https://github.com/tylerjereddy/diffusion_analysis_md_simulations

Python utility functions for the analysis of diffusion in molecular dynamics simulation trajectories.
https://github.com/tylerjereddy/diffusion_analysis_md_simulations

Last synced: 11 days ago
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Python utility functions for the analysis of diffusion in molecular dynamics simulation trajectories.

• Host: GitHub
• URL: https://github.com/tylerjereddy/diffusion_analysis_md_simulations
• Owner: tylerjereddy
• License: mit
• Created: 2014-09-19T09:05:50.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2022-06-21T21:15:49.000Z (about 3 years ago)
• Last Synced: 2025-03-28T02:45:49.634Z (3 months ago)
• Language: Jupyter Notebook
• Size: 835 KB
• Stars: 16
• Watchers: 3
• Forks: 7
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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Analysis of particle diffusion in molecular dynamics simulations

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Contains Python utility functions for the analysis of diffusion in molecular dynamics simulation trajectories.

The documentation for the project is available here: http://diffusion-analysis-md-simulations.readthedocs.org/en/latest/index.html

An IPython notebook containing an example diffusion calculation is available: https://github.com/tylerjereddy/diffusion_analysis_MD_simulations/blob/master/diffusion_analysis_sim126_extended.ipynb 

Please cite: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11827.svg)](https://doi.org/10.5281/zenodo.11827)

And even better if you cite the original paper: Reddy *et al.* (2015) *Structure* **23**: 584-97. [[DOI]](http://dx.doi.org/10.1016/j.str.2014.12.019)

For contributions:

  * ensure all unit tests pass (run pytest)

  * ensure all doctests pass (run doctesting.py)

  * if you import new modules, you may need to mock them in the Sphinx conf.py documentation file so that the docs are properly compiled by readthedocs

  * attempt to match the [numpy documentation standard](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt) as closely as possible