mirror of https://github.com/lammps/lammps.git
update kim examples log files
This commit is contained in:
Yaser Afshar
parent
7d49773294
commit
c16064d493
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@ -44,8 +44,8 @@ Created 32000 atoms
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kim interactions Ar
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#=== BEGIN kim interactions ==================================
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pair_style kim LennardJones_Ar
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WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1139)
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WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1145)
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WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1153)
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WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1159)
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pair_coeff * * Ar
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#=== END kim interactions ====================================
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@ -60,6 +60,26 @@ fix 1 all nve
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#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
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run 100
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
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@Article{tadmor:elliott:2011,
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author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
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title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
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journal = {{JOM}},
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year = 2011,
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volume = 63,
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number = 17,
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pages = {17},
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doi = {10.1007/s11837-011-0102-6}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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@ -76,20 +96,20 @@ Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 200 145069.63 0 164146.22 128015.94
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100 95.179703 154939.42 0 164017.94 131602.75
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Loop time of 2.8463 on 1 procs for 100 steps with 32000 atoms
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Loop time of 2.85673 on 1 procs for 100 steps with 32000 atoms
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Performance: 3.036 ns/day, 7.906 hours/ns, 35.133 timesteps/s
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Performance: 3.024 ns/day, 7.935 hours/ns, 35.005 timesteps/s
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.5046 | 2.5046 | 2.5046 | 0.0 | 88.00
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Neigh | 0.29437 | 0.29437 | 0.29437 | 0.0 | 10.34
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Comm | 0.01182 | 0.01182 | 0.01182 | 0.0 | 0.42
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Output | 7e-05 | 7e-05 | 7e-05 | 0.0 | 0.00
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Modify | 0.024522 | 0.024522 | 0.024522 | 0.0 | 0.86
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Other | | 0.01091 | | | 0.38
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Pair | 2.4805 | 2.4805 | 2.4805 | 0.0 | 86.83
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Neigh | 0.32948 | 0.32948 | 0.32948 | 0.0 | 11.53
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Comm | 0.012038 | 0.012038 | 0.012038 | 0.0 | 0.42
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Output | 7.4e-05 | 7.4e-05 | 7.4e-05 | 0.0 | 0.00
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Modify | 0.023745 | 0.023745 | 0.023745 | 0.0 | 0.83
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Other | | 0.01084 | | | 0.38
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Nlocal: 32000.0 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -44,8 +44,8 @@ Created 32000 atoms
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kim interactions Ar
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#=== BEGIN kim interactions ==================================
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pair_style kim LennardJones_Ar
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WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1139)
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WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1145)
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WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1153)
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WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1159)
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pair_coeff * * Ar
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#=== END kim interactions ====================================
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@ -60,6 +60,26 @@ fix 1 all nve
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#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
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run 100
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
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@Article{tadmor:elliott:2011,
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author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
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title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
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journal = {{JOM}},
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year = 2011,
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volume = 63,
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number = 17,
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pages = {17},
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doi = {10.1007/s11837-011-0102-6}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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@ -76,20 +96,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.791 | 9.791 | 9.791 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 200 145069.63 0 164146.22 128015.94
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100 95.179703 154939.42 0 164017.94 131602.75
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Loop time of 0.857614 on 4 procs for 100 steps with 32000 atoms
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Loop time of 0.843382 on 4 procs for 100 steps with 32000 atoms
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Performance: 10.074 ns/day, 2.382 hours/ns, 116.603 timesteps/s
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99.6% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 10.244 ns/day, 2.343 hours/ns, 118.570 timesteps/s
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99.8% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.73048 | 0.73398 | 0.73855 | 0.3 | 85.58
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Neigh | 0.083739 | 0.083964 | 0.084335 | 0.1 | 9.79
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Comm | 0.017996 | 0.022912 | 0.026515 | 2.1 | 2.67
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Output | 2.7e-05 | 3.5e-05 | 4.5e-05 | 0.0 | 0.00
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Modify | 0.010073 | 0.010158 | 0.010271 | 0.1 | 1.18
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Other | | 0.006571 | | | 0.77
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Pair | 0.71505 | 0.71942 | 0.72345 | 0.4 | 85.30
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Neigh | 0.089886 | 0.090153 | 0.090611 | 0.1 | 10.69
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Comm | 0.016342 | 0.020141 | 0.024546 | 2.5 | 2.39
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Output | 2.4e-05 | 2.625e-05 | 3.2e-05 | 0.0 | 0.00
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Modify | 0.008197 | 0.0083267 | 0.008504 | 0.1 | 0.99
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Other | | 0.005318 | | | 0.63
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Nlocal: 8000.00 ave 8018 max 7967 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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@ -96,7 +96,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- @Comment
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- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
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@Article{tadmor:elliott:2011,
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author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
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title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
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journal = {{JOM}},
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year = 2011,
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volume = 63,
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number = 17,
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pages = {17},
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doi = {10.1007/s11837-011-0102-6}
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}
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- OpenKIM potential: https://openkim.org/cite/MO_126566794224_004#item-citation
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@Comment
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{
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\documentclass{article}
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\usepackage{url}
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@ -175,9 +190,9 @@ Neighbor list info ...
