mooonpy.template.mapfile module

Reaction map-file writer for LAMMPS fix bond/react.

mooonpy.template.mapfile.write_mapfile(filename, rxn_map)[source]

Write a reaction map file.

Parameters:

  • filename (str or Path) – Output path.

  • rxn_map (dict) –

    Map data structure. Required keys:

    • 'Comment' (str): free-form comment for the header.

    • 'InitiatorIDs' (list[int]): the two initiator atom ids.

    • 'EdgeIDs' (list[int]): may be empty.

    • 'DeleteIDs' (list[int]): may be empty.

    • 'Equivalences' (list[tuple[int, int]]): (pre_id, post_id) pairs.

    • 'CustomChargesQedge' (list[int], optional): if non-empty, emits a CustomChargesQedge section so fix bond/react knows which atoms get charges remapped.