atomistics.calculators.lammps.libcalculator.calc_molecular_dynamics_thermal_expansion_with_lammpslib

atomistics.calculators.lammps.libcalculator.calc_molecular_dynamics_thermal_expansion_with_lammpslib#

atomistics.calculators.lammps.libcalculator.calc_molecular_dynamics_thermal_expansion_with_lammpslib(structure: Atoms, potential_dataframe: pandas.DataFrame, Tstart: float = 15.0, Tstop: float = 1500.0, Tstep: int = 5, Tdamp: float = 0.1, run: int = 100, thermo: int = 100, timestep: float = 0.001, Pstart: float = 0.0, Pstop: float = 0.0, Pdamp: float = 1.0, seed: int = 4928459, dist: str = 'gaussian', couple_xyz: bool = False, lmp: LammpsASELibrary | None = None, output_keys: Iterable[str] = ('temperatures', 'volumes'), **kwargs) → dict[source]#

Compute thermal expansion via NPT MD across a temperature range using the LAMMPS library interface.

Runs lammps_thermal_expansion_loop over temperatures from Tstart to Tstop in steps of Tstep.

Parameters:

  • structure (Atoms) – The input structure.

  • potential_dataframe (pandas.DataFrame) – DataFrame with "Species" and "Config" columns.

  • Tstart (float) – Starting temperature in K. Defaults to 15.0.

  • Tstop (float) – Ending temperature in K (inclusive). Defaults to 1500.0.

  • Tstep (int) – Temperature increment in K. Defaults to 5.

  • Tdamp (float) – Thermostat damping parameter in ps. Defaults to 0.1.

  • run (int) – Number of MD timesteps per temperature point. Defaults to 100.

  • thermo (int) – Thermo output frequency in timesteps. Defaults to 100.

  • timestep (float) – MD timestep in ps. Defaults to 0.001.

  • Pstart (float) – Starting pressure in bar. Defaults to 0.0.

  • Pstop (float) – Ending pressure in bar. Defaults to 0.0.

  • Pdamp (float) – Barostat damping parameter in ps. Defaults to 1.0.

  • seed (int) – Random seed for velocity initialisation. Defaults to 4928459.

  • dist (str) – Velocity distribution type. Defaults to "gaussian".

  • couple_xyz (bool) – Whether to couple all three box dimensions (isotropic pressure). Defaults to False.

  • lmp (LammpsASELibrary | None) – Existing LAMMPS library instance to reuse.

  • output_keys (Iterable[str]) – Which output quantities to return.

  • **kwargs – Additional keyword arguments forwarded to lammps_thermal_expansion_loop.

Returns:

Thermal expansion output (temperatures and volumes) keyed by quantity name.

Return type:

dict