update kim command examples
This commit is contained in:
Yaser Afshar
@ -1,35 +1,35 @@
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# 3d Lennard-Jones melt
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#
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# This example requires that the example models provided with
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# the kim-api package are installed. see the ./lib/kim/README or
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# ./lib/kim/Install.py files for details on how to install these
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# the kim-api package are installed. see the `./lib/kim/README` or
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# `./lib/kim/Install.py` files for details on how to install these
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# example models.
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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 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*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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kim_init LennardJones_Ar real
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kim init LennardJones_Ar real
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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kim_interactions Ar
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kim interactions Ar
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mass 1 39.95
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velocity all create 200.0 232345 loop geom
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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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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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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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run 100
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@ -1,34 +1,34 @@
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# kim-property example
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# kim property example
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#
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# For detailed information of this example please refer to:
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# https://openkim.org/doc/evaluation/tutorial-lammps/
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# `https://openkim.org/doc/evaluation/tutorial-lammps/`
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#
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# Description:
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#
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# This example is designed to calculate the cohesive energy corresponding to
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# the equilibrium FCC lattice constant for
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# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
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# argon. The material properties computed in LAMMPS are represented as a
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# standard KIM property instance format. (See
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# https://openkim.org/doc/schema/properties-framework/ and
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# https://lammps.sandia.gov/doc/kim_commands.html for further details).
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# Then the created property instance is written to a file named results.edn
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# using the `kim_property dump` commands.
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# This example is designed to calculate the cohesive energy corresponding to
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# the equilibrium FCC lattice constant for
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# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
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# argon. The material properties computed in LAMMPS are represented as a
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# standard KIM property instance format. (See
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# `https://openkim.org/doc/schema/properties-framework/` and
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# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
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# Then the created property instance is written to a file named `results.edn`
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# using the `kim property dump` command.
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#
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# Requirement:
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#
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# This example requires LAMMPS built with the Python 3.6 or later package
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# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
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#
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# This example requires LAMMPS built with the Python 3.6 or later package
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# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
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# more info on building LAMMPS with the version of Python on your system.
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# After successfully building LAMMPS with Python, you need to install the
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# kim-property Python package, See the
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# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
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# After successfully building LAMMPS with Python, you need to install the
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# kim-property Python package, See the
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# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
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# further details.
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#
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# This example requires that the KIM Portable Model (PM)
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# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
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# is installed. This can be done with the command
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# `kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
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# is installed. This can be done with the command
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# kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
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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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@ -38,14 +38,14 @@
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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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# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
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#
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# Initialize interatomic potential (KIM model) and units
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atom_style atomic
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# Set the OpenKIM model that will be used
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kim_init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
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kim init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
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# the equilibrium lattice constant for the fcc structure
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variable lattice_constant equal 5.248509056866169
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@ -55,14 +55,14 @@ boundary p p p
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# Create an FCC lattice with the lattice spacing
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# using a single conventional (orthogonal) unit cell
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lattice fcc ${lattice_constant}
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region box block 0 1 0 1 0 1 units lattice
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create_box 1 box
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lattice fcc ${lattice_constant}
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region box block 0 1 0 1 0 1 units lattice
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create_box 1 box
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create_atoms 1 box
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mass 1 39.948
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mass 1 39.948
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# Specify the KIM interactions
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kim_interactions Ar
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kim interactions Ar
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# Compute energy
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run 0
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@ -72,10 +72,10 @@ variable natoms equal "count(all)"
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variable ecohesive equal "-pe/v_natoms"
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# Create a property instance
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kim_property create 1 cohesive-potential-energy-cubic-crystal
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kim property create 1 cohesive-potential-energy-cubic-crystal
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# Set all the key-value pairs for this property instance
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kim_property modify 1 key short-name source-value 1 fcc &
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kim property modify 1 key short-name source-value 1 fcc &
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key species source-value 1 Ar &
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key a source-value ${lattice_constant} &
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source-unit angstrom &
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@ -88,4 +88,4 @@ kim_property modify 1 key short-name source-value 1 fcc
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source-unit eV
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# Dump the results in a file
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kim_property dump "results.edn"
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kim property dump "results.edn"
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@ -1,7 +1,7 @@
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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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# `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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@ -13,34 +13,34 @@
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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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# 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 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 yy equal 20*$y
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variable zz equal 20*$z
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
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kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
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kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
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kim query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
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lattice fcc ${a0}
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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lattice fcc ${a0}
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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kim_interactions Si
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kim interactions Si
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mass 1 39.95
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velocity all create 200.0 232345 loop geom
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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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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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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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run 100
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@ -1,7 +1,7 @@
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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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# `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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@ -13,33 +13,33 @@
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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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# 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 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 yy equal 20*$y
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variable zz equal 20*$z
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
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kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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kim_interactions Si
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kim interactions Si
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mass 1 39.95
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velocity all create 200.0 232345 loop geom
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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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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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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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run 100
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@ -1,8 +1,8 @@
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# 3d Lennard-Jones melt
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#
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# This example requires that the KIM Simulator Model (PM)
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# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
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# is installed. This can be done with the command
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# `Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000`
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# is installed. This can be done with the command
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# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
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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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@ -13,33 +13,33 @@
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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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# See https://openkim.org/doc/obtaining-models for alternative options.
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# 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 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 yy equal 20*$y
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variable zz equal 20*$z
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
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kim init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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kim_interactions O
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kim interactions O
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mass 1 39.95
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velocity all create 200.0 232345 loop geom
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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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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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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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run 100
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@ -1,33 +1,33 @@
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# 3d Lennard-Jones melt
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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 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 yy equal 20*$y
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variable zz equal 20*$z
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units real
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units real
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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pair_style lj/cut 8.1500
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pair_coeff 1 1 0.0104 3.4000
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pair_style lj/cut 8.1500
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pair_coeff 1 1 0.0104 3.4000
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#pair_style kim LennardJones_Ar
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#pair_coeff * * Ar
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#pair_style kim LennardJones_Ar
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#pair_coeff * * Ar
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mass 1 39.95
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velocity all create 200.0 232345 loop geom
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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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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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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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run 100
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