pyJac 1.0.3a4

Create analytical Jacobian matrix source code for chemical kinetics

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/.

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/

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.

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.

Authors

Created by Kyle Niemeyer ([e-mail]) and Nicholas Curtis ([e-mail])

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 build

• Adds minimal unittest test suite for module imports

Fixed

Changed

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}
    }

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 build

• Adds minimal unittest test suite for module imports

Fixed

Changed

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}
    }