shnitsel.data.dataset_containers.data_series ============================================ .. py:module:: shnitsel.data.dataset_containers.data_series Classes ------- .. autoapisummary:: shnitsel.data.dataset_containers.data_series.MetaInformation shnitsel.data.dataset_containers.data_series.DataSeries Module Contents --------------- .. py:class:: MetaInformation Meta information for trajectory setup .. py:attribute:: input_format :type: Literal['sharc', 'newtonx', 'ase', 'pyrai2md'] | None :value: None .. py:attribute:: input_type :type: Literal['static', 'dynamic'] | None :value: None .. py:attribute:: input_format_version :type: str | None :value: None .. py:attribute:: theory_basis_set :type: str | None :value: None .. py:attribute:: est_level :type: str | None :value: None .. py:class:: DataSeries(ds) Bases: :py:obj:`shnitsel.data.dataset_containers.shared.ShnitselDataset` Definition of the protocol to support instantiation from xarray dataset structs. .. py:attribute:: _is_multi_trajectory :type: bool :value: False .. py:property:: per_state :type: 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** :rtype: The wrapper for the per-state properties .. py:property:: inter_state :type: 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** :rtype: The wrapper for the inter-state properties .. py:property:: leading_dim :type: str The leading dimension along which consistent configurations are indexed. Usually `time` or `frame`. .. py:property:: positions The atom position data stored in this dataset if accessible. Will throw a `KeyError` if no data is accessible. .. py:property:: atXYZ The positional data for atoms stored in this dataset if accessible. Will throw a `KeyError` if no data is accessible. .. py:property:: energy The energy information stored in this dataset if accessible. Will throw a `KeyError` if no data is accessible. .. py: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. .. py:property:: nacs The non adiabatic coupling data stored in this dataset if accessible. Will throw a `KeyError` if no data is accessible. .. py:property:: socs The spin orbit coupling data stored in this dataset if accessible. Will throw a `KeyError` if no data is accessible. .. py:property:: dipole_permanent The permanent dipole data stored in this dataset if accessible. Will throw a `KeyError` if no data is accessible. .. py:property:: dipole_transition The transition dipole data stored in this dataset if accessible. Will throw a `KeyError` if no data is accessible. .. py:property:: e_kin The kinetic energy information stored in this dataset if accessible. Will throw a `KeyError` if no data is accessible. .. py:property:: velocities The velocity information stored in this dataset if accessible. Will throw a `KeyError` if no data is accessible. .. py:method:: _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 :param key: The key under which we expect to find the data :type key: str :returns: the value associated with the key that has been found :rtype: Any|None .. py:property:: t_max :type: float Maximum time up to which the simulation could have run if not interrupted. It may actually have run to this time. .. py:property:: delta_t :type: float The simulation timestep usually in the same units as `time` .. py:property:: trajid :type: 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. .. py:property:: trajectory_id :type: int | str | None An alias for `trajid` with a more telling name .. py:property:: max_timestep :type: int Alias for `max_ts` with a more telling name .. py:property:: max_ts :type: int The maximum time step to which the simulation progressed before termination. .. py:property:: completed :type: bool A flag whether the imported Trajectory had successfully completed. .. py:property:: input_format :type: Literal['sharc', 'newtonx', 'ase', 'pyrai2md', 'unknown'] | str Name of the simulation software or input file type from which the data was originally imported. .. py:property:: input_type :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 .. py:property:: input_format_version :type: str The version of the simulation software used to create this trajectory .. py:property:: num_singlets :type: int Number of singlet states in the system .. py:property:: num_doublets :type: int Number of doublet states in the system .. py:property:: num_triplets :type: int Number of triplet states in the system .. py:property:: forces_format :type: 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. .. py:property:: trajectory_input_path :type: str | None Input path from which the trajectory was loaded .. py:property:: theory_basis_set :type: str | None The theory basis set identifier for the underlying simulation .. py:property:: est_level :type: str | None The electronic structure theory level used during the simulation. .. py:property:: misc_input_settings :type: dict | None A dictionary of miscalleneous input settings read from trajectory output Arbitrary mapping from file names to settings within those files. .. py:property:: attrs :type: dict A dictionary of the attributes set on this Trajectory. Arbitrary mapping from attribute keys (str) to attribute values. .. py:method:: get_grouping_metadata() .. py:property:: is_multi_trajectory :type: bool Flag whether this is a multi-trajectory container. Overwritten by child classes that combine multiple trajectories into one object .. py:method:: get_type_marker() :classmethod: