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from hashlib import blake2b
from typing import Any, Dict, Optional, Type, TypeVar
from pydantic import Field
from emmet.core.qchem.task import TaskDocument
from emmet.core.qchem.molecule import MoleculeDoc
from emmet.core.material import PropertyOrigin
from emmet.core.molecules.molecule_property import PropertyDoc
from emmet.core.molecules.thermo import get_free_energy, MoleculeThermoDoc
from emmet.core.mpid import MPID, MPculeID
__author__ = "Evan Spotte-Smith <ewcspottesmith@lbl.gov>"
reference_potential = 4.44
T = TypeVar("T", bound="RedoxDoc")
class RedoxDoc(PropertyDoc):
"""
Molecular properties related to reduction and oxidation, including
vertical ionization energies and electron affinities, as well as reduction
and oxidation potentials
"""
property_name: str = "redox"
base_property_id: str = Field(
description="Property ID for the thermodynamic data of the " "base molecule"
)
electron_affinity: Optional[float] = Field(
None, description="Vertical electron affinity (units: eV)"
)
ea_task_id: Optional[MPID] = Field(
None, description="Task ID for the electron affinity calculation"
)
ionization_energy: Optional[float] = Field(
None, description="Vertical ionization energy (units: eV)"
)
ie_task_id: Optional[MPID] = Field(
None, description="Task ID for the ionization energy calculation"
)
reduction_energy: Optional[float] = Field(
None, description="Adiabatic electronic energy of reduction (units: eV)"
)
reduction_free_energy: Optional[float] = Field(
None, description="Adiabatic free energy of reduction (units: eV)"
)
red_molecule_id: Optional[MPculeID] = Field(
None, description="Molecule ID for adiabatic reduction"
)
red_property_id: Optional[str] = Field(
None,
description="Property ID for the thermodynamic data of the " "reduced molecule",
)
oxidation_energy: Optional[float] = Field(
None, description="Adiabatic electronic energy of oxidation (units: eV)"
)
oxidation_free_energy: Optional[float] = Field(
None, description="Adiabatic free energy of oxidation (units: eV)"
)
ox_molecule_id: Optional[MPculeID] = Field(
None, description="Molecule ID for adiabatic oxidation"
)
ox_property_id: Optional[str] = Field(
None,
description="Property ID for the thermodynamic data of the "
"oxidized molecule",
)
reduction_potential: Optional[float] = Field(
None,
description="Reduction potential referenced to the standard hydrogen electrode (SHE) (units: V)",
)
oxidation_potential: Optional[float] = Field(
None,
description="Oxidation potential referenced to the standard hydrogen electrode (SHE) (units: V)",
)
@classmethod
def _g_or_e(cls: Type[T], entry: Dict[str, Any]) -> float:
"""
Single atoms may not have free energies like more complex molecules do.
This function returns the free energy of a TaskDocument entry if
possible, and otherwise returns the electronic energy.
:param entry: dict representation of a TaskDocument
:return:
"""
try:
result = get_free_energy(
entry["output"]["final_energy"],
entry["output"]["enthalpy"],
entry["output"]["entropy"],
)
# Single atoms won't have enthalpy and entropy
except TypeError:
result = entry["output"]["final_energy"]
return result
@classmethod
def from_docs(
cls: Type[T],
base_molecule_doc: MoleculeDoc,
base_thermo_doc: MoleculeThermoDoc,
red_doc: Optional[MoleculeThermoDoc] = None,
ox_doc: Optional[MoleculeThermoDoc] = None,
ea_doc: Optional[TaskDocument] = None,
ie_doc: Optional[TaskDocument] = None,
deprecated: bool = False,
**kwargs,
): # type: ignore[override]
"""
Construct a document describing molecular redox properties from
MoleculeThermoDocs (for adiabatic redox potentials and thermodynamics)
and TaskDocs (for vertical ionization energies and electron
affinities)
:param base_molecule_doc: MoleculeDoc of interest
:param base_thermo_doc: MoleculeThermoDoc for the molecule of interest. All properties
will be calculated in reference to this document
:param red_doc: MoleculeThermoDoc for the reduced molecule. This molecule will
