tidynamics 1.1.2
Tiny package to compute dynamics correlations
License: BSD-3-Clause
Requires Python: >=3.7

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 <http://dirac.cnrs-orleans.fr/nMOLDYN.html>`_ analysis program.
- depends only `Python <https://www.python.org/>`_ and `NumPy <http://www.numpy.org/>`_.

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 <https://pypi.python.org/pypi/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
<https://www.kuleuven.be/wieiswie/nl/person/00092351>`_ or use the `issue tracker
<https://github.com/pdebuyl-lab/tidynamics/issues>`_ 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.