pymatgen.io.xtb package
This package implements modules for input and output to and from CREST.
Submodules
pymatgen.io.xtb.inputs module
Classes for writing XTB input files.
- class CRESTInput(molecule: Molecule, working_dir: str = '.', coords_filename: str | None = 'crest_in.xyz', constraints: dict[str, list[int] | float] | None = None)[source]
Bases:
MSONableAn object representing CREST input files. Because CREST is controlled through command line flags and external files, the CRESTInput class mainly consists of methods for containing and writing external files.
- Parameters:
molecule (Molecule) – Molecule object
working_dir (str) – Directory to write input files to
coords_filename (str) – Name of input coordinates file
constraints (dict) – Dictionary of common editable parameters for .constrains file. {“atoms”: [List of 1-indexed atoms to fix], “force_constant”: float]
- static constrains_template(molecule, reference_fnm, constraints) str[source]
- Parameters:
molecule (Molecule) – Molecule the constraints will be performed on
reference_fnm (str) – Name of file containing reference structure in same directory
constraints (dict) – Dictionary of common editable parameters for .constrains file. {“atoms”: [List of 1-indexed atoms to fix], “force_constant”: float]
- Returns:
for .constrains file
- Return type:
str
pymatgen.io.xtb.outputs module
Parsers for XTB output files and directories.
- class CRESTOutput(output_filename, path='.')[source]
Bases:
MSONableClass to parse CREST output files.
Assumes runtype is iMTD-GC [default].
- Parameters:
output_filename (str) – Filename to parse
path (str) – Path to directory including output_filename and all other xtb output files (crest_best.xyz, etc.)