sith.readers package

Submodules

class sith.readers.g09_reader.FileReader(path: Path | str, extract_data: bool = True)

Bases: object

Object used to read info in a .fchk file and store it into a Geometry object.

Parameters:

• path (Path or str) – Path to the fchk file to extract into a Geometry object.

• extract_data (bool. Default=True) – Automatically try to extract the data from the .fchk file. If False, the user should run _extract. Defatult=True

dims

counter of the DOFs, organized as: [0] Total number of DOFs [1] Number of distances [2] Number of angles [3] Number of dihedrals

Type:

np.array

geometry

object where the info is stored.

Type:

sith.Utilities.Geometry

block_readers

dictionary with the header and the respective reader that stores the values in Geometry.

Type:

dict

Note

This class should be used only for developers. Use this as a template to create other readers. Readers should assign the values to the attributes of the class Geometry.

build_atoms() → Atoms

Creates a ase.Atoms object of the structure in the fchk file.

Returns:

• (ase.Atoms) Atoms object with the molecular information of the

• structure.

• Note (Before using this method, FileReader.cartesian_coordinates and)

• FileReader.atomic_nums must have an assigned value.

class sith.readers.g09_reader.G09Reader(inputfiles: list | str)

Bases: object

Tool to read a set of fchk files of g09 corresponding to stretched molecules. It creates the geometries for each stretched configuration.

Parameters:

inputfiles (list or str) – list of paths to the fchk files (as strings or paths). The order of the elements matters according to the energy anaylis applied. This parameter could be also a string of the path to the a directory containing the fchk files in alphabetic order.

inputfiles

paths to the fchk files.

Type:

list[Path]

structures

list of sith.Utilities.Geometrys for each deformed configuration.

Type:

list[Geometry]

Module contents