Metadata-Version: 1.1
Name: pyjac
Version: 1.0.6
Summary: Create analytical Jacobian matrix source code for chemical kinetics
Home-page: https://github.com/slackha/pyJac
Author: Kyle E. Niemeyer
Author-email: kyle.niemeyer@gmail.com
License: MIT License
Description-Content-Type: UNKNOWN
Description: 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 <https://groups.io/g/slackha-users>`__, or by `opening an
        issue <https://github.com/SLACKHA/pyJac/issues>`__ on our github repo.
        
        Installation
        ------------
        
        Detailed installation instructions can be found in the `full
        documentation <http://slackha.github.io/pyJac/>`__. 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]`` <https://arxiv.org/abs/1605.03262>`__.
        
        License
        -------
        
        pyJac is released under the MIT license; see the
        `LICENSE <https://github.com/slackha/pyJac/blob/master/LICENSE>`__ for
        details.
        
        If you use this package as part of a scholarly publication, please see
        `CITATION.md <https://github.com/slackha/pyJac/blob/master/CITATION.md>`__
        for the appropriate citation(s).
        
        Contributing
        ------------
        
        We welcome contributions to pyJac! Please see the guide to making
        contributions in the
        `CONTRIBUTING.md <https://github.com/slackha/pyJac/blob/master/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 <http://contributor-covenant.org>`__ 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](https://github.com/kyleniemeyer) or
        [@arghdos](https://github.com/arghdos), via email at
        slackha@googlegroups.com) know and we will address it as soon as
        possible.
        
        Authors
        -------
        
        Created by `Kyle Niemeyer <http://kyleniemeyer.com>`__
        (kyle.niemeyer@gmail.com) and Nicholas Curtis (arghdos@gmail.com)
        
        Change Log
        ==========
        
        All notable changes to this project will be documented in this file.
        
        The format is based on `Keep a Changelog <http://keepachangelog.com/>`__
        and this project adheres to `Semantic
        Versioning <http://semver.org/>`__.
        
        [1.0.6] - 2018-02-21
        --------------------
        
        Added
        ~~~~~
        
        -  DOI for 1.0.4
        
        Fixed
        ~~~~~
        
        -  Syntax errors in readme.md
        -  Conda install instructions in install.md
        -  Corrected TRange columns in parser
        -  Minor documentation fixes
        
        Added
        ~~~~~
        
        -  Add check to reactions to test that all species exist
        -  Duplicate warning from falloff->chemically-activated TROE reactions
           for zero-parameters
        -  Add handling of non-unity default third body efficiency
        
        Changed
        ~~~~~~~
        
        -  Bump internal version to 1.0.5.c
        
        [1.0.5.b0] - 2017-06-02
        -----------------------
        
        Added
        ~~~~~
        
        -  Added usergroup info to README and documentation
        
        Fixed
        ~~~~~
        
        Changed
        ~~~~~~~
        
        -  Now strip whitespace from mechanism file lines prior to parsing
           keywords
        
        Removed
        ~~~~~~~
        
        -  Removed plotting scripts specific to first paper on pyJac
        
        `1.0.4 <https://github.com/slackha/pyJac/compare/v1.0.3...v1.0.4>`__ - 2017-04-18
        ---------------------------------------------------------------------------------
        
        Added
        ~~~~~
        
        -  Adds Travis config for automatic PyPI and conda builds
        -  Adds minimal unittest test suite for module imports
        -  Adds code of conduct
        
        Changed
        ~~~~~~~
        
        -  Changed README back to Markdown for simplicity
        -  Updated citation instructions
        
        `1.0.3 <https://github.com/slackha/pyJac/compare/v1.0.2...v1.0.3>`__ - 2017-04-01
        ---------------------------------------------------------------------------------
        
        Fixed
        ~~~~~
        
        -  Fix for SRI Falloff functions with non-default third bodies (`issue
           #12 <https://github.com/SLACKHA/pyJac/issues/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 <https://github.com/slackha/pyJac/compare/v1.0.1...v1.0.2>`__ - 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 <https://github.com/slackha/pyJac/compare/v1.0...v1.0.1>`__ - 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 <https://github.com/slackha/pyJac/compare/v0.9.1-beta...v1.0>`__ - 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 <https://github.com/slackha/pyJac/compare/v0.9-beta...v0.9.1-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
        
        Citation of pyJac
        =================
        
        |DOI|
        
        If you use pyJac in a scholarly article, please cite it directly as
        
            Kyle E. Niemeyer and Nicholas J. Curtis (2017). pyJac v1.0.4
            [Software]. Zenodo.
            `https://doi.org/10.5281/zenodo.###### <https://doi.org/10.5281/zenodo.######>`__
        
        A BibTeX entry for LaTeX users is
        
        BibTeX entry:
        -------------
        
        .. code:: tex
        
            @misc{pyJac,
                author = {Kyle E Niemeyer and Nicholas J Curtis},
                year = 2017,
                title = {{pyJac} v1.0.4},
                doi = {10.5281/zenodo.######},
                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:
        
        -  v1.0.4:
           `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>`__
        
        .. |DOI| image:: https://zenodo.org/badge/19829533.svg
           :target: https://zenodo.org/badge/latestdoi/19829533
        .. |Code of Conduct| image:: https://img.shields.io/badge/code%20of%20conduct-contributor%20covenant-green.svg
           :target: http://contributor-covenant.org/version/1/4/
        .. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg
           :target: https://opensource.org/licenses/MIT
        .. |PyPI| image:: https://badge.fury.io/py/pyJac.svg
           :target: https://badge.fury.io/py/pyJac
        .. |Anaconda| image:: https://anaconda.org/slackha/pyjac/badges/version.svg
           :target: https://anaconda.org/slackha/pyjac
        
Keywords: chemical_kinetics analytical_Jacobian
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
