LAMMPS (10 Feb 2021) # kim property example # # For detailed information of this example please refer to: # `https://openkim.org/doc/evaluation/tutorial-lammps/` # # Description: # # This example is designed to calculate the cohesive energy corresponding to # the equilibrium FCC lattice constant for # `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for # argon. The material properties computed in LAMMPS are represented as a # standard KIM property instance format. (See # `https://openkim.org/doc/schema/properties-framework/` and # `https://docs.lammps.org/kim_commands.html` for further details). # Then the created property instance is written to a file named `results.edn` # using the `kim property dump` command. # # Requirement: # # This example requires LAMMPS built with the Python 3.6 or later package # installed. See the `https://docs.lammps.org/python.html` doc page for # more info on building LAMMPS with the version of Python on your system. # After successfully building LAMMPS with Python, you need to install the # kim-property Python package, See the # `https://docs.lammps.org/Build_extras.html#kim` doc page for # further details. # # This example requires that the KIM Portable Model (PM) # `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` # is installed. This can be done with the command # kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 # 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. # # Initialize interatomic potential (KIM model) and units atom_style atomic # Set the OpenKIM model that will be used kim init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal #=== BEGIN kim init ========================================== units metal neighbor 2.0 bin # Angstroms timestep 1.0e-3 # picoseconds This model has 3 mutable parameters. No. | Parameter name | data type | extent ----------------------------------------------------- 1 | cutoff | "Double" | 1 2 | epsilon | "Double" | 1 3 | sigma | "Double" | 1 #=== END kim init ============================================ # the equilibrium lattice constant for the fcc structure variable lattice_constant equal 5.248509056866169 # Periodic boundary conditions along all three dimensions boundary p p p # Create an FCC lattice with the lattice spacing # using a single conventional (orthogonal) unit cell lattice fcc ${lattice_constant} lattice fcc 5.24850905686617 Lattice spacing in x,y,z = 5.2485091 5.2485091 5.2485091 region box block 0 1 0 1 0 1 units lattice create_box 1 box Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.2485091 5.2485091 5.2485091) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4 atoms create_atoms CPU = 0.001 seconds mass 1 39.948 # Specify the KIM interactions kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 pair_coeff * * Ar #=== END kim interactions ==================================== # Compute energy run 0 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_126566794224_004#item-citation @Comment { \documentclass{article} \usepackage{url} \begin{document} This Model originally published in \cite{MO_126566794224_004a} is archived in OpenKIM~\cite{MO_126566794224_004, MD_498634107543_004, tadmor:elliott:2011, elliott:tadmor:2011}. \bibliographystyle{vancouver} \bibliography{kimcite-MO_126566794224_004.bib} \end{document} } @Misc{MO_126566794224_004, author = {Ellad Tadmor}, title = {{L}ennard-{J}ones model (shifted) for {A}r with parameters from {B}ernardes (1958) (medium precision cutoff) v004}, doi = {10.25950/9f98b989}, howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}}, keywords = {OpenKIM, Model, MO_126566794224_004}, publisher = {OpenKIM}, year = 2020, } @Misc{MD_498634107543_004, author = {Ellad Tadmor}, title = {{D}river for the {L}ennard-{J}ones model uniformly shifted to have zero energy at the cutoff radius v004}, doi = {10.25950/bdffd6a6}, howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}}, keywords = {OpenKIM, Model Driver, MD_498634107543_004}, publisher = {OpenKIM}, year = 2020, } @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_126566794224_004a, author = {Newton Bernardes}, doi = {10.1103/PhysRev.112.1534}, issue = {5}, journal = {Physical Review}, pages = {1534--1539}, publisher = {American Physical Society}, title = {Theory of Solid {N}e, {A}, {K}r, and {X}e at 0{K}}, volume = {112}, year = {1958}, } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 1 1 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 15.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.165 | 3.165 | 3.165 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -0.34602203 0 -0.34602203 0.00061471244 Loop time of 1.5e-06 on 4 procs for 0 steps with 4 atoms 100.0% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.5e-06 | | |100.00 Nlocal: 1.00000 ave 1 max 1 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 935.000 ave 935 max 935 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 428.000 ave 428 max 428 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1712 Ave neighs/atom = 428.00000 Neighbor list builds = 0 Dangerous builds = 0 # Get cohesive energy variable natoms equal "count(all)" variable ecohesive equal "-pe/v_natoms" # Create a property instance kim property create 1 cohesive-potential-energy-cubic-crystal #=== kim property =========================================== # Set all the key-value pairs for this property instance kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value ${lattice_constant} source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value ${ecohesive} source-unit eV kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value 5.24850905686617 source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value ${ecohesive} source-unit eV kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value 5.24850905686617 source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value 0.0865055084950538 source-unit eV #=== kim property =========================================== # Dump the results in a file kim property dump "results.edn" #=== kim property =========================================== Total wall time: 0:00:00