from __future__ import annotations
import itertools
import warnings
from functools import cache, lru_cache
from json import loads
from os import environ
from typing import Literal
from emmet.core.electronic_structure import BSPathType
from emmet.core.mpid import MPID
from emmet.core.settings import EmmetSettings
from emmet.core.tasks import TaskDoc
from emmet.core.vasp.calc_types import CalcType
from packaging import version
from pymatgen.analysis.phase_diagram import PhaseDiagram
from pymatgen.analysis.pourbaix_diagram import IonEntry
from pymatgen.core import SETTINGS, Element, Structure
from pymatgen.core.ion import Ion
from pymatgen.entries.computed_entries import ComputedStructureEntry
from pymatgen.io.vasp import Chgcar
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from requests import Session, get
from mp_api.client.core import BaseRester, MPRestError
from mp_api.client.core.settings import MAPIClientSettings
from mp_api.client.core.utils import validate_ids
from mp_api.client.routes import GeneralStoreRester, MessagesRester, UserSettingsRester
from mp_api.client.routes.materials import (
AbsorptionRester,
AlloysRester,
BandStructureRester,
BondsRester,
ChargeDensityRester,
ChemenvRester,
DielectricRester,
DOIRester,
DosRester,
ElasticityRester,
ElectrodeRester,
ElectronicStructureRester,
EOSRester,
FermiRester,
GrainBoundaryRester,
MagnetismRester,
OxidationStatesRester,
PhononRester,
PiezoRester,
ProvenanceRester,
RobocrysRester,
SimilarityRester,
SubstratesRester,
SummaryRester,
SurfacePropertiesRester,
SynthesisRester,
TaskRester,
ThermoRester,
XASRester,
)
from mp_api.client.routes.materials.materials import MaterialsRester
from mp_api.client.routes.molecules import MoleculeRester
_DEPRECATION_WARNING = (
"MPRester is being modernized. Please use the new method suggested and "
"read more about these changes at https://docs.materialsproject.org/api. The current "
"methods will be retained until at least January 2022 for backwards compatibility."
)
_EMMET_SETTINGS = EmmetSettings()
_MAPI_SETTINGS = MAPIClientSettings()
DEFAULT_API_KEY = environ.get("MP_API_KEY", None)
DEFAULT_ENDPOINT = environ.get("MP_API_ENDPOINT", "https://api.materialsproject.org/")
[docs]
class MPRester:
"""Access the new Materials Project API."""
# Type hints for all routes
# To re-generate this list, use:
# for rester in MPRester()._all_resters:
# print(f"{rester.suffix.replace('/', '_')}: {rester.__class__.__name__}")
# Materials
eos: EOSRester
materials: MaterialsRester
similarity: SimilarityRester
tasks: TaskRester
xas: XASRester
fermi: FermiRester
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
charge_density: ChargeDensityRester
electronic_structure: ElectronicStructureRester
electronic_structure_bandstructure: BandStructureRester
electronic_structure_dos: DosRester
oxidation_states: OxidationStatesRester
provenance: ProvenanceRester
bonds: BondsRester
alloys: AlloysRester
absorption: AbsorptionRester
chemenv: ChemenvRester
# Molecules
molecules: MoleculeRester
# Generic
doi: DOIRester
_user_settings: UserSettingsRester
_general_store: GeneralStoreRester
_messages: MessagesRester
[docs]
def __init__(
self,
api_key: str | None = None,
endpoint: str = DEFAULT_ENDPOINT,
notify_db_version: bool = False,
include_user_agent: bool = True,
monty_decode: bool = True,
use_document_model: bool = True,
session: Session = None,
headers: dict = None,
mute_progress_bars: bool = _MAPI_SETTINGS.MUTE_PROGRESS_BARS,
):
"""Args:
api_key (str): A String API key for accessing the MaterialsProject
REST interface. Please obtain your API key at
https://next-gen.materialsproject.org/api. If this is None,
the code will check if there is a "MP_API_KEY" setting.
If so, it will use that environment variable. This makes
easier for heavy users to simply add this environment variable to
their setups and MPRester can then be called without any arguments.
endpoint (str): Url of endpoint to access the MaterialsProject REST
interface. Defaults to the standard Materials Project REST
address at "https://api.materialsproject.org", but
can be changed to other urls implementing a similar interface.
notify_db_version (bool): If True, the current MP database version will
be retrieved and logged locally in the ~/.mprester.log.yaml. If the database
version changes, you will be notified. The current database version is
also printed on instantiation. These local logs are not sent to
materialsproject.org and are not associated with your API key, so be
aware that a notification may not be presented if you run MPRester
from multiple computing environments.
include_user_agent (bool): If True, will include a user agent with the
HTTP request including information on pymatgen and system version
making the API request. This helps MP support pymatgen users, and
is similar to what most web browsers send with each page request.
Set to False to disable the user agent.
monty_decode: Decode the data using monty into python objects
use_document_model: If False, skip the creating the document model and return data
as a dictionary. This can be simpler to work with but bypasses data validation
and will not give auto-complete for available fields.
session (Session): Session object to use. By default (None), the client will create one.
headers (dict): Custom headers for localhost connections.
mute_progress_bars (bool): Whether to mute progress bars.
"""
# SETTINGS tries to read API key from ~/.config/.pmgrc.yaml
api_key = api_key or DEFAULT_API_KEY or SETTINGS.get("PMG_MAPI_KEY")
if api_key and len(api_key) != 32:
raise ValueError(
"Please use a new API key from https://materialsproject.org/api "
"Keys for the new API are 32 characters, whereas keys for the legacy "
"API are 16 characters."
