yamlpaths: Simple and beautiful reaction path energy diagrams

yamlpaths is a command line interface (CLI) based on reaction_pypaths that generates reaction path energy diagrams based on YAML files that contain energies or point to Gaussian 16 .log files.

Installation

To be able to execute yamlpaths.py anywhere download the source code and make it executable and export it to $PATH:

chmod +x yamlpaths.py
export PATH="/path/to/PAHMC/RRKM:$PATH"

Usage

Create a YAML file containg the following:

File location: /path/to/gaussian/output/
Energy type: Sum of electronic and zero-point Energies 
Diagrams: 
  title:
    x: x.log
    y: 1.5
    z: x 

The program will create all Diagrams as title.png which contains a diagram of the reaction along the path x > y > z. The values can be set as int or float numbers or they will be gathered using the Energy type from the Gaussian .log files. The program can use aliases to use the energy of another state in case of symmetries z: x.

usage: yamlpaths.py [-h] [-n NORMALIZE] [-o OUTPUT] yaml_file

Generate reaction path energy diagrams from YAML

positional arguments:
  yaml_file             The path to the YAML file

options:
  -h, --help            show this help message and exit
  -n, --normalize NORMALIZE
                        The key to normalize the values
  -o, --output OUTPUT   Output directory

For documentation on how to use reaction_pypaths.py and config.py see MFTabriz/reaction_pypaths

Example using values

Diagrams:
  Anthracene:
    D9: 0.00
    D9to9a: 1.35
    D9a: 1.32
    D9ato1: 1.57
    D1: 0.42
    D1to2: 1.06
    D2: 0.50

Example using Gaussian

File location: /Data/Phenanthrene/DFT/
Energy type: Sum of electronic and zero-point Energies
Diagrams:
  D9toD1:
    D9: D10
    D9to10: C14H10-D9to10.log
    D10: C14H10-D10.log
    D10to10a: C14H10-D10to10a.log
    D10a: C14H10-D10a.log
    D1to10a: C14H10-D1to10a.log
    D1: C14H10-D1.log

License and attributions

yamlpaths is available under the GNU GPL v3+ (attribution: MFTabriz@github, tim-degroot@github)