python-crunchflow -- A Python Library for Working with the CrunchFlow Reactive Transport Code
=============================================================================================

``python-crunchflow`` is an open source python package designed for working with the the reactive
transport model `CrunchFlow <https://github.com/CISteefel/CrunchTope>`_. This library provides a set
of tools for managing and manipulating CrunchFlow input files, as well as quickly reading and
plotting model output.

If you use the ``crunchflow`` package in published work, please cite the paper for which it was originally developed:

Perzan, Z., Babey, T., Caers, J., Bargar, J.R. and Maher, K., 2021, Local and global sensitivity analysis of a reactive transport model simulating floodplain redox cycling, *Water Resources Research*, doi: `10.1029/2021WR029723 <https://dx.doi.org/10.1029/2021WR029723>`_

This library consists of two main subpackages:

- ``crunchflow.output`` contains the ``TimeSeries`` and ``SpatialProfile`` classes for working with CrunchFlow ``time_series`` and ``spatial_profile`` output, respectively. These include concentration histories at a given grid cell as well as spatially-variable geochemical conditions and sediment properties at a given snapshot in time.
- ``crunchflow.input`` contains the ``InputFile`` and ``KeywordBlock`` classes for working with CrunchFlow input files.

Contents
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.. toctree::
   :maxdepth: 3
   :hidden:

   Home page <self>
   Tutorials <tutorials>

- **Tutorials**. Most of the functionality of this package is documented in the `Tutorials <tutorials.html>`_ section. There is one tutorial each for the ``crunchflow.input`` and ``crunchflow.output`` subpackages.
- **Documentation**. Some documentation of individual classes and functions is also included in the `API Reference <autoapi/index.html>`_.

Indices and tables
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* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`