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add references
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‎docs/source/conf.py‎

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'sphinx.ext.mathjax',
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'sphinx.ext.ifconfig',
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'sphinx.ext.viewcode',
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'sphinxcontrib.bibtex',
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'sphinx.ext.autosummary',
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'nbsphinx',
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'numpydoc',

‎docs/source/diffusion_basics.rst‎

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implicit discretization forms a Helmholtz equation solved by the pyro
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multigrid class. The main parameters that affect this solver are:
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+---------------------------------------------------------------------------+
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| ``[driver]`` |
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+===================+=======================================================+
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|``cfl`` | the "CFL" number for the diffusion equation. Since we |
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| | are doing an implicit discretization, this is the |
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| | multiple of the explicit timestep to take. |
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+-------------------+-------------------------------------------------------+
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+---------------------------------------------------------------------------+
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| ``[diffusion]`` |
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+===================+=======================================================+
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|``k`` | the conductivity (constant) |
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+-------------------+-------------------------------------------------------+
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.. include:: diffusion_defaults.inc
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Examples
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--------

‎docs/source/incompressible_basics.rst‎

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solving the incompressible equations. At the moment, only periodic BCs
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are supported.
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The main parameters that affect this solver are:
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.. include:: incompressible_defaults.inc
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Examples
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--------
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‎docs/source/index.rst‎

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diffusion_basics
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incompressible_basics
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lowmach_basics
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particles_basics
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swe_basics
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particles_basics
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.. toctree::
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:maxdepth: 1
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.. toctree::
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:maxdepth: 1
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:caption: Reference
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:caption: Software Reference
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API <modules>
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.. toctree::
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:caption: Bibliography
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references
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Indices and tables
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==================

‎docs/source/lowmach_basics.rst‎

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As with the incompressible solver, we implement a cell-centered approximate projection method.
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The main parameters that affect this solver are:
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.. include:: lm_atm_defaults.inc
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Examples
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--------
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‎docs/source/references.rst‎

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**********
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References
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**********
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.. bibliography:: refs.bib
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‎docs/source/refs.bib‎

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@ARTICLE{colella:1990,
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author = {{Colella}, P.},
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title = "{Multidimensional upwind methods for hyperbolic conservation laws}",
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journal = {Journal of Computational Physics},
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keywords = {ADVECTION, BOUNDARY VALUE PROBLEMS, COMPUTATIONAL GRIDS, CONSERVATION LAWS, FINITE DIFFERENCE THEORY, HYPERBOLIC FUNCTIONS, ALGORITHMS, CAUCHY PROBLEM, PREDICTOR-CORRECTOR METHODS},
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year = 1990,
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month = mar,
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volume = 87,
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pages = {171-200},
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doi = {10.1016/0021-9991(90)90233-Q},
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adsurl = {http://adsabs.harvard.edu/abs/1990JCoPh..87..171C},
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adsnote = {Provided by the SAO/NASA Astrophysics Data System}
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}
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@ARTICLE{mccorquodalecolella,
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author = {{McCorquodale}, P. and {Colella}, P.},
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title = "{A high-order finite-volume method for conservation laws on
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locally refined grids}",
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journal = {Communication in Applied Mathematics and Computational Science},
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year = {2011},
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volume = {6},
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number = {1},
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pages = {1--25}
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}
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@article{ZALESAK1979335,
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title = "Fully multidimensional flux-corrected transport algorithms for fluids",
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journal = "Journal of Computational Physics",
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volume = "31",
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number = "3",
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pages = "335 - 362",
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year = "1979",
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issn = "0021-9991",
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doi = "https://doi.org/10.1016/0021-9991(79)90051-2",
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url = "http://www.sciencedirect.com/science/article/pii/0021999179900512",
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author = "Steven T Zalesak",
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abstract = "The theory of flux-corrected transport (FCT) developed by Boris and Book [J. Comput. Phys. 11 (1973) 38; 18 (1975) 248; 20 (1976) 397] is placed in a simple, generalized format, and a new algorithm for implementing the critical flux limiting stage' in multidimensions without resort to time splitting is presented. The new flux limiting algorithm allows the use of FCT techniques in multidimensional fluid problems for which time splitting would produce unacceptable numerical results, such as those involving incompressible or nearly incompressible flow fields. The “clipping” problem associated with the original one dimensional flux limiter is also eliminated or alleviated. Test results and applications to a two dimensional fluid plasma problem are presented."
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}

‎docs/source/swe_basics.rst‎

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The main parameters that affect this solver are:
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+-----------------------------------------------------------------------------+
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|``[driver]`` |
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+==================+==========================================================+
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|``cfl`` | the advective CFL number (what fraction of a zone can |
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| | we cross in a single timestep) |
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+------------------+----------------------------------------------------------+
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+-------------------------------------------------------------------------------+
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|``[swe]`` |
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+====================+==========================================================+
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|``use_flattening`` | do we flatten the profiles at shocks? (0=no, 1=yes) |
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+--------------------+----------------------------------------------------------+
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|``z0`` | |
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+--------------------+ |
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|``z1`` | the parameters that affect the flattening algorithm |
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+--------------------+ |
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| ``delta`` | |
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+--------------------+----------------------------------------------------------+
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|``limiter`` | what type of limiting to use in reconstructing the |
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| | slopes. 0 means use an unlimited second-order centered |
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| | difference. 1 is the MC limiter, and 2 is the 4th-order |
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| | MC limiter |
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+--------------------+----------------------------------------------------------+
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|``riemann`` | which Riemann solver do we use? "HLLC" for the HLLC |
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| | solver, or "Roe" for the Roe fix |
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| | solver |
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+--------------------+----------------------------------------------------------+
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|``grav`` | the gravitational acceleration (must be > 0) |
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+--------------------+----------------------------------------------------------+
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.. include:: swe_defaults.inc
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Example problems
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----------------

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