kim command

Syntax

kim sub-command args

Examples

kim init args
kim interactions args
kim query args
kim param args
kim property args

Description

The kim command includes a set of sub-commands that allow LAMMPS users to use interatomic models (IM) (potentials and force fields) and their predictions for various physical properties archived in the Open Knowledgebase of Interatomic Models (OpenKIM) repository.

Using OpenKIM provides LAMMPS users with immediate access to a large number of verified IMs and their predictions. OpenKIM IMs have multiple benefits including reliability, reproducibility and convenience.

There are two types of IMs archived in OpenKIM:

  1. The first type is called a KIM Portable Model (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface (KIM API) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see complete list of supported codes).

  2. The second type is called a KIM Simulator Model (SM). A KIM SM is an IM that is implemented natively within a simulation code (simulator) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS.

With these two IM types, OpenKIM can archive and test almost all IMs that can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see the upload instructions.)

OpenKIM IMs are uniquely identified by a KIM ID. The extended KIM ID consists of a human-readable prefix identifying the type of IM, authors, publication year, and supported species, separated by two underscores from the KIM ID itself, which begins with an IM code (MO for a KIM Portable Model, and SM for a KIM Simulator Model) followed by a unique 12-digit code and a 3-digit version identifier. By convention SM prefixes begin with Sim_ to readily identify them.

SW_StillingerWeber_1985_Si__MO_405512056662_005
Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_001

Each OpenKIM IM has a dedicated “Model Page” on OpenKIM providing all the information on the IM including a title, description, authorship and citation information, test and verification check results, visualizations of results, a wiki with documentation and user comments, and access to raw files, and other information. The URL for the Model Page is constructed from the extended KIM ID of the IM:

https://openkim.org/id/extended_KIM_ID

For example, for the Stillinger-Weber potential listed above the Model Page is located at:

https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005

See the current list of KIM PMs and SMs archived in OpenKIM. This list is sorted by species and can be filtered to display only IMs for certain species combinations.

See Obtaining KIM Models to learn how to install a pre-built binary of the OpenKIM Repository of Models.

Note

It is also possible to locally install IMs not archived in OpenKIM, in which case their names do not have to conform to the KIM ID format.

Using OpenKIM IMs with LAMMPS (kim init, kim interactions)

Two sub-commands are employed when using OpenKIM IMs in LAMMPS, one to select the IM and perform necessary initialization (kim init), and the second to set up the IM for use by executing any necessary LAMMPS commands (kim interactions). Both are required.

Syntax

kim init model user_units unitarg
kim interactions typeargs

  • model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM)

  • user_units = the LAMMPS units style assumed in the LAMMPS input script

  • unitarg = unit_conversion_mode (optional)

  • typeargs = atom type to species mapping (one entry per atom type) or fixed_types for models with a preset fixed mapping

Examples

kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
kim interactions Si

kim init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_001 real
kim init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_001 metal unit_conversion_mode
kim interactions C H O

kim init Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolventsPolymers__SM_039297821658_000 real
kim interactions fixed_types

See the examples/kim directory for example input scripts that use KIM PMs and KIM SMs.

OpenKIM IM Initialization (kim init)

The kim command followed by init sub-command must be issued before the simulation box is created (normally at the top of the file). This command sets the OpenKIM IM that will be used and may issue additional commands changing LAMMPS default settings that are required for using the selected IM (such as units or atom_style). If needed, those settings can be overridden, however, typically a script containing a kim init command would not include units and atom_style commands.

The required arguments of kim init are the model name of the IM to be used in the simulation (for an IM archived in OpenKIM this is its extended KIM ID, and the user_units, which are the LAMMPS units style used in the input script. (Any dimensioned numerical values in the input script and values read in from files are expected to be in the user_units system.)

The selected IM can be either a KIM PM or a KIM SM. For a KIM SM, the kim init command verifies that the SM is designed to work with LAMMPS (and not another simulation code). In addition, the LAMMPS version used for defining the SM and the LAMMPS version being currently run are printed to help diagnose any incompatible changes to input script or command syntax between the two LAMMPS versions.

Based on the selected model kim init may modify the atom_style. Some SMs have requirements for this setting. If this is the case, then atom_style will be set to the required style. Otherwise, the value is left unchanged (which in the absence of an atom_style command in the input script is the default atom_style value).

Regarding units, the kim init behaves in different ways depending on whether or not unit conversion mode is activated as indicated by the optional unitarg argument. If unit conversion mode is not active, then user_units must either match the required units of the IM or the IM must be able to adjust its units to match. (The latter is only possible with some KIM PMs; SMs can never adjust their units.) If a match is possible, the LAMMPS units command is called to set the units to user_units. If the match fails, the simulation is terminated with an error. The kim init command also sets the default value for the skin (extra distance beyond force cutoff) as 2.0 Angstroms and sets the default value for the timestep size as 1.0 femtosecond.

Here is an example of a LAMMPS script to compute the cohesive energy of a face-centered cubic (fcc) lattice for the MEAM potential by Pascuet and Fernandez (2015) for Al.

kim          init Sim_LAMMPS_MEAM_PascuetFernandez_2015_Al__SM_811588957187_000 metal
boundary     p p p
lattice      fcc 4.049
region       simbox block 0 1 0 1 0 1 units lattice
create_box   1 simbox
create_atoms 1 box
mass         1 26.981539
kim          interactions Al
run          0
variable     Ec equal (pe/count(all))
print        "Cohesive Energy = ${Ec} eV"

The above script will end with an error in the kim init line if the IM is changed to another potential for Al that does not work with metal units. To address this, kim init offers the unit_conversion_mode as shown below.

If unit conversion mode is active, then kim init calls the LAMMPS units command to set the units to the IM’s required or preferred units. Conversion factors between the IM’s units and the user_units are defined for all physical quantities (mass, distance, etc.). (Note that converting to or from the “lj” unit style is not supported.) These factors are stored as internal style variables with the following standard names:

_u_mass
_u_distance
_u_time
_u_energy
_u_velocity
_u_force
_u_torque
_u_temperature
_u_pressure
_u_viscosity
_u_charge
_u_dipole
_u_efield
_u_density

If desired, the input script can be designed to work with these conversion factors so that the script will work without change with any OpenKIM IM. (This approach is used in the OpenKIM Testing Framework.)

For example, the script given above for the cohesive energy of fcc Al can be rewritten to work with any IM regardless of units. The following script constructs an fcc lattice with a lattice parameter defined in meters, computes the total energy, and prints the cohesive energy in Joules regardless of the units of the IM.

kim          init Sim_LAMMPS_MEAM_PascuetFernandez_2015_Al__SM_811588957187_000 si unit_conversion_mode
boundary     p p p
lattice      fcc $(4.049e-10*v__u_distance)
region       simbox block 0 1 0 1 0 1 units lattice
create_box   1 simbox
create_atoms 1 box
mass         1 $(4.480134e-26*v__u_mass)
kim          interactions Al
neighbor     $(2e-10*v__u_distance) bin
run          0
variable     Ec_in_J equal (pe/count(all))/v__u_energy
print        "Cohesive Energy = ${Ec_in_J} J"

Note the multiplication by v__u_distance and v__u_mass to convert from SI units (specified in the kim init command) to whatever units the IM uses (metal in this case), and the division by v__u_energy to convert from the IM’s energy units to SI units (Joule). This script will work correctly for any IM for Al (KIM PM or SM) selected by the kim init command.

Care must be taken to apply unit conversion to dimensional variables read in from a file. For example, if a configuration of atoms is read in from a dump file using the read_dump command, the following can be done to convert the box and all atomic positions to the correct units:

change_box all x scale ${_u_distance} &
               y scale ${_u_distance} &
               z scale ${_u_distance} &
               xy final $(xy*v__u_distance) &
               xz final $(xz*v__u_distance) &
               yz final $(yz*v__u_distance) &
               remap

Note

Unit conversion will only work if the conversion factors are placed in all appropriate places in the input script. It is up to the user to do this correctly.

OpenKIM IM Execution (kim interactions)

The second and final step in using an OpenKIM IM is to execute the kim interactions command. This command must be preceded by a kim init command and a command that defines the number of atom types N (such as create_box). The kim interactions command has one argument typeargs. This argument contains either a list of N chemical species, which defines a mapping between atom types in LAMMPS to the available species in the OpenKIM IM, or the keyword fixed_types for models that have a preset fixed mapping (i.e. the mapping between LAMMPS atom types and chemical species is defined by the model and cannot be changed). In the latter case, the user must consult the model documentation to see how many atom types there are and how they map to the chemical species.

For example, consider an OpenKIM IM that supports Si and C species. If the LAMMPS simulation has four atom types, where the first three are Si, and the fourth is C, the following kim interactions command would be used:

kim interactions Si Si Si C

Alternatively, for a model with a fixed mapping the command would be:

kim interactions fixed_types

The kim interactions command performs all the necessary steps to set up the OpenKIM IM selected in the kim init command. The specific actions depend on whether the IM is a KIM PM or a KIM SM. For a KIM PM, a pair_style kim command is executed followed by the appropriate pair_coeff command. For example, for the Ercolessi and Adams (1994) KIM PM for Al set by the following commands:

kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
...
...  box specification lines skipped
...
kim interactions Al

the kim interactions command executes the following LAMMPS input commands:

pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005
pair_coeff * * Al

For a KIM SM, the generated input commands may be more complex and require that LAMMPS is built with the required packages included for the type of potential being used. The set of commands to be executed is defined in the SM specification file, which is part of the SM package. For example, for the Strachan et al. (2003) ReaxFF SM set by the following commands:

kim init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
...
...  box specification lines skipped
...
kim interactions C H N O

the kim interactions command executes the following LAMMPS input commands:

pair_style reaxff lmp_control safezone 2.0 mincap 100
pair_coeff * * ffield.reax.rdx C H N O
fix reaxqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 param.qeq

Note

The files lmp_control, ffield.reax.rdx and param.qeq are specific to the Strachan et al. (2003) ReaxFF parameterization and are archived as part of the SM package in OpenKIM.

