- class matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature(integrator: MDIntegratorBase, n_run: int, rnemd_n_slab: int = 20, rnemd_interval: int = 100, init_time: float = 0.0, md_feature_args: Optional[Dict[str, Any]] = None)#
-
Bases:
FeatureBase
The matlantis-feature for calculating viscosity related properties.
This feature calls both MDFeature with RNEMDExtension and PostNEMDViscosityFeature.
Methods
__init__
(integrator, n_run[, rnemd_n_slab, …])Initialize an instance.
__call__
(system)Run the rNEMD simulation and calculate the viscosity.
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__(integrator: MDIntegratorBase, n_run: int, rnemd_n_slab: int = 20, rnemd_interval: int = 100, init_time: float = 0.0, md_feature_args: Optional[Dict[str, Any]] = None)#
-
Initialize an instance.
- Parameters
-
-
integrator (MDIntegratorBase) – Integrator used for the MD simulation run.
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n_run (int) – Number of time steps of the MD simulation.
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rnemd_n_slab (int, optional) – Number of the slabs used for the rNEMD calculation. Defaults to 20.
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rnemd_interval (int, optional) – Number of the timestep interval for the rNEMD calculation.
Defaults to 100. -
init_time (float, optional) – Trajectory frames before this time (in fs) is ignored for the calculation.
Defaults to 0.0 (i.e., all frames are used for calculation). -
md_feature_args (dict[str, Any] or None, optional) – Additional options for MDFeature
-
- __call__(system: MDSystemBase) ComplexNEMDViscosityFeatureResult #
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Run the rNEMD simulation and calculate the viscosity.
- Parameters
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system (MDSystemBase) – Target system to calculate the viscosity.
- Returns
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Result dataclass object.
- Return type
- attach_ctx(ctx: Optional[Context] = None) None #
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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 #
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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 #
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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 #
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Construct a FeatureBase object from serialized dict.
- Parameters
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res (dict[str, Any]) – A dict containing a serialized FeatureBase from to_dict().
- Returns
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The deserialized object from provided dict.
- Return type
- get_savedir_from_ctx() Path #
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Get the temporary save directory from the context.
- Returns
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The temporary save directory .
- Return type
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pathlib.Path
- init_scope() Iterator[None] #
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Context manager that enable to set attribution of the feature.
- Returns
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Init_scope context manager.
- Return type
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Iterator[None]
- repeat(n_repeat: int) Self #
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Set the maximum number of times that allowed to run the __call__ function.
- Parameters
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n_repeat (int) – The maximum number of repeats.
- Returns
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The feature.
- Return type
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Self
- to_dict() Dict[str, Any] #
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Dictionary representation of the FeatureBase.
- Returns
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A dict containing a serialized FeatureBase.
- Return type
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dict[str, Any]
Resource Library
matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature