uf3.data.io.atoms_from_df

atoms_from_df(df: pandas.core.frame.DataFrame, element_key: str = 'element', lammps_aliases: Optional[Dict[int, str]] = None, info: Optional[Dict[str, float]] = None, **atom_kwargs) → ase.atoms.Atoms[source]

Create ase.Atoms from DataFrame. Minimum required columns include: x, y, z, [element_key]

Parameters

  • df (pandas.DataFrame) – DataFrame of interest.

  • element_key (str) – column name corresponding to species.

  • lammps_aliases (dict) – optional map of aliases to species e.g. for LAMMPS atom types.

  • info (dict) – optional dictionary of scalars.

  • **atom_kwargs – arguments to pass to ase.Atoms, e.g. cell and pbc.

Returns

atoms (ase.Atoms)