pymatgen.entries.computed_entries module

This module implements equivalents of the basic ComputedEntry objects, which is the basic entity that can be used to perform many analyses. ComputedEntries contain calculated information, typically from VASP or other electronic structure codes. For example, ComputedEntries can be used as inputs for phase diagram analysis.

class CompositionEnergyAdjustment(adj_per_atom, n_atoms, uncertainty_per_atom=nan, name='', cls=None, description='Composition-based energy adjustment')

Bases: EnergyAdjustment

An energy adjustment applied to a ComputedEntry based on the atomic composition. Used in various DFT energy correction schemes.

Parameters:

• adj_per_atom – float, energy adjustment to apply per atom, in eV/atom

• n_atoms – float or int, number of atoms.

• uncertainty_per_atom – float, uncertainty in energy adjustment to apply per atom, in eV/atom. (Default: np.nan)

• name – str, human-readable name of the energy adjustment. (Default: “”)

• cls – dict, Serialized Compatibility class used to generate the energy adjustment. (Default: None)

• description – str, human-readable explanation of the energy adjustment.

property explain

Return an explanation of how the energy adjustment is calculated.

normalize(factor)

Normalize energy adjustment (in place), dividing value/uncertainty by a factor. :param factor: factor to divide by

property uncertainty

Return the value of the energy adjustment in eV.

property value

Return the value of the energy adjustment in eV.

class ComputedEntry(composition: Composition | str | dict[str, float], energy: float, correction: float = 0.0, energy_adjustments: list | None = None, parameters: dict | None = None, data: dict | None = None, entry_id: object | None = None)

Bases: Entry

Lightweight Entry object for computed data. Contains facilities for applying corrections to the energy attribute and for storing calculation parameters.

Initializes a ComputedEntry.

Parameters:

• composition (Composition) – Composition of the entry. For flexibility, this can take the form of all the typical input taken by a Composition, including a {symbol: amt} dict, a string formula, and others.

• energy (float) – Energy of the entry. Usually the final calculated energy from VASP or other electronic structure codes.

• correction (float) – Manually set an energy correction, will ignore energy_adjustments if specified.

• energy_adjustments – An optional list of EnergyAdjustment to be applied to the energy. This is used to modify the energy for certain analyses. Defaults to None.

• parameters – An optional dict of parameters associated with the entry. Defaults to None.

• data – An optional dict of any additional data associated with the entry. Defaults to None.

• entry_id – An optional id to uniquely identify the entry.

as_dict() → dict

Returns:

MSONable dict.

copy() → ComputedEntry

Returns a copy of the ComputedEntry.

property correction: float

Returns: float: the total energy correction / adjustment applied to the entry,

in eV.

property correction_per_atom: float

Returns: float: the total energy correction / adjustment applied to the entry,

normalized by atoms (units of eV/atom)

property correction_uncertainty: float

Returns: float: the uncertainty of the energy adjustments applied to the entry, in eV

property correction_uncertainty_per_atom: float

Returns: float: the uncertainty of the energy adjustments applied to the entry,

normalized by atoms (units of eV/atom)

property energy: float

the corrected energy of the entry.

Type:

return

classmethod from_dict(d) → ComputedEntry

Parameters:

d – Dict representation.

Returns:

ComputedEntry

normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → ComputedEntry

Normalize the entry’s composition and energy.

Parameters:

mode ("formula_unit" | "atom") – “formula_unit” (the default) normalizes to composition.reduced_formula. “atom” normalizes such that the composition amounts sum to 1.

property uncorrected_energy: float

Returns: float: the uncorrected energy of the entry

property uncorrected_energy_per_atom: float

Returns: float: the uncorrected energy of the entry, normalized by atoms

(units of eV/atom)

class ComputedStructureEntry(structure: Structure, energy: float, correction: float = 0.0, composition: Composition | str | dict[str, float] | None = None, energy_adjustments: list | None = None, parameters: dict | None = None, data: dict | None = None, entry_id: object | None = None)

Bases: ComputedEntry

A heavier version of ComputedEntry which contains a structure as well. The structure is needed for some analyses.

Initializes a ComputedStructureEntry.

Parameters:

• structure (Structure) – The actual structure of an entry.

• energy (float) – Energy of the entry. Usually the final calculated energy from VASP or other electronic structure codes.

• correction (float, optional) – A correction to the energy. This is mutually exclusive with energy_adjustments, i.e. pass either or neither but not both. Defaults to 0.

