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|
from __future__ import annotations
from emmet.core.settings import EmmetSettings
from emmet.core.symmetry import CrystalSystem
from emmet.core.vasp.material import MaterialsDoc
from pymatgen.core.structure import Structure
from mp_api.client.core import BaseRester, MPRestError
from mp_api.client.core.utils import validate_ids
from mp_api.client.routes.materials import (
AbsorptionRester,
AlloysRester,
BandStructureRester,
BondsRester,
ChemenvRester,
DielectricRester,
DosRester,
ElasticityRester,
ElectrodeRester,
ElectronicStructureRester,
EOSRester,
GrainBoundaryRester,
MagnetismRester,
OxidationStatesRester,
PhononRester,
PiezoRester,
ProvenanceRester,
RobocrysRester,
SimilarityRester,
SubstratesRester,
SummaryRester,
SurfacePropertiesRester,
SynthesisRester,
TaskRester,
ThermoRester,
XASRester,
)
_EMMET_SETTINGS = EmmetSettings() # type: ignore
class MaterialsRester(BaseRester[MaterialsDoc]):
suffix = "materials/core"
document_model = MaterialsDoc # type: ignore
supports_versions = True
primary_key = "material_id"
_sub_resters = [
"eos",
"similarity",
"tasks",
"xas",
"grain_boundaries",
"substrates",
"surface_properties",
"phonon",
"elasticity",
"thermo",
"dielectric",
"piezoelectric",
"magnetism",
"summary",
"robocrys",
"synthesis",
"insertion_electrodes",
"electronic_structure",
"electronic_structure_bandstructure",
"electronic_structure_dos",
"oxidation_states",
"provenance",
"bonds",
"alloys",
"absorption",
"chemenv",
]
# Materials subresters
eos: EOSRester
materials: MaterialsRester
similarity: SimilarityRester
tasks: TaskRester
xas: XASRester
grain_boundary: GrainBoundaryRester
substrates: SubstratesRester
surface_properties: SurfacePropertiesRester
phonon: PhononRester
elasticity: ElasticityRester
thermo: ThermoRester
dielectric: DielectricRester
piezoelectric: PiezoRester
magnetism: MagnetismRester
summary: SummaryRester
robocrys: RobocrysRester
synthesis: SynthesisRester
insertion_electrodes: ElectrodeRester
electronic_structure: ElectronicStructureRester
electronic_structure_bandstructure: BandStructureRester
electronic_structure_dos: DosRester
oxidation_states: OxidationStatesRester
provenance: ProvenanceRester
bonds: BondsRester
alloys: AlloysRester
absorption: AbsorptionRester
chemenv: ChemenvRester
def __dir__(self):
return dir(MaterialsRester) + self._sub_resters
def get_structure_by_material_id(
self, material_id: str, final: bool = True
) -> Structure | list[Structure]:
"""Get a structure for a given Materials Project ID.
Arguments:
material_id (str): Materials project ID
final (bool): Whether to get the final structure, or the list of initial
(pre-relaxation) structures. Defaults to True.
Returns:
structure (Union[Structure, List[Structure]]): Pymatgen structure object or list of
pymatgen structure objects.
"""
field = "structure" if final else "initial_structures"
response = self.search(material_ids=material_id, fields=[field])
if response:
response = (
response[0].model_dump() if self.use_document_model else response[0] # type: ignore
)
return response[field] if response else response # type: ignore
def search(
self,
material_ids: str | list[str] | None = None,
chemsys: str | list[str] | None = None,
crystal_system: CrystalSystem | None = None,
density: tuple[float, float] | None = None,
deprecated: bool | None = False,
elements: list[str] | None = None,
exclude_elements: list[str] | None = None,
formula: str | list[str] | None = None,
num_elements: tuple[int, int] | None = None,
num_sites: tuple[int, int] | None = None,
spacegroup_number: int | None = None,
spacegroup_symbol: str | None = None,
task_ids: list[str] | None = None,
volume: tuple[float, float] | None = None,
num_chunks: int | None = None,
chunk_size: int = 1000,
all_fields: bool = True,
fields: list[str] | None = None,
) -> list[MaterialsDoc] | list[dict]:
"""Query core material docs using a variety of search criteria.
