point_defect_diffusion Input Terms

Calculation Metadata

Specifies metadata descriptors common to all calculation styles.

  • branch: A metadata group name that the calculation can be parsed by. Primarily meant for differentiating runs with different settings parameters.

LAMMPS and MPI Commands

Specifies the external commands for running LAMMPS and MPI.

  • lammps_command: The path to the executable for running LAMMPS on your system. Don’t include command line options.

  • mpi_command: The path to the MPI executable and any command line options to use for calling LAMMPS to run in parallel on your system. LAMMPS will run as a serial process if not given.

Interatomic Potential

Specifies the interatomic potential to use and the directory where any associated parameter files are located.

  • potential_file: The path to the potential_LAMMPS or potential_LAMMPS_KIM record that defines the interatomic potential to use for LAMMPS calculations.

  • potential_kim_id: If potential_file is a potential_LAMMPS_KIM record, this allows for the specification of which version of the KIM model to use by specifying a full kim model id. If not given, the newest known version of the kim model will be assumed.

  • potential_kim_potid: Some potential_LAMMPS_KIM records are associated with multiple potential entries. This allows for the clear specification of which potential (by potid) to associate with those kim models.This will affect the list of available symbols for the calculation.

  • potential_dir: The path to the directory containing any potential parameter files (eg. eam.alloy setfl files) that are needed for the potential. If not given, then any required files are expected to be in the working directory where the calculation is executed.

Initial System Configuration

Specifies the file and options to load for the initial atomic configuration.

  • load_file: The path to the initial configuration file to load.

  • load_style: The atomman.load() style indicating the format of the load_file.

  • load_options: A space-delimited list of key-value pairs for optional style-specific arguments used by atomman.load().

  • family: A metadata descriptor for relating the load_file back to the original crystal structure or prototype that the load_file was based on. If not given, will use the family field in load_file if load_style is ‘system_model’, or the file’s name otherwise.

  • symbols: A space-delimited list of the potential’s atom-model symbols to associate with the loaded system’s atom types. Required if load_file does not contain symbol/species information.

  • box_parameters: Specifies new box parameters to scale the loaded configuration by. Can be given either as a list of three or six numbers: ‘a b c’ for orthogonal boxes, or ‘a b c alpha beta gamma’ for triclinic boxes. The a, b, c parameters are in units of length and the alpha, beta, gamma angles are in degrees.

System Manipulations

Performs simple manipulations on the loaded initial system.

  • a_uvw: The Miller(-Bravais) crystal vector relative to the loaded system to orient with the a box vector of a resulting rotated system. Specified as three or four space-delimited numbers. Either all or none of the uvw parameters must be given.

  • b_uvw: The Miller(-Bravais) crystal vector relative to the loaded system to orient with the b box vector of a resulting rotated system. Specified as three or four space-delimited numbers. Either all or none of the uvw parameters must be given.

  • c_uvw: The Miller(-Bravais) crystal vector relative to the loaded system to orient with the c box vector of a resulting rotated system. Specified as three or four space-delimited numbers. Either all or none of the uvw parameters must be given.

  • atomshift: A rigid-body shift vector to apply to all atoms in the rotated configuration. Specified as three space-delimited numbers that are relative to the size of the system after rotating, but before sizemults have been applied. This allows for the same relative shift of similar systems regardless of box_parameters and sizemults. Default value is ‘0.0 0.0 0.0’ (i.e. no shift).

  • sizemults: Multiplication parameters to construct a supercell from the rotated system. Given as either three or six space-delimited integers. For three integers, each value indicates the number of replicas to make along the corresponding a, b, c box vector with negative values replicating in the negative Cartesian space. For six integers, the values are divided into three pairs with each pair indicating the number of ‘negative’ and ‘positive’ replications to make for a given a, b, c box vector.

Point Defect

Specifies the parameter set that defines a point defect.

  • pointdefect_file: The path to a point_defect record file that contains input parameters associated with a specific point defect or a set of point defects.

  • pointdefect_type: Indicates which type of point defect to generate. ‘v’ or ‘vacancy’ for a vacancy, ‘i’ or ‘interstitial’ for a position-based interstitial, ‘s’ or ‘substitutional’ for a substitutional, and ‘d’, ‘db’ or ‘dumbbell’ for a dumbbell interstitial.

  • pointdefect_atype: Indicates the integer atom type to assign to an interstitial, substitutional, or dumbbell interstitial atom.

  • pointdefect_pos: Indicates the position where the point defect is to be placed. For the interstitial type, this cannot correspond to a current atom’s position. For the other styles, this must correspond to a current atom’s position.

  • pointdefect_dumbbell_vect: Specifies the dumbbell vector to use for a dumbbell interstitial. The atom defined by pointdefect_pos is shifted by -pointdefect_dumbbell_vect, and the inserted interstitial atom is placed at pointdefect_pos + pointdefect_dumbbell_vect.

  • pointdefect_scale: Boolean indicating if pointdefect_pos and pointdefect_dumbbell_vect are taken as absolute Cartesian vectors, or taken as scaled values relative to the loaded system. Default value is False.

Input/Output Units

Specifies the default units to use for the other input keys and to use for saving to the results file.

  • length_unit: The unit of length to use. Default value is ‘angstrom’.

  • pressure_unit: The unit of pressure to use. Default value is ‘GPa’.

  • energy_unit: The unit of energy to use. Default value is ‘eV’.

  • force_unit: The unit of force to use. Default value is ‘eV/angstrom’.

Run Parameters

  • temperature: Target temperature for the simulations. The NVT equilibrium steps will use this for the thermostat, then the energy scaled to try to capture this temperature for the NVE runs.

  • thermosteps: How often LAMMPS will print thermo data. Default value is runsteps//1000 or 1 if runsteps is less than 1000.

  • dumpsteps: How often LAMMPS will save the atomic configuration to a LAMMPS dump file. Default value is runsteps, meaning only the first and last states are saved.

  • runsteps: The number of MD integration steps to perform in the NVE run.

  • equilsteps: The number of NVT MD integration steps to perform prior to the NVE runsteps to allow the system to equilibriate.

  • randomseed: An int random number seed to use for generating initial velocities. A random int will be selected if not given.