- class matlantis_features.features.phonon.mode.PostPhononModeFeature#
-
Bases:
FeatureBase
The matlantis-feature to visualize how atoms move under a certain phonon mode.
Methods
__init__
()Initialize an instance.
__call__
(force_constant[, k_point, …])Calculates the phonon mode 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 the temporary save directory from the context.
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, 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
- 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
- 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]
Resource Library
matlantis_features.features.phonon.mode.PostPhononModeFeature