matlantis_features.features.md.md.MDFeature

class matlantis_features.features.md.md.MDFeature(integrator: MDIntegratorBase, n_run: int, checkpoint_file_name: Optional[str] = None, checkpoint_freq: Optional[int] = 10, traj_file_name: Optional[str] = None, traj_freq: Optional[int] = 1, traj_props: Optional[List[str]] = None, traj_append: bool = False, traj_init_frame: bool = False, show_progress_bar: bool = False, tqdm_options: Optional[Dict[str, Any]] = None, show_logger: bool = False, logger_interval: int = 100, estimator_fn: Optional[Callable[[], Estimator]] = None)#

Bases: FeatureBase

The matlantis-feature for molecular dynamics simulation.

Methods

`__init__`(integrator, n_run[, …])	Initialize an instance.
`__call__`(system[, extensions])	Run the MD simulation.
`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.
`get_temp_dir`()	Create temperory directory.
`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__(integrator: MDIntegratorBase, n_run: int, checkpoint_file_name: Optional[str] = None, checkpoint_freq: Optional[int] = 10, traj_file_name: Optional[str] = None, traj_freq: Optional[int] = 1, traj_props: Optional[List[str]] = None, traj_append: bool = False, traj_init_frame: bool = False, show_progress_bar: bool = False, tqdm_options: Optional[Dict[str, Any]] = None, show_logger: bool = False, logger_interval: int = 100, estimator_fn: Optional[Callable[[], Estimator]] = None)#

Initialize an instance.

Parameters

integrator (MDIntegratorBase) – Integrator object used for the simulation.
n_run (int) – Number or the steps to be run.
checkpoint_file_name (str or None, optional) – Checkpoint file name. If this value is None and checkpoint_freq>0,
checkpoint file name is automatically generated.
If relative path name is given,
the file is stored in the current working directory.
Defaults to None.
checkpoint_freq (int or None, optional) – Checkpoint creation frequency.
If this value is None or non positive, no checkpoit file is created.
Defaults to 10.
traj_file_name (str or None, optional) – Trajectory file name. If this value is None and traj_freq>0,
trajectory file name is automatically generated.
If relative path name is given,
the file is stored in the current working directory.
Defaults to None.
traj_freq (int or None, optional) – Trajectory saving frequency.
If this value is None or non positive, no trajectory file is created.
Defaults to 1.
traj_props (list[str] or None, optional) – Names of the properties stored in the trajectory file.
If None, energy, forces, and stress properties are stored.
Defaults to None.
traj_append (bool, optional) – If True and trajectory file exists, trajectory will be
appended to the existing file. Defaults to False.
traj_init_frame (bool, optional) – If True, the initial structure of the simulation is
also stored in the trajectory file. Defaults to False.
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.
logger_interval (int, optional) – The interval of when to print out logger information.
Defaults to 100.
estimator_fn (EstimatorFnType or None, optional) – A factory method to create a custom estimator.
Please refer Customizing estimator used in matlantis-features for detail.

__call__(system: MDSystemBase, extensions: Optional[List[Tuple[MDExtensionBase, int]]] = None) → MDFeatureResult#

Run the MD simulation.

Parameters

system (MDSystemBase) – Target system of the MD simulation.
extensions (MDExtensionList or None, optional) – Extension list (tuple of extension object and interval) used for the simulation.
Defaults to None.

Returns

Result object for the MD simulation.

Return type

MDFeatureResult

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