Note

Parameters like cutoff radii and charge tolerances, which have an effect on IM predictions, are also included in the SM definition ensuring reproducibility.

Note

When using kim init and kim interactions to select and set up an OpenKIM IM, other LAMMPS commands for the same functions (such as pair_style, pair_coeff, bond_style, bond_coeff, fixes related to charge equilibration, etc.) should normally not appear in the input script.

Note

kim interactions must be called each time after the change_box command to provide the correct settings (it should be called with the same typeargs as the first call.) The reason is that changing a periodic boundary to a non-periodic one, or in general, using the change_box command after the interactions are set via kim interactions or pair_coeff commands might affect some of the settings. For example, SM models containing Coulombic terms in the interactions require different settings if a periodic boundary changes to a non-periodic one. In other cases, the second call to kim interactions does not affect any other settings.

Using OpenKIM Web Queries in LAMMPS (kim query)

The kim query command performs a web query to retrieve the predictions of an IM set by kim init for material properties archived in OpenKIM.

Syntax

kim query variable formatarg query_function queryargs

  • variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command

  • formatarg = list, split, or index (optional):

    list = returns a single string with a list of space separated values
       (e.g. "1.0 2.0 3.0"), which is placed in a LAMMPS variable as
       defined by the variable argument. [default]
split = returns the values separately in new variables with names based
       on the prefix specified in variable and a number appended to
       indicate which element in the list of values is in the variable
index = returns a variable style index that can be incremented via the
       next command.  This enables the construction of simple loops

  • query_function = name of the OpenKIM web API query function to be used

  • queryargs = a series of keyword=value pairs that represent the web query; supported keywords depend on the query function

Examples

kim query a0 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom]
kim query model index get_available_models species=[Al] potential_type=[eam]

The result of the query is stored in one or more string style variables as determined by the optional formatarg argument. For the “list” setting of formatarg (or if formatarg is not specified), the result is returned as a space-separated list of values in variable. The formatarg keyword “split” separates the result values into individual variables of the form prefix_I, where prefix is set to the kim query variable argument and I ranges from 1 to the number of returned values. The number and order of the returned values is determined by the type of query performed. The formatarg keyword “index” returns a variable style index that can be incremented via the next command. This enables the construction of simple loops over the returned values by the type of query performed.

Note

kim query only supports queries that return a single result or an array of values. More complex queries that return a JSON structure are not currently supported. An attempt to use kim query in such cases will generate an error.

The second required argument query_function is the name of the query function to be called (e.g. get_lattice_constant_cubic). All following arguments are parameters handed over to the web query in the format keyword=value, where value is always an array of one or more comma-separated items in brackets. The list of supported keywords and the type and format of their values depend on the query function used. The current list of query functions is available on the OpenKIM webpage at https://openkim.org/doc/usage/kim-query.

Note

All query functions, except get_available_models, require the model keyword, which identifies the IM whose predictions are being queried. kim query automatically generates the model keyword based on the IM set in by kim init, and it can be overwritten if specified as an argument to the kim query. Where kim init is not specified, the model keyword must be provided as an argument to the kim query.

Note

Each query_function is associated with a default method (implemented as a KIM Test) used to compute this property. In cases where there are multiple methods in OpenKIM for computing a property, a method keyword can be provided to select the method of choice. See the query documentation to see which methods are available for a given query_function.

kim query Usage Examples and Further Clarifications

The data obtained by kim query commands can be used as part of the setup or analysis phases of LAMMPS simulations. Some examples are given below.

Define an equilibrium fcc crystal

kim      init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
boundary p p p
kim      query a0 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom]
lattice  fcc ${a0}
...

units   metal
kim     query a0 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]
lattice fcc ${a0}
...

The kim query command retrieves from OpenKIM the equilibrium lattice constant predicted by the Ercolessi and Adams (1994) potential for the fcc structure and places it in variable a0. This variable is then used on the next line to set up the crystal. By using kim query, the user is saved the trouble and possible error of tracking this value down, or of having to perform an energy minimization to find the equilibrium lattice constant.

