Compares zeolite structures using graphs and structural similarities. This implementation in Python was made by Daniel Schwalbe-Koda. If you use this code, please cite

D. Schwalbe-Koda, Z. Jensen, E. Olivetti and R. Gómez-Bombarelli. "Graph similarity drives zeolite diffusionless transformations and intergrowth". Nature Materials 18, 1177-1181 (2019). Link: https://www.nature.com/articles/s41563-019-0486-1

BibTeX format:

@article{10.1038/s41563-019-0486-1,
    title={Graph similarity drives zeolite diffusionless transformations and intergrowth},
    author={Schwalbe-Koda, Daniel and Jensen, Zach and Olivetti, Elsa and Gómez-Bombarelli, Rafael},
    journal={Nature Materials},
    year={2019},
    volume={18},
    number={11},
    pages={1177--1181},
    doi={10.1038/s41563-019-0486-1}
}

This repository contains:

• Data of the Supplementary Information of the article.
• Code implementing the equations of relevance of the article.
• Tutorials on how to use our code and reproduce our results. We cover:
  • How to open and read the data of the article
  • How to verify the existence of isomorphism between periodic graphs of zeolite structures
  • How to calculate the D-measure between graphs
  • How to calculate the SOAP distance between zeolites
  • How to match supercells and calculate the graph distance using our methods of supercell matching.

The tutorials are self-explanatory. This code was tested with the following dependencies:

python==3.7.4,
numpy==1.16.4,
ase==3.18.1
pymatgen==2019.5.8,
soaplite==1.0.3,
networkx==2.3

To use the code, you can create an anaconda environment. Learn more on how to manage anaconda environments by reading this page. To create a new environment working with the current code, run the following commands:

conda create -n zeograph python=3.7 numpy networkx pymatgen=2019.5.8 ase -c anaconda -c matsci -c conda-forge

After the installation is complete, install soaplite by entering the environment and installing this package using pip:

conda activate zeograph
pip install soaplite

This should provide an environment adequate for running the tutorials.