tidynamics 0.1.0

tidynamics
==========

.. image:: https://travis-ci.org/pdebuyl-lab/tidynamics.svg?branch=master
:target: https://travis-ci.org/pdebuyl-lab/tidynamics
:alt: Test Status

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/plone/software/nmoldyn/>`_ 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

It is also possible to download the source code and execute the setup.py file.

I ran the tests with Python 2.7, 3.5 and 3.6 and NumPy 1.11 and 1.13. If you encounter any
issue, let me know (see :ref:`Contact` below).

Testing
-------

We use `pytest <https://pypi.python.org/pypi/pytest/>`_ for testing::

python -m pytest

.. _contact:

Contact
-------

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.