Note

In unit_conversion_mode the results obtained from a kim query would need to be converted to the appropriate units system. For example, in the above script, the lattice command would need to be changed to: “lattice fcc $(v_a0*v__u_distance)”.

Define an equilibrium hcp crystal

kim      init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal
boundary p p p
kim      query latconst split get_lattice_constant_hexagonal crystal=[hcp] species=[Zr] units=[angstrom]
lattice  custom ${latconst_1} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 $(latconst_2/latconst_1) &
         basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75
...

In this case the kim query returns two arguments (since the hexagonal close packed (hcp) structure has two independent lattice constants). The formatarg keyword “split” places the two values into the variables latconst_1 and latconst_2. (These variables are created if they do not already exist.)

Define a crystal at finite temperature accounting for thermal expansion

kim      init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
boundary p p p
kim      query a0 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom]
kim      query alpha get_linear_thermal_expansion_coefficient_cubic crystal=[fcc] species=[Al] units=[1/K] temperature=[293.15] temperature_units=[K]
variable DeltaT equal 300
lattice  fcc $(v_a0*v_alpha*v_DeltaT)
...

As in the previous example, the equilibrium lattice constant is obtained for the Ercolessi and Adams (1994) potential. However, in this case the crystal is scaled to the appropriate lattice constant at room temperature (293.15 K) by using the linear thermal expansion constant predicted by the potential.

Note

When passing numerical values as arguments (as in the case of the temperature in the above example) it is also possible to pass a tolerance indicating how close to the value is considered a match. If no tolerance is passed a default value is used. If multiple results are returned (indicating that the tolerance is too large), kim query will return an error. See the query documentation to see which numerical arguments and tolerances are available for a given query_function.

Compute defect formation energy

kim      init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
...
... Build fcc crystal containing some defect and compute the total energy
... which is stored in the variable *Etot*
...
kim      query Ec get_cohesive_energy_cubic crystal=[fcc] species=[Al] units=[eV]
variable Eform equal ${Etot} - count(all)*${Ec}
...

The defect formation energy Eform is computed by subtracting the ideal fcc cohesive energy of the atoms in the system from Etot. The ideal fcc cohesive energy of the atoms is obtained from OpenKIM for the Ercolessi and Adams (1994) potential.

Retrieve equilibrium fcc crystal of all EAM potentials that support a specific species

kim   query model index get_available_models species=[Al] potential_type=[eam]
label model_loop
kim   query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
print "FCC lattice constant (${model} potential) = ${latconst}"
...
...   do something with current value of latconst
...
next  model
jump  SELF model_loop

In this example, the index mode of formatarg is used. The first kim query returns the list of all available EAM potentials that support the Al species and archived in OpenKIM. The result of the query operation is stored in the LAMMPS variable model as an index variable. This variable is used later to access the values one at a time within a loop as shown in the example. The second kim query command retrieves from OpenKIM the equilibrium lattice constant predicted by each potential for the fcc structure and places it in variable latconst.

Note

kim query commands return results archived in OpenKIM. These results are obtained using programs for computing material properties (KIM Tests and KIM Test Drivers) that were contributed to OpenKIM. In order to give credit to Test developers, the number of times results from these programs are queried is tracked. No other information about the nature of the query or its source is recorded.

Accessing KIM Model Parameters from LAMMPS (kim param)

All IMs are functional forms containing a set of parameters. These parameters’ values are typically selected to best reproduce a training set of quantum mechanical calculations or available experimental data. For example, a Lennard-Jones potential intended to model argon might have the values of its two parameters, epsilon, and sigma, fit to the dimer dissociation energy or thermodynamic properties at a critical point of the phase diagram.

Normally a user employing an IM should not modify its parameters since, as noted above, these are selected to reproduce material properties. However, there are cases where accessing and modifying IM parameters is desired, such as for assessing uncertainty, fitting an IM, or working with an ensemble of IMs. As explained above, IMs archived in OpenKIM are either Portable Models (PMs) or Simulator Models (SMs). KIM PMs are complete independent implementations of an IM, whereas KIM SMs are wrappers to an IM implemented within LAMMPS. Two different mechanisms are provided for accessing IM parameters in these two cases:

  • For a KIM PM, the kim param command can be used to get and set the values of the PM’s parameters as explained below.

  • For a KIM SM, the user should consult the documentation page for the specific IM and follow instructions there for how to modify its parameters (if possible).

The kim param get and kim param set commands provide an interface to access and change the parameters of a KIM PM that “publishes” its parameters and makes them publicly available (see the KIM API documentation for details).

Note

The kim param set/get command must be preceded by a kim interactions command (or alternatively by a pair_style kim and pair_coeff commands). The kim param set command may be used wherever a pair_coeff command may occur.

