relax_liquid 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.

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: The target temperature to relax to. Required.

  • pressure: The target hydrostatic pressure to relax to. Default value is 0.0 GPa

  • temperature_melt: The elevated temperature to first use to hopefully melt the initial configuration.

  • rdfcutoff: The cutoff distance to use for the RDF cutoff. If not given then will use 4 * r0, where r0 is the shortest atomic distance found in the given system configuration.

  • meltsteps: The number of npt integration steps to perform during the melting stage at the melt temperature to create an amorphous liquid structure. Default value is 50000.

  • coolsteps: The number of npt integration steps to perform during the cooling stage where the temperature is reduced from the melt temperature to the target temperature. Default value is 10000.

  • equilvolumesteps: The number of npt integration steps to perform during the volume equilibration stage where the system is held at the target temperature and pressure to obtain an estimate for the relaxed volume. Default value is 50000.

  • equilvolumesamples: The number of thermo samples from the end of the volume equilibration stage to use in computing the average volume. Cannot be larger than equilvolumesteps / 100. It is recommended to set smaller than the max to allow for some convergence time. Default value is 300.

  • equilenergysteps: The number of nvt integration steps to perform during the energy equilibration stage where the system is held at the target temperature to obtain an estimate for the total energy. Default value is 10000.

  • equilenergysamples: The number of thermo samples from the end of the energy equilibrium stage to use in computing the target total energy. Cannot be larger than equilenergysteps / 100. Default value is 100.

  • equilenergystyle: Indicates which scheme to use for computing the target total energy. Allowed values are ‘pe’ or ‘te’. For ‘te’, the average total energy from the equilenergysamples is used as the target energy. For ‘pe’, the average potential energy plus 3/2 N kB T is used as the target energy. Default value is ‘pe’.

  • runsteps: The number of nve integration steps to perform on the system to obtain measurements of MSD and RDF of the liquid. Default value is 50000.

  • dumpsteps: Dump files will be saved every this many steps during the runsteps simulation. Default is None, which sets dumpsteps equal to the sum of all other steps values so only the final configuration is saved.

  • restartsteps: Restart files will be saved every this many steps. Default is None which sets restartsteps equal to the sum of all other steps values so only the final configuration is saved.

  • randomseed: Random number seed used by LAMMPS in creating velocities and with the Langevin thermostat. Default is None which will select a random int between 1 and 900000000.