• composition (Composition) – Composition of the entry. For flexibility, this can take the form of all the typical input taken by a Composition, including a {symbol: amt} dict, a string formula, and others.

• energy_adjustments – An optional list of EnergyAdjustment to be applied to the energy. This is used to modify the energy for certain analyses. Defaults to None.

• parameters – An optional dict of parameters associated with the entry. Defaults to None.

• data – An optional dict of any additional data associated with the entry. Defaults to None.

• entry_id – An optional id to uniquely identify the entry.

as_dict() → dict

Returns:

MSONable dict.

copy() → ComputedStructureEntry

Returns a copy of the ComputedStructureEntry.

classmethod from_dict(d) → ComputedStructureEntry

Parameters:

d – Dict representation.

Returns:

ComputedStructureEntry

normalize(mode: Literal['formula_unit', 'atom'] = 'formula_unit') → ComputedStructureEntry

Normalize the entry’s composition and energy. The structure remains unchanged.

Parameters:

mode ("formula_unit" | "atom") – “formula_unit” (the default) normalizes to composition.reduced_formula. “atom” normalizes such that the composition amounts sum to 1.

property structure: Structure

the structure of the entry.

Type:

return

class ConstantEnergyAdjustment(value, uncertainty=nan, name='Constant energy adjustment', cls=None, description='Constant energy adjustment')

Bases: EnergyAdjustment

A constant energy adjustment applied to a ComputedEntry. Useful in energy referencing schemes such as the Aqueous energy referencing scheme.

Parameters:

• value – float, value of the energy adjustment in eV

• uncertainty – float, uncertainty of the energy adjustment in eV. (Default: np.nan)

• name – str, human-readable name of the energy adjustment. (Default: Constant energy adjustment)

• cls – dict, Serialized Compatibility class used to generate the energy adjustment. (Default: None)

• description – str, human-readable explanation of the energy adjustment.

property explain

Return an explanation of how the energy adjustment is calculated.

normalize(factor)

Normalize energy adjustment (in place), dividing value/uncertainty by a factor. :param factor: factor to divide by

class EnergyAdjustment(value, uncertainty=nan, name='Manual adjustment', cls=None, description='')

Bases: MSONable

Lightweight class to contain information about an energy adjustment or energy correction.

Parameters:

• value – float, value of the energy adjustment in eV

• uncertainty – float, uncertainty of the energy adjustment in eV. Default: np.nan

• name – str, human-readable name of the energy adjustment. (Default: Manual adjustment)

• cls – dict, Serialized Compatibility class used to generate the energy adjustment. (Default: None)

• description – str, human-readable explanation of the energy adjustment.

abstract property explain

Return an explanation of how the energy adjustment is calculated.

abstract normalize(factor)

Scale the value of the current energy adjustment by factor in-place.

This method is utilized in ComputedEntry.normalize() to scale the energies to a formula unit basis (e.g. E_Fe6O9 = 3 x E_Fe2O3).

property uncertainty

Return the uncertainty in the value of the energy adjustment in eV

property value

Return the value of the energy correction in eV.

class GibbsComputedStructureEntry(structure: Structure, formation_enthalpy_per_atom: float, temp: float = 300, gibbs_model: Literal['SISSO'] = 'SISSO', composition: Composition | None = None, correction: float = 0.0, energy_adjustments: list | None = None, parameters: dict | None = None, data: dict | None = None, entry_id: object | None = None)

Bases: ComputedStructureEntry

An extension to ComputedStructureEntry which includes the estimated Gibbs free energy of formation via a machine-learned model.

Parameters:

• structure (Structure) – The pymatgen Structure object of an entry.

• formation_enthalpy_per_atom (float) – Formation enthalpy of the entry;

• be (must) – calculated using phase diagram construction (eV)

• temp (float) – Temperature in Kelvin. If temperature is not selected from one of [300, 400, 500, … 2000 K], then free energies will be interpolated. Defaults to 300 K.

• gibbs_model ('SISSO') – Model for Gibbs Free energy. “SISSO”, the descriptor created by Bartel et al. (2018) – see reference in documentation, is currently the only supported) option.

• composition (Composition) – The composition of the entry. Defaults to None.

• correction (float) – A correction to be applied to the energy. Defaults to 0.

• energy_adjustments (list) – A list of energy adjustments to be applied to the energy. Defaults to None.

