"""Converts ASE Atoms objects into MDMC Molecules."""
from typing import TYPE_CHECKING, List, Union, Optional
import numpy as np
import ase
from ase.geometry.analysis import Analysis
from MDMC.MD.structures import Atom, Molecule
from MDMC.MD.interactions import Bond, BondAngle, DihedralAngle
if TYPE_CHECKING:
from MDMC.MD import Structure, Universe, BondedInteraction
[docs]
def ASE_to_MDMC(atoms: ase.Atoms) -> List[Atom]:
"""
Convert an ASE Atoms object to a list of Atoms.
Parameters
----------
atoms: ase.Atoms
an ASE Atoms object.
Returns
-------
List[Atom]
a list of Atoms with bonds corresponding to the ASE Atoms object.
"""
# create MDMC Atom objects
atoms_list = [Atom(atom.symbol, atom.position, charge=atom.charge) for atom in atoms]
# the ASE Analysis object contains bond information; the properties unique_bonds,
# unique_angles and unique_dihedrals contain Bond, BondAngle and DihedralAngle
# information respectively.
analysis = Analysis(atoms)
interactions_list: List['BondedInteraction'] = []
# ase bond lists have the following structure:
# index X of the list contains all bonds that start at atom number X.
# e.g. if index 0 of unique_angles contains (1, 3) that means
# there is a bond angle of atoms 0—1—3
# (the same order as MDMC)
# one bond list is generated per neighbour list; we should only
# have one neighbour list here.
for index, bonds in enumerate(analysis.unique_bonds[0]):
interactions_list.extend([Bond(atoms_list[index],
atoms_list[bonded_atom])
for bonded_atom in bonds])
for index, bonds in enumerate(analysis.unique_angles[0]):
interactions_list.extend([BondAngle(atoms_list[index],
atoms_list[bonded_atoms[0]],
atoms_list[bonded_atoms[1]])
for bonded_atoms in bonds])
for index, bonds in enumerate(analysis.unique_dihedrals[0]):
interactions_list.extend([DihedralAngle(atoms_list[index],
atoms_list[bonded_atoms[0]],
atoms_list[bonded_atoms[1]],
atoms_list[bonded_atoms[2]])
for bonded_atoms in bonds])
return atoms_list
def _convert_to_ase_atom(atom: Atom) -> ase.Atom:
"""
Converts an MDMC ``Atom`` to an ``ase.Atom``
Parameters
----------
atom : Atom
An MDMC ``Atom`` object to be converted to an ``ase.Atom`` object
Returns
-------
ase.atom.Atom
An ``ASE.Atom`` object which is equivalent to ``atom``
"""
return ase.atom.Atom(position=atom.position,
mass=atom.mass,
symbol=atom.element.symbol,
charge=atom.charge)
[docs]
def MDMC_to_ASE(structure: Union['Structure', 'Universe', List[Atom]],
cell: Optional[np.ndarray] = None) -> ase.Atoms:
"""
Convert an MDMC Structure into an ase.Atoms object.
Note that ASE infers bonds from the atoms' covalent radius.
Parameters:
-----------
structure: Structure, Universe or List[Atom]
the MDMC object to convert.
cell: np.array, optional, default None
provides cell dimensions for the ASE Atoms object.
If None, the default cell size (0,0,0) is used.
Returns:
--------
ase.Atoms
an ASE Atoms object corresponding to the same structure.
"""
if isinstance(structure, list): # if list of atoms, compile into molecule
structure = Molecule(atoms=structure)
if cell is None:
cell = np.array([0., 0., 0.,])
return ase.Atoms([_convert_to_ase_atom(atom) for atom in structure.atoms], cell=cell)