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AutoTST: A framework to perform automated transition state theory calculations

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Automated Transition State Theory Calculator | AutoTST

Build Status codecov MIT license Release

Descritpion

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.

How to Install

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

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