Source code for moyopy.interface

from __future__ import annotations

from warnings import warn

try:
    import ase
    from pymatgen.core import Composition, Element, Structure
    from pymatgen.io.ase import MSONAtoms
except ImportError:
    raise ImportError("Try installing dependencies with `pip install moyopy[interface]`")

import moyopy




class MoyoAdapter:
    @staticmethod


    def get_structure(
        cell: moyopy.Cell, unique_species_mapping: dict[int, Composition] | None = None
    ) -> Structure:
        """Convert a Moyo Cell to a pymatgen Structure.

        If the Cell was created from a disordered Structure, the unique_species_mapping should be
        provided to reconstruct the original species.

        Parameters
        ----------
        cell : moyopy.Cell
            The Moyo Cell to convert.
        unique_species_mapping : dict[int, Composition] | None
            A mapping from integer indices used in the Moyo Cell to the original pymatgen
            SpeciesLike objects. If None, assumes the Cell was created from an ordered Structure.

        Returns
        -------
        structure : Structure
            The converted pymatgen Structure object.
        """
        if unique_species_mapping:
            species = [unique_species_mapping[number] for number in cell.numbers]
        else:
            species = [Element.from_Z(number) for number in cell.numbers]
        return Structure(lattice=cell.basis, species=species, coords=cell.positions)


    @staticmethod


    def get_atoms(cell: moyopy.Cell) -> ase.Atoms:
        atoms = ase.Atoms(
            cell=cell.basis,
            scaled_positions=cell.positions,
            numbers=cell.numbers,
            pbc=True,
        )
        return atoms


    @staticmethod


    def from_structure(structure: Structure) -> moyopy.Cell:
        if not structure.is_ordered:
            raise ValueError("Structure must be ordered. Use from_disordered_structure instead.")

        basis = structure.lattice.matrix.tolist()
        positions = structure.frac_coords.tolist()
        numbers = [site.specie.Z for site in structure]

        return moyopy.Cell(
            basis=basis,
            positions=positions,
            numbers=numbers,
        )


    @staticmethod


    def from_disordered_structure(
        structure: Structure,
    ) -> tuple[moyopy.Cell, dict[int, Composition]]:
        """Convert a disordered pymatgen Structure to a Moyo Cell.

        Parameters
        ----------
        structure : Structure
            A pymatgen Structure object, which may contain disordered sites.

        Returns
        -------
        cell : moyopy.Cell
            The converted Moyo Cell object.
        unique_species_mapping : dict[int, Composition]
            A mapping from integer indices used in the Moyo Cell to the original pymatgen
            SpeciesLike objects.
        """
        if structure.is_ordered:
            warn("Structure is ordered. Consider using from_structure.")

        unique_species = {}
        for site in structure:
            key = site.species
            if key not in unique_species:
                unique_species[key] = len(unique_species)
        unique_species_mapping = {i: species for i, species in enumerate(unique_species)}

        basis = structure.lattice.matrix.tolist()
        positions = structure.frac_coords.tolist()
        numbers = [unique_species[site.species] for site in structure]
        cell = moyopy.Cell(
            basis=basis,
            positions=positions,
            numbers=numbers,
        )

        return cell, unique_species_mapping


    @staticmethod


    def from_atoms(atoms: ase.Atoms) -> moyopy.Cell:
        basis = list(atoms.cell)
        positions = atoms.get_scaled_positions()
        numbers = atoms.get_atomic_numbers()

        return moyopy.Cell(
            basis=basis,
            positions=positions,
            numbers=numbers,
        )


    @staticmethod


    def from_py_obj(struct: Structure | ase.Atoms | MSONAtoms) -> moyopy.Cell:
        """Convert a Python atomic structure object to a Moyo Cell.

        Args:
            struct: Currently supports pymatgen Structure, ASE Atoms, and MSONAtoms

        Returns:
            moyopy.Cell: The converted Moyo cell
        """
        if isinstance(struct, (ase.Atoms, MSONAtoms)):
            return MoyoAdapter.from_atoms(struct)
        elif isinstance(struct, Structure):
            return MoyoAdapter.from_structure(struct)
        else:
            cls_name = type(struct).__name__
            raise TypeError(f"Expected Structure, Atoms, or MSONAtoms, got {cls_name}")