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import logging
from collections import defaultdict
from typing import Dict, List, Optional
import numpy as np
from pydantic import Field
from pymatgen.analysis.bond_valence import BVAnalyzer
from pymatgen.core import Structure
from pymatgen.core.periodic_table import Specie
from emmet.core.material_property import PropertyDoc
from emmet.core.mpid import MPID
class OxidationStateDoc(PropertyDoc):
"""Oxidation states computed from the structure"""
property_name: str = "oxidation"
structure: Structure = Field(
...,
description="The structure used in the generation of the oxidation state data.",
)
possible_species: List[str] = Field(
description="Possible charged species in this material."
)
possible_valences: List[float] = Field(
description="List of valences for each site in this material."
)
average_oxidation_states: Dict[str, float] = Field(
description="Average oxidation states for each unique species."
)
method: Optional[str] = Field(
None, description="Method used to compute oxidation states."
)
@classmethod
def from_structure(cls, structure: Structure, material_id: MPID, **kwargs): # type: ignore[override]
# TODO: add check for if it already has oxidation states, if so pass this along unchanged ("method": "manual")
structure.remove_oxidation_states()
# Null document
d = {
"possible_species": [],
"possible_valences": [],
"average_oxidation_states": {},
} # type: dict
try:
bva = BVAnalyzer()
valences = bva.get_valences(structure)
possible_species = {
str(Specie(structure[idx].specie, oxidation_state=valence))
for idx, valence in enumerate(valences)
}
structure.add_oxidation_state_by_site(valences)
# construct a dict of average oxi_states for use
# by MP2020 corrections. The format should mirror
# the output of the first element from Composition.oxi_state_guesses()
# e.g. {'Li': 1.0, 'O': -2.0}
site_oxidation_list = defaultdict(list)
for site in structure:
site_oxidation_list[site.specie.element].append(site.specie.oxi_state)
oxi_state_dict = {
str(el): np.mean(oxi_states) for el, oxi_states in site_oxidation_list.items() # type: ignore
}
d = {
"possible_species": list(possible_species),
"possible_valences": valences,
"average_oxidation_states": oxi_state_dict,
"method": "Bond Valence Analysis",
}
except Exception as e:
logging.error("BVAnalyzer failed with: {}".format(e))
try:
first_oxi_state_guess = structure.composition.oxi_state_guesses(
max_sites=-50
)[0]
valences = [
first_oxi_state_guess[site.species_string] for site in structure
]
possible_species = {
str(Specie(el, oxidation_state=valence))
for el, valence in first_oxi_state_guess.items()
}
structure.add_oxidation_state_by_site(valences)
d = {
"possible_species": list(possible_species),
"possible_valences": valences,
"average_oxidation_states": first_oxi_state_guess,
"method": "Oxidation State Guess",
}
except Exception as e:
logging.error("Oxidation state guess failed with: {}".format(e))
d["warnings"] = ["Oxidation state guessing failed."]
d["state"] = "unsuccessful"
return super().from_structure(
meta_structure=structure,
material_id=material_id,
structure=structure,
**d,
**kwargs
)
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