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 ============================================ kim query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"] #=== BEGIN kim-query ========================================= variable a0 string "4.146581932902336" #=== END kim-query =========================================== lattice fcc ${a0} lattice fcc 4.146581932902336 Lattice spacing in x,y,z = 4.1465819 4.1465819 4.1465819 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 (82.931639 82.931639 82.931639) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.001 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}, } - OpenKIM query: https://doi.org/10.1063/5.0014267 @Article{karls:bierbaum:2020, author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott and J. P. Sethna and E. B. Tadmor}, title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic material property computation engine}, journal = {{T}he {J}ournal of {C}hemical {P}hysics}, year = 2020, volume = 153, number = 6, pages = {064104}, doi = {10.1063/5.0014267} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... 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 = 41 41 41 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) = 3.489 | 3.489 | 3.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 200 -126084.25 0 -107007.66 1528.8768 100 94.450495 -116016.03 0 -107007.07 2282.2685 Loop time of 5.33871 on 4 procs for 100 steps with 32000 atoms Performance: 1.618 ns/day, 14.830 hours/ns, 18.731 timesteps/s 99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.244 | 5.2604 | 5.2753 | 0.5 | 98.53 Neigh | 0.027617 | 0.027767 | 0.027955 | 0.1 | 0.52 Comm | 0.017101 | 0.031947 | 0.04856 | 6.3 | 0.60 Output | 3.4e-05 | 4.525e-05 | 5.6e-05 | 0.0 | 0.00 Modify | 0.011577 | 0.01165 | 0.011709 | 0.0 | 0.22 Other | | 0.0069 | | | 0.13 Nlocal: 8000.00 ave 8029 max 7968 min Histogram: 1 1 0 0 0 0 0 0 0 2 Nghost: 4259.00 ave 4303 max 4202 min Histogram: 1 0 0 0 0 0 2 0 0 1 Neighs: 0.00000 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 112548.0 ave 113091 max 111995 min Histogram: 1 0 0 1 0 0 0 1 0 1 Total # of neighbors = 450192 Ave neighs/atom = 14.068500 Neighbor list builds = 3 Dangerous builds = 0 Total wall time: 0:00:07