239 lines
8.6 KiB
Groff
239 lines
8.6 KiB
Groff
LAMMPS (10 Feb 2021)
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# 3d Lennard-Jones melt
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#
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# This example requires that the KIM Portable Model (PM)
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# `SW_StillingerWeber_1985_Si__MO_405512056662_005`
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# is installed. This can be done with the command
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# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
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# If this command does not work, you may need to setup your PATH to find the utility.
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# If you installed the kim-api using the LAMMPS CMake build, you can do the following
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# (where the current working directory is assumed to be the LAMMPS build directory)
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# source ./kim_build-prefix/bin/kim-api-activate
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# If you installed the kim-api using the LAMMPS Make build, you can do the following
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# (where the current working directory is assumed to be the LAMMPS src directory)
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# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
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# (where you should relplace X.Y.Z with the appropriate kim-api version number).
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#
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# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
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#
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
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#=== BEGIN kim init ==========================================
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units real
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neighbor 2.0 bin # Angstroms
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timestep 1.0 # femtoseconds
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This model has 9 mutable parameters.
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No. | Parameter name | data type | extent
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-----------------------------------------------------
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1 | A | "Double" | 1
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2 | B | "Double" | 1
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3 | p | "Double" | 1
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4 | q | "Double" | 1
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5 | sigma | "Double" | 1
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6 | gamma | "Double" | 1
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7 | cutoff | "Double" | 1
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8 | lambda | "Double" | 1
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9 | costheta0 | "Double" | 1
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#=== END kim init ============================================
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kim query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
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#=== BEGIN kim-query =========================================
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variable a0 string "4.146581932902336"
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#=== END kim-query ===========================================
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lattice fcc ${a0}
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lattice fcc 4.146581932902336
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Lattice spacing in x,y,z = 4.1465819 4.1465819 4.1465819
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (82.931639 82.931639 82.931639)
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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 32000 atoms
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create_atoms CPU = 0.001 seconds
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kim interactions Si
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#=== BEGIN kim interactions ==================================
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pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
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pair_coeff * * Si
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#=== END kim interactions ====================================
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mass 1 39.95
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velocity all create 200.0 232345 loop geom
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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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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- 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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\begin{document}
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This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_005b} is archived in OpenKIM~\cite{MO_405512056662_005, MD_335816936951_004, tadmor:elliott:2011, elliott:tadmor:2011}.
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\bibliographystyle{vancouver}
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\bibliography{kimcite-MO_405512056662_005.bib}
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\end{document}
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}
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@Misc{MO_405512056662_005,
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author = {Amit K Singh},
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title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005},
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doi = {10.25950/c74b293f},
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howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
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keywords = {OpenKIM, Model, MO_405512056662_005},
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publisher = {OpenKIM},
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year = 2018,
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}
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@Misc{MD_335816936951_004,
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author = {Mingjian Wen},
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title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004},
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doi = {10.25950/f3abd2d6},
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howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
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keywords = {OpenKIM, Model Driver, MD_335816936951_004},
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publisher = {OpenKIM},
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year = 2018,
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}
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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 = {7},
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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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@Misc{elliott:tadmor:2011,
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author = {Ryan S. Elliott and Ellad B. Tadmor},
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title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
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howpublished = {\url{https://openkim.org/kim-api}},
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publisher = {OpenKIM},
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year = 2011,
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doi = {10.25950/ff8f563a},
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}
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@Article{MO_405512056662_005a,
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author = {Stillinger, Frank H. and Weber, Thomas A.},
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doi = {10.1103/PhysRevB.31.5262},
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issue = {8},
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journal = {Physical Review B},
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month = {Apr},
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pages = {5262--5271},
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publisher = {American Physical Society},
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title = {Computer simulation of local order in condensed phases of silicon},
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volume = {31},
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year = {1985},
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}
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@Book{MO_405512056662_005b,
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author = {Tadmor, Ellad B. and Miller, Ronald E.},
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doi = {10.1017/CBO9781139003582},
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publisher = {Cambridge University Press},
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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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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 4.07118
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ghost atom cutoff = 4.07118
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binsize = 2.03559, bins = 41 41 41
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair kim, perpetual
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attributes: full, newton off, cut 4.07118
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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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 5.33871 on 4 procs for 100 steps with 32000 atoms
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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 | 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
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Comm | 0.017101 | 0.031947 | 0.04856 | 6.3 | 0.60
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Output | 3.4e-05 | 4.525e-05 | 5.6e-05 | 0.0 | 0.00
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Modify | 0.011577 | 0.01165 | 0.011709 | 0.0 | 0.22
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Other | | 0.0069 | | | 0.13
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Nlocal: 8000.00 ave 8029 max 7968 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 4259.00 ave 4303 max 4202 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 112548.0 ave 113091 max 111995 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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Total # of neighbors = 450192
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Ave neighs/atom = 14.068500
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Neighbor list builds = 3
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Dangerous builds = 0
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Total wall time: 0:00:07
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