matlantis_features.features.phonon.mode.PostPhononModeFeature

Bases: FeatureBase

The matlantis-feature to visualize how atoms move under a certain phonon mode.

Methods

__init__() → None#

Initialize an instance.

__call__(force_constant: ForceConstantFeatureResult, k_point: Tuple[float, float, float] = (0.0, 0.0, 0.0), repeat_of_cell: Tuple[int, int, int] = (3, 3, 3), mode_indices: Optional[Union[int, List[int]]] = None, n_images: int = 20, amplitude: float = 5.0, q_point: Optional[Tuple[float, float, float]] = None) → PostPhononModeFeatureResult#

Calculates the phonon mode from the force constant.

Parameters

• force_constant (ForceConstantFeatureResult) – The force contant result obtained from
  matlantis_features.features.phonon.RunForceConstantFeature

• k_point (tuple[float, float, float], optional) – The k-point in which the phonon mode
  will be calculated and the atom movement will be viewed. Defaults to [0., 0., 0.].

• repeat_of_cell (tuple[int, int, int], optional) – To view the phonon mode at a large
  supercell. Defaults to [3, 3, 3].

• mode_indices (int or list[int] or None, optional) – The index of branches.
  If None is provided, the phonon modes will be calculated in all branches.

• n_images (int, optional) – Number of images in one period. Defaults to 20.

• amplitude (float, optional) – The amplitude of vibration. Defaults to 1.0.

• q_point (tuple[float, float, float] or None, optional) – Deprecated parameter.
  The q-vector in which the phonon mode will be calculated and the atom movement
  will be viewed. Defaults to [0., 0., 0.].

Returns

A set of structure images that show the periodic movement of each atom under phonon
modes of given a k-point.

Return type

PostPhononModeFeatureResult

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]