Syntax

kim param get param_name index_range variable formatarg
kim param set param_name index_range values

  • param_name = name of a KIM portable model parameter (which is published by the PM and available for access). The specific string used to identify a parameter is defined by the PM. For example, for the Stillinger-Weber (SW) potential in OpenKIM, the parameter names are A, B, p, q, sigma, gamma, cutoff, lambda, costheta0

  • index_range = KIM portable model parameter index range (an integer for a single element, or pair of integers separated by a colon for a range of elements)

  • variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command

  • formatarg = list, split, or explicit (optional): .. parsed-literal:

    *list* = returns a single string with a list of space separated values
       (e.g. "1.0 2.0 3.0"), which is placed in a LAMMPS variable as
       defined by the *variable* argument.
*split* = returns the values separately in new variables with names based
       on the prefix specified in *variable* and a number appended to
       indicate which element in the list of values is in the variable
*explicit* = returns the values separately in one more more variable names
       provided as arguments that precede *formatarg*\ . [default]

  • values = new value(s) to replace the current value(s) of a KIM portable model parameter

Note

The list of all the parameters that a PM exposes for access/mutation are automatically written to the lammps log file when kim init is called.

Each published parameter of a KIM PM takes the form of an array of numerical values. The array can contain one element for a single-valued parameter, or a set of values. For example, the multispecies SW potential for the Zn-Cd-Hg-S-Se-Te system has the same parameter names as the single-species SW potential, but each parameter array contains 21 entries that correspond to the parameter values used for each pairwise combination of the model’s six supported species (this model does not have parameters specific to individual ternary combinations of its supported species).

The index_range argument may either be an integer referring to a specific element within the array associated with the parameter specified by param_name, or a pair of integers separated by a colon that refer to a slice of this array. In both cases, one-based indexing is used to refer to the entries of the array.

The result of a get operation for a specific index_range is stored in one or more LAMMPS string style variables as determined by the optional formatarg argument documented above. If not specified, the default for formatarg is “explicit” for the kim param command.

For the case where the result is an array with multiple values (i.e. index_range contains a range), the optional “split” or “explicit” formatarg keywords can be used to separate the results into multiple variables; see the examples below. Multiple parameters can be retrieved with a single call to kim param get by repeating the argument list following get.

For a set operation, the values argument contains the new value(s) for the element(s) of the parameter specified by index_range. For the case where multiple values are being set, values contains a set of values separated by spaces. Multiple parameters can be set with a single call to kim param set by repeating the argument list following set.

kim param Usage Examples and Further Clarifications

Examples of getting and setting KIM PM parameters with further clarifications are provided below.

Getting a scalar parameter

kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
...
kim interactions Si
kim param get A 1 VARA

or

...
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si
kim param get A 1 VARA

In these cases, the value of the SW A parameter is retrieved and placed in the LAMMPS variable VARA. The variable VARA can be used in the remainder of the input script in the same manner as any other LAMMPS variable.

Getting multiple scalar parameters with a single call

...
kim interactions Si
kim param get A 1 VARA B 1 VARB

In this example, it is shown how to retrieve the A and B parameters of the SW potential and store them in the LAMMPS variables VARA and VARB.

Getting a range of values from a parameter

There are several options when getting a range of values from a parameter determined by the formatarg argument.

kim init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
...
kim interactions Te Zn Se
kim param get lambda 7:9 LAM_TeTe LAM_TeZn LAM_TeSe

In this case, formatarg is not specified and therefore the default “explicit” mode is used. (The behavior would be the same if the word explicit were added after LAM_TeSe.) Elements 7, 8 and 9 of parameter lambda retrieved by the get operation are placed in the LAMMPS variables LAM_TeTe, LAM_TeZn and LAM_TeSe, respectively.

Note

In the above example, elements 7-9 of the lambda parameter correspond to Te-Te, Te-Zm and Te-Se interactions. This can be determined by visiting the model page for the specified potential and looking at its parameter file linked to at the bottom of the page (file with .param ending) and consulting the README documentation provided with the driver for the PM being used. A link to the driver is provided at the top of the model page.

...
kim      interactions Te Zn Se
kim      param get lambda 15:17 LAMS list
variable LAM_VALUE index ${LAMS}
label    loop_on_lambda
...
...      do something with the current value of lambda
...
next     LAM_VALUE
jump     SELF loop_on_lambda

In this case, the “list” mode of formatarg is used. The result of the get operation is stored in the LAMMPS variable LAMS as a string containing the three retrieved values separated by spaces, e.g “1.0 2.0 3.0”. This can be used in LAMMPS with an index variable to access the values one at a time within a loop as shown in the example. At each iteration of the loop LAM_VALUE contains the current value of lambda.

...
kim interactions Te Zn Se
kim param get lambda 15:17 LAM split

In this case, the “split” mode of formatarg is used. The three values retrieved by the get operation are stored in the three LAMMPS variables LAM_15, LAM_16 and LAM_17. The provided name “LAM” is used as prefix and the location in the lambda array is appended to create the variable names.

