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from pydantic import Field
from hashlib import blake2b
from typing import Optional
from emmet.core.mpid import MPculeID
from emmet.core.qchem.calc_types import LevelOfTheory
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>"
def get_free_energy(energy, enthalpy, entropy, temperature=298.15, convert_energy=True):
"""
Helper function to calculate Gibbs free energy from electronic energy, enthalpy, and entropy
:param energy: Electronic energy in Ha
:param enthalpy: Enthalpy in kcal/mol
:param entropy: Entropy in csal/mol-K
:param temperature: Temperature in K. Default is 298.15, 25C
returns: Free energy in eV
"""
if convert_energy:
e = energy * 27.2114
else:
e = energy
return e + enthalpy * 0.043363 - temperature * entropy * 0.000043363
class MoleculeThermoDoc(PropertyDoc):
property_name: str = "thermo"
electronic_energy: float = Field(
..., description="Electronic energy of the molecule (units: eV)"
)
correction: bool = Field(
False,
description="Was a single-point calculation at higher level of "
"theory used to correct the electronic energy?",
)
base_level_of_theory: Optional[LevelOfTheory] = Field(
None, description="Level of theory used for uncorrected thermochemistry."
)
base_solvent: Optional[str] = Field(
None,
description="String representation of the solvent "
"environment used for uncorrected thermochemistry.",
)
base_lot_solvent: Optional[str] = Field(
None,
description="String representation of the level of theory and solvent "
"environment used for uncorrected thermochemistry.",
)
correction_level_of_theory: Optional[LevelOfTheory] = Field(
None, description="Level of theory used to correct the electronic energy."
)
correction_solvent: Optional[str] = Field(
None,
description="String representation of the solvent "
"environment used to correct the electronic energy.",
)
correction_lot_solvent: Optional[str] = Field(
None,
description="String representation of the level of theory and solvent "
"environment used to correct the electronic energy.",
)
combined_lot_solvent: Optional[str] = Field(
None,
description="String representation of the level of theory and solvent "
"environment used to generate this ThermoDoc, combining "
"both the frequency calculation and (potentially) the "
"single-point energy correction.",
)
zero_point_energy: Optional[float] = Field(
None, description="Zero-point energy of the molecule (units: eV)"
)
rt: Optional[float] = Field(
None,
description="R*T, where R is the gas constant and T is temperature, taken "
"to be 298.15K (units: eV)",
)
total_enthalpy: Optional[float] = Field(
None, description="Total enthalpy of the molecule at 298.15K (units: eV)"
)
total_entropy: Optional[float] = Field(
None, description="Total entropy of the molecule at 298.15K (units: eV/K)"
)
translational_enthalpy: Optional[float] = Field(
None,
description="Translational enthalpy of the molecule at 298.15K (units: eV)",
)
translational_entropy: Optional[float] = Field(
None,
description="Translational entropy of the molecule at 298.15K (units: eV/K)",
)
rotational_enthalpy: Optional[float] = Field(
None, description="Rotational enthalpy of the molecule at 298.15K (units: eV)"
)
rotational_entropy: Optional[float] = Field(
None, description="Rotational entropy of the molecule at 298.15K (units: eV/K)"
)
vibrational_enthalpy: Optional[float] = Field(
None, description="Vibrational enthalpy of the molecule at 298.15K (units: eV)"
)
vibrational_entropy: Optional[float] = Field(
None, description="Vibrational entropy of the molecule at 298.15K (units: eV/K)"
)
free_energy: Optional[float] = Field(
None, description="Gibbs free energy of the molecule at 298.15K (units: eV)"
)
@classmethod
def from_task(
cls,
task: TaskDocument,
molecule_id: MPculeID,
correction_task: Optional[TaskDocument] = None,
deprecated: bool = False,
**kwargs,
): # type: ignore[override]
"""
Construct a thermodynamics document from a task
:param task: document from which thermodynamic properties can be extracted
:param molecule_id: MPculeID
:param deprecated: bool. Is this document deprecated?
:param kwargs: to pass to PropertyDoc
:return:
"""
if task.output.optimized_molecule is not None:
mol = task.output.optimized_molecule
else:
mol = task.output.initial_molecule
if correction_task is None:
energy = task.output.final_energy
correction = False
correction_lot = None
correction_solvent = None
correction_lot_solvent = None
level_of_theory = task.level_of_theory
solvent = task.solvent
lot_solvent = task.lot_solvent
combined_lot_solvent = task.lot_solvent
else:
energy = correction_task.output.final_energy
correction = True
correction_lot = correction_task.level_of_theory
correction_solvent = correction_task.solvent
correction_lot_solvent = correction_task.lot_solvent
combined_lot_solvent = f"{task.lot_solvent}//{correction_lot_solvent}"
level_of_theory = correction_lot
solvent = correction_solvent
lot_solvent = combined_lot_solvent
total_enthalpy = task.output.enthalpy
total_entropy = task.output.entropy
origins = [PropertyOrigin(name="thermo", task_id=task.task_id)]
id_string = f"thermo-{molecule_id}-{task.task_id}-{task.lot_solvent}"
if correction and correction_task is not None:
origins.append(
PropertyOrigin(
name="thermo_energy_correction", task_id=correction_task.task_id
)
)
id_string += f"-{correction_task.task_id}-{correction_task.lot_solvent}"
h = blake2b()
h.update(id_string.encode("utf-8"))
property_id = h.hexdigest()
if total_enthalpy is not None and total_entropy is not None:
free_energy = get_free_energy(energy, total_enthalpy, total_entropy)
for calc in task.calcs_reversed:
if all(
[
calc.get(x) is not None
for x in [
"ZPE",
"trans_enthalpy",
"rot_enthalpy",
"vib_enthalpy",
"gas_constant",
"trans_entropy",
"rot_entropy",
"vib_entropy",
]
]
):
return super().from_molecule(
meta_molecule=mol,
property_id=property_id,
molecule_id=molecule_id,
level_of_theory=level_of_theory,
solvent=solvent,
lot_solvent=lot_solvent,
correction=correction,
base_level_of_theory=task.level_of_theory,
base_solvent=task.solvent,
base_lot_solvent=task.lot_solvent,
correction_level_of_theory=correction_lot,
correction_solvent=correction_solvent,
correction_lot_solvent=correction_lot_solvent,
combined_lot_solvent=combined_lot_solvent,
electronic_energy=energy * 27.2114,
zero_point_energy=calc["ZPE"] * 0.043363,
rt=calc["gas_constant"] * 0.043363,
total_enthalpy=total_enthalpy * 0.043363,
translational_enthalpy=calc["trans_enthalpy"] * 0.043363,
rotational_enthalpy=calc["rot_enthalpy"] * 0.043363,
vibrational_enthalpy=calc["vib_enthalpy"] * 0.043363,
total_entropy=total_entropy * 0.000043363,
translational_entropy=calc["trans_entropy"] * 0.000043363,
rotational_entropy=calc["rot_entropy"] * 0.000043363,
vibrational_entropy=calc["vib_entropy"] * 0.000043363,
free_energy=free_energy,
deprecated=deprecated,
origins=origins,
**kwargs,
)
# If all thermodynamic data is not available
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,
correction=correction,
correction_level_of_theory=correction_lot,
correction_solvent=correction_solvent,
correction_lot_solvent=correction_lot_solvent,
combined_lot_solvent=combined_lot_solvent,
electronic_energy=energy * 27.2114,
deprecated=deprecated,
origins=origins,
**kwargs,
)
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