{"id":14977859,"url":"https://github.com/pdebuyl-lab/tidynamics","last_synced_at":"2025-10-28T07:30:29.974Z","repository":{"id":60723470,"uuid":"113866245","full_name":"pdebuyl-lab/tidynamics","owner":"pdebuyl-lab","description":"A tiny package to compute the dynamics of stochastic and molecular 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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://github.com/pdebuyl-lab/tidynamics/actions/workflows/test.yml/badge.svg\n   :target: https://github.com/pdebuyl-lab/tidynamics/actions/workflows/test.yml\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\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1401184.svg\n   :target: https://doi.org/10.5281/zenodo.1401184\n   :alt: Link Zenodo archive\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 \u003chttp://dirac.cnrs-orleans.fr/nMOLDYN.html\u003e`_ analysis program.\n- depends only `Python \u003chttps://www.python.org/\u003e`_ and `NumPy \u003chttp://www.numpy.org/\u003e`_.\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 pip locally.\n \nTests are run with Python 3.7 to 3.11. Python 2 is not supported anymore.  If\nyou encounter any issue, let me know (see Contact below).\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 \u003chttps://pypi.python.org/pypi/pytest/\u003e`_ 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\u003chttps://www.kuleuven.be/wieiswie/nl/person/00092351\u003e`_ or use the `issue tracker\n\u003chttps://github.com/pdebuyl-lab/tidynamics/issues\u003e`_ 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","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdebuyl-lab%2Ftidynamics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpdebuyl-lab%2Ftidynamics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdebuyl-lab%2Ftidynamics/lists"}