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tidynamics

tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations - Published in JOSS (2018)

https://github.com/pdebuyl-lab/tidynamics

Science Score: 98.0%

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    Found 9 DOI reference(s) in README and JOSS metadata
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    Published in Journal of Open Source Software

Keywords

correlation molecular-dynamics numpy stochastic-process
Last synced: 6 months ago · JSON representation ·

Repository

A tiny package to compute the dynamics of stochastic and molecular simulations

Basic Info
Statistics
  • Stars: 28
  • Watchers: 2
  • Forks: 4
  • Open Issues: 0
  • Releases: 3
Topics
correlation molecular-dynamics numpy stochastic-process
Created about 8 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.rst 

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.

Owner

  • Name: Pierre de Buyl's lab
  • Login: pdebuyl-lab
  • Kind: organization

JOSS Publication

tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations
Published
August 27, 2018
DOI
Volume 3, Issue 28, Page 877
Authors
Pierre de Buyl ORCID
Instituut voor Theoretische Fysica, KU Leuven, B-3001 Leuven, Belgium
Editor
Kyle Niemeyer ORCID
Tags
physics time series stochastic processes
View PDF Review Thread Software Archive

Citation (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

.. 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

~~~
@article{tidynamics_2018,
  doi = {10.21105/joss.00877}
  year  = {2018},
  publisher = {Open Journals},
  volume = {3},
  number = {28},
  pages = {877},
  author = {Pierre de Buyl},
  title = {{tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations}},
  journal = {Journal of Open Source Software},
}
~~~

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 146
  • Total Committers: 2
  • Avg Commits per committer: 73.0
  • Development Distribution Score (DDS): 0.007
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Pierre de Buyl p****l@p****e 145
Malcolm Ramsay m****4@g****m 1
Committer Domains (Top 20 + Academic)
pdebuyl.be: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 13
  • Total pull requests: 3
  • Average time to close issues: 2 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 5
  • Total pull request authors: 2
  • Average comments per issue: 2.23
  • Average comments per pull request: 0.33
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • malramsay64 (8)
  • richardjgowers (2)
  • AlphonsG (1)
  • abhijeetdhakane (1)
  • kain88-de (1)
Pull Request Authors
  • malramsay64 (2)
  • pdebuyl (1)
Top Labels
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Packages

  • Total packages: 2
  • Total downloads:
    • pypi 5,305 last-month
  • Total docker downloads: 326
  • Total dependent packages: 8
    (may contain duplicates)
  • Total dependent repositories: 5
    (may contain duplicates)
  • Total versions: 11
  • Total maintainers: 1
pypi.org: tidynamics

Tiny package to compute dynamics correlations

  • Versions: 9
  • Dependent Packages: 6
  • Dependent Repositories: 4
  • Downloads: 5,305 Last month
  • Docker Downloads: 326
Rankings
Dependent packages count: 1.6%
Docker downloads count: 3.0%
Average: 4.5%
Downloads: 5.7%
Dependent repos count: 7.5%
Maintainers (1)
pdebuyl
Last synced: 6 months ago
conda-forge.org: tidynamics

tidynamics performs the computation of mean-square displacements and correlation functions. tidynamics implements the so-called Fast Correlation Algorithm proposed by Kneller and others for the nMOLDYN analysis program. tidynamics depends only Python and NumPy.

  • Versions: 2
  • Dependent Packages: 2
  • Dependent Repositories: 1
Rankings
Dependent packages count: 19.6%
Dependent repos count: 24.4%
Average: 37.4%
Stargazers count: 51.3%
Forks count: 54.2%
Last synced: 6 months ago

Dependencies

.github/workflows/test.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.binder/requirements.txt pypi
  • matplotlib *
  • numpy *
pyproject.toml pypi
  • numpy *