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atoms

Schemas for storing metadata about Atoms objects.

atoms_to_metadata 

atoms_to_metadata(
    atoms: Atoms,
    additional_fields: dict[str, Any] | None = None,
) -> AtomsSchema

Convert an ASE Atoms object to a dict suitable for storage in MongoDB.

Parameters:

  • atoms (Atoms) –

    ASE Atoms object to store in {"atoms": atoms}

  • additional_fields (dict[str, Any] | None, default: None ) –

    Additional fields to add to the document.

Returns:

  • AtomsSchema –

    Dict of metadata about the Atoms object.

Source code in quacc/schemas/atoms.py 
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def atoms_to_metadata(
    atoms: Atoms, additional_fields: dict[str, Any] | None = None
) -> AtomsSchema:
    """
    Convert an ASE Atoms object to a dict suitable for storage in MongoDB.

    Parameters
    ----------
    atoms
        ASE Atoms object to store in {"atoms": atoms}
    additional_fields
        Additional fields to add to the document.

    Returns
    -------
    AtomsSchema
        Dict of metadata about the Atoms object.
    """
    additional_fields = additional_fields or {}
    atoms = copy_atoms(atoms)
    results = {}
    atoms.calc = None

    # Strip the dummy atoms, if present
    if "X" in atoms.get_chemical_symbols():
        del atoms[[atom.index for atom in atoms if atom.symbol == "X"]]

    # Get Pymatgen Structure/Molecule metadata
    if atoms.pbc.any():
        structure = AseAtomsAdaptor().get_structure(atoms)
        structure_metadata = StructureMetadata().from_structure(structure).model_dump()
        results["structure_metadata"] = structure_metadata
    else:
        mol = AseAtomsAdaptor().get_molecule(atoms, charge_spin_check=False)
        molecule_metadata = MoleculeMetadata().from_molecule(mol).model_dump()
        for key in ["charge", "spin_multiplicity", "nelectrons"]:
            del molecule_metadata[key]
        results["molecule_metadata"] = molecule_metadata

    # Store Atoms object
    results["atoms"] = atoms

    return results | additional_fields