)
self.api_key = api_key
self.endpoint = endpoint
self.headers = headers or {}
self.session = session or BaseRester._create_session(
api_key=self.api_key,
include_user_agent=include_user_agent,
headers=self.headers,
)
self.use_document_model = use_document_model
self.monty_decode = monty_decode
self.mute_progress_bars = mute_progress_bars
self._deprecated_attributes = [
"eos",
"similarity",
"tasks",
"xas",
"fermi",
"grain_boundary",
"substrates",
"surface_properties",
"phonon",
"elasticity",
"thermo",
"dielectric",
"piezoelectric",
"magnetism",
"summary",
"robocrys",
"synthesis",
"insertion_electrodes",
"charge_density",
"electronic_structure",
"electronic_structure_bandstructure",
"electronic_structure_dos",
"oxidation_states",
"provenance",
"bonds",
"alloys",
"absorption",
"chemenv",
]
# Check if emmet version of server is compatible
emmet_version = MPRester.get_emmet_version(self.endpoint)
try:
from mpcontribs.client import Client
self.contribs = Client(api_key, headers=self.headers, session=self.session)
except ImportError:
self.contribs = None
warnings.warn(
"mpcontribs-client not installed. "
"Install the package to query MPContribs data, or construct pourbaix diagrams: "
"'pip install mpcontribs-client'"
)
except Exception as error:
self.contribs = None
warnings.warn(f"Problem loading MPContribs client: {error}")
if version.parse(emmet_version.base_version) < version.parse(
_MAPI_SETTINGS.MIN_EMMET_VERSION
):
warnings.warn(
"The installed version of the mp-api client may not be compatible with the API server. "
"Please install a previous version if any problems occur."
)
if notify_db_version:
raise NotImplementedError("This has not yet been implemented.")
if not self.endpoint.endswith("/"):
self.endpoint += "/"
# Dynamically set rester attributes.
# First, materials and molecules top level resters are set.
# Nested rested are then setup to be loaded dynamically with custom __getattr__ functions.
self._all_resters = []
# Get all rester classes
for _cls in BaseRester.__subclasses__():
sub_resters = _cls.__subclasses__()
if sub_resters:
self._all_resters.extend(sub_resters)
else:
self._all_resters.append(_cls)
# Instantiate top level molecules and materials resters and set them as attributes
core_suffix = ["molecules/core", "materials/core"]
core_resters = {
cls.suffix.split("/")[0]: cls(
api_key=api_key,
endpoint=endpoint,
include_user_agent=include_user_agent,
session=self.session,
monty_decode=monty_decode,
use_document_model=use_document_model,
headers=self.headers,
mute_progress_bars=self.mute_progress_bars,
)
for cls in self._all_resters
if cls.suffix in core_suffix
}
# Set remaining top level resters, or get an attribute-class name mapping
# for all sub-resters
_sub_rester_suffix_map = {"materials": {}, "molecules": {}}
for cls in self._all_resters:
if cls.suffix not in core_suffix:
suffix_split = cls.suffix.split("/")
if len(suffix_split) == 1:
rester = cls(
api_key=api_key,
endpoint=endpoint,
include_user_agent=include_user_agent,
session=self.session,
monty_decode=monty_decode
if cls not in [TaskRester, ProvenanceRester] # type: ignore
else False, # Disable monty decode on nested data which may give errors
use_document_model=use_document_model,
headers=self.headers,
mute_progress_bars=self.mute_progress_bars,
) # type: BaseRester
setattr(
self,
suffix_split[0],
rester,
)
else:
attr = "_".join(suffix_split[1:])
if "materials" in suffix_split:
_sub_rester_suffix_map["materials"][attr] = cls
elif "molecules" in suffix_split:
_sub_rester_suffix_map["molecules"][attr] = cls
# Allow lazy loading of nested resters under materials and molecules using custom __getattr__ methods
def __core_custom_getattr(_self, _attr, _rester_map):
if _attr in _rester_map:
cls = _rester_map[_attr]
rester = cls(
api_key=api_key,
endpoint=endpoint,
include_user_agent=include_user_agent,
session=self.session,
monty_decode=monty_decode
if cls not in [TaskRester, ProvenanceRester] # type: ignore
else False, # Disable monty decode on nested data which may give errors
use_document_model=use_document_model,
headers=self.headers,
mute_progress_bars=self.mute_progress_bars,
) # type: BaseRester
setattr(
_self,
_attr,
rester,
)
return rester
else:
raise AttributeError(
f"{_self.__class__.__name__!r} object has no attribute {attr!r}"
)
def __materials_getattr__(_self, attr):
_rester_map = _sub_rester_suffix_map["materials"]
rester = __core_custom_getattr(_self, attr, _rester_map)
return rester
def __molecules_getattr__(_self, attr):
_rester_map = _sub_rester_suffix_map["molecules"]
rester = __core_custom_getattr(_self, attr, _rester_map)
return rester
MaterialsRester.__getattr__ = __materials_getattr__
MoleculeRester.__getattr__ = __molecules_getattr__
for attr, rester in core_resters.items():
setattr(
self,
attr,
rester,
)
def __enter__(self):
"""Support for "with" context."""
return self
def __exit__(self, exc_type, exc_val, exc_tb):
"""Support for "with" context."""
self.session.close()
def __getattr__(self, attr):
if attr in self._deprecated_attributes:
warnings.warn(
f"Accessing {attr} data through MPRester.{attr} is deprecated. "
f"Please use MPRester.materials.{attr} instead.",
DeprecationWarning,
stacklevel=2,
)
return getattr(super().__getattribute__("materials"), attr)
else:
raise AttributeError(
f"{self.__class__.__name__!r} object has no attribute {attr!r}"
)
def __getattribute__(self, attr):
if "molecules" in attr:
warnings.warn(
"NOTE: You are accessing a new set of molecules data to be officially released very soon. "
"This dataset includes many new properties, and is designed to be more easily expanded. "
"For the previous (legacy) molecules data, use the MPRester.molecules.jcesr rester. "
)
return super().__getattribute__(attr)
def __dir__(self):
return dir(MPRester) + self._deprecated_attributes + ["materials", "molecules"]
[docs]
def get_task_ids_associated_with_material_id(
self, material_id: str, calc_types: list[CalcType] | None = None
) -> list[str]:
""":param material_id:
:param calc_types: if specified, will restrict to certain task types, e.g. [CalcType.GGA_STATIC]
:return:
"""
tasks = self.materials.get_data_by_id(
material_id, fields=["calc_types"]
).calc_types
if calc_types:
return [
task for task, calc_type in tasks.items() if calc_type in calc_types
]
else:
return list(tasks.keys())
[docs]
def get_structure_by_material_id(
self, material_id: str, final: bool = True, conventional_unit_cell: bool = False
) -> Structure | list[Structure]:
"""Get a Structure corresponding to a material_id.
