calc_phonon.py

Calculation functions

phonon_quasiharmonic(lammps_command: str, ucell: System, potential: Potential, mpi_command: str | None = None, a_mult: int = 2, b_mult: int = 2, c_mult: int = 2, distance: float = 0.01, symprec: float = 1e-05, strainrange: float = 0.01, numstrains: int = 5) → dict

Function that performs phonon and quasiharmonic approximation calculations using phonopy and LAMMPS.

Parameters:

  • lammps_command (str) – Command for running LAMMPS.

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

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

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

  • a_mult (int, optional) – The a size multiplier to use on ucell before running the phonon calculation. Must be an int and not a tuple. Default value is 2.

  • b_mult (int, optional) – The b size multiplier to use on ucell before running the phonon calculation. Must be an int and not a tuple. Default value is 2.

  • c_mult (int, optional) – The c size multiplier to use on ucell before running the phonon calculation. Must be an int and not a tuple. Default value is 2.

  • distance (float, optional) – The atomic displacement distance used for computing the phonons. Default value is 0.01.

  • symprec (float, optional) – Absolute length tolerance to use in identifying symmetry of atomic sites and system boundaries. Default value is 1e-5.

  • strainrange (float, optional) – The range of strains to apply to the unit cell to use with the quasiharmonic calculations. Default value is 0.01.

  • numstrains (int, optional) – The number of strains to use for the quasiharmonic calculations. Must be an odd integer. If 1, then the quasiharmonic calculations will not be performed. Default value is 5.

phononcalc(lammps_command: str, ucell: System, potential: Potential, mpi_command: str | None = None, a_mult: int = 2, b_mult: int = 2, c_mult: int = 2, distance: float = 0.01, symprec: float = 1e-05, istrain: str = '', plot: bool = True, lammps_date: date | None = None) → dict

Uses phonopy to compute the phonons for a unit cell structure using a LAMMPS interatomic potential.

Parameters:

  • lammps_command (str) – Command for running LAMMPS.

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

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

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

  • a_mult (int, optional) – The a size multiplier to use on ucell before running the phonon calculation. Must be an int and not a tuple. Default value is 2.

  • b_mult (int, optional) – The b size multiplier to use on ucell before running the phonon calculation. Must be an int and not a tuple. Default value is 2.

  • c_mult (int, optional) – The c size multiplier to use on ucell before running the phonon calculation. Must be an int and not a tuple. Default value is 2.

  • distance (float, optional) – The atomic displacement distance used for computing the phonons. Default value is 0.01.

  • symprec (float, optional) – Absolute length tolerance to use in identifying symmetry of atomic sites and system boundaries. Default value is 1e-5.

  • istrain (str, optional) – A string to add to saved yaml files to ensure their uniqueness for the different strains explored by QHA. Default value is ‘’, which assumes only one calculation is being performed.

  • plot (bool, optional) – Flag indicating if band structure and DOS figures are to be generated. Default value is True.

  • lammps_date (datetime.date, optional) – The version date associated with lammps_command. If not given, the version will be identified.