Arguments:
material_ids (str, List[str]): A single Material ID string or list of strings
(e.g., mp-149, [mp-149, mp-13]).
chemsys (str, List[str]): A chemical system or list of chemical systems
(e.g., Li-Fe-O, Si-*, [Si-O, Li-Fe-P]).
crystal_system (CrystalSystem): Crystal system of material.
density (Tuple[float,float]): Minimum and maximum density to consider.
deprecated (bool): Whether the material is tagged as deprecated.
elements (List[str]): A list of elements.
exclude_elements (List[str]): A list of elements to exclude.
formula (str, List[str]): A formula including anonymized formula
or wild cards (e.g., Fe2O3, ABO3, Si*). A list of chemical formulas can also be passed
(e.g., [Fe2O3, ABO3]).
num_elements (Tuple[int,int]): Minimum and maximum number of elements to consider.
num_sites (Tuple[int,int]): Minimum and maximum number of sites to consider.
spacegroup_number (int): Space group number of material.
spacegroup_symbol (str): Space group symbol of the material in international short symbol notation.
task_ids (List[str]): List of Materials Project IDs to return data for.
volume (Tuple[float,float]): Minimum and maximum volume to consider.
num_chunks (int): Maximum number of chunks of data to yield. None will yield all possible.
chunk_size (int): Number of data entries per chunk.
all_fields (bool): Whether to return all fields in the document. Defaults to True.
fields (List[str]): List of fields in MaterialsCoreDoc to return data for.
Default is material_id, last_updated, and formula_pretty if all_fields is False.
Returns:
([MaterialsDoc], [dict]) List of material documents or dictionaries.
"""
query_params = {"deprecated": deprecated} # type: dict
if material_ids:
if isinstance(material_ids, str):
material_ids = [material_ids]
query_params.update({"material_ids": ",".join(validate_ids(material_ids))})
if formula:
if isinstance(formula, str):
formula = [formula]
query_params.update({"formula": ",".join(formula)})
if chemsys:
if isinstance(chemsys, str):
chemsys = [chemsys]
query_params.update({"chemsys": ",".join(chemsys)})
if elements:
query_params.update({"elements": ",".join(elements)})
if exclude_elements:
query_params.update({"exclude_elements": ",".join(exclude_elements)})
if task_ids:
query_params.update({"task_ids": ",".join(validate_ids(task_ids))})
query_params.update(
{
"crystal_system": crystal_system,
"spacegroup_number": spacegroup_number,
"spacegroup_symbol": spacegroup_symbol,
}
)
if num_sites:
query_params.update(
{"nsites_min": num_sites[0], "nsites_max": num_sites[1]}
)
if num_elements:
if isinstance(num_elements, int):
num_elements = (num_elements, num_elements)
query_params.update(
{"nelements_min": num_elements[0], "nelements_max": num_elements[1]}
)
if volume:
query_params.update({"volume_min": volume[0], "volume_max": volume[1]})
if density:
query_params.update({"density_min": density[0], "density_max": density[1]})
query_params = {
entry: query_params[entry]
for entry in query_params
if query_params[entry] is not None
}
return super()._search(
num_chunks=num_chunks,
chunk_size=chunk_size,
all_fields=all_fields,
fields=fields,
**query_params,
)
def find_structure(
self,
filename_or_structure,
ltol=_EMMET_SETTINGS.LTOL,
stol=_EMMET_SETTINGS.STOL,
angle_tol=_EMMET_SETTINGS.ANGLE_TOL,
allow_multiple_results=False,
) -> list[str] | str:
"""Finds matching structures from the Materials Project database.
Multiple results may be returned of "similar" structures based on
distance using the pymatgen StructureMatcher algorithm, however only
a single result should match with the same spacegroup, calculated to the
default tolerances.
Args:
filename_or_structure: filename or Structure object
ltol: fractional length tolerance
stol: site tolerance
angle_tol: angle tolerance in degrees
allow_multiple_results: changes return type for either
a single material_id or list of material_ids
Returns:
A matching material_id if one is found or list of results if allow_multiple_results
is True
Raises:
MPRestError
"""
params = {"ltol": ltol, "stol": stol, "angle_tol": angle_tol, "_limit": 1}
if isinstance(filename_or_structure, str):
s = Structure.from_file(filename_or_structure)
elif isinstance(filename_or_structure, Structure):
s = filename_or_structure
else:
raise MPRestError("Provide filename or Structure object.")
results = self._post_resource(
body=s.as_dict(),
params=params,
suburl="find_structure",
use_document_model=False,
).get("data")
if len(results) > 1: # type: ignore
if not allow_multiple_results:
raise ValueError(
"Multiple matches found for this combination of tolerances, but "
"`allow_multiple_results` set to False."
)
return results # type: ignore
if results:
return results[0]["material_id"]
else:
return []
|
