toxyz

Generates an xyz file from the provided gaussian files. For output files, it extracts the last geometry (unless --step is specified). This util is meant for quick inspections of gaussian outputs using other GUI tools such as jmol.

usage: pyssianutils toxyz [-h] [-l] [-o OUTFILE] [--step STEP]
                          files [files ...]

Positional Arguments

files

Gaussian Input/Output Files

Named Arguments

-l, --listfile

When enabled instead of considering the files provided as the gaussian output files considers the file provided as a list of gaussian output files

Default: False

-o, --outfile

Name of the xyz file with all the provided geometries sorted by filename

Default: all_geometries.xyz

--step

Will attempt to access the ith optimization step of a gaussian output file to extract its geometry on all files provided. 'initial geometry'='1'

Usage

If we aim to extract a specific step of a given gaussian minimization or transition state search toxyz allows its extraction with the --step However the main motivation for the development of this util was to simplify the visual inspection of the final geometries of multiple conformers. Lets say that we 10 conformers in a folder with the names molecule_{00..10}.log. Using toxyz we can generate an xzy with the last geometry of each conformer optimization by:

$ pyssianutils toxyz molecule_*.log -o all_conformers.xyz
molecule_00.log
molecule_01.log
molecule_02.log
molecule_03.log
molecule_04.log
molecule_05.log
molecule_06.log
molecule_07.log
molecule_08.log
molecule_09.log
molecule_10.log

Now we can easily open the all conformers with jmol, or any other visualization software in which we can easily switch between the different frames of a multimolecular xyz file.