Kudi is a tool that allows effortless extraction of chemically relevant data along a reaction path of a chemical reaction. It is build in python 3 and its straightforward structure makes userfriendly and allows for effortless implementation of new capabilities, and extension to any quantum chemistry package. Currently Kudi can be used in conjunction with Gaussian16
git clone https://github.com/stvogt/kudi
cd /path/to/kudi
Install within your prefered python environment:
python -m pip install .
The Kudi objects containing all the reaction path data, is initialized with an output file. This output file contains a series of single point computations, one for each point of the reaction path. This file has a special structure and needs to be created using a kudi pre-processing script.
- From an existing IRC
Use the make_sp script to create the input_sp.dat file that can be run with
Gaussian. To list the different options run (python make_sp_g16.py -h). This will create an input file of single point computations for each reaction coordinate structure. This file contains
the lines:
"Single Point computation for reaction coordinate: "
followed by the corresponding reaction coordinate of the single point computation. The resulting output_sp.dat file can then be used as an input for Kudi.
- From an transition state structure
If you only have a optimized transition state structure and have not yet obtained the reaction path, Kudi can help you generate the IRC or output file, with the make_irc_g16.py script. To check the options run python make_irc_g16.py -h in your shell.
In the tutorials folder there are several tutorials that ilustrates the capabilities of Kudi. A complete Manual is currently under construction.