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(): 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