https://github.com/reactionmechanismgenerator/autotst
AutoTST: A framework to perform automated transition state theory calculations
https://github.com/reactionmechanismgenerator/autotst
chemistry combustion kinetics quantum-chemistry
Last synced: 4 months ago
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AutoTST: A framework to perform automated transition state theory calculations
- Host: GitHub
- URL: https://github.com/reactionmechanismgenerator/autotst
- Owner: ReactionMechanismGenerator
- License: other
- Created: 2018-02-12T19:22:37.000Z (over 8 years ago)
- Default Branch: main
- Last Pushed: 2024-08-13T11:41:23.000Z (almost 2 years ago)
- Last Synced: 2024-08-13T14:38:34.112Z (almost 2 years ago)
- Topics: chemistry, combustion, kinetics, quantum-chemistry
- Language: Python
- Homepage:
- Size: 11.8 MB
- Stars: 31
- Watchers: 10
- Forks: 16
- Open Issues: 23
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Automated Transition State Theory Calculator | AutoTST
[](https://travis-ci.com/ReactionMechanismGenerator/AutoTST)
[](https://codecov.io/gh/reactionmechanismgenerator/autotst)
[](http://opensource.org/licenses/MIT)
## 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**](rmg.mit.edu), [**RDKit**](http://www.rdkit.org/), and [**ASE**](https://wiki.fysik.dtu.dk/ase/) to automatically create three dimentional geometries of transition states, reactants, and products;
optimize them using the [**Gaussian 09**](http://gaussian.com/) 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](https://github.com/ReactionMechanismGenerator/RMG-database/blob/master/families/rmg_reaction_families.pdf)
However, we intend to introduce support for new reaction families and quantum packages.
## How to Install
Before installing AutoTST, download [Anaconda](anaconda.com/download/) and [Git](https://git-scm.com/downloads)
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`
## How to Give Feedback
Please post any issues you may have to the [issues page](https://github.com/ReactionMechanismGenerator/AutoTST/issues/)
or drop in to the [chat room](https://gitter.im/ReactionMechanismGenerator/AutoTST)
## Credits
- [Professor Richard H. West's research group](http://www.northeastern.edu/comocheng/) at
[Northeastern University](http://www.northeastern.edu/).
- Dr. Pierre L. Bhoorasingh