Metadata-Version: 2.1
Name: chemreac
Version: 0.8.2
Summary: Python package for modeling chemical kinetics with diffusion and drift.
Home-page: https://github.com/chemreac/chemreac
Author: Bjoern I. Dahlgren
Author-email: bjodah@gmail.com
License: BSD
Description: chemreac
        ========
        .. image:: http://hera.physchem.kth.se:9090/api/badges/chemreac/chemreac/status.svg
           :target: http://hera.physchem.kth.se:9090/chemreac/chemreac
           :alt: Build status
        .. image:: https://img.shields.io/pypi/v/chemreac.svg
           :target: https://pypi.python.org/pypi/chemreac
           :alt: PyPI version
        .. image:: https://img.shields.io/badge/python-3.5,3.6-blue.svg
           :target: https://www.python.org/
           :alt: Python version
        .. image:: https://zenodo.org/badge/8840/chemreac/chemreac.svg
           :target: https://zenodo.org/badge/latestdoi/8840/chemreac/chemreac
           :alt: DOI (digital object identifier) for latest release on Zenodo
        .. image:: https://img.shields.io/pypi/l/chemreac.svg
           :target: https://github.com/bjodah/chemreac/blob/master/LICENSE
           :alt: License
        .. image:: http://img.shields.io/badge/benchmarked%20by-asv-green.svg?style=flat
           :target: http://hera.physchem.kth.se/~chemreac/benchmarks
           :alt: airspeedvelocity
        .. image:: http://hera.physchem.kth.se/~chemreac/branches/master/htmlcov/coverage.svg
           :target: http://hera.physchem.kth.se/~chemreac/branches/master/htmlcov
           :alt: coverage
        
        .. image:: http://chemreac.github.io/chemreac_logo.svg
           :alt: chemreac logotype
           :align: left
        
        chremreac is an open source library which aims to collect tools and utilities for
        modeling of chemical kinetics problems. It is primarily designed to
        be useful in the context of aqueous phase with external radiation fields (including
        advection/diffusion processes).
        
        The (heavy) numerical processing is done in rountines written in C++ which have
        been wrapped in a `Python <https://www.python.org>`_ interface using
        `Cython <https://www.cython.org>`_.
        
        Documentation
        =============
        
        - Documentation for the latest stable release is found here:
          `<http://chemreac.github.io/chemreac/latest/>`_
        - and development documentation for the current master branch is found here:
          `<http://hera.physchem.kth.se/~chemreac/branches/master/html>`_).
        
        
        Installation
        ============
        .. install-start
        
        The easiest way to install ``chemreac`` (on linux) is to use
        `conda <http://docs.continuum.io/anaconda/index.html>`_:
        
        ::
        
           $ conda install -c chemreac chemreac pytest
        
        and you're done! To check if ``chemreac`` is installed correctly you may run:
        
        ::
        
            $ pytest --pyargs chemreac
        
        which should run the test suite (all tests should pass or xfail).
        If you are using a special platform with non-standard math libraries you
        may need to compile your own pacakges. The "recipes" for the conda packages
        are kept `here <https://github.com/chemreac/chemreac_anaconda/>`_.
        
        If you are not using the conda package manager you can still install
        ``chemreac`` from source. You will find the instructions for doing so below.
        
        Building from source
        --------------------
        Below you will find instructions for installation by building ``chemreac`` from source.
        You may also look in ``scripts/`` folder for automated install scripts used
        on the continuous integration servers.
        
        Prerequisites
        ~~~~~~~~~~~~~
        Version numbers of dependencies indicate what has been tested:
        
        - C++ compiler with C++11 support (e.g. `GCC <https://gcc.gnu.org/>`_ >= 4.8)
        - LAPACK (provided by e.g. `OpenBLAS <http://www.openblas.net/>`_)
        - `Sundials <http://computation.llnl.gov/casc/sundials/main.html>`_ 2.6.2
        - Python (2.7 or >=3.4)
        
        In addition to the standard library provided by Python, a number of python
        packages are required (see `setup.py <./setup.py>`_), they are found on `PyPI
        <https://pypi.python.org/pypi>`_ and are automatically installed when
        using ``pip``.
        
