Convert an OPTIMADE structure, in the format of
StructureResource
to an ASE Atoms object.
This conversion function relies on the ASE code.
For more information on the ASE code see their documentation.
from_ase_atoms(atoms)
Convert an ASE Atoms object into an OPTIMADE StructureResourceAttributes model.
Parameters:
| Name |
Type |
Description |
Default |
atoms
|
Atoms
|
The ASE Atoms object to convert.
|
required
|
Returns:
| Type |
Description |
StructureResourceAttributes
|
An OPTIMADE StructureResourceAttributes model, which can be converted to a raw Python
dictionary with .model_dump() or to JSON with .model_dump_json().
|
Source code in optimade/adapters/structures/ase.py
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158 | def from_ase_atoms(atoms: Atoms) -> StructureResourceAttributes:
"""Convert an ASE `Atoms` object into an OPTIMADE `StructureResourceAttributes` model.
Parameters:
atoms: The ASE `Atoms` object to convert.
Returns:
An OPTIMADE `StructureResourceAttributes` model, which can be converted to a raw Python
dictionary with `.model_dump()` or to JSON with `.model_dump_json()`.
"""
if not isinstance(atoms, Atoms):
raise RuntimeError(
f"Cannot convert type {type(atoms)} into an OPTIMADE `StructureResourceAttributes` model."
)
attributes = {}
attributes["cartesian_site_positions"] = atoms.positions.tolist()
attributes["lattice_vectors"] = atoms.cell.tolist()
attributes["species_at_sites"] = atoms.get_chemical_symbols()
attributes["elements_ratios"] = elements_ratios_from_species_at_sites(
attributes["species_at_sites"]
)
attributes["species"] = species_from_species_at_sites(
attributes["species_at_sites"]
)
attributes["dimension_types"] = [int(_) for _ in atoms.pbc.tolist()]
attributes["nperiodic_dimensions"] = sum(attributes["dimension_types"])
attributes["nelements"] = len(attributes["species"])
attributes["elements"] = sorted([_.name for _ in attributes["species"]])
attributes["nsites"] = len(attributes["species_at_sites"])
attributes["chemical_formula_descriptive"] = atoms.get_chemical_formula()
attributes["chemical_formula_reduced"] = reduce_formula(
atoms.get_chemical_formula()
)
attributes["chemical_formula_anonymous"] = anonymize_formula(
attributes["chemical_formula_reduced"],
)
attributes["last_modified"] = None
attributes["immutable_id"] = None
attributes["structure_features"] = []
for key in atoms.info:
optimade_key = key.lower()
if not key.startswith(f"_{EXTRA_FIELD_PREFIX}"):
optimade_key = f"_{EXTRA_FIELD_PREFIX}_{optimade_key}"
attributes[optimade_key] = atoms.info[key]
return StructureResourceAttributes(**attributes)
|
get_ase_atoms(optimade_structure)
Get ASE Atoms from OPTIMADE structure.
Caution
Cannot handle partial occupancies (this includes vacancies).
Parameters:
Returns:
Source code in optimade/adapters/structures/ase.py
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106 | def get_ase_atoms(optimade_structure: OptimadeStructure) -> Atoms:
"""Get ASE `Atoms` from OPTIMADE structure.
Caution:
Cannot handle partial occupancies (this includes vacancies).
Parameters:
optimade_structure: OPTIMADE structure.
Returns:
ASE `Atoms` object.
"""
if "optimade.adapters" in repr(globals().get("Atoms")):
warn(ASE_NOT_FOUND, AdapterPackageNotFound)
return None
attributes = optimade_structure.attributes
# Cannot handle partial occupancies
if StructureFeatures.DISORDER in attributes.structure_features:
raise ConversionError(
"ASE cannot handle structures with partial occupancies, sorry."
)
species = attributes.species
# If species is missing, infer data from species_at_sites
if not species:
species = species_from_species_at_sites(attributes.species_at_sites) # type: ignore[arg-type]
optimade_species: dict[str, OptimadeStructureSpecies] = {_.name: _ for _ in species}
# Since we've made sure there are no species with more than 1 chemical symbol,
# asking for index 0 will always work.
if "X" in [specie.chemical_symbols[0] for specie in optimade_species.values()]:
raise ConversionError(
"ASE cannot handle structures with unknown ('X') chemical symbols, sorry."
)
atoms = []
for site_number in range(attributes.nsites): # type: ignore[arg-type]
species_name = attributes.species_at_sites[site_number] # type: ignore[index]
site = attributes.cartesian_site_positions[site_number] # type: ignore[index]
current_species = optimade_species[species_name]
# Argument above about chemical symbols also holds here
mass = None
if current_species.mass:
mass = current_species.mass[0]
atoms.append(
Atom(symbol=current_species.chemical_symbols[0], position=site, mass=mass)
)
info = {}
for key in attributes.model_dump().keys():
if key.startswith("_"):
ase_key = key
if key.startswith(f"_{EXTRA_FIELD_PREFIX}_"):
ase_key = "".join(key.split(f"_{EXTRA_FIELD_PREFIX}_")[1:])
info[ase_key] = getattr(attributes, key)
return Atoms(
symbols=atoms,
cell=attributes.lattice_vectors,
pbc=attributes.dimension_types,
info=info if info else None,
)
|