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

get_savedir_from_ctx() Path#

Get the temporary save directory from the context.

Returns

The temporary save directory .

Return type

pathlib.Path

get_temp_dir() Path#

Create temperory directory.

Returns

The location of temperory directory.

Return type

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]