have the same (covalent) bonding as base_thermo_doc but will differ in
charge by -1
:param ox_doc: MoleculeThermoDoc for the oxidized molecule. This molecule will
have the same (covalent) bonding as the base_thermo_doc but will differ
in charge by +1
:param ea_doc: A TaskDocument performed at the same structure as
base_thermo_doc, but at a charge that differs by -1. This document will
be used to calculate the electron affinity of the molecule
:param ie_doc: A TaskDocument performed at the same structure as
base_thermo_doc, but at a charge that differs by +1. This document will
be used to calculate the ionization energy of the molecule
:param kwargs: To be passed to PropertyDoc
:return:
"""
if all([x is None for x in [red_doc, ox_doc, ea_doc, ie_doc]]):
# No redox properties can be extracted
return None
base_has_g = base_thermo_doc.free_energy is not None
base_property_id = base_thermo_doc.property_id
red_molecule_id = None
red_property_id = None
reduction_energy = None
reduction_free_energy = None
reduction_potential = None
ox_molecule_id = None
ox_property_id = None
oxidation_energy = None
oxidation_free_energy = None
oxidation_potential = None
ea_task_id = None
electron_affinity = None
ie_task_id = None
ionization_energy = None
id_string = (
f"redox-{base_molecule_doc.molecule_id}-{base_thermo_doc.lot_solvent}-"
f"{base_thermo_doc.property_id}"
)
origins = list()
# Adiabatic reduction properties
if red_doc is not None:
red_molecule_id = red_doc.molecule_id
red_property_id = red_doc.property_id
id_string += f"-{red_doc.property_id}"
reduction_energy = (
red_doc.electronic_energy - base_thermo_doc.electronic_energy
)
if base_has_g and red_doc.free_energy is not None:
reduction_free_energy = (
red_doc.free_energy - base_thermo_doc.free_energy
)
else:
reduction_free_energy = None
red = reduction_free_energy or reduction_energy
reduction_potential = -1 * red - reference_potential
# Adiabatic oxidation properties
if ox_doc is not None:
ox_molecule_id = ox_doc.molecule_id
ox_property_id = ox_doc.property_id
id_string += f"-{ox_doc.property_id}"
oxidation_energy = (
ox_doc.electronic_energy - base_thermo_doc.electronic_energy
)
if base_has_g and ox_doc.free_energy is not None:
oxidation_free_energy = ox_doc.free_energy - base_thermo_doc.free_energy
else:
oxidation_free_energy = None
ox = oxidation_free_energy or oxidation_energy
oxidation_potential = ox - reference_potential
# Electron affinity
if ea_doc is not None:
ea_task_id = ea_doc.task_id
id_string += f"-{ea_task_id}"
origins.append(PropertyOrigin(name="electron_affinity", task_id=ea_task_id))
electron_affinity = (
ea_doc.output.final_energy * 27.2114 - base_thermo_doc.electronic_energy
)
# Ionization energy
if ie_doc is not None:
ie_task_id = ie_doc.task_id
id_string += f"-{ie_task_id}"
origins.append(PropertyOrigin(name="ionization_energy", task_id=ie_task_id))
ionization_energy = (
ie_doc.output.final_energy * 27.2114 - base_thermo_doc.electronic_energy
)
h = blake2b()
h.update(id_string.encode("utf-8"))
property_id = h.hexdigest()
return super().from_molecule(
meta_molecule=base_molecule_doc.molecule,
property_id=property_id,
molecule_id=base_molecule_doc.molecule_id,
base_property_id=base_property_id,
level_of_theory=base_thermo_doc.level_of_theory,
solvent=base_thermo_doc.solvent,
lot_solvent=base_thermo_doc.lot_solvent,
red_molecule_id=red_molecule_id,
red_property_id=red_property_id,
reduction_energy=reduction_energy,
reduction_free_energy=reduction_free_energy,
reduction_potential=reduction_potential,
ox_molecule_id=ox_molecule_id,
ox_property_id=ox_property_id,
oxidation_energy=oxidation_energy,
oxidation_free_energy=oxidation_free_energy,
oxidation_potential=oxidation_potential,
ea_task_id=ea_task_id,
electron_affinity=electron_affinity,
ie_task_id=ie_task_id,
ionization_energy=ionization_energy,
deprecated=deprecated,
origins=origins,
**kwargs,
)
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