Zeolite Simulation Environment

Authors: Jerry T. Crum, Justin R. Crum

Description

This is a package to automate zeolite structure generation and characterization for computational chemistry.

Requirements

This package is built around the ASE atoms object, and thus requires installation of ASE, available at: https://wiki.fysik.dtu.dk/ase/install.html.

Ring finding uses graph theory implemented by NetworkX, available at: https://networkx.github.io.

Numpy is also required.

Installation

The package can be installed from PyPI, where it is listed as zeose, using pip or uv:

pip install zeose

The other package listed on PyPI under the name zse is not affiliated with this package.

Installing to contribute

Clone this git repository,

git clone https://github.com/jtcrum/zse

and then install it with pip:

pip install -e ./zse

Current Modules

To see how to use each of the modules, please visit examples, which contains several Python notebooks that show how to use the tools in this repository.

• zse.cation
• zse.cif_tools
• zse.collections
• zse.protonate
• zse.rings
• zse.substitute
• zse.tpairs
• zse.utilities

Contributions

If there is something you would like to see added to this package, or if you would like to contribute, please email me at jcrum@nd.edu.

Acknowledgments

Contributors

Sichi Li, Craig Waitt, Yujia Wang, William Schneider, Alex Hoffman

Testers

Jian Ren Lim, Elsa Koninckx

Funding Sources

• Center for Innovative and Strategic Transformation of Alkane Resources
• Designing Materials to Revolutionize and Engineer our Future
• Arthur J. Schmitt Leadership Fellowship

Computational Resources

This research was supported in part by the Notre Dame Center for Research Computing through access to the HPC clusters.

Research Group

Many thanks to all the members of the Schneider Group who listened to me present this material over and over again, and provided input into how to make ZSE more useful.

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