shnitsel.data.dataset_containers.data_series#
Classes#
Meta information for trajectory setup |
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Definition of the protocol to support instantiation from |
Module Contents#
- class MetaInformation#
Meta information for trajectory setup
- class DataSeries(ds)#
Bases:
shnitsel.data.dataset_containers.shared.ShnitselDatasetDefinition of the protocol to support instantiation from xarray dataset structs.
- Parameters:
ds (xarray.Dataset)
- property per_state: shnitsel.data.dataset_containers.per_state.PerState#
Convert this trajectory to a PerState object only allowing access to the per-state data encoded in this entity
- Returns:
PerState
- Return type:
The wrapper for the per-state properties
- property inter_state: shnitsel.data.dataset_containers.inter_state.InterState#
Convert this trajectory to an InterState object only allowing access to the inter-state data encoded in this entity.
Will calculate some interstate properties like state-to-state energy differences.
- Returns:
InterState
- Return type:
The wrapper for the inter-state properties
- property leading_dim: str#
The leading dimension along which consistent configurations are indexed. Usually time or frame.
- Return type:
- property positions#
The atom position data stored in this dataset if accessible.
Will throw a KeyError if no data is accessible.
- property atXYZ#
The positional data for atoms stored in this dataset if accessible.
Will throw a KeyError if no data is accessible.
- property energy#
The energy information stored in this dataset if accessible.
Will throw a KeyError if no data is accessible.
- property forces#
The force data stored in this dataset if accessible. Note that depending on forces_format, there may only be data for the active state or for some of the states.
Will throw a KeyError if no data is accessible.
- property nacs#
The non adiabatic coupling data stored in this dataset if accessible.
Will throw a KeyError if no data is accessible.
- property socs#
The spin orbit coupling data stored in this dataset if accessible.
Will throw a KeyError if no data is accessible.
- property dipole_permanent#
The permanent dipole data stored in this dataset if accessible.
Will throw a KeyError if no data is accessible.
- property dipole_transition#
The transition dipole data stored in this dataset if accessible.
Will throw a KeyError if no data is accessible.
- property e_kin#
The kinetic energy information stored in this dataset if accessible.
Will throw a KeyError if no data is accessible.
- property velocities#
The velocity information stored in this dataset if accessible.
Will throw a KeyError if no data is accessible.
- _param_from_vars_or_attrs(key)#
Helper function to extract information either from a data var or from a coordinate or from the attributes of the dataset
- Parameters:
key (str) – The key under which we expect to find the data
- Returns:
the value associated with the key that has been found
- Return type:
Any|None
- property t_max: float#
Maximum time up to which the simulation could have run if not interrupted.
It may actually have run to this time.
- Return type:
- property trajid: int | str | None#
Id of the trajectory. If assigned it is expected to be unique across the same input but may clash with other trajectory ids if multiple separate imports are combined or indepdendent simulation data is combined.
- property max_ts: int#
The maximum time step to which the simulation progressed before termination.
- Return type:
- property completed: bool#
A flag whether the imported Trajectory had successfully completed.
- Return type:
- property input_format: Literal['sharc', 'newtonx', 'ase', 'pyrai2md', 'unknown'] | str#
Name of the simulation software or input file type from which the data was originally imported.
- Return type:
Literal[‘sharc’, ‘newtonx’, ‘ase’, ‘pyrai2md’, ‘unknown’] | str
- property input_type: Literal['static', 'dynamic', 'unknown']#
Whether the data in this trajectory is static (independently optimized) or continuous time-resolved data or whether the type is not known
- Return type:
Literal[‘static’, ‘dynamic’, ‘unknown’]
- property input_format_version: str#
The version of the simulation software used to create this trajectory
- Return type:
- property forces_format: bool | Literal['all', 'active_only'] | None#
The forces format in the trajectory.
Options are a binary flag to signify whether there are forces or not. If the flag is True, the forces still might not be available for all states but only for the active state. If ‘all’ is the format, then there will be forces for all states. If the mode is ‘active_only’ there will definitely only be forces for the active state in the trajectory. If The mode is None, more specific manual analysis may be required.
- Return type:
bool | Literal[‘all’, ‘active_only’] | None
- property trajectory_input_path: str | None#
Input path from which the trajectory was loaded
- Return type:
str | None
- property theory_basis_set: str | None#
The theory basis set identifier for the underlying simulation
- Return type:
str | None
- property est_level: str | None#
The electronic structure theory level used during the simulation.
- Return type:
str | None
- property misc_input_settings: dict | None#
A dictionary of miscalleneous input settings read from trajectory output
Arbitrary mapping from file names to settings within those files.
- Return type:
dict | None
- property attrs: dict#
A dictionary of the attributes set on this Trajectory.
Arbitrary mapping from attribute keys (str) to attribute values.
- Return type:
- get_grouping_metadata()#