rename viscous_burgers -> burgers_viscous (#267)

this is consistent with incompressible and also allows it to
appear next to burgers in a listing (alphabetically)

README.md

@@ -138,7 +138,7 @@ pyro provides the following solvers (all in 2-d):
   - `burgers`: a second-order unsplit solver for invsicid Burgers'
     equation.
 
-  - `viscous_burgers`: a second-order unsplit solver for viscous
+  - `burgers_viscous`: a second-order unsplit solver for viscous
     Burgers' equation with constant-coefficient diffusion. It uses
     Crank-Nicolson time-discretized solver for solving diffusion.
 

docs/source/burgers_basics.rst

@@ -45,19 +45,28 @@ A 2D viscous Burgers' Equation has the following form:
    u_t + u u_x + v u_y = \epsilon \left( u_{xx} + u_{yy}\right) \\
    v_t + u v_x + v v_y = \epsilon \left( v_{xx} + v_{yy}\right)
 
-The viscous Burgers' equation has an additional velocity diffusion term on the RHS compared to the inviscid Burgers' equation. Here :math:`\epsilon` represents the constant viscosity.
+The viscous Burgers' equation has an additional velocity diffusion
+term on the RHS compared to the inviscid Burgers' equation. Here
+:math:`\epsilon` represents the constant viscosity.
 
-:py:mod:`pyro.viscous_burgers` is inherited from :py:mod:`pyro.burgers`, where we added an additional diffusion term when constructing the interface states. We then solve for diffusion along with the extra advective source to the Helmholtz equation by using the Crank-Nicolson discretization and multigrid solvers.
+:py:mod:`pyro.burgers_viscous` is inherited from
+:py:mod:`pyro.burgers`, where we added an additional diffusion term
+when constructing the interface states. We then solve for diffusion
+along with the extra advective source to the Helmholtz equation by
+using the Crank-Nicolson discretization and multigrid solvers.
 
 
 The parameters for this solver are:
 
-.. include:: viscous_burgers_defaults.inc
+.. include:: burgers_viscous_defaults.inc
 
 
 .. image:: viscous_burgers.png
    :align: center
 
-The figure above is generated using ``viscous_burgers/problems/test.py``, which has the identical setup as in ``burgers/problems/test.py``. With diffusion added to the system, we see the shock (discontinuity) is smeared out as system evolves.
+The figure above is generated using
+``burgers_viscous/problems/test.py``, which has the identical setup as
+in ``burgers/problems/test.py``. With diffusion added to the system,
+we see the shock (discontinuity) is smeared out as system evolves.
 
 

docs/source/pyro.advection.rst

@@ -25,6 +25,14 @@ pyro.advection.advective\_fluxes module
    :undoc-members:
    :show-inheritance:
 
+pyro.advection.interface module
+-------------------------------
+
+.. automodule:: pyro.advection.interface
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pyro.advection.simulation module
 --------------------------------
 

docs/source/pyro.advection_fv4.problems.rst

@@ -16,3 +16,19 @@ pyro.advection\_fv4.problems.smooth module
    :members:
    :undoc-members:
    :show-inheritance:
+
+pyro.advection\_fv4.problems.test module
+----------------------------------------
+
+.. automodule:: pyro.advection_fv4.problems.test
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.advection\_fv4.problems.tophat module
+------------------------------------------
+
+.. automodule:: pyro.advection_fv4.problems.tophat
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pyro.burgers.problems.rst

@@ -1,5 +1,5 @@
 pyro.burgers.problems package
-===============================
+=============================
 
 .. automodule:: pyro.burgers.problems
    :members:
@@ -9,27 +9,34 @@ pyro.burgers.problems package
 Submodules
 ----------
 
-pyro.burgers.problems.test module
+pyro.burgers.problems.converge module
 -------------------------------------
 
-.. automodule:: pyro.burgers.problems.test
+.. automodule:: pyro.burgers.problems.converge
    :members:
    :undoc-members:
    :show-inheritance:
 
+pyro.burgers.problems.test module
+---------------------------------
 
-pyro.burgers.problems.converge module
--------------------------------------
-
-.. automodule:: pyro.burgers.problems.converge
+.. automodule:: pyro.burgers.problems.test
    :members:
    :undoc-members:
    :show-inheritance:
 
 pyro.burgers.problems.tophat module
--------------------------------------
+-----------------------------------
 
