Reaction-network is a Python package for predicting likely inorganic chemical reaction pathways using graph theory.
Project description
Reaction network (rxn-network) is a Python package for predicting chemical reaction pathways in solid-state materials synthesis using graph theory.
Installing rxn-network
The rxn-network package has several dependencies, most of which can be installed through PyPI. However, graph-tool must be installed through a more customized method; please see https://graph-tool.skewed.de/ for more details. We recommend the following installation procedure to create a new conda environment:
conda create -n gt python=3.9
And then install graph-tool through conda-forge:
conda install -c conda-forge graph-tool
To install an editable version of the rxn-network code, simply download (clone) the code from this repository, navigate to its directory in terminal, and then run the following command to install the requirements:
pip install -r requirements.txt
And then to finally install an editable version of the package:
pip install -e .
Demo
A demo Jupyter notebook (demo.ipynb) contains the code necessary to replicate the results of the paper and is a good starting template for using the rxn-network package.
Note: the demo NB is currently being updated with refactored code; please see one of the previous releases if you wish to use it!
How to cite rxn-network
The following paper explains the methodology of the rxn-network package:
McDermott, M. J., Dwaraknath, S. S., and Persson, K. A. (2021). A graph-based network for predicting chemical reaction pathways in solid-state materials synthesis. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-23339-x
Acknowledgements
This work was supported as part of GENESIS: A Next Generation Synthesis Center, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award Number DE-SC0019212.
Learn more about the GENESIS EFRC here: https://www.stonybrook.edu/genesis/
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