uf3.data.io.parse_lammps_outputs

parse_lammps_outputs(path: str, lammps_aliases: Dict[int, str], prefix: Optional[str] = None, column_subs: Dict[str, str] = {'PotEng': 'energy'}, log_fname: str = 'log.lammps', dump_fname: str = 'dump.lammpstrj', atoms_key: str = 'geometry', size_key: str = 'size', log_regex: Optional[str] = None) → pandas.core.frame.DataFrame[source]

Convenience wrapper for parsing both LAMMPS log and dump in a run directory.

Parameters

  • path (str) – path to run directory.

  • lammps_aliases (dict) – optional map of LAMMPS atom types to species.

  • prefix (str) – prefix for DataFrame index. e.g. “bulk” -> [bulk_0, bulk_1, bulk_2, …]

  • column_subs (dict) – column name substitutions for DataFrame. Default {“PotEng”: “energy”}.

  • log_fname – log filenane, default “log.lammps”.

  • dump_fname (str) – dump filename, default “dump.lammpstrj”.

  • atoms_key (str) – column name for geometries, default “geometry”. Modify when parsed geometries are part of a larger pipeline.

  • size_key (str) – column name for number of atoms per geometry, default “size”.

  • log_regex (str) – Regular expression for identifying step information. Defaults to “n(Step[^n]+n[^A-Za-z]+)(?:Loop time of)”

Returns

Indexed by timestep, containing

columns from log (e.g. Temp, PotEng) and column containing corresponding ase.Atoms snapshots.

Return type

df (pandas.DataFrame)