Args:
material_id (str): Materials Project material_id (a string,
e.g., mp-1234).
final (bool): Whether to get the final structure, or the list of initial
(pre-relaxation) structures. Defaults to True.
conventional_unit_cell (bool): Whether to get the standard
conventional unit cell for the final or list of initial structures.
Returns:
Structure object or list of Structure objects.
"""
structure_data = self.materials.get_structure_by_material_id(
material_id=material_id, final=final
)
if conventional_unit_cell and structure_data:
if final:
structure_data = SpacegroupAnalyzer(
structure_data
).get_conventional_standard_structure()
else:
structure_data = [
SpacegroupAnalyzer(structure).get_conventional_standard_structure()
for structure in structure_data
]
return structure_data
[docs]
def get_database_version(self):
"""The Materials Project database is periodically updated and has a
database version associated with it. When the database is updated,
consolidated data (information about "a material") may and does
change, while calculation data about a specific calculation task
remains unchanged and available for querying via its task_id.
The database version is set as a date in the format YYYY_MM_DD,
where "_DD" may be optional. An additional numerical suffix
might be added if multiple releases happen on the same day.
Returns: database version as a string
"""
return get(url=self.endpoint + "heartbeat").json()["db_version"]
[docs]
@staticmethod
@cache
def get_emmet_version(endpoint):
"""Get the latest version emmet-core and emmet-api used in the
current API service.
Returns: version as a string
"""
response = get(url=endpoint + "heartbeat").json()
error = response.get("error", None)
if error:
raise MPRestError(error)
return version.parse(response["version"])
[docs]
def get_material_id_from_task_id(self, task_id: str) -> str | None:
"""Returns the current material_id from a given task_id. The
material_id should rarely change, and is usually chosen from
among the smallest numerical id from the group of task_ids for
that material. However, in some circumstances it might change,
and this method is useful for finding the new material_id.
Args:
task_id (str): A task id.
Returns:
material_id (MPID)
"""
docs = self.materials.search(task_ids=[task_id], fields=["material_id"])
if len(docs) == 1: # pragma: no cover
return str(docs[0].material_id) # type: ignore
elif len(docs) > 1: # pragma: no cover
raise ValueError(
f"Multiple documents return for {task_id}, this should not happen, please report it!"
)
else: # pragma: no cover
warnings.warn(
f"No material found containing task {task_id}. Please report it if you suspect a task has gone missing."
)
return None
[docs]
def get_materials_id_from_task_id(self, task_id: str) -> str | None:
"""This method is deprecated, please use get_material_id_from_task_id."""
warnings.warn(
"This method is deprecated, please use get_material_id_from_task_id.",
DeprecationWarning,
)
return self.get_material_id_from_task_id(task_id)
[docs]
def get_material_id_references(self, material_id: str) -> list[str]:
"""Returns all references for a material id.
Args:
material_id (str): A material id.
Returns:
List of BibTeX references ([str])
"""
return self.provenance.get_data_by_id(material_id).references
[docs]
def get_materials_id_references(self, material_id: str) -> list[str]:
"""This method is deprecated, please use get_material_id_references."""
warnings.warn(
"This method is deprecated, please use get_material_id_references instead.",
DeprecationWarning,
)
return self.get_material_id_references(material_id)
[docs]
def get_material_ids(
self,
chemsys_formula: str | list[str],
) -> list[MPID]:
"""Get all materials ids for a formula or chemsys.
Args:
chemsys_formula (str, List[str]): A chemical system, list of chemical systems
(e.g., Li-Fe-O, Si-*, [Si-O, Li-Fe-P]), or single formula (e.g., Fe2O3, Si*).
Returns:
List of all materials ids ([MPID])
"""
if isinstance(chemsys_formula, list) or (
isinstance(chemsys_formula, str) and "-" in chemsys_formula
):
input_params = {"chemsys": chemsys_formula}
else:
input_params = {"formula": chemsys_formula}
return sorted(
doc.material_id
for doc in self.materials.search(
**input_params, # type: ignore
all_fields=False,
fields=["material_id"],
)
)
[docs]
def get_materials_ids(
self,
chemsys_formula: str | list[str],
) -> list[MPID]:
"""This method is deprecated, please use get_material_ids."""
warnings.warn(
"This method is deprecated, please use get_material_ids.",
DeprecationWarning,
)
return self.get_material_ids(chemsys_formula)
[docs]
def get_structures(
self, chemsys_formula: str | list[str], final=True
) -> list[Structure]:
"""Get a list of Structures corresponding to a chemical system or formula.
Args:
chemsys_formula (str, List[str]): A chemical system, list of chemical systems
(e.g., Li-Fe-O, Si-*, [Si-O, Li-Fe-P]), or single formula (e.g., Fe2O3, Si*).
final (bool): Whether to get the final structure, or the list of initial
(pre-relaxation) structures. Defaults to True.