Setting a scalar parameter

kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
...
kim interactions Si
kim param set gamma 1 2.6

Here, the SW potential’s gamma parameter is set to 2.6. Note that the get and set commands work together, so that a get following a set operation will return the new value that was set. For example,

...
kim interactions Si
kim param get gamma 1 ORIG_GAMMA
kim param set gamma 1 2.6
kim param get gamma 1 NEW_GAMMA
...
print "original gamma = ${ORIG_GAMMA}, new gamma = ${NEW_GAMMA}"

Here, ORIG_GAMMA will contain the original gamma value for the SW potential, while NEW_GAMMA will contain the value 2.6.

Setting multiple scalar parameters with a single call

kim      init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
...
kim      interactions Cd Te
variable VARG equal 2.6
variable VARS equal 2.0951
kim      param set gamma 1 ${VARG} sigma 3 ${VARS}

In this case, the first element of the gamma parameter and third element of the sigma parameter are set to 2.6 and 2.0951, respectively. This example also shows how LAMMPS variables can be used when setting parameters.

Setting a range of values of a parameter

kim init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
...
kim interactions Cd Te Zn Se Hg S
kim param set sigma 2:6 2.35214 2.23869 2.04516 2.43269 1.80415

In this case, elements 2 through 6 of the parameter sigma are set to the values 2.35214, 2.23869, 2.04516, 2.43269 and 1.80415 in order.

Writing material properties in standard KIM Property Instance format (kim property)

The OpenKIM system includes a collection of Tests (material property calculation codes), Models (interatomic potentials), Predictions, and Reference Data (DFT or experiments). Specifically, a KIM Test is a computation that when coupled with a KIM Model generates the prediction of that model for a specific material property rigorously defined by a KIM Property Definition (see the KIM Properties Framework for further details). A prediction of a material property for a given model is a specific numerical realization of a property definition, referred to as a “Property Instance.” The objective of the kim property command is to make it easy to output material properties in a standardized, machine readable, format that can be easily ingested by other programs. Additionally, it aims to make it as easy as possible to convert a LAMMPS script that computes a material property into a KIM Test that can then be uploaded to openkim.org

A developer interested in creating a KIM Test using a LAMMPS script should first determine whether a property definition that applies to their calculation already exists in OpenKIM by searching the properties page. If none exists, it is possible to use a locally defined property definition contained in a file until it can be uploaded to the official repository (see below). Once one or more applicable property definitions have been identified, the kim property create, kim property modify, kim property remove, and kim property destroy, commands provide an interface to create, set, modify, remove, and destroy instances of them within a LAMMPS script.

Syntax

kim property create  instance_id property_id
kim property modify  instance_id key key_name key_name_key key_name_value
kim property remove  instance_id key key_name
kim property destroy instance_id
kim property dump    file

  • instance_id = a positive integer identifying the KIM property instance; (note that the results file can contain multiple property instances)

  • property_id = identifier of a KIM Property Definition, which can be (1) a property short name, (2) the full unique ID of the property (including the contributor and date), (3) a file name corresponding to a local property definition file

  • key_name = one of the keys belonging to the specified KIM property definition

  • key_name_key = a key belonging to a key-value pair (standardized in the KIM Properties Framework)

  • key_name_value = value to be associated with a key_name_key in a key-value pair

  • file = name of a file to write the currently defined set of KIM property instances to

Examples of each of the three property_id cases are shown below,

kim property create 1 atomic-mass
kim property create 2 cohesive-energy-relation-cubic-crystal

kim property create 1 tag:brunnels@noreply.openkim.org,2016-05-11:property/atomic-mass
kim property create 2 tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal

kim property create 1 new-property.edn
kim property create 2 /home/mary/marys-kim-properties/dissociation-energy.edn

In the last example, “new-property.edn” and “/home/mary/marys-kim-properties/dissociation-energy.edn” are the names of files that contain user-defined (local) property definitions.

A KIM property instance takes the form of a “map,” i.e. a set of key-value pairs akin to Perl’s hash, Python’s dictionary, or Java’s Hashtable. It consists of a set of property key names, each of which is referred to here by the key_name argument, that are defined as part of the relevant KIM Property Definition and include only lowercase alphanumeric characters and dashes. The value paired with each property key is itself a map whose possible keys are defined as part of the KIM Properties Framework; these keys are referred to by the key_name_key argument and their associated values by the key_name_value argument. These values may either be scalars or arrays, as stipulated in the property definition.

Note

Each map assigned to a key_name must contain the key_name_key “source-value” and an associated key_name_value of the appropriate type (as defined in the relevant KIM Property Definition). For keys that are defined as having physical units, the “source-unit” key_name_key must also be given a string value recognized by GNU units.

