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
Last synced: 7 months ago
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A tiny package to compute the dynamics of stochastic and molecular simulations
- Host: GitHub
- URL: https://github.com/pdebuyl-lab/tidynamics
- Owner: pdebuyl-lab
- License: bsd-3-clause
- Created: 2017-12-11T14:05:49.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2023-07-11T12:37:28.000Z (almost 3 years ago)
- Last Synced: 2025-02-01T12:44:04.609Z (over 1 year ago)
- Topics: correlation, molecular-dynamics, numpy, stochastic-process
- Language: Python
- Homepage: http://lab.pdebuyl.be/tidynamics/
- Size: 137 KB
- Stars: 27
- Watchers: 3
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
- Citation: CITATION
Awesome Lists containing this project
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.