.. ATS documentation master file, created by
   sphinx-quickstart on Thu Mar 12 14:16:05 2020.
   You can adapt this file completely to your liking, but it should at least
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Advanced Terrestrial Simulator
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.. image:: _static/images/coweeta.png

The Advanced Terrestrial Simulator is a code for solving ecosystem-based, integrated, distributed hydrology.

Capabilities are largely based on solving various forms of Richards equation, coupled to a surface flow equation, along with the needed sources and sinks for ecosystem and climate models. This can (but need not) include thermal processes (especially ice for frozen soils), evapotranspiration, surface energy balances, snow, biogeochemistry, plant dynamics, deformation, transport, and much more.

ATS is a suite of physics processes built for Amanzi.  As such documentation is split between process documentation here and framework documentation in Amanzi.  Links across the related projects attempt to build a uniform interface for the user.


Join the Community
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ATS is more than just a code, but a community of users with a lot of experience in both integrated hydrology, Arctic hydrology, reactive transport, and ATS code development.  Please join us on our `Google group <https://groups.google.com/forum/#!forum/ats-users>`_.  We try very hard to create a welcoming community that supports and enables our users to do their science.


Installation
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ATS is now built as a part of Amanzi directly. Please see the `ATS installation instructions <https://github.com/amanzi/amanzi/blob/master/INSTALL_ATS.md>`_ on Amanzi's site.


License and Copyright
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Please see the `LICENSE <https://github.com/amanzi/ats/blob/master/LICENSE>`_ and `COPYRIGHT <https://github.com/amanzi/ats/blob/master/COPYRIGHT>`_ files included in the top level directory of your ATS download.



Citation
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In all works, please cite the code:

E.T. Coon, M. Berndt, A. Jan, D. Svyatsky, A.L. Atchley, E. Kikinzon, D.R. Harp, G. Manzini, E. Shelef, K. Lipnikov, R. Garimella, C. Xu, J.D. Moulton, S. Karra, S.L. Painter, E. Jafarov, and S. Molins. 2020. Advanced Terrestrial Simulator. U.S. Department of Energy, USA. Version 1.0. `DOI <https://doi.org/10.11578/dc.20190911.1>`_

Additionally, consider citing one or more of the below, depending upon the application space:

**Watershed Hydrology:** Coon, Ethan T., et al. "Coupling surface flow and subsurface flow in complex soil structures using mimetic finite differences." Advances in Water Resources 144 (2020): 103701. `DOI <https://doi.org/10.1016/j.advwatres.2020.103701>`_

**Arctic Hydrology:** Painter, Scott L., et al. "Integrated surface/subsurface permafrost thermal hydrology: Model formulation and proof‐of‐concept simulations." Water Resources Research 52.8 (2016): 6062-6077. `DOI <https://doi.org/10.1002/2015WR018427>`_

**Reactive Transport:**  Molins, Sergi, et al. "A Multicomponent Reactive Transport Model for Integrated Surface‐Subsurface Hydrology Problems." Water Resources Research 58.8 (2022): e2022WR032074. `DOI <https://doi.org/10.1029/2022WR032074>`_

**Multiphysics Modeling:** Coon, Ethan T., J. David Moulton, and Scott L. Painter. "Managing complexity in simulations of land surface and near-surface processes." Environmental modelling & software 78 (2016): 134-149. `DOI <https://doi.org/10.1016/j.envsoft.2015.12.017>`_


Wiki
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Please see our `Wiki Page <https://github.com/amanzi/ats/wiki>`_ for frequently asked questions and a Developer's Guide.


.. toctree::
   :maxdepth: 2
   :caption: User Guide:

   demos
   input_spec


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