Returns:
List of Structure objects. ([Structure])
"""
if isinstance(chemsys_formula, list) or (
isinstance(chemsys_formula, str) and "-" in chemsys_formula
):
input_params = {"chemsys": chemsys_formula}
else:
input_params = {"formula": chemsys_formula}
if final:
return [
doc.structure
for doc in self.materials.search(
**input_params, # type: ignore
all_fields=False,
fields=["structure"],
)
]
else:
structures = []
for doc in self.materials.search(
**input_params, # type: ignore
all_fields=False,
fields=["initial_structures"],
):
structures.extend(doc.initial_structures)
return structures
[docs]
def find_structure(
self,
filename_or_structure: str | Structure,
ltol: float = _EMMET_SETTINGS.LTOL,
stol: float = _EMMET_SETTINGS.STOL,
angle_tol: float = _EMMET_SETTINGS.ANGLE_TOL,
allow_multiple_results: bool = 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
"""
return self.materials.find_structure(
filename_or_structure,
ltol=ltol,
stol=stol,
angle_tol=angle_tol,
allow_multiple_results=allow_multiple_results,
)
[docs]
def get_entries(
self,
chemsys_formula_mpids: str | list[str],
compatible_only: bool = True,
inc_structure: bool = None,
property_data: list[str] = None,
conventional_unit_cell: bool = False,
additional_criteria: dict = None,
) -> list[ComputedStructureEntry]:
"""Get a list of ComputedEntries or ComputedStructureEntries corresponding
to a chemical system or formula. This returns entries for all thermo types
represented in the database. Each type corresponds to a different mixing scheme
(i.e. GGA/GGA+U, GGA/GGA+U/R2SCAN, R2SCAN). By default the thermo_type of the
entry is also returned.
Args:
chemsys_formula_mpids (str, List[str]): A chemical system, list of chemical systems
(e.g., Li-Fe-O, Si-*, [Si-O, Li-Fe-P]), formula, list of formulas
(e.g., Fe2O3, Si*, [SiO2, BiFeO3]), Materials Project ID, or list of Materials
Project IDs (e.g., mp-22526, [mp-22526, mp-149]).
compatible_only (bool): Whether to return only "compatible"
entries. Compatible entries are entries that have been
processed using the MaterialsProject2020Compatibility class,
which performs adjustments to allow mixing of GGA and GGA+U
calculations for more accurate phase diagrams and reaction
energies. This data is obtained from the core "thermo" API endpoint.
inc_structure (str): *This is a deprecated argument*. Previously, if None, entries
returned were ComputedEntries. If inc_structure="initial",
ComputedStructureEntries with initial structures were returned.
Otherwise, ComputedStructureEntries with final structures
were returned. This is no longer needed as all entries will contain
structure data by default.
property_data (list): Specify additional properties to include in
entry.data. If None, only default data is included. Should be a subset of
input parameters in the 'MPRester.thermo.available_fields' list.
conventional_unit_cell (bool): Whether to get the standard
conventional unit cell
additional_criteria (dict): Any additional criteria to pass. The keys and values should
correspond to proper function inputs to `MPRester.thermo.search`. For instance,
if you are only interested in entries on the convex hull, you could pass
{"energy_above_hull": (0.0, 0.0)} or {"is_stable": True}.
Returns:
List ComputedStructureEntry objects.
"""
if inc_structure is not None:
warnings.warn(
"The 'inc_structure' argument is deprecated as structure "
"data is now always included in all returned entry objects."
)
if isinstance(chemsys_formula_mpids, str):
chemsys_formula_mpids = [chemsys_formula_mpids]
try:
input_params = {"material_ids": validate_ids(chemsys_formula_mpids)}
except ValueError:
if any("-" in entry for entry in chemsys_formula_mpids):
input_params = {"chemsys": chemsys_formula_mpids}
else:
input_params = {"formula": chemsys_formula_mpids}
if additional_criteria:
input_params = {**input_params, **additional_criteria}
entries = []
fields = (
["entries", "thermo_type"]
if not property_data
else ["entries", "thermo_type"] + property_data
)
docs = self.thermo.search(
**input_params,
all_fields=False,
fields=fields, # type: ignore
)
for doc in docs:
entry_list = (
doc.entries.values()
if self.use_document_model
else doc["entries"].values()
)
for entry in entry_list:
entry_dict = entry.as_dict() if self.monty_decode else entry
if not compatible_only:
entry_dict["correction"] = 0.0
entry_dict["energy_adjustments"] = []
if property_data:
for property in property_data:
entry_dict["data"][property] = (
doc.model_dump()[property]
if self.use_document_model
else doc[property]
)
if conventional_unit_cell:
entry_struct = Structure.from_dict(entry_dict["structure"])
s = SpacegroupAnalyzer(
entry_struct
).get_conventional_standard_structure()
site_ratio = len(s) / len(entry_struct)
new_energy = entry_dict["energy"] * site_ratio
entry_dict["energy"] = new_energy
entry_dict["structure"] = s.as_dict()
entry_dict["correction"] = 0.0
for element in entry_dict["composition"]:
entry_dict["composition"][element] *= site_ratio
for correction in entry_dict["energy_adjustments"]:
if "n_atoms" in correction:
correction["n_atoms"] *= site_ratio
entry = (
ComputedStructureEntry.from_dict(entry_dict)
if self.monty_decode
else entry_dict
)
entries.append(entry)
return entries
[docs]
def get_pourbaix_entries(
self,
chemsys: str | list,
solid_compat="MaterialsProject2020Compatibility",
use_gibbs: Literal[300] | None = None,
):
"""A helper function to get all entries necessary to generate
a Pourbaix diagram from the rest interface.
Args:
chemsys (str or [str]): Chemical system string comprising element
symbols separated by dashes, e.g., "Li-Fe-O" or List of element
symbols, e.g., ["Li", "Fe", "O"].
solid_compat: Compatibility scheme used to pre-process solid DFT energies prior
to applying aqueous energy adjustments. May be passed as a class (e.g.
MaterialsProject2020Compatibility) or an instance
(e.g., MaterialsProject2020Compatibility()). If None, solid DFT energies
are used as-is. Default: MaterialsProject2020Compatibility
use_gibbs: Set to 300 (for 300 Kelvin) to use a machine learning model to
estimate solid free energy from DFT energy (see GibbsComputedStructureEntry).
This can slightly improve the accuracy of the Pourbaix diagram in some
cases. Default: None. Note that temperatures other than 300K are not
permitted here, because MaterialsProjectAqueousCompatibility corrections,
used in Pourbaix diagram construction, are calculated based on 300 K data.
