matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature

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