GPS-TS: Geodesic Path Search for Transition States

GPS-TS contains gpsts, a simple package to expore chemical reactivity. It consists of three main parts:

• Generating entrance and exit complexes, using Architector and xTB to pose reacting molecules close to each other
• Generating plausible reaction pathways by interpolating along a geodesic in internal coordinate space (see geodesic_interpolate)
• Analyzing the energy profile along the geodesic path to identify regions for transition-state searches, using QuAcc as a workflow manager and the Atomic Simulation Environment (ASE) to perform Q-Chem or ORCA calculations.

Installation

GPS-TS requires Python version 3.9+. These installation instructions assume that you have access to pip. Note that we also recommend that you use conda or a related package manager to ensure a clean installation environment.

Before installing GPS-TS, you will need to install versions of ASE, QuAcc, and Architector outside of PyPI. You'll also need to install geodesic_interpolate.

To install ASE and QuAcc:

pip install --force-reinstall --no-deps https://gitlab.com/ase/ase/-/archive/master/ase-master.zip
pip install git+https://github.com/quantum-accelerators/quacc.git

To install Architector:

git clone https://github.com/lanl/Architector
cd Architector
git checkout Secondary_Solvation_Shell
pip install -e .

To install geodesic_interpolate:

git clone https://github.com/virtualzx-nad/geodesic-interpolate
cd geodesic-interpolate
pip install -e .

And finally, with these steps taken, you should be able to install GPS-TS:

git clone https://github.com/CoReACTER/GPS-TS
cd GPS-TS
pip install -e .

Tests

GPS-TS uses pytest for unit testing. Testing is currently a work in progress, and specifically, functions related to our benchmark dataset (see src/gpsts/benchmark) and automated calculations (see src/gpsts/quacc.py) are not tested.

To run tests, first ensure that you have pytest installed:

pip install pytest

And then:

cd GPS-TS
pytest tests

Documentation

TODO!

Citation

TODO!

License

GPS-TS is released under a GNU General Public License (GPL), version 3.0. This means that you, as a user, can copy, distribute, or modify GPS-TS, as long as your modified code is licensed under the GPL and is released publicly with installation instructions. For more information, read the LICENSE file provided in this repo!