shnitsel.io.sharc.format_reader

Attributes

_sharc_default_pattern_regex
_sharc_default_pattern_glob_traj
_sharc_default_pattern_glob_icond
DataType

Classes

SHARCDynamicFormatInformation	Information to keep track of relevant information for
SHARCInitialFormatInformation	Information to keep track of relevant information for
SHARCMultiInitialFormatInformation	Information to keep track of relevant information for
SHARCFormatReader	Class for providing the SHARC format reading functionality in the standardized FormatReader interface

Module Contents

class SHARCDynamicFormatInformation

Bases: shnitsel.io.format_reader_base.FormatInformation

Information to keep track of relevant information for

class SHARCInitialFormatInformation

Bases: shnitsel.io.format_reader_base.FormatInformation

Information to keep track of relevant information for

class SHARCMultiInitialFormatInformation

Bases: shnitsel.io.format_reader_base.FormatInformation

Information to keep track of relevant information for

list_of_iconds: list | None = None

_sharc_default_pattern_regex

_sharc_default_pattern_glob_traj = 'TRAJ_*'

_sharc_default_pattern_glob_icond = 'ICOND_*'

DataType

class SHARCFormatReader

Bases: shnitsel.io.format_reader_base.FormatReader

Class for providing the SHARC format reading functionality in the standardized FormatReader interface

find_candidates_in_directory(path)

Function to return a all potential matches for the current file format within a provided directory at path. Parameters

Returns:

• list[pathlib.Path] – A list of paths that should be checked in detail for whether they represent the format of this FormatReader.

• None – If no potential candidates were found

Parameters:

path (shnitsel.io.shared.helpers.PathOptionsType)

Return type:

list[pathlib.Path] | None

check_path_for_format_info(path, hints_or_settings=None)

Check if the path is a SHARC-style output directory.

Designed for a single input trajectory.

Parameters:

• path (PathOptionsType) – The path to check for SHARC data

• hints_or_settings (dict | None, optional) – Configuration options provided to the reader by the user, by default None

Returns:

The object holding all relevant format information for the path contents if it matches the SHARC format

Return type:

FormatInformation

Raises:

• FileNotFoundError – If the path is not a directory.

• FileNotFoundError – If path is a directory but does not contain the required SHARC output files

read_from_path(path, *, format_info, loading_parameters=None, expect_dtype=None)

Read a SHARC-style trajcetory from path at path. Implements FormatReader.read_from_path().

Designed for a single input trajectory.

Parameters:

• path (pathlib.Path) – Path to a SHARC-format directory.

• format_info (FormatInformation) – Format information on the provided path that has been previously parsed.

• loading_parameters (LoadingParameters | None, optional) – Loading parameters to e.g. override default state names, units or configure the error reporting behavior, by default None

• expect_dtype (type[DataType] | UnionType | None, optional) – An optional parameter to specify the return type. For this class, it should be xr.Dataset, Trajectory or Frames, by default None

Returns:

The loaded Shnitsel-conforming trajectory.

Return type:

xr.Dataset | Trajectory | Frames | None

Raises:

• ValueError – Not enough loading information was provided via path and format_info, e.g. if both are None.

• FileNotFoundError – Path was not found or was not of appropriate SHARC format

get_units_with_defaults(unit_overrides=None)

Apply units to the default unit dictionary of the format SHARC

Parameters:

unit_overrides (Dict[str, str] | None, optional) – Units denoted by the user to override format default settings., by default None

Returns:

The resulting, overridden default units

Return type:

dict[str, str]