point_defect_diffusion.py

Calculation functions

pointdiffusion(lammps_command: str, system: System, potential: Potential, point_kwargs: list | dict, mpi_command: str | None = None, temperature: float = 300.0, runsteps: int = 200000, thermosteps: int | None = None, dumpsteps: int = 0, equilsteps: int = 20000, randomseed: int | None = None) → dict

Evaluates the diffusion rate of a point defect at a given temperature. This method will run two simulations: an NVT run at the specified temperature to equilibrate the system, then an NVE run to measure the defect’s diffusion rate. The diffusion rate is evaluated using the mean squared displacement of all atoms in the system, and using the assumption that diffusion is only due to the added defect(s).

Parameters:

  • lammps_command (str) – Command for running LAMMPS.

  • system (atomman.System) – The system to perform the calculation on.

  • potential (atomman.lammps.Potential) – The LAMMPS implemented potential to use.

  • point_kwargs (dict or list of dict) – One or more dictionaries containing the keyword arguments for the atomman.defect.point() function to generate specific point defect configuration(s).

  • mpi_command (str, optional) – The MPI command for running LAMMPS in parallel. If not given, LAMMPS will run serially.

  • temperature (float, optional) – The temperature to run at (default is 300.0).

  • runsteps (int, optional) – The number of integration steps to perform (default is 200000).

  • thermosteps (int, optional) – Thermo values will be reported every this many steps (default is 100).

  • dumpsteps (int or None, optional) – Dump files will be saved every this many steps (default is 0, which does not output dump files).

  • equilsteps (int, optional) – The number of timesteps at the beginning of the simulation to exclude when computing average values (default is 20000).

  • randomseed (int or None, optional) – 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.)

Returns:

Dictionary of results consisting of keys:

  • ’natoms’ (int) - The number of atoms in the system.

  • ’temp’ (float) - The mean measured temperature.

  • ’pxx’ (float) - The mean measured normal xx pressure.

  • ’pyy’ (float) - The mean measured normal yy pressure.

  • ’pzz’ (float) - The mean measured normal zz pressure.

  • ’Epot’ (numpy.array) - The mean measured total potential energy.

  • ’temp_std’ (float) - The standard deviation in the measured temperature values.

  • ’pxx_std’ (float) - The standard deviation in the measured normal xx pressure values.

  • ’pyy_std’ (float) - The standard deviation in the measured normal yy pressure values.

  • ’pzz_std’ (float) - The standard deviation in the measured normal zz pressure values.

  • ’Epot_std’ (float) - The standard deviation in the measured total potential energy values.

  • ’dx’ (float) - The computed diffusion constant along the x-direction.

  • ’dy’ (float) - The computed diffusion constant along the y-direction.

  • ’dz’ (float) - The computed diffusion constant along the y-direction.

  • ’d’ (float) - The total computed diffusion constant.

Return type:

dict