"""
# imports are not top-level due to expense
from pymatgen.analysis.pourbaix_diagram import PourbaixEntry
from pymatgen.entries.compatibility import (
Compatibility,
MaterialsProject2020Compatibility,
MaterialsProjectAqueousCompatibility,
MaterialsProjectCompatibility,
)
from pymatgen.entries.computed_entries import ComputedEntry
if solid_compat == "MaterialsProjectCompatibility":
solid_compat = MaterialsProjectCompatibility()
elif solid_compat == "MaterialsProject2020Compatibility":
solid_compat = MaterialsProject2020Compatibility()
elif isinstance(solid_compat, Compatibility):
pass
else:
raise ValueError(
"Solid compatibility can only be 'MaterialsProjectCompatibility', "
"'MaterialsProject2020Compatibility', or an instance of a Compatibility class"
)
pbx_entries = []
if isinstance(chemsys, str):
chemsys = chemsys.split("-")
# capitalize and sort the elements
chemsys = sorted(e.capitalize() for e in chemsys)
# Get ion entries first, because certain ions have reference
# solids that aren't necessarily in the chemsys (Na2SO4)
# download the ion reference data from MPContribs
ion_data = self.get_ion_reference_data_for_chemsys(chemsys)
# build the PhaseDiagram for get_ion_entries
ion_ref_comps = [
Ion.from_formula(d["data"]["RefSolid"]).composition for d in ion_data
]
ion_ref_elts = set(
itertools.chain.from_iterable(i.elements for i in ion_ref_comps)
)
# TODO - would be great if the commented line below would work
# However for some reason you cannot process GibbsComputedStructureEntry with
# MaterialsProjectAqueousCompatibility
ion_ref_entries = self.get_entries_in_chemsys(
list([str(e) for e in ion_ref_elts] + ["O", "H"]),
# use_gibbs=use_gibbs
)
# suppress the warning about supplying the required energies; they will be calculated from the
# entries we get from MPRester
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore",
message="You did not provide the required O2 and H2O energies.",
)
compat = MaterialsProjectAqueousCompatibility(solid_compat=solid_compat)
# suppress the warning about missing oxidation states
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore", message="Failed to guess oxidation states.*"
)
ion_ref_entries = compat.process_entries(ion_ref_entries)
# TODO - if the commented line above would work, this conditional block
# could be removed
if use_gibbs:
# replace the entries with GibbsComputedStructureEntry
from pymatgen.entries.computed_entries import GibbsComputedStructureEntry
ion_ref_entries = GibbsComputedStructureEntry.from_entries(
ion_ref_entries, temp=use_gibbs
)
ion_ref_pd = PhaseDiagram(ion_ref_entries)
ion_entries = self.get_ion_entries(ion_ref_pd, ion_ref_data=ion_data)
pbx_entries = [PourbaixEntry(e, f"ion-{n}") for n, e in enumerate(ion_entries)]
# Construct the solid pourbaix entries from filtered ion_ref entries
extra_elts = (
set(ion_ref_elts)
- {Element(s) for s in chemsys}
- {Element("H"), Element("O")}
)
for entry in ion_ref_entries:
entry_elts = set(entry.composition.elements)
# Ensure no OH chemsys or extraneous elements from ion references
if not (
entry_elts <= {Element("H"), Element("O")}
or extra_elts.intersection(entry_elts)
):
# Create new computed entry
form_e = ion_ref_pd.get_form_energy(entry)
new_entry = ComputedEntry(
entry.composition, form_e, entry_id=entry.entry_id
)
pbx_entry = PourbaixEntry(new_entry)
pbx_entries.append(pbx_entry)
return pbx_entries
[docs]
@lru_cache
def get_ion_reference_data(self) -> list[dict]:
"""Download aqueous ion reference data used in the construction of Pourbaix diagrams.
Use this method to examine the ion reference data and to add additional
ions if desired. The data returned from this method can be passed to
get_ion_entries().
Data are retrieved from the Aqueous Ion Reference Data project
hosted on MPContribs. Refer to that project and its associated documentation
for more details about the format and meaning of the data.
Returns:
[dict]: Among other data, each record contains 1) the experimental ion free energy, 2) the
formula of the reference solid for the ion, and 3) the experimental free energy of the
reference solid. All energies are given in kJ/mol. An example is given below.
{'identifier': 'Li[+]',
'formula': 'Li[+]',
'data': {'charge': {'display': '1.0', 'value': 1.0, 'unit': ''},
'ΔGᶠ': {'display': '-293.71 kJ/mol', 'value': -293.71, 'unit': 'kJ/mol'},
'MajElements': 'Li',
'RefSolid': 'Li2O',
'ΔGᶠRefSolid': {'display': '-561.2 kJ/mol',
'value': -561.2,
'unit': 'kJ/mol'},
'reference': 'H. E. Barner and R. V. Scheuerman, Handbook of thermochemical data for
compounds and aqueous species, Wiley, New York (1978)'}}
"""
return self.contribs.query_contributions(
query={"project": "ion_ref_data"},
fields=["identifier", "formula", "data"],
paginate=True,
).get("data")
[docs]
def get_ion_reference_data_for_chemsys(self, chemsys: str | list) -> list[dict]:
"""Download aqueous ion reference data used in the construction of Pourbaix diagrams.
Use this method to examine the ion reference data and to add additional
ions if desired. The data returned from this method can be passed to
get_ion_entries().
Data are retrieved from the Aqueous Ion Reference Data project
hosted on MPContribs. Refer to that project and its associated documentation
for more details about the format and meaning of the data.
Args:
chemsys (str or [str]): Chemical system string comprising element
symbols separated by dashes, e.g., "Li-Fe-O" or List of element
symbols, e.g., ["Li", "Fe", "O"].
