a kim-property command example

# 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://lammps.sandia.gov/doc/kim_commands.html for further details).

# Then the created property instance is written to a file named results.edn 

# using the `kim_property dump` commands.  

#

# Requirement:

# 

# This example requires LAMMPS built with the Python 3.6 or later package 

# installed. See the `https://lammps.sandia.gov/doc/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://lammps.sandia.gov/doc/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

# 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}

region box block 0 1 0 1 0 1 units lattice

create_box 1 box

create_atoms 1 box

mass 1 39.948

# Specify the KIM interactions

kim_interactions Ar

# Compute energy

run 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

# 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

# Dump the results in a file

kim_property dump "results.edn"