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from typing import List
from hashlib import blake2b
from pydantic import Field
from emmet.core.mpid import MPculeID
from emmet.core.qchem.task import TaskDocument
from emmet.core.material import PropertyOrigin
from emmet.core.molecules.molecule_property import PropertyDoc
__author__ = "Evan Spotte-Smith <ewcspottesmith@lbl.gov>"
CHARGES_METHODS = ["nbo", "resp", "critic2", "mulliken"]
SPINS_METHODS = ["nbo", "mulliken"]
class PartialChargesDoc(PropertyDoc):
"""Atomic partial charges of a molecule"""
property_name: str = "partial_charges"
method: str = Field(
..., description="Method used to compute atomic partial charges"
)
partial_charges: List[float] = Field(
..., description="Atomic partial charges for the molecule"
)
@classmethod
def from_task(
cls,
task: TaskDocument,
molecule_id: MPculeID,
preferred_methods: List[str],
deprecated: bool = False,
**kwargs,
): # type: ignore[override]
"""
Determine partial charges from a task document
:param task: task document from which partial charges can be extracted
:param molecule_id: MPculeID
:param preferred_methods: list of methods; by default, NBO7, RESP, Critic2, and Mulliken, in that order
:param kwargs: to pass to PropertyDoc
:return:
"""
charges = None
method = None
if task.output.optimized_molecule is not None:
mol = task.output.optimized_molecule
else:
mol = task.output.initial_molecule
for m in preferred_methods:
if m == "nbo" and task.output.nbo is not None:
method = m
charges = [
float(task.output.nbo["natural_populations"][0]["Charge"][str(i)])
for i in range(len(mol))
]
break
elif m == "resp" and task.output.resp is not None:
method = m
charges = [float(i) for i in task.output.resp]
break
elif m == "critic2" and task.critic2 is not None:
method = m
charges = list([float(i) for i in task.critic2["processed"]["charges"]])
break
elif m == "mulliken" and task.output.mulliken is not None:
method = m
if isinstance(task.output.mulliken[0], list):
charges = [float(mull[0]) for mull in task.output.mulliken]
else:
charges = [float(i) for i in task.output.mulliken]
break
id_string = (
f"partial_charges-{molecule_id}-{task.task_id}-{task.lot_solvent}-{method}"
)
h = blake2b()
h.update(id_string.encode("utf-8"))
property_id = h.hexdigest()
if charges is None:
raise Exception("No valid partial charge information!")
return super().from_molecule(
meta_molecule=mol,
property_id=property_id,
molecule_id=molecule_id,
level_of_theory=task.level_of_theory,
solvent=task.solvent,
lot_solvent=task.lot_solvent,
partial_charges=charges,
method=method,
origins=[PropertyOrigin(name="partial_charges", task_id=task.task_id)],
deprecated=deprecated,
**kwargs,
)
class PartialSpinsDoc(PropertyDoc):
"""Atomic partial charges of a molecule"""
property_name: str = "partial_spins"
method: str = Field(..., description="Method used to compute atomic partial spins")
partial_spins: List[float] = Field(
..., description="Atomic partial spins for the molecule"
)
@classmethod
def from_task(
cls,
task: TaskDocument,
molecule_id: MPculeID,
preferred_methods: List[str],
deprecated: bool = False,
**kwargs,
): # type: ignore[override]
"""
Determine partial spins from a task document
:param task: task document from which partial spins can be extracted
:param molecule_id: MPculeID
:param preferred_methods: list of methods; by default, NBO7 and Mulliken, in that order
:param kwargs: to pass to PropertyDoc
:return:
"""
spins = None
method = None
if task.output.optimized_molecule is not None:
mol = task.output.optimized_molecule
else:
mol = task.output.initial_molecule
if mol.spin_multiplicity == 1:
raise Exception("Closed-shell molecule has no partial spins!")
for m in preferred_methods:
if m == "nbo" and task.output.nbo is not None:
method = m
spins = [
float(task.output.nbo["natural_populations"][0]["Density"][str(i)])
for i in range(len(mol))
]
break
elif m == "mulliken" and task.output.mulliken is not None:
method = m
spins = [float(mull[1]) for mull in task.output.mulliken]
break
id_string = (
f"partial_spins-{molecule_id}-{task.task_id}-{task.lot_solvent}-{method}"
)
h = blake2b()
h.update(id_string.encode("utf-8"))
property_id = h.hexdigest()
if spins is None:
raise Exception("No valid partial spin information!")
return super().from_molecule(
meta_molecule=mol,
property_id=property_id,
molecule_id=molecule_id,
level_of_theory=task.level_of_theory,
solvent=task.solvent,
lot_solvent=task.lot_solvent,
partial_spins=spins,
method=method,
origins=[PropertyOrigin(name="partial_spins", task_id=task.task_id)],
deprecated=deprecated,
**kwargs,
)
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