Once a kim property create command has been given to instantiate a property instance, maps associated with the property’s keys can be edited using the kim property modify command. In using this command, the special keyword “key” should be given, followed by the property key name and the key-value pair in the map associated with the key that is to be set. For example, the atomic-mass property definition consists of two property keys named “mass” and “species.” An instance of this property could be created like so:

kim property create 1 atomic-mass
kim property modify 1 key species source-value Al
kim property modify 1 key mass    source-value 26.98154
kim property modify 1 key mass    source-unit amu

or, equivalently,

kim property create 1 atomic-mass
kim property modify 1 key species source-value Al       &
                      key mass    source-value 26.98154 &
                                  source-unit  amu

kim property Usage Examples and Further Clarifications

Create

kim property create instance_id property_id

The kim property create command takes as input a property instance ID and the property definition name, and creates an initial empty property instance data structure. For example,

kim property create 1 atomic-mass
kim property create 2 cohesive-energy-relation-cubic-crystal

creates an empty property instance of the “atomic-mass” property definition with instance ID 1 and an empty instance of the “cohesive-energy-relation-cubic-crystal” property with ID 2. A list of published property definitions in OpenKIM can be found on the properties page.

One can also provide the name of a file in the current working directory or the path of a file containing a valid property definition. For example,

kim property create 1 new-property.edn

where “new-property.edn” refers to a file name containing a new property definition that does not exist in OpenKIM.

If the property_id given cannot be found in OpenKIM and no file of this name containing a valid property definition can be found, this command will produce an error with an appropriate message. Calling kim property create with the same instance ID multiple times will also produce an error.

Modify

kim property modify instance_id key key_name key_name_key key_name_value

The kim property modify command incrementally builds the property instance by receiving property definition keys along with associated arguments. Each key_name is associated with a map containing one or more key-value pairs (in the form of key_name_key-key_name_value pairs). For example,

kim property modify 1 key species source-value Al
kim property modify 1 key mass    source-value 26.98154
kim property modify 1 key mass    source-unit  amu

where the special keyword “key” is followed by a key_name (“species” or “mass” in the above) and one or more key-value pairs. These key-value pairs may continue until either another “key” keyword is given or the end of the command line is reached. Thus, the above could equivalently be written as

kim property modify 1 key species source-value Al       &
                      key mass    source-value 26.98154 &
                      key mass    source-unit  amu

As an example of modifying multiple key-value pairs belonging to the map of a single property key, the following command modifies the map of the “cohesive-potential-energy” property key to contain the key “source-unit” which is assigned a value of “eV” and the key “digits” which is assigned a value of 5,

kim property modify 2 key cohesive-potential-energy source-unit eV digits 5

Note

The relevant data types of the values in the map are handled automatically based on the specification of the key in the KIM Property Definition. In the example above, this means that the value “eV” will automatically be interpreted as a string while the value 5 will be interpreted as an integer.

The values contained in maps can either be scalars, as in all of the examples above, or arrays depending on which is stipulated in the corresponding Property Definition. For one-dimensional arrays, a single one-based index must be supplied that indicates which element of the array is to be modified. For multidimensional arrays, multiple indices must be given depending on the dimensionality of the array.

Note

All array indexing used by kim property modify is one-based, i.e. the indices are enumerated 1, 2, 3, …

Note

The dimensionality of arrays are defined in the the corresponding Property Definition. The extent of each dimension of an array can either be a specific finite number or indefinite and determined at run time. If an array has a fixed extent, attempting to modify an out-of-range index will fail with an error message.

For example, the “species” property key of the cohesive-energy-relation-cubic-crystal property is a one-dimensional array that can contain any number of entries based on the number of atoms in the unit cell of a given cubic crystal. To assign an array containing the string “Al” four times to the “source-value” key of the “species” property key, we can do so by issuing:

kim property modify 2 key species source-value 1 Al
kim property modify 2 key species source-value 2 Al
kim property modify 2 key species source-value 3 Al
kim property modify 2 key species source-value 4 Al

Note

No declaration of the number of elements in this array was given; kim property modify will automatically handle memory management to allow an arbitrary number of elements to be added to the array.

Note

In the event that kim property modify is used to set the value of an array index without having set the values of all lesser indices, they will be assigned default values based on the data type associated with the key in the map:

Data type

Default value

int

0

float

0.0

string

""

file

""

For example, doing the following:

kim property create 2 cohesive-energy-relation-cubic-crystal
kim property modify 2 key species source-value 4 Al

will result in the “source-value” key in the map for the property key “species” being assigned the array [“”, “”, “”, “Al”].

