Added docs for nonuniform advection problem

Author: harpolea

docs/source/advection_basics.rst

@@ -12,11 +12,16 @@ numerical methods for advection that we implement in pyro.
 
 pyro has several solvers for linear advection:
 
-* :py:mod:`advection` implements the directionally unsplit corner transport upwind algorithm with piecewise linear reconstruction
+* :py:mod:`advection` implements the directionally unsplit corner transport upwind
+  algorithm with piecewise linear reconstruction
 
 * :py:mod:`advection_fv4` uses a fourth-order accurate finite-volume
   method with RK4 time integration
 
+* :py:mod:`advection_nonuniform` models advection with a non-uniform velocity field.
+  This is used to implement
+  `Zalesak (1979) <https://doi.org/10.1016/0021-9991(79)90051-2>`_'s slotted disk problem.
+
 * :py:mod:`advection_rk` uses a method of lines time-integration
   approach with piecewise linear spatial reconstruction for linear
   advection
@@ -146,4 +151,3 @@ Extensions
 
   The neat thing about Burger's equation is that it admits shocks and
   rarefactions, so some very interesting flow problems can be setup.
-

docs/source/advection_nonuniform.problems.rst

@@ -0,0 +1,34 @@
+advection\_nonuniform\.problems package
+=======================================
+
+.. automodule:: advection_nonuniform.problems
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+advection\_nonuniform\.problems\.slotted module
+-----------------------------------------------
+
+.. automodule:: advection_nonuniform.problems.slotted
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+advection\_nonuniform\.problems\.smooth module
+----------------------------------------------
+
+.. automodule:: advection_nonuniform.problems.smooth
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+advection\_nonuniform\.problems\.tophat module
+----------------------------------------------
+
+.. automodule:: advection_nonuniform.problems.tophat
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/advection_nonuniform.rst

@@ -0,0 +1,33 @@
+advection\_nonuniform package
+=============================
+
+.. automodule:: advection_nonuniform
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+    advection_nonuniform.problems
+
+Submodules
+----------
+
+advection\_nonuniform\.advective\_fluxes module
+-----------------------------------------------
+
+.. automodule:: advection_nonuniform.advective_fluxes
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+advection\_nonuniform\.simulation module
+----------------------------------------
+
+.. automodule:: advection_nonuniform.simulation
+    :members:
+    :undoc-members:
+    :show-inheritance:

paper/paper.bib

@@ -16,8 +16,8 @@ @ARTICLE{pyroI
 }
 
 @ARTICLE{castro,
-   author = {{Almgren}, A.~S. and {Beckner}, V.~E. and {Bell}, J.~B. and 
-	{Day}, M.~S. and {Howell}, L.~H. and {Joggerst}, C.~C. and {Lijewski}, M.~J. and 
+   author = {{Almgren}, A.~S. and {Beckner}, V.~E. and {Bell}, J.~B. and
+	{Day}, M.~S. and {Howell}, L.~H. and {Joggerst}, C.~C. and {Lijewski}, M.~J. and
 	{Nonaka}, A. and {Singer}, M. and {Zingale}, M.},
     title = "{CASTRO: A New Compressible Astrophysical Solver. I. Hydrodynamics and Self-gravity}",
   journal = {Astrophysical Journal},
@@ -35,7 +35,7 @@ @ARTICLE{castro
 }
 
 @ARTICLE{maestro,
-   author = {{Nonaka}, A. and {Almgren}, A.~S. and {Bell}, J.~B. and {Lijewski}, M.~J. and 
+   author = {{Nonaka}, A. and {Almgren}, A.~S. and {Bell}, J.~B. and {Lijewski}, M.~J. and
 	{Malone}, C.~M. and {Zingale}, M.},
     title = "{MAESTRO: An Adaptive Low Mach Number Hydrodynamics Algorithm for Stellar Flows}",
   journal = {Astrophysical Journal Supplement},

paper/paper.md

@@ -63,30 +63,29 @@ to science codes.
 
 The current pyro solvers are:
 
-  * linear advection (including a second-order unsplit CTU scheme, a
-    method-of-lines piecewise linear solver$^\star$, a 4th-order
-    finite-volume scheme$^\star$, and a WENO method$^\star$)
+-   linear advection (including a second-order unsplit CTU scheme, a
+    method-of-lines piecewise linear solver$^\\star$, a 4th-order
+    finite-volume scheme$^\\star$, a WENO method$^\\star$, and
+    advection with a non-uniform velocity field$^\\star$)
 
-  * compressible hydrodynamics (including a second-order unsplit CTU
-    scheme, a method-of-lines piecewise linear solver$^\star$, and two
+-   compressible hydrodynamics (including a second-order unsplit CTU
+    scheme, a method-of-lines piecewise linear solver$^\\star$, and two
     4th-order finite-volume schemes, one with Runge-Kutta integration
     and the other using a spectral deferred corrections
-    method$^\star$)
+    method$^\\star$)
 
-  * diffusion using a second-order implicit discretization
+-   diffusion using a second-order implicit discretization
 
-  * incompressible hydrodynamics using a second-order approximate
+-   incompressible hydrodynamics using a second-order approximate
     projection method.
 
-  * low Mach number atmospheric solver$^\star$, using an approximate
+-   low Mach number atmospheric solver$^\\star$, using an approximate
     projection method.
 
-  * shallow water equations solver$^\star$
+-   shallow water equations solver$^\\star$
 
-(solvers since the first pyro paper are marked with a $^\star$).  Also
+(solvers since the first pyro paper are marked with a $^\\star$).  Also
 new is support for Lagrangian tracer particles, which can be added to
 any solver that has a velocity field.
 
-
-
 # References