class matlantis_features.features.common.neb.NEBFeatureResult(feature: NEBFeature, call_params: Dict[str, Any], output: NEBFeatureOutput, calculator_info: Optional[Dict[str, Any]], version_info: Dict[str, Any], user_info: Dict[str, Any])#

Bases: FeatureBaseResult

A dataclass for result of NEBFeature.

Methods

__init__(feature, call_params, output, …)

from_dict(res)

Construct a FeatureBaseResult object from serialized dict.

load(filename)

Construct a FeatureBaseResult object from serialized dict.

plot([plt_name])

Plots the energy profile along the NEB pathway.

save(filename)

Construct a FeatureBaseResult object from serialized dict.

to_dataframe([csv_name])

Saves the NEB information to pandas.DataFrame.

to_dict()

Dictionary representation of the FeatureBaseResult.

to_gif([gif_name, rotation])

Creates gif file to show the movement of atoms along the NEB pathway.

to_traj(traj_name)

Creates ase.io.Trajectory to save the movement of atoms.
__init__(feature: NEBFeature, call_params: Dict[str, Any], output: NEBFeatureOutput, calculator_info: Optional[Dict[str, Any]], version_info: Dict[str, Any], user_info: Dict[str, Any]) → None#
classmethod from_dict(res: Dict[str, Any]) → FeatureBaseResult#

Construct a FeatureBaseResult object from serialized dict.

Parameters

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

Returns

The deserialized object from provided dict.

Return type

FeatureBaseResult

classmethod load(filename: str) → FeatureBaseResult#

Construct a FeatureBaseResult object from serialized dict.

Parameters

filename (str) – Name of file to save the FeatureBaseResult to.

Returns

The FeatureBaseResult object if loading was successful.

Return type

FeatureBaseResult

plot(plt_name: Optional[str] = None) → Figure#

Plots the energy profile along the NEB pathway.

Parameters

plt_name (str or None, optional) – The file name to which the plot of the energy profile
will be saved. Supported formats include ‘png’ ‘jpg’ ‘jpeg’ ‘webp’ ‘svg’
and ‘pdf’. If ‘None’ is provided, the figure will not be saved. Defaults to None.

Returns

The plot of the NEB energy profile as a plotly.graph_objects.Figure instance.

Return type

go.Figure

save(filename: str) → bool#

Construct a FeatureBaseResult object from serialized dict.

Parameters

filename (str) – Name of file to save the FeatureBaseResult to.

Returns

Whether saving the result was successful or not.

Return type

bool

to_dataframe(csv_name: Optional[str] = None) → DataFrame#

Saves the NEB information to pandas.DataFrame.

Parameters

csv_name (str or None, optional) – The file name to which the NEB information will be
saved. Defaults to None.

Returns

The pandas.DataFrame which contains the energy and max force of each image during
the optimization.

Return type

pd.DataFrame

to_dict() → Dict[str, Any]#

Dictionary representation of the FeatureBaseResult.

Returns

A dict containing a serialized FeatureBaseResult.

Return type

dict[str, Any]

to_gif(gif_name: Optional[str] = None, rotation: str = ‘0x,0y,0z’) → None#

Creates gif file to show the movement of atoms along the NEB pathway.

Parameters

  • gif_name (str or None, optional) – The file name to which the NEB pathway will be
    saved. Defaults to None.

  • rotation (str, optional) – The viewing angle. Defaults to ‘0x,0y,0z’.

to_traj(traj_name: str) → None#

Creates ase.io.Trajectory to save the movement of atoms.

Parameters

traj_name (str) – The file name to which the NEB trajectory will be saved.

Attributes

feature: NEBFeature#
output: NEBFeatureOutput#
call_params: Dict[str, Any]#
calculator_info: Optional[Dict[str, Any]]#
version_info: Dict[str, Any]#
user_info: Dict[str, Any]#