Returns:
[dict]: Among other data, each record contains 1) the experimental ion free energy, 2) the
formula of the reference solid for the ion, and 3) the experimental free energy of the
reference solid. All energies are given in kJ/mol. An example is given below.
{'identifier': 'Li[+]',
'formula': 'Li[+]',
'data': {'charge': {'display': '1.0', 'value': 1.0, 'unit': ''},
'ΔGᶠ': {'display': '-293.71 kJ/mol', 'value': -293.71, 'unit': 'kJ/mol'},
'MajElements': 'Li',
'RefSolid': 'Li2O',
'ΔGᶠRefSolid': {'display': '-561.2 kJ/mol',
'value': -561.2,
'unit': 'kJ/mol'},
'reference': 'H. E. Barner and R. V. Scheuerman, Handbook of thermochemical data for
compounds and aqueous species, Wiley, New York (1978)'}}
"""
ion_data = self.get_ion_reference_data()
if isinstance(chemsys, str):
chemsys = chemsys.split("-")
return [d for d in ion_data if d["data"]["MajElements"] in chemsys]
[docs]
def get_ion_entries(
self, pd: PhaseDiagram, ion_ref_data: list[dict] = None
) -> list[IonEntry]:
"""Retrieve IonEntry objects that can be used in the construction of
Pourbaix Diagrams. The energies of the IonEntry are calculaterd from
the solid energies in the provided Phase Diagram to be
consistent with experimental free energies.
NOTE! This is an advanced method that assumes detailed understanding
of how to construct computational Pourbaix Diagrams. If you just want
to build a Pourbaix Diagram using default settings, use get_pourbaix_entries.
Args:
pd: Solid phase diagram on which to construct IonEntry. Note that this
Phase Diagram MUST include O and H in its chemical system. For example,
to retrieve IonEntry for Ti, the phase diagram passed here should contain
materials in the H-O-Ti chemical system. It is also assumed that solid
energies have already been corrected with MaterialsProjectAqueousCompatibility,
which is necessary for proper construction of Pourbaix diagrams.
ion_ref_data: Aqueous ion reference data. If None (default), the data
are downloaded from the Aqueous Ion Reference Data project hosted
on MPContribs. To add a custom ionic species, first download
data using get_ion_reference_data, then add or customize it with
your additional data, and pass the customized list here.
Returns:
[IonEntry]: IonEntry are similar to PDEntry objects. Their energies
are free energies in eV.
"""
# determine the chemsys from the phase diagram
chemsys = "-".join([el.symbol for el in pd.elements])
# raise ValueError if O and H not in chemsys
if "O" not in chemsys or "H" not in chemsys:
raise ValueError(
"The phase diagram chemical system must contain O and H! Your"
f" diagram chemical system is {chemsys}."
)
if not ion_ref_data:
ion_data = self.get_ion_reference_data_for_chemsys(chemsys)
else:
ion_data = ion_ref_data
# position the ion energies relative to most stable reference state
ion_entries = []
for _n, i_d in enumerate(ion_data):
ion = Ion.from_formula(i_d["formula"])
refs = [
e
for e in pd.all_entries
if e.composition.reduced_formula == i_d["data"]["RefSolid"]
]
if not refs:
raise ValueError("Reference solid not contained in entry list")
stable_ref = sorted(refs, key=lambda x: x.energy_per_atom)[0]
rf = stable_ref.composition.get_reduced_composition_and_factor()[1]
# TODO - need a more robust way to convert units
# use pint here?
if i_d["data"]["ΔGᶠRefSolid"]["unit"] == "kJ/mol":
# convert to eV/formula unit
ref_solid_energy = i_d["data"]["ΔGᶠRefSolid"]["value"] / 96.485
elif i_d["data"]["ΔGᶠRefSolid"]["unit"] == "MJ/mol":
# convert to eV/formula unit
ref_solid_energy = i_d["data"]["ΔGᶠRefSolid"]["value"] / 96485
else:
raise ValueError(
f"Ion reference solid energy has incorrect unit {i_d['data']['ΔGᶠRefSolid']['unit']}"
)
solid_diff = pd.get_form_energy(stable_ref) - ref_solid_energy * rf
elt = i_d["data"]["MajElements"]
correction_factor = ion.composition[elt] / stable_ref.composition[elt]
# TODO - need a more robust way to convert units
# use pint here?
if i_d["data"]["ΔGᶠ"]["unit"] == "kJ/mol":
# convert to eV/formula unit
ion_free_energy = i_d["data"]["ΔGᶠ"]["value"] / 96.485
elif i_d["data"]["ΔGᶠ"]["unit"] == "MJ/mol":
# convert to eV/formula unit
ion_free_energy = i_d["data"]["ΔGᶠ"]["value"] / 96485
else:
raise ValueError(
f"Ion free energy has incorrect unit {i_d['data']['ΔGᶠ']['unit']}"
)
energy = ion_free_energy + solid_diff * correction_factor
ion_entries.append(IonEntry(ion, energy))
return ion_entries
[docs]
def get_entry_by_material_id(
self,
material_id: str,
compatible_only: bool = True,
inc_structure: bool = None,
property_data: list[str] = None,
conventional_unit_cell: bool = False,
):
"""Get all ComputedEntry objects corresponding to a material_id.
Args:
material_id (str): Materials Project material_id (a string,
e.g., mp-1234).
compatible_only (bool): Whether to return only "compatible"
entries. Compatible entries are entries that have been
processed using the MaterialsProject2020Compatibility class,
which performs adjustments to allow mixing of GGA and GGA+U
calculations for more accurate phase diagrams and reaction
energies. This data is obtained from the core "thermo" API endpoint.
inc_structure (str): *This is a deprecated argument*. Previously, if None, entries
returned were ComputedEntries. If inc_structure="initial",
ComputedStructureEntries with initial structures were returned.