        For rendering the documentation you also need:
        
        - `Sphinx <http://sphinx-doc.org/>`_
        - `numpydoc <https://pypi.python.org/pypi/numpydoc>`_
        - `sphinx_rtd_theme <https://pypi.python.org/pypi/sphinx_rtd_theme>`_
        
        to run all the tests you also need these tools:
        
        - valgrind
        - graphviz
        - dot2tex
        - pdflatex
        
        
        Building and installing
        ~~~~~~~~~~~~~~~~~~~~~~~
        Once non-python prerequisites are in installed, you may procede e.g. as:
        
        ::
        
            $ git clone https://github.com/chemreac/chemreac.git
            $ cd chemreac
            $ pip install --user -e .[all]
            $ ./scripts/run_tests.sh
        
        
        the above procedure works on Ubuntu 14.04 for example.
        
        To specify an alternative LAPACK lib, set the environment variable LLAPACK, e.g.:
        
        ::
        
            $ LLAPACK=openblas python setup.py build_ext --inplace
        
        The following environment variables are also supported by
        ``setup.py`` (defaults to "0", enable by setting them to "1"):
        
        +-----------------------------------------+-------+--------------------------------------------------+
        |Environament variable                    |Default|Action                                            |
        +=========================================+=======+==================================================+
        |``WITH_OPENMP``                          |0      |Enable parallell evaluation of rhs and jac.       |
        +-----------------------------------------+-------+--------------------------------------------------+
        |``WITH_BLOCK_DIAG_ILU_DGETRF``           |0      |Use unblocked version of dgetrf instead of LAPACK |
        +-----------------------------------------+-------+--------------------------------------------------+
        |``WITH_BLOCK_DIAG_ILU_OPENMP``           |0      |Evaluate LU decomposition of blocks in parallel   |
        +-----------------------------------------+-------+--------------------------------------------------+
        |``WITH_DATA_DUMPING``                    |0      |For debugging purposes only                       |
        +-----------------------------------------+-------+--------------------------------------------------+
        |``WITH_DEBUG``                           |0      |For debugging purposes only                       |
        +-----------------------------------------+-------+--------------------------------------------------+
        
        Enabling the first three is known to provide significant speed up for some scenarios (performance is
        system dependent, hence recommendations are not possible to give without benchmarking).
        
        Tests
        -----
        If you have ``py.test`` installed you may run the test suite on the
        installed package:
        
        ::
        
            $ py.test --pyargs chemreac
        
        All tests should pass (or xfail). If they do not, please `file an
        issue <https://github.com/chemreac/chemreac/issues>`_.
        
        .. install-end
        
        Status
        ======
        Both the correctness (continuous integration) and the performance
        (benchmarks) of the code base is monitored continuously.
        
        Continuous integration
        ----------------------
        .. ci-start
        
        In order to minimize the risk of (re)introducing bugs into the code
        base, it is continuously built on a CI server:
        
        .. image:: http://hera.physchem.kth.se:9090/api/badges/chemreac/chemreac/status.svg
           :target: http://hera.physchem.kth.se:9090/chemreac/chemreac
           :alt: Build status
        
        .. ci-end
        
        Performace tracking
        -------------------
        Benchmarks for tracking the performance of the library are kept at
        https://github.com/chemreac/chemreac-benchmarks
        
        
        License
        =======
        The source code is Open Source and is released under the very permissive
        "simplified (2-clause) BSD license". See ``LICENSE.txt`` for further details.
        Contributors are welcome to suggest improvements at https://github.com/chemreac/chemreac
        
        Author
        ======
        Björn Dahlgren, contact:
         - gmail address: bjodah
         - kth.se address: bda
        
Keywords: chemical kinetics,Smoluchowski equation,advection-diffusion-reaction
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Mathematics
Requires-Python: >=3.5
Provides-Extra: all
