class matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature#

Bases: FeatureBase

The matlantis-feature for calculating thermochemistry properties from phonon.

Methods

__init__()

Initialize an instance.

__call__(force_constant, kpts[, tmin, tmax, …])

Calculates the thermochemistry properties from the force constant.

attach_ctx([ctx])

Attach the feature to matlantis_features.utils.Context.

check_estimator_fn(estimator_fn)

Checks if the given estimator function is None and output a warning if so.

cost_estimate([atoms])

Estimate the cost of the feature.

from_dict(res)

Construct a FeatureBase object from serialized dict.

get_savedir_from_ctx()

Get the temporary save directory from the context.

init_scope()

Context manager that enable to set attribution of the feature.

repeat(n_repeat)

Set the maximum number of times that allowed to run the __call__ function.

to_dict()

Dictionary representation of the FeatureBase.

__init__() None#

Initialize an instance.

__call__(force_constant: ForceConstantFeatureResult, kpts: List[int], tmin: float = 0.0, tmax: float = 1000.0, tstep: float = 10.0, temperatures: Optional[List[float]] = None, include_lattice_energy: bool = False, scheme: str = ‘mp’, shift: Optional[ndarray] = None, cutoff_frequency: float = 0.0) PostPhononThermochemistryFeatureResult#

Calculates the thermochemistry properties from the force constant.

Parameters
  • force_constant (ForceConstantFeatureResult) – The calculation result of
    the ForceConstantFeature.

  • kpts (list[int]) – The number of mesh points along each axis.

  • tmin (float, optional) – The lower limit of temperate range to be calculated.
    Defaults to 0.0.

  • tmax (float, optional) – The upper limit of temperate range to be calculated.
    Defaults to 1000.0.

  • tstep (float, optional) – Creates a evenly spaced set of temperatures in the range of
    [tmin, tmax) at intervals of tstep, at which the thermochemical
    properties will be calculated. Defaults to 10.0.

  • temperatures (list[float] or None, optional) – The temperatures at which the thermochemistry properties will be calculated. If
    None is provided, the calculation temperatures will be generated according to
    ‘tmin’, ‘tmax’ and ‘tstep’. Defaults to None.

  • include_lattice_energy (bool, optional) – Add the potential energy of the input
    structure to the result of internal energy and helmholtz free energy. Defaults
    to False.

  • scheme (str, optional) – The type of mesh grid: either ‘mp’ or ‘gamma’. The mesh grid is
    determined by the Monkhorst-Pack scheme (‘mp’) or Gamma-centered scheme (‘gamma’).
    Defaults to ‘mp’.

  • shift (np.ndarray or None, optional) – An array of shape (3,) containing the shift of
    the mesh grid in the direction along the corresponding reciprocal axes. Defaults
    to None.

  • cutoff_frequency (float, optional) – The vibration modes with frequency smaller than
    ‘cutoff_frequency’ will not be used in the thermochemical property calculation.
    Imaginary frequencies will be regarded as negative. Defaults to 0.0.

Returns

The calculation results of thermochemical properties from phonons.

Return type

PostPhononThermochemistryFeatureResult

attach_ctx(ctx: Optional[Context] = None) None#

Attach the feature to matlantis_features.utils.Context.

Parameters

ctx (Context or None, optional) – The matlantis_features.utils.Context object. Defaults to None.

check_estimator_fn(estimator_fn: Optional[Callable[[], Estimator]]) None#

Checks if the given estimator function is None and output a warning if so.

Parameters

estimator_fn (EstimatorFnType or None, optional) – A factory method to create a custom estimator.
Please refer Customizing estimator used in matlantis-features for detail. Defaults to None.

cost_estimate(atoms: Optional[Union[Atoms, MatlantisAtoms]] = None) FeatureCost#

Estimate the cost of the feature.

Parameters

atoms (ASEAtoms or MatlantisAtoms or None, optional) – The input atoms. Defaults to None.

Returns

The cost of the feature.

Return type

FeatureCost

classmethod from_dict(res: Dict[str, Any]) FeatureBase#

Construct a FeatureBase object from serialized dict.

Parameters

res (dict[str, Any]) – A dict containing a serialized FeatureBase from to_dict().

Returns

The deserialized object from provided dict.

Return type

FeatureBase

get_savedir_from_ctx() Path#

Get the temporary save directory from the context.

Returns

The temporary save directory .

Return type

pathlib.Path

init_scope() Iterator[None]#

Context manager that enable to set attribution of the feature.

Returns

Init_scope context manager.

Return type

Iterator[None]

repeat(n_repeat: int) Self#

Set the maximum number of times that allowed to run the __call__ function.

Parameters

n_repeat (int) – The maximum number of repeats.

Returns

The feature.

Return type

Self

to_dict() Dict[str, Any]#

Dictionary representation of the FeatureBase.

Returns

A dict containing a serialized FeatureBase.

Return type

dict[str, Any]