run_packmol

mbgdml.structure_gen.packmol_gen.run_packmol(work_dir, packmol_input_lines, packmol_path='packmol')

Generate structure by running packmol.

Output must be in the xyz format.

Parameters:

• work_dir (str) – Work directory to write input file and run packmol.

• packmol_input_lines (list) – Lines to a packmol input file.

• packmol_path (str, default: packmol) – Path to packmol binary. Default value assumes it can be located in your PATH.

Returns:

• numpy.ndarray – Atomic numbers of the structure

• numpy.ndarray – Cartesian coordinates of the structure.