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pyjac

Creates C and CUDA analytical Jacobians for chemical kinetics ODE systems

https://github.com/slackha/pyjac

Science Score: 51.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: arxiv.org, zenodo.org
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.2%) to scientific vocabulary

Keywords from Contributors

code-generation
Last synced: 7 months ago · JSON representation ·

Repository

Creates C and CUDA analytical Jacobians for chemical kinetics ODE systems

Basic Info
Statistics
  • Stars: 51
  • Watchers: 13
  • Forks: 24
  • Open Issues: 18
  • Releases: 0
Created almost 12 years ago · Last pushed about 4 years ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

pyJac

DOI Code of Conduct License PyPI Anaconda

This utility creates source code to calculate the Jacobian matrix analytically for a chemical reaction mechanism.

Documentation

The full documentation for pyJac can be found at http://slackha.github.io/pyJac/.

User Group

Further support can be found at our user group, or by opening an issue on our github repo.

Installation

Detailed installation instructions can be found in the full documentation. The easiest way to install pyJac is via conda. You can install to your environment with ```

conda install -c slackha pyjac ```

pyJac can also be installed from PyPI using pip: pip install pyjac or, using the downloaded source code, installed as a Python module: ```

python setup.py install ```

Usage

pyJac can be run as a python module: ```

python -m pyjac [options] ```

The generated source code is placed within the out (by default) directory, which is created if it doesn't exist initially. See the documentation or use python pyjac -h for the full list of options.

Theory

Theory, derivations, validation and performance testing can be found in the paper fully describing version 1.0.2 of pyJac: https://niemeyer-research-group.github.io/pyJac-paper/, now published via https://doi.org/10.1016/j.cpc.2017.02.004 and available openly via arXiv:1605.03262 [physics.comp-ph].

License

pyJac is released under the MIT license; see the LICENSE for details.

If you use this package as part of a scholarly publication, please see CITATION.md for the appropriate citation(s).

Contributing

We welcome contributions to pyJac! Please see the guide to making contributions in the CONTRIBUTING.md file.

Code of Conduct

In order to have a more open and welcoming community, pyJac adheres to a code of conduct adapted from the Contributor Covenant code of conduct.

Please adhere to this code of conduct in any interactions you have in the pyJac community. It is strictly enforced on all official pyJac repositories, websites, and resources. If you encounter someone violating these terms, please let a maintainer (@kyleniemeyer or @arghdos, via email at slackha@googlegroups.com) know and we will address it as soon as possible.

Authors

Created by Kyle Niemeyer (kyle.niemeyer@gmail.com) and Nicholas Curtis (arghdos@gmail.com)

Owner

  • Name: SLACKHA
  • Login: SLACKHA
  • Kind: organization
  • Location: Corvallis, OR

SLACKHA is a Software Library for Accelerating Chemical Kinetics on Hybrid Architectures

Citation (CITATION.md) 

# Citation of pyJac

[![DOI](https://zenodo.org/badge/19829533.svg)](https://zenodo.org/badge/latestdoi/19829533)

If you use pyJac in a scholarly article, please cite it directly as

> Kyle E. Niemeyer and Nicholas J. Curtis (2018). pyJac v1.0.6 [Software]. Zenodo.
<https://doi.org/10.5281/zenodo.1182789>

A BibTeX entry for LaTeX users is

## BibTeX entry:

```TeX
@misc{pyJac,
    author = {Kyle E Niemeyer and Nicholas J Curtis},
    year = 2018,
    title = {{pyJac} v1.0.6},
    doi = {https://doi.org/10.5281/zenodo.1182789},
    url = {https://github.com/slackha/pyJac},
}
```

In both cases, please update the entry with the version used. The DOI for the
latest version can be found in the badge at the top. If you would like to cite
a specific, older version, the DOIs for each release are:

 * v1.0.6: [10.5281/zenodo.1182789](https://doi.org/10.5281/zenodo.1182789)
 * v1.0.4: [10.5281/zenodo.555950](https://doi.org/10.5281/zenodo.555950)
 * v1.0.3: [10.5281/zenodo.439682](https://doi.org/10.5281/zenodo.439682)
 * v1.0.2: [10.5281/zenodo.251144](https://doi.org/10.5281/zenodo.251144)

GitHub Events

Total
  • Watch event: 2
  • Issue comment event: 2
  • Fork event: 2
Last Year
  • Watch event: 2
  • Issue comment event: 2
  • Fork event: 2

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 1,312
  • Total Committers: 4
  • Avg Commits per committer: 328.0
  • Development Distribution Score (DDS): 0.468
Top Committers
Name Email Commits
arghdos a****s@g****m 698
Nick-lab n****s@u****u 300
Kyle Niemeyer k****r@g****m 276
arghdos a****s@u****m 38
Committer Domains (Top 20 + Academic)
uconn.edu: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 41
  • Total pull requests: 8
  • Average time to close issues: 7 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 22
  • Total pull request authors: 2
  • Average comments per issue: 2.63
  • Average comments per pull request: 1.88
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kyleniemeyer (10)
  • michael-a-hansen (4)
  • arghdos (4)
  • ghost (3)
  • kahilah (2)
  • stgeke (2)
  • sandeepjella (1)
  • TJaravel (1)
  • mgoodson-cvd (1)
  • synjon-symthe (1)
  • Tom-Y-Liu (1)
  • syoukera (1)
  • GontzalLopez (1)
  • BarrySmith (1)
  • testcan (1)
Pull Request Authors
  • arghdos (6)
  • kyleniemeyer (2)
Top Labels
Issue Labels
enhancement (7) v1.0 task (3) bug (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 49 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 8
  • Total maintainers: 1
pypi.org: pyjac

Create analytical Jacobian matrix source code for chemical kinetics

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 49 Last month
Rankings
Forks count: 8.4%
Stargazers count: 9.6%
Dependent packages count: 10.1%
Average: 16.1%
Dependent repos count: 21.5%
Downloads: 30.6%
Maintainers (1)
kyleniemeyer
Last synced: 8 months ago

Dependencies

setup.py pypi
  • Cython >=0.23.1
  • bitarray >=0.8.1
  • numpy >=1.12.0
  • optionloop >1.0.3
  • pyyaml >=3.11