shnitsel.io.sharc.parse_initial_conditions

Attributes

_re_grads
_re_nacs
_re_state_map_entry
_transition_identification_re

Classes

IcondPath

Functions

nans(*dims)
list_iconds([iconds_path, glob_expr])	Retrieve a list of all potential initial condition directories to be parsed given the input path and matching patter.
dims_from_QM_out(f)	Function to also read the relevant dimensions (number of atoms, number of states) from WM.out
dims_from_QM_log(log)	Function to retrieve the listed number of states and the number of atoms from the Qm.log file of initial conditions
check_dims(pathlist)	Function to obtain the number of atoms and states across all input paths.
finalize_icond_dataset(dataset, loading_parameters, ...)	Function to expand the initial conditions dataset with a time dimension.
read_iconds_individual(path[, loading_parameters])	Function to read initial a single initial condition directory into a Dataset with standard shnitsel annotations and units
parse_QM_in(qm_in)	Function to read settings of initial conditions from QM.in file.
parse_QM_log(log)	Function to parse main information from the QM.log file
parse_QM_log_geom(f, out)	Read geometry into an xr.Dataset object from the provided file input stream f.
_read_dim_or_transition_identification_line(f, ...)	Function to optionally read the current state id or transition identification line.
parse_QM_out(f, out[, loading_parameters])	Function to read all information about forces, energies, dipoles, nacs, etc. from initial condition QM.out files.
iconds_to_frames(iconds)	Function to convert the icond coordinate into a trajid coordinate and also build a combined frame`+`time multiindex as frame

Module Contents

_re_grads

_re_nacs

_re_state_map_entry

class IcondPath

Bases: NamedTuple

idx: int

path: pathlib.Path

nans(*dims)

list_iconds(iconds_path='./iconds/', glob_expr='**/ICOND_*')

Retrieve a list of all potential initial condition directories to be parsed given the input path and matching patter.

Parameters:

• iconds_path (str | os.PathLike, optional) – The path where to look for initial condition directories. Defaults to ‘./iconds/’.

• glob_expr (str, optional) – The pattern for finding initial conditions. Defaults to ‘**/ICOND_*’.

Raises:

FileNotFoundError – If no directories match the pattern.

Returns:

The list of Tuples of the parsed ID and the full path of the initial conditions

Return type:

List[IcondPath]

dims_from_QM_out(f)

Function to also read the relevant dimensions (number of atoms, number of states) from WM.out

Parameters:

f (TextIOWrapper) – The QM.out file to read from

Returns:

First the number of states, second the number of atoms or respectively None if not found.

Return type:

Tuple[int,int]

dims_from_QM_log(log)

Function to retrieve the listed number of states and the number of atoms from the Qm.log file of initial conditions

Parameters:

log (TextIOWrapper) – Input file handle to read the log file contents from

Raises:

ValueError – If the log file contains an inconsistently structured Line about states but does neither specify Singlet nor Triplet states.

Returns:

First the number of states, then the number of atoms. This is followed by the number of singlet, doublet and triplet states (if available). If a value is not available, it will default to 0.

Return type:

Tuple[int,int,int,int,int]

check_dims(pathlist)

Function to obtain the number of atoms and states across all input paths.

Will only return the tuple of (number_states, number_atoms) if these numbers are consistent across all paths. Otherwise, an error will be raised.

Parameters:

pathlist (Sequence[pathlib.Path]) – The list of paths belonging to the same system to check for consistent dimensions

Raises:

• FileNotFoundError – If the number of valid input paths in pathlist is zero, a FileNotFoundError is raised

• ValueError – If the number of states and the number of atoms does not agree across all systems a ValueError is raised

Returns:

The number of states and the number of atoms, then the number of singlets, doublets and triplets in this order

Return type:

Tuple[int, int, int, int, int]

finalize_icond_dataset(dataset, loading_parameters, default_format_attributes)

Function to expand the initial conditions dataset with a time dimension.

Also sets the default unit on the time dimension based on default_format_attributes.

Parameters:

• dataset (xr.Dataset) – The initial conditions dataset. Should not have a “time” dimension yet.

• loading_parameters (LoadingParameters) – Loading parameters to override units

• default_format_attributes (Dict[str, Dict[str, Any]]) – Default attributes to set on variables, mostly used to set the time dimension attributes

Returns:

The modified dataset

Return type:

xr.Dataset

read_iconds_individual(path, loading_parameters=None)

Function to read initial a single initial condition directory into a Dataset with standard shnitsel annotations and units

Parameters:

• path (PathOptionsType) – The path to a initial conditions directory

• loading_parameters (LoadingParameters | None, optional) – Parameter settings for e.g. standard units or state names.

Returns:

The Dataset object containing all of the loaded data from the initial condition in default shnitsel units

Return type:

xr.Dataset

parse_QM_in(qm_in)

Function to read settings of initial conditions from QM.in file.

Will attempt to read key settings and initial positions that would usually be read form QM.log.

Parameters:

qm_in (TextIOWrapper) – File stream of the found QM.in file containing some key settings and positional information.

Raises:

FileNotFoundError – If parts of the file are malformed or missing.

Returns:

the resulting settings in a key-value pair. Contains num_atoms, num_states, atNames and atXYZ.

Return type:

Dict[str, Any]

parse_QM_log(log)

Function to parse main information from the QM.log file

Parameters:

log (TextIOWrapper) – Input file wrapper to read the information from

Raises:

ValueError – If there are neither singlet nor triplet states listed in the QM.log file

Returns:

Dictionary with key information about the system

Return type:

Dict[str, Any]

parse_QM_log_geom(f, out)

Read geometry into an xr.Dataset object from the provided file input stream f.

f must be the contents of a QM.log file.

Parameters:

• f (TextIOWrapper) – File wrapper for a QM.log file’s contents

• out (xr.Dataset) – The dataset to write the resulting geometry to

_transition_identification_re

_read_dim_or_transition_identification_line(f, main_version)

Function to optionally read the current state id or transition identification line.

Only for versions 3.0 and up do we need to read the identification. :param f: Input stream of text file :type f: TextIOWrapper :param main_version: The main sharc version to switch the behavior :type main_version: int

Raises:

ValueError – _description_

Returns:

_description_

Return type:

_type_

Parameters:

• f (io.TextIOWrapper)

• main_version (int)

parse_QM_out(f, out, loading_parameters=None)

Function to read all information about forces, energies, dipoles, nacs, etc. from initial condition QM.out files.

if out=None is provided, a new Dataset is constructed and returned by the function

Parameters:

• f (TextIOWrapper) – File input of the QM.out file to parse the data from

• out (xr.Dataset) – Target Dataset to write the loaded data into. Defaults to None.

• loading_parameters (LoadingParameters,optional) – Optional loading parameters to override variable mappings and units.

Returns:

If a new Dataset was constructed instead of being written to out, it will be returned.

Return type:

xr.Dataset | None

iconds_to_frames(iconds)

Function to convert the icond coordinate into a trajid coordinate and also build a combined frame`+`time multiindex as frame

Will exempt atNames and atNums from the rearrangement.

Parameters:

iconds (xr.Dataset) – input dataset to replace the dimension in

Raises:

ValueError – Raised if at least one array has size 0 in one coordinate

Returns:

The transformed dataset

Return type:

xr.Dataset