Otherwise, ComputedStructureEntries with final structures
were returned. This is no longer needed as all entries will contain
structure data by default.
property_data (list): Specify additional properties to include in
entry.data. If None, only default data is included. Should be a subset of
input parameters in the 'MPRester.thermo.available_fields' list.
conventional_unit_cell (bool): Whether to get the standard
conventional unit cell
Returns:
List of ComputedEntry or ComputedStructureEntry object.
"""
return self.get_entries(
material_id,
compatible_only=compatible_only,
inc_structure=inc_structure,
property_data=property_data,
conventional_unit_cell=conventional_unit_cell,
)
[docs]
def get_entries_in_chemsys(
self,
elements: str | list[str],
use_gibbs: int | None = None,
compatible_only: bool = True,
inc_structure: bool = None,
property_data: list[str] = None,
conventional_unit_cell: bool = False,
additional_criteria=None,
):
"""Helper method to get a list of ComputedEntries in a chemical system.
For example, elements = ["Li", "Fe", "O"] will return a list of all
entries in the Li-Fe-O chemical system, i.e., all LixOy,
FexOy, LixFey, LixFeyOz, Li, Fe and O phases. Extremely useful for
creating phase diagrams of entire chemical systems.
Note that by default this returns mixed GGA/GGA+U entries. For others,
pass GGA/GGA+U/R2SCAN, or R2SCAN as thermo_types in additional_criteria.
Args:
elements (str or [str]): Chemical system string comprising element
symbols separated by dashes, e.g., "Li-Fe-O" or List of element
symbols, e.g., ["Li", "Fe", "O"].
use_gibbs: If None (default), DFT energy is returned. If a number, return
the free energy of formation estimated using a machine learning model
(see GibbsComputedStructureEntry). The number is the temperature in
Kelvin at which to estimate the free energy. Must be between 300 K and
2000 K.
compatible_only (bool): Whether to return only "compatible"
entries. Compatible entries are entries that have been
processed using the MaterialsProject2020Compatibility class,
which performs adjustments to allow mixing of GGA and GGA+U
calculations for more accurate phase diagrams and reaction
energies. This data is obtained from the core "thermo" API endpoint.
inc_structure (str): *This is a deprecated argument*. Previously, if None, entries
returned were ComputedEntries. If inc_structure="initial",
ComputedStructureEntries with initial structures were returned.
Otherwise, ComputedStructureEntries with final structures
were returned. This is no longer needed as all entries will contain
structure data by default.
property_data (list): Specify additional properties to include in
entry.data. If None, only default data is included. Should be a subset of
input parameters in the 'MPRester.thermo.available_fields' list.
conventional_unit_cell (bool): Whether to get the standard
conventional unit cell
additional_criteria (dict): Any additional criteria to pass. The keys and values should
correspond to proper function inputs to `MPRester.thermo.search`. For instance,
if you are only interested in entries on the convex hull, you could pass
{"energy_above_hull": (0.0, 0.0)} or {"is_stable": True}, or if you are only interested
in entry data
Returns:
List of ComputedStructureEntries.
"""
if isinstance(elements, str):
elements = elements.split("-")
elements_set = set(elements) # remove duplicate elements
all_chemsyses = []
for i in range(len(elements_set)):
for els in itertools.combinations(elements_set, i + 1):
all_chemsyses.append("-".join(sorted(els)))
entries = [] # type: List[ComputedEntry]
entries.extend(
self.get_entries(
all_chemsyses,
compatible_only=compatible_only,
inc_structure=inc_structure,
property_data=property_data,
conventional_unit_cell=conventional_unit_cell,
additional_criteria=additional_criteria
or {"thermo_types": ["GGA_GGA+U"]},
)
)
if not self.monty_decode:
entries = [ComputedStructureEntry.from_dict(entry) for entry in entries]
if use_gibbs:
# replace the entries with GibbsComputedStructureEntry
from pymatgen.entries.computed_entries import GibbsComputedStructureEntry
entries = GibbsComputedStructureEntry.from_entries(entries, temp=use_gibbs)
if not self.monty_decode:
entries = [entry.as_dict() for entry in entries]
return entries
[docs]
def get_bandstructure_by_material_id(
self,
material_id: str,
path_type: BSPathType = BSPathType.setyawan_curtarolo,
line_mode=True,
):
"""Get the band structure pymatgen object associated with a Materials Project ID.
Arguments:
material_id (str): Materials Project ID for a material
path_type (BSPathType): k-point path selection convention
line_mode (bool): Whether to return data for a line-mode calculation
Returns:
bandstructure (Union[BandStructure, BandStructureSymmLine]): BandStructure or BandStructureSymmLine object
"""
return self.electronic_structure_bandstructure.get_bandstructure_from_material_id( # type: ignore
material_id=material_id, path_type=path_type, line_mode=line_mode
)
[docs]
def get_dos_by_material_id(self, material_id: str):
"""Get the complete density of states pymatgen object associated with a Materials Project ID.
Arguments:
material_id (str): Materials Project ID for a material
Returns:
dos (CompleteDos): CompleteDos object
"""
return self.electronic_structure_dos.get_dos_from_material_id(material_id=material_id) # type: ignore
[docs]
def get_phonon_dos_by_material_id(self, material_id: str):
"""Get phonon density of states data corresponding to a material_id.
Args:
material_id (str): Materials Project material_id.
Returns:
CompletePhononDos: A phonon DOS object.
"""
return self.phonon.get_data_by_id(material_id, fields=["ph_dos"]).ph_dos
[docs]
def get_phonon_bandstructure_by_material_id(self, material_id: str):
"""Get phonon dispersion data corresponding to a material_id.
Args:
material_id (str): Materials Project material_id.
Returns:
PhononBandStructureSymmLine: phonon band structure.
"""
return self.phonon.get_data_by_id(material_id, fields=["ph_bs"]).ph_bs
[docs]
def get_wulff_shape(self, material_id: str):
"""Constructs a Wulff shape for a material.
Args:
material_id (str): Materials Project material_id, e.g. 'mp-123'.
Returns:
pymatgen.analysis.wulff.WulffShape
"""
from pymatgen.analysis.wulff import WulffShape
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
structure = self.get_structure_by_material_id(material_id)
surfaces = surfaces = self.surface_properties.get_data_by_id(
material_id
).surfaces
lattice = (
SpacegroupAnalyzer(structure).get_conventional_standard_structure().lattice
)
miller_energy_map = {}
for surf in surfaces:
miller = tuple(surf.miller_index)
# Prefer reconstructed surfaces, which have lower surface energies.
if (miller not in miller_energy_map) or surf.is_reconstructed:
miller_energy_map[miller] = surf.surface_energy
millers, energies = zip(*miller_energy_map.items())
return WulffShape(lattice, millers, energies)
[docs]
def get_charge_density_from_material_id(
self, material_id: str, inc_task_doc: bool = False
) -> Chgcar | None:
"""Get charge density data for a given Materials Project ID.
Arguments:
material_id (str): Material Project ID
inc_task_doc (bool): Whether to include the task document in the returned data.
Returns:
chgcar: Pymatgen Chgcar object.
"""
if not hasattr(self, "charge_density"):
raise MPRestError(
"boto3 not installed. "
"To query charge density data install the boto3 package."
)
# TODO: really we want a recommended task_id for charge densities here
# this could potentially introduce an ambiguity
task_ids = self.get_task_ids_associated_with_material_id(
material_id, calc_types=[CalcType.GGA_Static, CalcType.GGA_U_Static]
)
results: list[TaskDoc] = self.tasks.search(task_ids=task_ids, fields=["last_updated", "task_id"]) # type: ignore
if len(results) == 0:
return None
latest_doc = max(results, key=lambda x: x.last_updated)
result = (
self.tasks._query_open_data(
bucket="materialsproject-parsed",
prefix="chgcars",
key=str(latest_doc.task_id),
)
or {}
)
chgcar = result.get("data", None)
if chgcar is None:
raise MPRestError(f"No charge density fetched for {material_id}.")
if inc_task_doc:
task_doc = self.tasks.get_data_by_id(latest_doc.task_id)
return chgcar, task_doc
return chgcar
[docs]
def get_download_info(self, material_ids, calc_types=None, file_patterns=None):
"""Get a list of URLs to retrieve raw VASP output files from the NoMaD repository
Args:
material_ids (list): list of material identifiers (mp-id's)
task_types (list): list of task types to include in download (see CalcType Enum class)
file_patterns (list): list of wildcard file names to include for each task
Returns:
a tuple of 1) a dictionary mapping material_ids to task_ids and
calc_types, and 2) a list of URLs to download zip archives from
NoMaD repository. Each zip archive will contain a manifest.json with
metadata info, e.g. the task/external_ids that belong to a directory.
"""
# task_id's correspond to NoMaD external_id's
calc_types = (
[t.value for t in calc_types if isinstance(t, CalcType)]
if calc_types
else []
)
meta = {}
for doc in self.materials.search(
task_ids=material_ids,
fields=["calc_types", "deprecated_tasks", "material_id"],
):
for task_id, calc_type in doc.calc_types.items():
if calc_types and calc_type not in calc_types:
continue
mp_id = doc.material_id
if meta.get(mp_id) is None:
meta[mp_id] = [{"task_id": task_id, "calc_type": calc_type}]
else:
meta[mp_id].append({"task_id": task_id, "calc_type": calc_type})
if not meta:
raise ValueError(f"No tasks found for material id {material_ids}.")
# return a list of URLs for NoMaD Downloads containing the list of files
# for every external_id in `task_ids`
# For reference, please visit https://nomad-lab.eu/prod/rae/api/
# check if these task ids exist on NOMAD
prefix = "https://nomad-lab.eu/prod/rae/api/repo/?"
if file_patterns is not None:
for file_pattern in file_patterns:
prefix += f"file_pattern={file_pattern}&"
prefix += "external_id="
task_ids = [t["task_id"] for tl in meta.values() for t in tl]
nomad_exist_task_ids = self._check_get_download_info_url_by_task_id(
prefix=prefix, task_ids=task_ids
)
if len(nomad_exist_task_ids) != len(task_ids):
self._print_help_message(
nomad_exist_task_ids, task_ids, file_patterns, calc_types
)
# generate download links for those that exist
prefix = "https://nomad-lab.eu/prod/rae/api/raw/query?"
if file_patterns is not None:
for file_pattern in file_patterns:
prefix += f"file_pattern={file_pattern}&"
prefix += "external_id="
urls = [prefix + tids for tids in nomad_exist_task_ids]
return meta, urls
def _check_get_download_info_url_by_task_id(self, prefix, task_ids) -> list[str]:
nomad_exist_task_ids: list[str] = []
prefix = prefix.replace("/raw/query", "/repo/")
for task_id in task_ids:
url = prefix + task_id
if self._check_nomad_exist(url):
nomad_exist_task_ids.append(task_id)
return nomad_exist_task_ids
@staticmethod
def _check_nomad_exist(url) -> bool:
response = get(url=url)
if response.status_code != 200:
return False
content = loads(response.text)
if content["pagination"]["total"] == 0:
return False
return True
@staticmethod
def _print_help_message(nomad_exist_task_ids, task_ids, file_patterns, calc_types):
non_exist_ids = set(task_ids) - set(nomad_exist_task_ids)
warnings.warn(
f"For file patterns [{file_patterns}] and calc_types [{calc_types}], \n"
f"the following ids are not found on NOMAD [{list(non_exist_ids)}]. \n"
f"If you need to upload them, please contact Patrick Huck at phuck@lbl.gov"
)
[docs]
def query(*args, **kwargs):
"""The MPRester().query method has been replaced with the MPRester().summary.search method.
Note this method also no longer supports direct MongoDB-type queries. For more information,
please see the new documentation.
"""
raise NotImplementedError(
"""
The MPRester().query method has been replaced with the MPRester().summary.search method.
Note this method also no longer supports direct MongoDB-type queries. For more information,
please see the new documentation.
"""
)
