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https://github.com/pdebuyl-lab/tidynamics

A tiny package to compute the dynamics of stochastic and molecular simulations
https://github.com/pdebuyl-lab/tidynamics

correlation molecular-dynamics numpy stochastic-process

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A tiny package to compute the dynamics of stochastic and molecular simulations

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README 

        
tidynamics

==========



.. image:: http://joss.theoj.org/papers/10.21105/joss.00877/status.svg

   :target: https://doi.org/10.21105/joss.00877

   :alt: DOI link to JOSS article



.. image:: https://github.com/pdebuyl-lab/tidynamics/actions/workflows/test.yml/badge.svg

   :target: https://github.com/pdebuyl-lab/tidynamics/actions/workflows/test.yml

   :alt: Test status



.. image:: https://anaconda.org/conda-forge/tidynamics/badges/version.svg

   :target: https://anaconda.org/conda-forge/tidynamics

   :alt: Link to conda-forge page



.. image:: https://mybinder.org/badge.svg

   :target: https://mybinder.org/v2/gh/pdebuyl-lab/tidynamics/master?filepath=doc%2Findex.ipynb

   :alt: Link to binder example notebook



.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1401184.svg

   :target: https://doi.org/10.5281/zenodo.1401184

   :alt: Link Zenodo archive



A tiny package to compute the dynamics of stochastic and molecular simulations.



:License: BSD 3-clause

:Author: Pierre de Buyl

:Website: http://lab.pdebuyl.be/tidynamics/



tidynamics



- performs the computation of mean-square displacements and correlation functions.

- accepts as input NumPy arrays storing the positions and velocities of particles.

- implements the so-called Fast Correlation Algorithm proposed by Kneller and others for the

  `nMOLDYN `_ analysis program.

- depends only `Python `_ and `NumPy `_.



For a quick jump into tidynamics, have a look at the examples.



Goals and plans:



- Minimal dependencies.

- Serve as a reference implementation for common algorithms that are useful for molecular

  and stochastic simulations.

- Provide later a bit more flexibility to handle cross correlations and many-body systems.



Installation

------------



It is necessary to have Python and NumPy to install and use tidynamics.



tidynamics can be installed with pip::



    pip install --user tidynamics



or with conda (via conda-forge)::



    conda install -c conda-forge tidynamics



It is also possible to download the source code and execute pip locally.

 

Tests are run with Python 3.7 to 3.11. Python 2 is not supported anymore.  If

you encounter any issue, let me know (see Contact below).



Citation

--------



When using tidynamics in a publication, please cite the following paper:



Pierre de Buyl (2018), *tidynamics: A tiny package to compute the dynamics of

stochastic and molecular simulations*, The Journal of Open Source

Software https://doi.org/10.21105/joss.00877



Testing

-------



We use `pytest `_ for testing::



    python -m pytest



Installing tidynamics does not install the tests. It is necessary to download tidynamics'

source and to install pytest to run the tests.



Contact, support, and contribution information

----------------------------------------------



To contact the author about tidynamics, you can either write an email to `Pierre de Buyl

`_ or use the `issue tracker

`_ of the GitHub project.

Existing contributors are listed in the file CONTRIBUTORS.



Bug reports are welcome. If you consider proposing a feature, please keep in mind the goals

and plans exposed above.