AutoTST is a framework to perform automated transition state theory calculations related to reaction families common in combustion. It is based off of the frame work of RMG, RDKit, and ASE to automatically create three dimentional geometries of transition states, reactants, and products; optimize them using the Gaussian 09 quantum chemistry package; and obtain kinetic parameters using Arkane (a canonical calculator included in RMG).
Currently, AutoTST supports three reaction families:
- Hydrogen Abstraction
- Disproportination
- Intra Hydrogen Migration
For general templates of these reaction families, click here
However, we intend to introduce support for new reaction families and quantum packages.
Before installing AutoTST, download Anaconda and Git
Install the latest version of AutoTST by cloning the source code via Git. Make sure to start in an appropriate local directory where you want the AutoTST folder to exist.
git clone https://github.com/ReactionMechanismGenerator/AutoTST.git
Now, create the anaconda environment for AutoTST
-
cd AutoTST -
conda env create -f environment.yml
Modify environment variables. Add AutoTST to the PYTHONPATH to ensure that you can access modules from any folder. Modify your ~/.bashrc file by adding the following line:
-
export AUTOTST="your_folder/AutoTST -
export PYTHONPATH=$AUTOTST:$PYTHONPATH
To be able to run AutoTST in any conda environment, you can set your path to the following by modifing your ~/.bashrc:
export PATH=~/anaconda/envs/tst_env/bin:$PATH
Finally either close and reopen your terminal to refresh your environment variables, or type the following command
source ~/.bashrc
Please post any issues you may have to the issues page or drop in to the chat room
- Professor Richard H. West's research group at Northeastern University.
- Dr. Pierre L. Bhoorasingh