmt::format("{}_{}", varname, nlbound); varsname[0] = fmt::format("{}_{}", varname, nlbound);
++i; ++i;
} else { } else {
if ((strcmp(arg[i], "list") == 0) || if (formatarg == "list" || formatarg == "explicit") ++i;
(strcmp(arg[i], "explicit") == 0)) ++i;
varsname[0] = varname; varsname[0] = varname;
} }
} else { } else {

19
src/KIM/kim_property.cpp
View File

@ -85,11 +85,10 @@ void KimProperty::command(int narg, char **arg)
#if LMP_PYTHON #if LMP_PYTHON
#if PY_MAJOR_VERSION >= 3 #if PY_MAJOR_VERSION >= 3
if (narg < 2) error->all(FLERR, "Invalid 'kim property' command"); if (narg < 2) error->all(FLERR, "Invalid 'kim property' command");
if (!(strcmp(arg[0], "create") == 0) &&
!(strcmp(arg[0], "destroy") == 0) && const std::string subcmd(arg[0]);
!(strcmp(arg[0], "modify") == 0) && if ((subcmd != "create") && (subcmd != "destroy") && (subcmd != "modify") &&
!(strcmp(arg[0], "remove") == 0) && (subcmd != "remove") && (subcmd != "dump")) {
!(strcmp(arg[0], "dump") == 0)) {
std::string msg("Incorrect arguments in 'kim property' command.\n"); std::string msg("Incorrect arguments in 'kim property' command.\n");
msg += "'kim property create/destroy/modify/remove/dump' is mandatory"; msg += "'kim property create/destroy/modify/remove/dump' is mandatory";
error->all(FLERR, msg); error->all(FLERR, msg);
@ -130,7 +129,7 @@ void KimProperty::command(int narg, char **arg)
} }
// kim_property create 1 cohesive-potential-energy-cubic-crystal // kim_property create 1 cohesive-potential-energy-cubic-crystal
if (strcmp(arg[0], "create") == 0) { if (subcmd == "create") {
if (narg != 3) { if (narg != 3) {
PyGILState_Release(gstate); PyGILState_Release(gstate);
error->all(FLERR, "Invalid 'kim property create' command"); error->all(FLERR, "Invalid 'kim property create' command");
@ -196,7 +195,7 @@ void KimProperty::command(int narg, char **arg)
Py_XDECREF(pArgs); Py_XDECREF(pArgs);
Py_XDECREF(pFunc); Py_XDECREF(pFunc);
Py_XDECREF(pValue); Py_XDECREF(pValue);
} else if (strcmp(arg[0], "destroy") == 0) { } else if (subcmd == "destroy") {
if (narg != 2) { if (narg != 2) {
PyGILState_Release(gstate); PyGILState_Release(gstate);
error->all(FLERR, "Invalid 'kim property destroy' command"); error->all(FLERR, "Invalid 'kim property destroy' command");
@ -256,7 +255,7 @@ void KimProperty::command(int narg, char **arg)
Py_XDECREF(pArgs); Py_XDECREF(pArgs);
Py_XDECREF(pFunc); Py_XDECREF(pFunc);
Py_XDECREF(pValue); Py_XDECREF(pValue);
} else if (strcmp(arg[0], "modify") == 0) { } else if (subcmd == "modify") {
if (narg < 6) { if (narg < 6) {
PyGILState_Release(gstate); PyGILState_Release(gstate);
error->all(FLERR, "Invalid 'kim property modify' command"); error->all(FLERR, "Invalid 'kim property modify' command");
@ -321,7 +320,7 @@ void KimProperty::command(int narg, char **arg)
Py_XDECREF(pArgs); Py_XDECREF(pArgs);
Py_XDECREF(pFunc); Py_XDECREF(pFunc);
Py_XDECREF(pValue); Py_XDECREF(pValue);
} else if (strcmp(arg[0], "remove") == 0) { } else if (subcmd == "remove") {
if (narg < 4) { if (narg < 4) {
PyGILState_Release(gstate); PyGILState_Release(gstate);
error->all(FLERR, "Invalid 'kim property remove' command"); error->all(FLERR, "Invalid 'kim property remove' command");
@ -386,7 +385,7 @@ void KimProperty::command(int narg, char **arg)
Py_XDECREF(pArgs); Py_XDECREF(pArgs);
Py_XDECREF(pFunc); Py_XDECREF(pFunc);
Py_XDECREF(pValue); Py_XDECREF(pValue);
} else if (strcmp(arg[0], "dump") == 0) { } else if (subcmd == "dump") {
if (narg != 2) { if (narg != 2) {
PyGILState_Release(gstate); PyGILState_Release(gstate);
error->all(FLERR, "Invalid 'kim property dump' command"); 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) // check the query_args format (a series of keyword=value pairs)
for (int i = 2; i < narg; ++i) { 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 " auto msg = fmt::format("Illegal query format.\nInput argument "
"of `{}` to 'kim query' is wrong. The query format is the " "of `{}` to 'kim query' is wrong. The query format is the "
"keyword=[value], where value is always an array of one or " "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") { if (query_function != "get_available_models") {
for (int i = 2; i < narg; ++i) { for (int i = 2; i < narg; ++i) {
// check if the model is specified as an argument // 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], "=[]"); ValueTokenizer values(arg[i], "=[]");
std::string key = values.next_string(); std::string key = values.next_string();
model_name = 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 "pair_kim.h"
#include "atom.h" #include "atom.h"
#include "citeme.h"
#include "comm.h" #include "comm.h"
#include "domain.h" #include "domain.h"
#include "error.h" #include "error.h"
@ -73,6 +74,21 @@
using namespace LAMMPS_NS; 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) : PairKIM::PairKIM(LAMMPS *lmp) :
@ -120,6 +136,8 @@ PairKIM::PairKIM(LAMMPS *lmp) :
// (used by kim_free(), etc.) // (used by kim_free(), etc.)
