Create analytical Jacobian matrix source code for chemical kinetics
Project description
pyJac
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/.
Installation
Detailed installation instructions can be found in the full documentation. However, pyJac can be installed as a Python module:
python setup.py install
or from PyPI using pip:
pip install pyjac
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] <https://arxiv.org/abs/1605.03262>`__.
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.
Change Log
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Unreleased
Added
Adds Travis config for automatic PyPI and conda builds
Adds minimal unittest test suite for module imports
Fixed
Changed
Changed README back to Markdown for simplicity
1.0.3 - 2017-04-01
Fixed
Fix for SRI Falloff functions with non-default third bodies (issue #12)
Fixed removal of jac/rate lists before libgen of functional_tester
Fixed pywrap module import
Changed
Issue warning in Cantera parsing if the installed version doesn’t have access to species thermo properties.
Added
Added significantly more documentation and examples for data ordering, the state vector / Jacobian, and using the python interface
1.0.2 - 2017-01-18
Added
Added CHANGELOG
Added documentation for libgen / pywrap features
Changed
Minor compilation fixes for including OpenMP
Updated github links to point to SLACKHA / Niemeyer Research Group
Deprecated
Shared library creation for CUDA disabled, as CUDA does not allow linkage of SO’s into another CUDA kernel
Fixed
Explicitly conserve mass in PaSR
Minor path fixes
Division by zero in some TROE parameter cases
1.0.1 - 2016-05-25
Added
Added GPU macros, e.g., THREAD_ID, GRID_SIZE
Changed
Much better handling of removal of files created during testing
Fixed
Bugfix that generates data.bin files correctly from .npy files for performance testing (important)
Explicit setting of OpenMP # threads for performance testing
1.0 - 2016-05-07
Added
pyJac is now a Python package
pyJac can now create a static/shared library for a mechanism (for external linkage)
Added documentation
Added examples
Changed
Handles CUDA compilation better via Cython
pointers are now restricted where appropriate
better Python3 compatibility
Fixed
other minor bugfixes
0.9.1-beta - 2015-10-29
Changed
Implemented the strict mass conservation formulation
Updated CUDA implementation such that it is testable vs. pyJac c-version (and Cantera where applicable)
More robust build folder management
More robust mapping for strict mass conservation
0.9-beta - 2015-10-02
Added
First working / tested version of pyJac
Cite As:
Kyle E. Niemeyer and Nicholas J. Curtis (2016). pyJac version 1.0.3 [Software]. Available from https://github.com/slackha/pyJac. doi:10.5281/zenodo.251144
BibTeX entry:
@misc{pyjac:2017, author = {Kyle E Niemeyer and Nicholas J Curtis}, title = {{pyJac}}, year = {2017}, howpublished = {Available via \url{https://github.com/slackha/pyJac}}, doi = {10.5281/zenodo.439682}, Note = {Version 1.0.3} }
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