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python-hydro · Sep 15, 2024 · 781f71f · 781f71f
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diff --git a/docs/source/advection_basics.rst b/docs/source/advection_basics.rst
@@ -1,6 +1,6 @@
-*****************
-Advection solvers
-*****************
+*********
+Advection
+*********
 
 The linear advection equation:
 

diff --git a/docs/source/compressible_basics.rst b/docs/source/compressible_basics.rst
@@ -1,6 +1,6 @@
-**********************************
-Compressible hydrodynamics solvers
-**********************************
+**************************
+Compressible hydrodynamics
+**************************
 
 The Euler equations of compressible hydrodynamics take the form:
 

diff --git a/docs/source/lowmach_basics.rst b/docs/source/lowmach_basics.rst
@@ -1,5 +1,6 @@
-Low Mach number hydrodynamics solver
-====================================
+*****************************
+Low Mach number hydrodynamics
+*****************************
 
 pyro's low Mach hydrodynamics solver is designed for atmospheric
 flows. It captures the effects of stratification on a fluid element by
@@ -14,24 +15,13 @@ governing equations are:
 
 with :math:`\nabla p_0 = \rho_0 g` and :math:`\beta_0 = p_0^{1/\gamma}`.
 
+``lm_atm`` solver
+=================
 
 As with the incompressible solver, we implement a cell-centered approximate projection method.
 
 The main parameters that affect this solver are:
 
 .. include:: lm_atm_defaults.inc
 
-Examples
---------
-
-bubble
-^^^^^^
-
-The bubble problem places a buoyant bubble in a stratified atmosphere
-and watches the development of the roll-up due to shear as it
-rises. This is run as:
-
-.. prompt:: bash
-
-   pyro_sim.py lm_atm bubble inputs.bubble
-
+.. include:: lm_atm_problems.inc
diff --git a/docs/source/swe_basics.rst b/docs/source/swe_basics.rst
@@ -1,5 +1,6 @@
-Shallow water solver
-====================
+***************************
+Shallow water hydrodynamics
+***************************
 
 The (augmented) shallow water equations take the form:
 
@@ -13,26 +14,32 @@ with :math:`h` is the fluid height, :math:`U` the fluid velocity, :math:`g` the
 gravitational acceleration and :math:`\psi = \psi(x, t)` represents some
 passive scalar.
 
+``swe`` solver
+==============
 
-The implementation here has flattening at shocks and a choice of Riemann solvers.
+The pyro ``swe`` implementation has flattening at shocks and a choice of Riemann solvers.
 
 The main parameters that affect this solver are:
 
 .. include:: swe_defaults.inc
 
-Example problems
-----------------
+.. include:: swe_problems.inc
 
-dam
-^^^
+Examples
+========
 
-The dam break problem is a standard hydrodynamics problem, analogous to the Sod
-shock tube problem in compressible hydrodynamics. It considers a one-multidimensional
-problem of two regions of fluid at different heights, initially separated by a dam.
-The problem then models the evolution of the system when this dam is removed.
-As for the Sod problem, there exists an exact solution for the dam break problem,
-so we can check our solution against the exact solutions. See Toro's shallow water
-equations book for details on this problem and the exact Riemann solver.
+dam
+---
+
+The dam break problem is a standard hydrodynamics problem, analogous
+to the Sod shock tube problem in compressible hydrodynamics. It
+considers a one-multidimensional problem of two regions of fluid at
+different heights, initially separated by a dam.  The problem then
+models the evolution of the system when this dam is removed.  As for
+the Sod problem, there exists an exact solution for the dam break
+problem, so we can check our solution against the exact solutions. See
+Toro's shallow water equations book for details on this problem and
+the exact Riemann solver.
 
 Because it is one-dimensional, we run it in narrow domains in the x- or
 y-directions. It can be run as:
@@ -57,40 +64,11 @@ slightly better than the HLLC solver, with less smearing at the shock
 and head/tail of the rarefaction.
 
 
-quad
-^^^^
-
-The quad problem sets up different states in four regions of the
-domain and watches the complex interfaces that develop as shocks
-interact. This problem has appeared in several places (and a `detailed
-investigation
-<http://planets.utsc.utoronto.ca/~pawel/Riemann.hydro.html>`_ is
-online by Pawel Artymowicz). It is run as:
-
-.. prompt:: bash
-
-   pyro_sim.py swe quad inputs.quad
-
-
-kh
-^^
-
-The Kelvin-Helmholtz problem models three layers of fluid: two at the top and
-bottom of the domain travelling in one direction, one in the central part of the
-domain travelling in the opposite direction. At the interface of the layers,
-shearing produces the characteristic Kelvin-Helmholtz instabilities, just as
-is seen in the standard compressible problem. It is run as:
-
-.. prompt:: bash
-
-   pyro_sim.py swe kh inputs.kh
-
-
 Exercises
----------
+=========
 
 Explorations
-^^^^^^^^^^^^
+------------
 
 * There are multiple Riemann solvers in the swe
   algorithm. Run the same problem with the different Riemann solvers
@@ -101,7 +79,7 @@ Explorations
 
 
 Extensions
-^^^^^^^^^^
+----------
 
 * Limit on the characteristic variables instead of the primitive
   variables. What changes do you see? (the notes show how to implement

diff --git a/pyro/mesh/patch.py b/pyro/mesh/patch.py
@@ -943,10 +943,6 @@ def cell_center_data_clone(old):
     old : CellCenterData2d object
         The CellCenterData2d object we wish to copy
 
-    Note
-    ----
-    It may be that this whole thing can be replaced with a copy.deepcopy()
-
     """
 
     if not isinstance(old, CellCenterData2d):