kim_init_ok = false; kim_init_ok = false;
kim_particle_codes_ok = false; kim_particle_codes_ok = false;
if (lmp->citeme) lmp->citeme->add(cite_openkim);
// END // END
} }
@ -291,10 +309,11 @@ void PairKIM::settings(int narg, char **arg)
init_style_call_count = 0; init_style_call_count = 0;
if (narg != 1) { if (narg != 1) {
if ((narg > 0) && ((0 == strcmp("KIMvirial", arg[0])) || const std::string arg_str(arg[0]);
(0 == strcmp("LAMMPSvirial", arg[0])))) { if ((narg > 0) &&
error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not " ((arg_str == "KIMvirial") || (arg_str == "LAMMPSvirial"))) {
"supported with kim-api"); error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not supported "
"with kim-api");
} else error->all(FLERR,"Illegal pair_style command"); } else error->all(FLERR,"Illegal pair_style command");
} }
// arg[0] is the KIM Model name // arg[0] is the KIM Model name
@ -337,14 +356,16 @@ void PairKIM::coeff(int narg, char **arg)
// insure I,J args are * * // 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 " error->all(FLERR,"Incorrect args for pair coefficients.\nThe first two "
"arguments of pair_coeff command must be * * to span " "arguments of pair_coeff command must be * * to span "
"all LAMMPS atom types"); "all LAMMPS atom types");
int ilo,ihi,jlo,jhi; int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); utils::bounds(FLERR,arg_0_str,1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); utils::bounds(FLERR,arg_1_str,1,atom->ntypes,jlo,jhi,error);
// read args that map atom species to KIM elements // read args that map atom species to KIM elements
// lmps_map_species_to_unique[i] = // lmps_map_species_to_unique[i] =
@ -426,12 +447,12 @@ void PairKIM::coeff(int narg, char **arg)
int kimerror; int kimerror;
// Parameter name // Parameter name
char *paramname = nullptr; std::string paramname;
for (int i = 2 + atom->ntypes; i < narg;) { for (int i = 2 + atom->ntypes; i < narg;) {
// Parameter name // Parameter name
if (i < narg) if (i < narg)
paramname = arg[i++]; paramname = std::string(arg[i++]);
else else
break; break;
@ -448,7 +469,8 @@ void PairKIM::coeff(int narg, char **arg)
if (kimerror) if (kimerror)
error->all(FLERR,"KIM GetParameterMetadata returned 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) { if (param_index >= numberOfParameters) {
@ -994,47 +1016,49 @@ void PairKIM::set_lmps_flags()
if (force->pair_match("hybrid",0)) if (force->pair_match("hybrid",0))
error->all(FLERR,"pair_kim does not support hybrid"); 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 // determine unit system and set lmps_units flag
if (strcmp(update->unit_style,"real") == 0) { if (unit_style_str == "real") {
lmps_units = REAL; lmps_units = REAL;
lengthUnit = KIM_LENGTH_UNIT_A; lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol; energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if (strcmp(update->unit_style,"metal") == 0) { } else if (unit_style_str == "metal") {
lmps_units = METAL; lmps_units = METAL;
lengthUnit = KIM_LENGTH_UNIT_A; lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV; energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps; timeUnit = KIM_TIME_UNIT_ps;
} else if (strcmp(update->unit_style,"si") == 0) { } else if (unit_style_str == "si") {
lmps_units = SI; lmps_units = SI;
lengthUnit = KIM_LENGTH_UNIT_m; lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J; energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C; chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s; timeUnit = KIM_TIME_UNIT_s;
} else if (strcmp(update->unit_style,"cgs") == 0) { } else if (unit_style_str == "cgs") {
lmps_units = CGS; lmps_units = CGS;
lengthUnit = KIM_LENGTH_UNIT_cm; lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg; energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC; chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s; timeUnit = KIM_TIME_UNIT_s;
} else if (strcmp(update->unit_style,"electron") == 0) { } else if (unit_style_str == "electron") {
lmps_units = ELECTRON; lmps_units = ELECTRON;
lengthUnit = KIM_LENGTH_UNIT_Bohr; lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree; energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if (strcmp(update->unit_style,"lj") == 0 || } else if ((unit_style_str == "lj") ||
strcmp(update->unit_style,"micro") == 0 || (unit_style_str == "micro") ||
strcmp(update->unit_style,"nano") == 0) { (unit_style_str == "nano")) {
error->all(FLERR,fmt::format("LAMMPS unit_style {} not supported " error->all(FLERR,fmt::format("LAMMPS unit_style {} not supported "
"by KIM models", update->unit_style)); "by KIM models", unit_style_str));
} else { } else {
error->all(FLERR,"Unknown unit_style"); 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.*", "one or more comma-separated items.*",
lmp->input->one(squery);); 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\"] " squery = "kim query a0 get_lattice_constant_cubic crystal=[\"fcc\"] "
"species=[\"Al\"]"; "species=[\"Al\"]";
TEST_FAILURE(".*ERROR: Illegal query format.\nMust use 'kim init' before " TEST_FAILURE(".*ERROR: Illegal query format.\nMust use 'kim init' before "