• parameters (dict) – An optional dict of parameters associated with the entry. Defaults to None.

• data (dict) – An optional dict of any additional data associated with the entry. Defaults to None.

• entry_id – An optional id to uniquely identify the entry.

as_dict() → dict

Returns:

MSONable dict.

classmethod from_dict(d) → GibbsComputedStructureEntry

Parameters:

d – Dict representation.

Returns:

GibbsComputedStructureEntry

classmethod from_entries(entries, temp=300, gibbs_model='SISSO') → list[pymatgen.entries.computed_entries.GibbsComputedStructureEntry]

Constructor method for initializing GibbsComputedStructureEntry objects from T = 0 K ComputedStructureEntry objects, as acquired from a thermochemical database e.g. The Materials Project.

Parameters:

• entries ([ComputedStructureEntry]) – List of ComputedStructureEntry objects, as downloaded from The Materials Project API.

• temp (int) – Temperature [K] for estimating Gibbs free energy of formation.

• gibbs_model (str) – Gibbs model to use; currently the only option is “SISSO”.

Returns:

list of new entries which replace the orig.

entries with inclusion of Gibbs free energy of formation at the specified temperature.

Return type:

[GibbsComputedStructureEntry]

classmethod from_pd(pd, temp=300, gibbs_model='SISSO') → list[pymatgen.entries.computed_entries.GibbsComputedStructureEntry]

Constructor method for initializing a list of GibbsComputedStructureEntry objects from an existing T = 0 K phase diagram composed of ComputedStructureEntry objects, as acquired from a thermochemical database; (e.g.. The Materials Project)

Parameters:

• pd (PhaseDiagram) – T = 0 K phase diagram as created in pymatgen. Must contain ComputedStructureEntry objects.

• temp (int) – Temperature [K] for estimating Gibbs free energy of formation.

• gibbs_model (str) – Gibbs model to use; currently the only option is “SISSO”.

Returns:

list of new entries which replace the orig.

entries with inclusion of Gibbs free energy of formation at the specified temperature.

Return type:

[GibbsComputedStructureEntry]

gf_sisso() → float

Gibbs Free Energy of formation as calculated by SISSO descriptor from Bartel et al. (2018). Units: eV (not normalized)

WARNING: This descriptor only applies to solids. The implementation here attempts to detect and use downloaded NIST-JANAF data for common experimental gases (e.g. CO2) where possible. Note that experimental data is only for Gibbs Free Energy of formation, so expt. entries will register as having a formation enthalpy of 0.

Reference: Bartel, C. J., Millican, S. L., Deml, A. M., Rumptz, J. R., Tumas, W., Weimer, A. W., … Holder, A. M. (2018). Physical descriptor for the Gibbs energy of inorganic crystalline solids and temperature-dependent materials chemistry. Nature Communications, 9(1), 4168. https://doi.org/10.1038/s41467-018-06682-4

Returns:

the difference between formation enthalpy (T=0 K, Materials Project) and the predicted Gibbs free energy of formation (eV)

Return type:

float

class ManualEnergyAdjustment(value)

Bases: ConstantEnergyAdjustment

A manual energy adjustment applied to a ComputedEntry.

Parameters:

value – float, value of the energy adjustment in eV

class TemperatureEnergyAdjustment(adj_per_deg, temp, n_atoms, uncertainty_per_deg=nan, name='', cls=None, description='Temperature-based energy adjustment')

Bases: EnergyAdjustment

An energy adjustment applied to a ComputedEntry based on the temperature. Used, for example, to add entropy to DFT energies.

Parameters:

• adj_per_deg – float, energy adjustment to apply per degree K, in eV/atom

• temp – float, temperature in Kelvin

• n_atoms – float or int, number of atoms

• uncertainty_per_deg – float, uncertainty in energy adjustment to apply per degree K, in eV/atom. (Default: np.nan)

• name – str, human-readable name of the energy adjustment. (Default: “”)

• cls – dict, Serialized Compatibility class used to generate the energy adjustment. (Default: None)

• description – str, human-readable explanation of the energy adjustment.

property explain

Return an explanation of how the energy adjustment is calculated.

normalize(factor)

Normalize energy adjustment (in place), dividing value/uncertainty by a factor. :param factor: factor to divide by

property uncertainty

Return the value of the energy adjustment in eV.

property value

Return the value of the energy correction in eV.