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Add-on to pymatgen for diffusion analysis.

Project description


This is an add-on to pymatgen for diffusion analysis that is developed by the Materials Virtual Lab. Note that it relies on pymatgen for structural manipulations, file io, and preliminary analyses. In particular, pymatgen’s DiffusionAnalyzer is used heavily. The purpose of this add-on is to provide other diffusion analyses, using trajectories extracted using the DiffusionAnalyzer class.

This is, and will always be, a scientific work in progress. Pls check back for more details.

Features (non-exhaustive!)

  1. Van-Hove analysis
  2. Probability density
  3. Clustering (e.g., k-means with periodic boundary conditions).


If you use pymatgen-diffusion in your research, please cite the following work:

Deng, Z.; Zhu, Z.; Chu, I.-H.; Ong, S. P. Data-Driven First-Principles
Methods for the Study and Design of Alkali Superionic Conductors,
Chem. Mater., 2016, acs.chemmater.6b02648, doi:10.1021/acs.chemmater.6b02648.

You should also include the following citation for the pymatgen core package given that it forms the basis for most of the analyses:

Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier,
Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent Chevrier, Kristin A.
Persson, Gerbrand Ceder. *Python Materials Genomics (pymatgen) : A Robust,
Open-Source Python Library for Materials Analysis.* Computational
Materials Science, 2013, 68, 314-319. doi:10.1016/j.commatsci.2012.10.028.

In addtion, some of the analyses may also have relevant publications that you should cite. Please consult the documentation of each module.


We welcome contributions in all forms. If you’d like to contribute, please fork this repository, make changes and send us a pull request!


This code is funded by the National Science Foundation’s Designing Materials to Revolutionize and Engineer our Future (DMREF) program under Grant No. 1436976.

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Files for pymatgen-diffusion, version 0.2.0
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