 .. automodule:: pyro.burgers.problems.tophat
    :members:
    :undoc-members:
    :show-inheritance:
+
+pyro.burgers.problems.verify module
+-----------------------------------
+
+.. automodule:: pyro.burgers.problems.verify
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pyro.burgers.rst

@@ -1,5 +1,5 @@
 pyro.burgers package
-======================
+====================
 
 .. automodule:: pyro.burgers
    :members:
@@ -18,15 +18,15 @@ Submodules
 ----------
 
 pyro.burgers.burgers\_interface module
----------------------------------------
+--------------------------------------
 
 .. automodule:: pyro.burgers.burgers_interface
    :members:
    :undoc-members:
    :show-inheritance:
 
 pyro.burgers.simulation module
---------------------------------
+------------------------------
 
 .. automodule:: pyro.burgers.simulation
    :members:

docs/source/pyro.burgers_viscous.problems.rst

@@ -0,0 +1,34 @@
+pyro.burgers\_viscous.problems package
+======================================
+
+.. automodule:: pyro.burgers_viscous.problems
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+pyro.burgers\_viscous.problems.converge module
+----------------------------------------------
+
+.. automodule:: pyro.burgers_viscous.problems.converge
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.burgers\_viscous.problems.test module
+------------------------------------------
+
+.. automodule:: pyro.burgers_viscous.problems.test
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.burgers\_viscous.problems.tophat module
+--------------------------------------------
+
+.. automodule:: pyro.burgers_viscous.problems.tophat
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pyro.burgers_viscous.rst

@@ -0,0 +1,34 @@
+pyro.burgers\_viscous package
+=============================
+
+.. automodule:: pyro.burgers_viscous
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pyro.burgers_viscous.problems
+
+Submodules
+----------
+
+pyro.burgers\_viscous.interface module
+--------------------------------------
+
+.. automodule:: pyro.burgers_viscous.interface
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.burgers\_viscous.simulation module
+---------------------------------------
+
+.. automodule:: pyro.burgers_viscous.simulation
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pyro.compressible.rst

@@ -49,6 +49,14 @@ pyro.compressible.interface module
    :undoc-members:
    :show-inheritance:
 
+pyro.compressible.riemann module
+--------------------------------
+
+.. automodule:: pyro.compressible.riemann
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pyro.compressible.simulation module
 -----------------------------------
 

docs/source/pyro.multigrid.examples.rst

@@ -0,0 +1,106 @@
+pyro.multigrid.examples package
+===============================
+
+.. automodule:: pyro.multigrid.examples
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+pyro.multigrid.examples.mg\_test\_general\_alphabeta\_only module
+-----------------------------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.mg_test_general_alphabeta_only
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.mg\_test\_general\_beta\_only module
+------------------------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.mg_test_general_beta_only
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.mg\_test\_general\_constant module
+----------------------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.mg_test_general_constant
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.mg\_test\_general\_dirichlet module
+-----------------------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.mg_test_general_dirichlet
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.mg\_test\_general\_inhomogeneous module
+---------------------------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.mg_test_general_inhomogeneous
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.mg\_test\_simple module
+-----------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.mg_test_simple
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.mg\_test\_vc\_constant module
+-----------------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.mg_test_vc_constant
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.mg\_test\_vc\_dirichlet module
+------------------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.mg_test_vc_dirichlet
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.mg\_test\_vc\_periodic module
+-----------------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.mg_test_vc_periodic
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.mg\_vis module
+--------------------------------------
+
+.. automodule:: pyro.multigrid.examples.mg_vis
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.project\_periodic module
+------------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.project_periodic
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyro.multigrid.examples.prolong\_restrict\_demo module
+------------------------------------------------------
+
+.. automodule:: pyro.multigrid.examples.prolong_restrict_demo
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pyro.multigrid.rst

@@ -6,6 +6,14 @@ pyro.multigrid package
    :undoc-members:
    :show-inheritance:
 
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pyro.multigrid.examples
+
 Submodules
 ----------