kim_init command
kim_interactions command
kim_query command
kim_param command
Syntax
kim_init model user_units unitarg
kim_interactions typeargs
kim_query variable formatarg query_function queryargs
kim_param get param_name index_range variables formatarg
kim_param set param_name index_range values
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
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):
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 for kim_query] 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 preceed formatarg. [default for kim_param]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
param_name = name of a KIM portable model parameter
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)
values = new value(s) to replace the current value(s) of a KIM portable model parameter
Examples
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
kim_interactions Si
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 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
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Al"] units=["angstrom"]
kim_param get gamma 1 varGamma
kim_param set gamma 1 3.0
Description
The set of kim_commands provide a high-level wrapper around the Open Knowledgebase of Interatomic Models (OpenKIM) repository of interatomic models (IMs) (potentials and force fields), so that they can be used by LAMMPS scripts. These commands do not implement any computations directly, but rather generate LAMMPS input commands based on the information retrieved from the OpenKIM repository to initialize and activate OpenKIM IMs and query their predictions for use in the LAMMPS script. All LAMMPS input commands generated and executed by kim_commands are echoed to the LAMMPS log file.
Benefits of Using OpenKIM IMs
Employing OpenKIM IMs provides LAMMPS users with multiple benefits:
Reliability
All content archived in OpenKIM is reviewed by the KIM Editor for quality.
IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded.
IMs in OpenKIM are exhaustively tested using KIM Tests that compute a host of material properties, and KIM Verification Checks that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM’s page accessible through the OpenKIM browse interface.
Reproducibility
Each IM in OpenKIM is issued a unique identifier (KIM ID), which includes a version number (last three digits). Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID.
OpenKIM is a member organization of DataCite and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility.
Convenience
IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the kim_init command documented on this page.
The kim_query web query tool provides the ability to use the predictions of IMs for supported material properties (computed via KIM Tests) as part of a LAMMPS input script setup and analysis.
Support is provided for unit conversion between the unit style used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units.
Types of IMs in OpenKIM
There are two types of IMs archived in OpenKIM:
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).
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_000
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-build 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
Two commands are employed when using OpenKIM IMs, 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.
See the examples/kim directory for example input scripts that use KIM PMs and KIM SMs.
OpenKIM IM Initialization (kim_init)
The kim_init mode 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 command 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.
Here is an example of a LAMMPS script to compute the cohesive energy of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994) potential for Al:
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
boundary p p p
lattice fcc 4.032
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))/${_u_energy}
print "Cohesive Energy = ${EcJ} eV"
The above script will end with an error in the kim_init line if the IM is changed to another potential for Al that does not work with metal units. To address this kim_init offers the unit_conversion_mode as shown below. If unit conversion mode is active, then kim_init calls the LAMMPS units command to set the units to the IM’s required or preferred units. Conversion factors between the IM’s units and the user_units are defined for all physical quantities (mass, distance, etc.). (Note that converting to or from the “lj” unit style is not supported.) These factors are stored as internal style variables with the following standard names:
_u_mass
_u_distance
_u_time
_u_energy
_u_velocity
_u_force
_u_torque
_u_temperature
_u_pressure
_u_viscosity
_u_charge
_u_dipole
_u_efield
_u_density
If desired, the input script can be designed to work with these conversion factors so that the script will work without change with any OpenKIM IM. (This approach is used in the OpenKIM Testing Framework.) For example, the script given above for the cohesive energy of fcc Al can be rewritten to work with any IM regardless of units. The following script constructs an fcc lattice with a lattice parameter defined in meters, computes the total energy, and prints the cohesive energy in Joules regardless of the units of the IM.
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode
boundary p p p
lattice fcc 4.032e-10*${_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*${_u_mass}
kim_interactions Al
run 0
variable Ec_in_J equal (pe/count(all))/${_u_energy}
print "Cohesive Energy = ${Ec_in_J} J"
Note the multiplication by ${_u_distance} and ${_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 ${_u_energy} to convert from the IM’s energy units to SI units (Joule). This script will work correctly for any IM for Al (KIM PM or SM) selected by the kim_init command.
Care must be taken to apply unit conversion to dimensional variables read in from a file. For example, if a configuration of atoms is read in from a dump file using the read_dump command, the following can be done to convert the box and all atomic positions to the correct units:
variable xyfinal equal xy*${_u_distance}
variable xzfinal equal xz*${_u_distance}
variable yzfinal equal yz*${_u_distance}
change_box all x scale ${_u_distance} &
y scale ${_u_distance} &
z scale ${_u_distance} &
xy final ${xyfinal} &
xz final ${xzfinal} &
yz final ${yzfinal} &
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 reax/c lmp_control safezone 2.0 mincap 100
pair_coeff * * ffield.reax.rdx C H N O
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
Note that 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 also that 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.
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.
Note
The kim_query command must be preceded by a kim_init command.
The syntax for the kim_query command is as follows:
kim_query variable formatarg query_function queryargs
The result of the query is stored in one or more string style variables as determined by the optional formatarg argument documented above. 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. (Note that the “explicit” setting of formatarg is not supported by kim_query.)
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 require the model keyword, which identifies the IM whose predictions are being queried. This keyword is automatically generated by kim_query based on the IM set in kim_init and must not be specified as an argument to 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}
...
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 that 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 ${a0}*${_u_distance}”.
Define an equilibrium hcp crystal
kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal
boundary p p p
kim_query latconst split get_lattice_constant_hexagonal crystal=["hcp"] species=["Zr"] units=["angstrom"]
variable a0 equal latconst_1
variable c0 equal latconst_2
variable c_to_a equal ${c0}/${a0}
lattice custom ${a0} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 ${c_to_a} &
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.) For convenience the variables a0 and c0 are created in order to make the remainder of the input script more readable.
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 ${a0}*${alpha}*${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 from Etot the ideal fcc cohesive energy of the atoms in the system obtained from OpenKIM for the Ercolessi and Adams (1994) potential.
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. The values of these parameters 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 get/set commands must be preceded by kim_init. The kim_param set command must additionally 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.
The syntax for the kim_param command is as follows:
kim_param get param_name index_range variable formatarg
kim_param set param_name index_range values
Here, param_name is the name of a KIM PM 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.
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_param get A 1 VARA
In this case, 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_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
...
kim_param get A 1 VARA B 1 VARB
This retrieves the A and B parameters of the SW potential and stores 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_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_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
...
kim_param get lambda 15:17 LAMS list
variable LAM_VALUE index ${LAMS}
label loop_on_lambda
...
... do something with 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_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
...
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.
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 log.cite file.
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 set of kim_commands 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. See the KIM section of the Packages details for details.
Furthermore, when using kim_commands to run KIM SMs, any packages required by the native potential being used or other commands or fixes that it invokes must be installed.