Source code for scm.appleandp.packmol

from scm.plams import packmol, Molecule
from .APPLEandP_atomtyper import get_APPLEandP_atomtypes
from typing import List


[docs]def appleandp_packmol(molecules: List[Molecule], forcefield_file: str, **kwargs):
    """
    molecules: list of Molecule
        If they are ions they should have the molecule.properties.charge set to the charge

    forcefield_file: str
        The force field file will be written here. It will be overwritten if it already exists

    ``**kwargs``: various options
        See the documentation for the ``packmol()`` function

    Returns: a PLAMS Molecule created with packmol

    This function differs from the PLAMS implementation of packmol in that it also writes out a force field file for use with APPLE&P.
    """

    # Build a box with packmol:
    box = packmol(molecules=molecules, **kwargs)

    # Define all the species we have in the box:
    label2charge = {mol.label(): int(mol.properties.get("charge", 0)) for mol in molecules}

    # Assign bonds and atom-types for the box and the .ff file for that system:
    box, forcefield = get_APPLEandP_atomtypes(box, label2charge=label2charge)

    with open(forcefield_file, "w") as f:
        f.write(forcefield)

    return box