Source code for pymatgen.io.ase

# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides conversion between the Atomic Simulation Environment
Atoms object and pymatgen Structure objects.
"""


__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Mar 8, 2012"

from pymatgen.core.structure import Molecule, Structure

try:
    from ase import Atoms
    ase_loaded = True
except ImportError:
    ase_loaded = False


[docs]class AseAtomsAdaptor: """ Adaptor serves as a bridge between ASE Atoms and pymatgen objects. """
[docs] @staticmethod def get_atoms(structure, **kwargs): """ Returns ASE Atoms object from pymatgen structure or molecule. Args: structure: pymatgen.core.structure.Structure or pymatgen.core.structure.Molecule **kwargs: other keyword args to pass into the ASE Atoms constructor Returns: ASE Atoms object """ if not structure.is_ordered: raise ValueError("ASE Atoms only supports ordered structures") if not ase_loaded: raise ImportError("AseAtomsAdaptor requires ase package.\n" "Use `pip install ase` or `conda install ase -c conda-forge`") symbols = [str(site.specie.symbol) for site in structure] positions = [site.coords for site in structure] if hasattr(structure, "lattice"): cell = structure.lattice.matrix pbc = True else: cell = None pbc = None return Atoms(symbols=symbols, positions=positions, pbc=pbc, cell=cell, **kwargs)
[docs] @staticmethod def get_structure(atoms, cls=None): """ Returns pymatgen structure from ASE Atoms. Args: atoms: ASE Atoms object cls: The Structure class to instantiate (defaults to pymatgen structure) Returns: Equivalent pymatgen.core.structure.Structure """ symbols = atoms.get_chemical_symbols() positions = atoms.get_positions() lattice = atoms.get_cell() cls = Structure if cls is None else cls return cls(lattice, symbols, positions, coords_are_cartesian=True)
[docs] @staticmethod def get_molecule(atoms, cls=None): """ Returns pymatgen molecule from ASE Atoms. Args: atoms: ASE Atoms object cls: The Molecule class to instantiate (defaults to pymatgen molecule) Returns: Equivalent pymatgen.core.structure.Molecule """ symbols = atoms.get_chemical_symbols() positions = atoms.get_positions() cls = Molecule if cls is None else cls return cls(symbols, positions)