re-org docs, add info

README.md

 # MFIX-Exa
-This is the public face of the MFiX-Exa project.
+This is the public face of the MFiX-Exa project, hosting the documentation,
+gallery of results, etc. The website is: https://amrex-codes.github.io/MFIX-Exa/
 
-The code for now lives at NETL; instructions for how to get access to the code
-will be given below.
+## Editing
 
-This repo is designed to host the documentation, gallery of results, etc.
+The documentation source is in `docs/source/` and the html source for the cover
+page is in `docs/webroot/`.
 
-## Editing
+:warning: **Do not push any edits to the `gh-pages` branch** as these will be
+overwritten. Instead, commit your changes to the `master` branch, and the
+`gh-pages` branch will be updated automatically a few minutes later.
+
+### Documentation
+
+The documentation is built using
+[sphinx](https://www.sphinx-doc.org/en/master/). The `docs/source/config.py`
+file contains the settings for building this documentation. The documentation
+can be built locally by:
+
+1. Install sphinx:
+
+```shell
+> pip install sphinx sphinx_rtd_theme
+```
+
+2. Build the documentation:
+
+```shell
+> mkdir build
+> sphinx-build -b html docs/source/ build
+```
+
+The HTML pages will now be located in the `build` directory. Open the
+`index.html` with your favorite browser:
 
-Do not push any edits to the `gh-pages` branch as these will be overwritten.
-Instead, commit your changes to the `master` branch, and the `gh-pages` branch
-will be updated automatially a few minutes later. The documentation source is
-in `docs/source/` and the html source for the cover page is in `docs/webroot/`.
+```shell
+> firefox build/index.html
+```
 
 ### Doxygen
 

docs/source/EB.rst → docs/source/EB_Chapter.rst

@@ -13,4 +13,4 @@ refining the computational meshes near walls.
    :maxdepth: 1
    :caption: Contents:
 
-   EBWalls
+   eb/EBWalls

docs/source/Fluids_Chapter.rst

@@ -8,5 +8,5 @@ Solving the Fluid Equations
 
 .. toctree::
 
-   FluidEquations
-   FluidTimeDiscretization
+   fluids/FluidEquations
+   fluids/FluidTimeDiscretization

docs/source/GettingStarted.rst → docs/source/GettingStarted_Chapter.rst

@@ -6,8 +6,6 @@ Getting Started
 .. toctree::
    :maxdepth: 1
 
-   Structure
-   BuildingCMake
-   BuildingGMake
-   RunningTestSuite
-   RegressionTesting
+   getting_started/Structure
+   getting_started/BuildingCMake
+   getting_started/BuildingGMake

docs/source/Inputs_Chapter.rst

@@ -3,16 +3,48 @@
 Run-time Inputs
 ===============
 
+Run-time inputs are used to control the simulation setup such as the grid,
+solver settings, geometry, boundary conditions etc. These ``<key> = <value(s)>``
+pairs are saved in a text file, with any file name, that is passed to the
+MFiX-Exa executable at run time:
+
+.. code-block:: shell
+
+   ./mfix my_project.inputs
+
+.. note::
+   Traditionally, input files have been named ``inputs``. However, it is
+   recommended that you provide a descriptive name with an extension of
+   ``.inputs`` such as ``fluid_bed.inputs``
+
+The input text file looks something like this:
+
+.. code-block::
+
+   # Run settings
+   mfix.stop_time = 10.0 # inline comment
+
+   # Solver settings
+   nodal_proj.verbose = 0
+   nodal_proj.maxiter = 1000
+
+where comments are denoted with a ``#``. If a value is not specified for a key,
+the default value will be used.
+
+The following sections contain information addressing the input keywords and
+values for setting up a problem. Pay special attention to any prefixes for the
+keywords such as ``mfix``, ``amr``, ``geometry``, ``nodal_proj`` etc.
+
 .. toctree::
    :maxdepth: 1
 
-   InputsProblemDefinition
-   InputsDrag
-   InputsTimeStepping 
-   InputsInitialization 
-   InputsLoadBalancing 
-   InputsMultigrid
-   InputsPlotFiles 
-   InputsCheckpoint
-   InputsMonitors
-   InputsVerbosity
+   Units, mesh, geometry, species, fluid, DEM, regions, inital and boundary conditions <inputs/InputsProblemDefinition>
+   Particle drag <inputs/InputsDrag>
+   inputs/InputsTimeStepping
+   inputs/InputsInitialization
+   inputs/InputsLoadBalancing
+   inputs/InputsMultigrid
+   inputs/InputsPlotFiles
+   inputs/InputsCheckpoint
+   inputs/InputsMonitors
+   inputs/InputsVerbosity

docs/source/Particles_Chapter.rst

@@ -23,7 +23,7 @@ particle-particle, particle-fluid, and particle-wall interactions.
    :maxdepth: 1
    :caption: Contents:
 
-   ParticleBasics
-   ParticleFluid
-   ParticleWalls
-   ParticlesOnGpus
+   particles/ParticleBasics
+   particles/ParticleFluid
+   particles/ParticleWalls
+   particles/ParticlesOnGpus

docs/source/index.rst

@@ -9,28 +9,40 @@ Welcome to MFiX-EXA's documentation!
 MFiX-Exa is a new multiphase modeling tool for the exascale.  It
 combines kernels from the existing MFiX code with the AMReX framework.
 
-MFiX-Exa is under active development as part of the MFiX-Exa 
-application project in DOE's Exascale Computing Project. 
+MFiX-Exa is under active development as part of the MFiX-Exa
+application project in DOE's Exascale Computing Project.
 
-All of MFiX-Exa's development is done in the NETL gitlab repository, with 
+All of MFiX-Exa's development is done in the NETL gitlab repository, with
 active development in the develop branch. Changes are merged into
 the master branch at the beginning of each month.
 
 .. toctree::
    :maxdepth: 1
-   :caption: Contents:
+   :caption: User guide:
 
    Introduction
-   GettingStarted
+   GettingStarted_Chapter
    Inputs_Chapter
    ManagingGridHierarchy_Chapter
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Reference:
+
    Fluids_Chapter
    Particles_Chapter
-   EB
+   EB_Chapter
+   Debugging
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Tests and Benchmarks:
+
+   RunningTestSuite
+   RegressionTesting
    CITests
    NightlyTests
    qb/index
-   Debugging
 
 Notice
 ------