- class matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity#
-
Bases:
PostNEMDViscosityFeature
The old version of PostNEMDViscosityFeature. This class is deprecated. Please use PostNEMDViscosityFeature instead.
Methods
__init__
()Initialize an instance.
__call__
(md_results[, init_time])Calculate the viscosity from the non-equilibrium MD trajectory.
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__(md_results: MDFeatureResult, init_time: float = 0.0) PostNEMDViscosityFeatureResult #
-
Calculate the viscosity from the non-equilibrium MD trajectory.
- Parameters
-
-
md_results (MDFeatureResult) – MD feature’s result object containing the trajectory.
The simulation must be run with the rNEMD extension. -
init_time (float, optional) – Trajectory frames before this time is ignored for the calculation.
Defaults to 0.0 (i.e., all frames are used for calculation).
-
- Returns
-
Result dataclass object.
- 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.md.post_features.nemd_viscosity.PostNEMDViscosity