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"description": "tidynamics\n==========\n\n.. image:: http://joss.theoj.org/papers/10.21105/joss.00877/status.svg\n :target: https://doi.org/10.21105/joss.00877\n :alt: DOI link to JOSS article\n\n.. image:: https://travis-ci.org/pdebuyl-lab/tidynamics.svg?branch=master\n :target: https://travis-ci.org/pdebuyl-lab/tidynamics\n :alt: Test status\n\n.. image:: https://anaconda.org/conda-forge/tidynamics/badges/version.svg\n :target: https://anaconda.org/conda-forge/tidynamics\n :alt: Link to conda-forge page\n\n.. image:: https://mybinder.org/badge.svg\n :target: https://mybinder.org/v2/gh/pdebuyl-lab/tidynamics/master?filepath=doc%2Findex.ipynb\n :alt: Link to binder example notebook\n\nA tiny package to compute the dynamics of stochastic and molecular simulations.\n\n:License: BSD 3-clause\n:Author: Pierre de Buyl\n:Website: http://lab.pdebuyl.be/tidynamics/\n\ntidynamics\n\n- performs the computation of mean-square displacements and correlation functions.\n- accepts as input NumPy arrays storing the positions and velocities of particles.\n- implements the so-called Fast Correlation Algorithm proposed by Kneller and others for the\n `nMOLDYN `_ analysis program.\n- depends only `Python `_ and `NumPy `_.\n\nFor a quick jump into tidynamics, have a look at the examples.\n\nGoals and plans:\n\n- Minimal dependencies.\n- Serve as a reference implementation for common algorithms that are useful for molecular\n and stochastic simulations.\n- Provide later a bit more flexibility to handle cross correlations and many-body systems.\n\n\nInstallation\n------------\n\nIt is necessary to have Python and NumPy to install and use tidynamics.\n\ntidynamics can be installed with pip::\n\n pip install --user tidynamics\n\nor with conda (via conda-forge)::\n\n conda install -c conda-forge tidynamics\n\nIt is also possible to download the source code and execute the setup.py file.\n\nI ran the tests with Python 2.7, 3.5 and 3.6 and NumPy 1.11 and 1.13. If you encounter any\nissue, let me know (see Contact below).\n\n\nCitation\n--------\n\nWhen using tidynamics in a publication, please cite the following paper:\n\nPierre de Buyl (2018), *tidynamics: A tiny package to compute the dynamics of\nstochastic and molecular simulations*, The Journal of Open Source\nSoftware https://doi.org/10.21105/joss.00877\n\n\nTesting\n-------\n\nWe use `pytest `_ for testing::\n\n python -m pytest\n\nInstalling tidynamics does not install the tests. It is necessary to download tidynamics'\nsource and to install pytest to run the tests.\n\nContact, support, and contribution information\n----------------------------------------------\n\nTo contact the author about tidynamics, you can either write an email to `Pierre de Buyl\n`_ or use the `issue tracker\n`_ of the GitHub project.\nExisting contributors are listed in the file CONTRIBUTORS.\n\nBug reports are welcome. If you consider proposing a feature, please keep in mind the goals\nand plans exposed above.\n\n\n",
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