.. chombo-discharge documentation master file, created by
   sphinx-quickstart on Thu Jul 26 21:03:53 2018.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

.. important::

   **This is a beta release. Development is still in progress, and various bugs may be present. Minor changes to the user interface can still occur.**

Welcome to ``chombo-discharge``'s user documentation
****************************************************

.. important::

   ``chombo-discharge`` is a modular and scalable research code for Cartesian two- and three-dimensional simulations of low-temperature plasmas in complex geometries.
   The code is hosted at `GitHub <https://github.com/chombo-discharge/chombo-discharge>`_ together with the source files for this documentation.

``chombo-discharge`` features include:

* Fully written in C++.
* Parallelized with OpenMP, MPI, or MPI+OpenMP.
* Support for complex geometries.
* Scalar advection-diffusion-reaction processes.
* Electrostatics with support for electrodes and dielectrics.
* Radiative transport as a diffusion or Monte Carlo process.
* Particle-mesh operations (like Particle-In-Cell)
* Parallel I/O with HDF5.
* Dual-grid simulations with individual load balancing of fluid and particles.
* Various multi-physics interfaces that use the above solvers.
* Various time integration schemes.  

.. * Îto particle models for microscopic drift-diffusion-reaction processes.  

Numerical solvers are designed to run either on their own, or as a part of a larger application.

For scalability, ``chombo-discharge`` is built on top of `Chombo 3 <https://github.com/applied-numerical-algorithms-group-lbnl/Chombo_3.2>`_, and therefore additionally features

* Cut-cell representation of multi-material geometries.
* Patch based adaptive mesh refinement.
* Weak and strong scalability to thousands of computer cores.

Our goal is that users will be able to use ``chombo-discharge`` without modifying the underlying solvers.
There are interfaces for describing e.g. the plasma physics, boundary conditions, mesh refinement, etc.
As ``chombo-discharge`` evolves, so will these interfaces.
We aim for (but cannot guarantee) backward compatibility such that existing ``chombo-discharge`` models can be run on future versions of ``chombo-discharge``.

.. This is for getting rid of the TOC in html view.
.. raw:: html

   <style>
   section#introduction,
   section#design,
   section#discretization,
   section#solvers,
   section#multi-physics-applications,
   section#single-solver-applications,
   section#tutorial,
   section#utilities,
   section#contributing,
   section#references,
   section#bibliography,
   section#epilogue {
	 display:none;
   }
   </style>   

.. only:: latex

   .. toctree::
      :caption: Contents

Introduction
************

.. toctree::
   :maxdepth: 3
   :caption: Introduction
   :hidden:

   Base/Documentation
   Base/Overview
   Base/Installation
   Base/Control
   Base/Examples
   Base/Testing
   Base/Acknowledgements

Design
******

.. toctree::
   :maxdepth: 3
   :caption: Design
   :hidden:

   Source/DesignOverview
   Source/Driver
   Source/ComputationalGeometry
   Source/TimeStepper
   Source/AmrMesh   
   Source/CellTagger

Discretization
**************

.. toctree::
   :maxdepth: 3
   :caption: Discretization
   :hidden:

   Source/SpatialDiscretization      
   Source/ChomboBasics      
   Source/MeshData
   Source/Particles
   Source/Realm
   Source/LinearSolvers
   Source/VV   

Solvers
*******

.. toctree::
   :maxdepth: 3
   :caption: Solvers
   :hidden:	     

   Solvers/CDR
   Solvers/Electrostatics
   Solvers/Ito   
   Solvers/KineticMonteCarlo
   Solvers/MeshODESolver
   Solvers/RTE
   Solvers/SurfaceODESolver
   Solvers/TracerParticles

Multi-physics applications
**************************

.. toctree::
   :maxdepth: 3
   :caption: Multi-physics applications
   :hidden:	     

   Applications/CdrPlasmaModel
   Applications/DischargeInceptionModel
   Applications/ItoKMC

Single-solver applications
**************************

.. toctree::
   :maxdepth: 3
   :caption: Single-solver applications
   :hidden:	     

   Applications/AdvectionDiffusionModel
   Applications/BrownianWalkerModel         
   Applications/ElectrostaticsModel
   Applications/GeometryModel
   Applications/MeshODEModel
   Applications/RadiativeTransferModel
   Applications/TracerParticleModel


..
   Tutorial
   ********

   .. toctree::
      :maxdepth: 3
      :caption: Tutorial
      :hidden:	     

      Tutorials/Tutorial
      
Utilities
*********  

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   :maxdepth: 3
   :caption: Utilities
   :hidden:	     

   Utilities/DataParser
   Utilities/LookupTable
   Utilities/RandomNumbers
   Utilities/LeastSquares

Contributing
************  

.. toctree::
   :maxdepth: 3
   :caption: Contributing
   :hidden:	     

   Contrib/Contributions
   Contrib/CodeStandard

.. only:: html
	  
   Bibliography
   ************

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   :maxdepth: 3
   :caption: Bibliography
   :hidden:	     

   ZZReferences