LAMMPS (10 Feb 2021) # 3d Lennard-Jones melt # # This example requires that the KIM Portable Model (PM) # `SW_StillingerWeber_1985_Si__MO_405512056662_005` # is installed. This can be done with the command # kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 # If this command does not work, you may need to setup your PATH to find the utility. # If you installed the kim-api using the LAMMPS CMake build, you can do the following # (where the current working directory is assumed to be the LAMMPS build directory) # source ./kim_build-prefix/bin/kim-api-activate # If you installed the kim-api using the LAMMPS Make build, you can do the following # (where the current working directory is assumed to be the LAMMPS src directory) # source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate # (where you should relplace X.Y.Z with the appropriate kim-api version number). # # Or, see `https://openkim.org/doc/obtaining-models` for alternative options. # variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real #=== BEGIN kim init ========================================== units real neighbor 2.0 bin # Angstroms timestep 1.0 # femtoseconds This model has 9 mutable parameters. No. | Parameter name | data type | extent ----------------------------------------------------- 1 | A | "Double" | 1 2 | B | "Double" | 1 3 | p | "Double" | 1 4 | q | "Double" | 1 5 | sigma | "Double" | 1 6 | gamma | "Double" | 1 7 | cutoff | "Double" | 1 8 | lambda | "Double" | 1 9 | costheta0 | "Double" | 1 #=== END kim init ============================================ lattice fcc 4.4300 Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.003 seconds kim interactions Si #=== BEGIN kim interactions ================================== pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 pair_coeff * * Si #=== END kim interactions ==================================== mass 1 39.95 velocity all create 200.0 232345 loop geom neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 all nve #fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 run 100 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 @Article{tadmor:elliott:2011, author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker}, title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels}, journal = {{JOM}}, year = 2011, volume = 63, number = 17, pages = {17}, doi = {10.1007/s11837-011-0102-6} } - OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation @Comment { \documentclass{article} \usepackage{url} \begin{document} 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}. \bibliographystyle{vancouver} \bibliography{kimcite-MO_405512056662_005.bib} \end{document} } @Misc{MO_405512056662_005, author = {Amit K Singh}, title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005}, doi = {10.25950/c74b293f}, howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}}, keywords = {OpenKIM, Model, MO_405512056662_005}, publisher = {OpenKIM}, year = 2018, } @Misc{MD_335816936951_004, author = {Mingjian Wen}, title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004}, doi = {10.25950/f3abd2d6}, howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}}, keywords = {OpenKIM, Model Driver, MD_335816936951_004}, 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_405512056662_005a, author = {Stillinger, Frank H. and Weber, Thomas A.}, doi = {10.1103/PhysRevB.31.5262}, issue = {8}, journal = {Physical Review B}, month = {Apr}, pages = {5262--5271}, publisher = {American Physical Society}, title = {Computer simulation of local order in condensed phases of silicon}, volume = {31}, year = {1985}, } @Book{MO_405512056662_005b, author = {Tadmor, Ellad B. and Miller, Ronald E.}, doi = {10.1017/CBO9781139003582}, publisher = {Cambridge University Press}, title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques}, year = {2011}, } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.07118 ghost atom cutoff = 4.07118 binsize = 2.03559, bins = 44 44 44 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 4.07118 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard 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 17.6645 on 1 procs for 100 steps with 32000 atoms 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 | 17.553 | 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 Nghost: 7760.00 ave 7760 max 7760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 402352.0 ave 402352 max 402352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402352 Ave neighs/atom = 12.573500 Neighbor list builds = 4 Dangerous builds = 0 Total wall time: 0:00:17