For convenience, the index argument provided may refer to an inclusive range of indices by specifying two integers separated by a colon (the first integer must be less than or equal to the second integer, and no whitespace should be included). Thus, the snippet above could equivalently be written:

kim property modify 2 key species source-value 1:4 Al Al Al Al

Calling this command with a non-positive index, e.g. kim property modify 2 key species source-value 0 Al, or an incorrect number of input arguments, e.g. kim property modify 2 key species source-value 1:4 Al Al, will result in an error.

As an example of modifying multidimensional arrays, consider the “basis-atoms” key in the cohesive-energy-relation-cubic-crystal property definition. This is a two-dimensional array containing the fractional coordinates of atoms in the unit cell of the cubic crystal. In the case of, e.g. a conventional fcc unit cell, the “source-value” key in the map associated with this key should be assigned the following value:

[[0.0, 0.0, 0.0],
 [0.5, 0.5, 0.0],
 [0.5, 0.0, 0.5],
 [0.0, 0.5, 0.5]]

While each of the twelve components could be set individually, we can instead set each row at a time using colon notation:

kim property modify 2 key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0
kim property modify 2 key basis-atom-coordinates source-value 2 1:3 0.5 0.5 0.0
kim property modify 2 key basis-atom-coordinates source-value 3 1:3 0.5 0.0 0.5
kim property modify 2 key basis-atom-coordinates source-value 4 1:3 0.0 0.5 0.5

Where the first index given refers to a row and the second index refers to a column. We could, instead, choose to set each column at a time like so:

kim property modify 2 key basis-atom-coordinates source-value 1:4 1 0.0 0.5 0.5 0.0 &
                      key basis-atom-coordinates source-value 1:4 2 0.0 0.5 0.0 0.5 &
                      key basis-atom-coordinates source-value 1:4 3 0.0 0.0 0.5 0.5

Note

Multiple calls of kim property modify made for the same instance ID can be combined into a single invocation, meaning the following are both valid:

kim property modify 2 key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 &
                      key basis-atom-coordinates source-value 2 1:3 0.5 0.5 0.0 &
                      key basis-atom-coordinates source-value 3 1:3 0.5 0.0 0.5 &
                      key basis-atom-coordinates source-value 4 1:3 0.0 0.5 0.5

kim property modify 2 key short-name source-value 1 fcc                         &
                      key species source-value 1:4 Al Al Al Al                  &
                      key a source-value 1:5 3.9149 4.0000 4.032 4.0817 4.1602  &
                            source-unit angstrom                                &
                            digits 5                                            &
                      key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 &
                      key basis-atom-coordinates source-value 2 1:3 0.5 0.5 0.0 &
                      key basis-atom-coordinates source-value 3 1:3 0.5 0.0 0.5 &
                      key basis-atom-coordinates source-value 4 1:3 0.0 0.5 0.5

Note

For multidimensional arrays, only one colon-separated range is allowed in the index listing. Therefore,

kim property modify 2 key basis-atom-coordinates 1 1:3 0.0 0.0 0.0

is valid but

kim property modify 2 key basis-atom-coordinates 1:2 1:3 0.0 0.0 0.0 0.0 0.0 0.0

is not.

Note

After one sets a value in a map with the kim property modify command, additional calls will overwrite the previous value.

Remove

kim property remove instance_id key key_name

The kim property remove command can be used to remove a property key from a property instance. For example,

kim property remove 2 key basis-atom-coordinates

Destroy

kim property destroy instance_id

The kim property destroy command deletes a previously created property instance ID. For example,

kim property destroy 2

Note

If this command is called with an instance ID that does not exist, no error is raised.

Dump

The kim property dump command can be used to write the content of all currently defined property instances to a file:

kim property dump file

For example,

kim property dump results.edn

Note

Issuing the kim property dump command clears all existing property instances from memory.

Citation of OpenKIM IMs

When publishing results obtained using OpenKIM IMs researchers are requested to cite the OpenKIM project (Tadmor), KIM API (Elliott), and the specific IM codes used in the simulations, in addition to the relevant scientific references for the IM. The citation format for an IM is displayed on its page on OpenKIM along with the corresponding BibTex file, and is automatically added to the LAMMPS citation reminder.

Citing the IM software (KIM infrastructure and specific PM or SM codes) used in the simulation gives credit to the researchers who developed them and enables open source efforts like OpenKIM to function.

Restrictions

The kim command is part of the KIM package. It is only enabled if LAMMPS is built with that package. A requirement for the KIM package, is the KIM API library that must be downloaded from the OpenKIM website and installed before LAMMPS is compiled. When installing LAMMPS from binary, the kim-api package is a dependency that is automatically downloaded and installed. The kim query command requires the libcurl library to be installed. The kim property command requires Python 3.6 or later and the kim-property python package to be installed. See the KIM section of the Packages details for details.

Furthermore, when using kim command to run KIM SMs, any packages required by the native potential being used or other commands or fixes that it invokes must be installed.