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Per MPI rank memory allocation (min/avg/max) = 3.119 | 3.119 | 3.119 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -0.34602203 0 -0.34602203 0.00061471244
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Loop time of 0 on 1 procs for 0 steps with 4 atoms
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Loop time of 3e-05 on 1 procs for 0 steps with 4 atoms
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0.0% CPU use with 1 MPI tasks x no OpenMP threads
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3.3% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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@ -187,7 +202,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0 | | | 0.00
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Other | | 3e-05 | | |100.00
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Nlocal: 4.00000 ave 4 max 4 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -78,7 +78,7 @@ Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.2485091 5.2485091
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 4 atoms
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create_atoms CPU = 0.000 seconds
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create_atoms CPU = 0.001 seconds
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mass 1 39.948
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# Specify the KIM interactions
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@ -96,7 +96,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- @Comment
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- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
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@Article{tadmor:elliott:2011,
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author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
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title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
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journal = {{JOM}},
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year = 2011,
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volume = 63,
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number = 17,
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pages = {17},
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doi = {10.1007/s11837-011-0102-6}
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}
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- OpenKIM potential: https://openkim.org/cite/MO_126566794224_004#item-citation
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@Comment
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{
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\documentclass{article}
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\usepackage{url}
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@ -90,7 +90,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- @Comment
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- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
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@Article{tadmor:elliott:2011,
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author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
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title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
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journal = {{JOM}},
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year = 2011,
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volume = 63,
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number = 17,
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pages = {17},
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doi = {10.1007/s11837-011-0102-6}
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}
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- OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation
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@Comment
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{
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\documentclass{article}
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\usepackage{url}
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@ -161,6 +176,19 @@ This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_0
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title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
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year = {2011},
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}
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- OpenKIM query: https://doi.org/10.1063/5.0014267
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@Article{karls:bierbaum:2020,
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author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott and J. P. Sethna and E. B. Tadmor},
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title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic material property computation engine},
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journal = {{T}he {J}ournal of {C}hemical {P}hysics},
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year = 2020,
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volume = 153,
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number = 6,
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pages = {064104},
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doi = {10.1063/5.0014267}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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@ -179,20 +207,20 @@ Per MPI rank memory allocation (min/avg/max) = 10.36 | 10.36 | 10.36 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 200 -126084.25 0 -107007.66 1528.8768
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100 94.450495 -116016.03 0 -107007.07 2282.2685
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Loop time of 18.2886 on 1 procs for 100 steps with 32000 atoms
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Loop time of 18.2008 on 1 procs for 100 steps with 32000 atoms
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Performance: 0.472 ns/day, 50.802 hours/ns, 5.468 timesteps/s
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Performance: 0.475 ns/day, 50.558 hours/ns, 5.494 timesteps/s
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 18.155 | 18.155 | 18.155 | 0.0 | 99.27
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Neigh | 0.087194 | 0.087194 | 0.087194 | 0.0 | 0.48
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Comm | 0.009477 | 0.009477 | 0.009477 | 0.0 | 0.05
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Output | 6.7e-05 | 6.7e-05 | 6.7e-05 | 0.0 | 0.00
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Modify | 0.02616 | 0.02616 | 0.02616 | 0.0 | 0.14
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Other | | 0.0111 | | | 0.06
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Pair | 18.058 | 18.058 | 18.058 | 0.0 | 99.21
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Neigh | 0.097367 | 0.097367 | 0.097367 | 0.0 | 0.53
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Comm | 0.009271 | 0.009271 | 0.009271 | 0.0 | 0.05
