matlantis_features.features.common.hessian.HessianFeature

class matlantis_features.features.common.hessian.HessianFeature(delta: float = 0.01, nfree: int = 2, method: str = ‘standard’, direction: str = ‘central’, show_progress_bar: bool = False, tqdm_options: Optional[Dict[str, Any]] = None, show_logger: bool = False, estimator_fn: Optional[Callable[[], Estimator]] = None, num_threads: int = 20)#

Bases: FeatureBase

The matlantis-feature for calculating molecular vibration.

The vibration properties, including the force constant, vibration frequencies and vibration modes are calculated with the finite displacement method.

Methods

`__init__`([delta, nfree, method, direction, …])	Initialize an instance.
`__call__`(atoms[, indices])	Calculate the hessian matrix.
`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__(delta: float = 0.01, nfree: int = 2, method: str = ‘standard’, direction: str = ‘central’, show_progress_bar: bool = False, tqdm_options: Optional[Dict[str, Any]] = None, show_logger: bool = False, estimator_fn: Optional[Callable[[], Estimator]] = None, num_threads: int = 20) → None#

Initialize an instance.

Parameters

delta (float, optional) – The distance of finite displacement applied to each atom.
The unit is Angstrom. Defaults to 0.01.
nfree (int, optional) – The number of displacements per atom. Must be 2 or 4. Defaults
to 2.
method (str, optional) – The method to calculate the force constant from the displaced
supercells and their forces. This parameter can be ‘Standard’ or ‘Frederiksen’.
Defaults to ‘standard’.
direction (str, optional) – This parameter discribe how the displacment is found. Must
be When ‘direction=forward’/’direction=backward’, each atom is displaced along the
positive/negative direction of the axis. When ‘direction=center’, each atom is
displaced along both positive and negative directions of the axis. Defaults to
‘central’.
show_progress_bar (bool, optional) – Show progress bar. Defaults to False.
tqdm_options (dict[str, Any] or None, optional) – Options for tqdm.
show_logger (bool, optional) – Show log information. Defaults to False.
estimator_fn (EstimatorFnType or None, optional) – A factory method to create a custom estimator.
Please refer Customizing estimator used in matlantis-features for detail.
num_threads (int, optional) – Number of threads for parallel calculation. Defaults to 10.

__call__(atoms: Union[MatlantisAtoms, Atoms], indices: Optional[List[int]] = None) → HessianFeatureResult#

Calculate the hessian matrix.

Parameters

atoms (MatlantisAtoms or ASEAtoms) – The input structure.
indices (list[int] or None, optional) – List of indices of atoms allowed to vibrate.
If ‘None’ is provided, all atoms are allowed to vibrate. Defaults to None.

Returns

The hessian matrix.

Return type

HessianFeatureResult

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