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Output | 6.1e-05 | 6.1e-05 | 6.1e-05 | 0.0 | 0.00
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Modify | 0.025469 | 0.025469 | 0.025469 | 0.0 | 0.14
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Other | | 0.01084 | | | 0.06
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Nlocal: 32000.0 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -90,7 +90,22 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- @Comment
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- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
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@Article{tadmor:elliott:2011,
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author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
|
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title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
|
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journal = {{JOM}},
|
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year = 2011,
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volume = 63,
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number = 17,
|
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pages = {17},
|
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doi = {10.1007/s11837-011-0102-6}
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}
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- OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation
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@Comment
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{
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\documentclass{article}
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\usepackage{url}
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@ -161,6 +176,19 @@ This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_0
|
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title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
|
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year = {2011},
|
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}
|
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- OpenKIM query: https://doi.org/10.1063/5.0014267
|
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|
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@Article{karls:bierbaum:2020,
|
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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},
|
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year = 2020,
|
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volume = 153,
|
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number = 6,
|
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pages = {064104},
|
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doi = {10.1063/5.0014267}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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@ -179,20 +207,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.489 | 3.489 | 3.489 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 200 -126084.25 0 -107007.66 1528.8768
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100 94.450495 -116016.03 0 -107007.07 2282.2685
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Loop time of 5.00432 on 4 procs for 100 steps with 32000 atoms
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Loop time of 5.33871 on 4 procs for 100 steps with 32000 atoms
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Performance: 1.727 ns/day, 13.901 hours/ns, 19.983 timesteps/s
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99.7% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 1.618 ns/day, 14.830 hours/ns, 18.731 timesteps/s
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99.6% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 4.9281 | 4.9366 | 4.9447 | 0.3 | 98.65
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Neigh | 0.02399 | 0.024135 | 0.024318 | 0.1 | 0.48
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Comm | 0.020646 | 0.029014 | 0.037515 | 4.3 | 0.58
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Output | 2.9e-05 | 3.325e-05 | 4.2e-05 | 0.0 | 0.00
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Modify | 0.008808 | 0.0088445 | 0.00888 | 0.0 | 0.18
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Other | | 0.005691 | | | 0.11
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Pair | 5.244 | 5.2604 | 5.2753 | 0.5 | 98.53
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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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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}
|
||||
|
|
@ -589,67 +604,19 @@ This Model originally published in \cite{MO_123629422045_005a} is archived in Op
|
|||
volume = {26},
|
||||
year = {1994},
|
||||
}
|
||||
- @Comment
|
||||
{
|
||||
\documentclass{article}
|
||||
\usepackage{url}
|
||||
\begin{document}
|
||||
This Model originally published in \cite{MO_004835508849_000a} is archived in OpenKIM~\cite{MO_004835508849_000, MD_120291908751_005, tadmor:elliott:2011, elliott:tadmor:2011}.
|
||||
\bibliographystyle{vancouver}
|
||||
\bibliography{kimcite-MO_004835508849_000.bib}
|
||||
\end{document}
|
||||
- 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}
|
||||
}
|
||||
|
||||
@Misc{MO_004835508849_000,
|
||||
author = {Ellad Tadmor},
|
||||
title = {{F}innis-{S}inclair potential ({LAMMPS} cubic hermite tabulation) for {Z}r developed by {M}endelev and {A}ckland (2007); version 3 refitted for radiation studies v000},
|
||||
doi = {10.25950/7b7b5ab5},
|
||||
howpublished = {OpenKIM, \url{https://doi.org/10.25950/7b7b5ab5}},
|
||||
keywords = {OpenKIM, Model, MO_004835508849_000},
|
||||
publisher = {OpenKIM},
|
||||
year = 2018,
|
||||
}
|
||||
|
||||
@Misc{MD_120291908751_005,
|
||||
author = {Ryan S. Elliott},
|
||||
title = {{EAM} {M}odel {D}river for tabulated potentials with cubic {H}ermite spline interpolation as used in {LAMMPS} v005},
|
||||
doi = {10.25950/68defa36},
|
||||
howpublished = {OpenKIM, \url{https://doi.org/10.25950/7b7b5ab5}},
|
||||
keywords = {OpenKIM, Model Driver, MD_120291908751_005},
|
||||
publisher = {OpenKIM},
|
||||
year = 2018,
|
||||
}
|
||||
|
||||
@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 = {7},
|
||||
pages = {17},
|
||||
doi = {10.1007/s11837-011-0102-6},
|
||||
}
|
||||
|
||||
@Misc{elliott:tadmor:2011,
|
||||
author = {Ryan S. Elliott and Ellad B. Tadmor},
|
||||
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
|
||||
howpublished = {\url{https://openkim.org/kim-api}},
|
||||
publisher = {OpenKIM},
|
||||
year = 2011,
|
||||
doi = {10.25950/ff8f563a},
|
||||
}
|
||||
|
||||
@Article{MO_004835508849_000a,
|
||||
author = {Mendelev, M. I. and Ackland, G. J.},
|
||||
doi = {10.1080/09500830701191393},
|
||||
journal = {Philosophical Magazine Letters},
|
||||
number = {5},
|
||||
pages = {349-359},
|
||||
title = {Development of an interatomic potential for the simulation of phase transformations in zirconium},
|
||||
volume = {87},
|
||||
year = {2007},
|
||||
}
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Total wall time: 0:01:58
|
||||
Total wall time: 0:01:56
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
Loading…
Reference in New Issue