clean-up and correct lab docs (#580)

* added new he plume; with write_up.

* added new break sim; with write_up.

* added Rec IC for VOF.

* updated all pdfs for write ups.

* updated xml and inpout file for examples.

* modify break write up

Author: spdomin

examples/hula/milestone.xml

@@ -14,7 +14,6 @@
 
   <Parameter        name="aggregation: type"                type="string"   value="uncoupled"/>
   <Parameter        name="aggregation: drop tol"            type="double"   value="0.02"/>
-  <Parameter        name="aggregation: phase2a include root" type="bool"   value="false"/>
   <Parameter        name="repartition: enable"              type="bool"     value="true"/>
   <Parameter        name="repartition: min rows per proc"   type="int"      value="1000"/>
   <Parameter        name="repartition: start level"         type="int"      value="2"/>

examples/shapes/dgSquare_R0.i

@@ -25,7 +25,7 @@ linear_solvers:
 realms:
 
   - name: realm_1
-    mesh: mesh/square_R0.g
+    mesh: square_R0.g
     use_edges: no       
     automatic_decomposition_type: rcb
    

examples/shapes/milestone.xml

@@ -14,7 +14,6 @@
 
   <Parameter        name="aggregation: type"                type="string"   value="uncoupled"/>
   <Parameter        name="aggregation: drop tol"            type="double"   value="0.02"/>
-  <Parameter        name="aggregation: phase2a include root" type="bool"   value="false"/>
   <Parameter        name="repartition: enable"              type="bool"     value="true"/>
   <Parameter        name="repartition: min rows per proc"   type="int"      value="1000"/>
   <Parameter        name="repartition: start level"         type="int"      value="2"/>

examples/street/milestone_aspect_ratio_smooth.xml

@@ -15,7 +15,6 @@
   <Parameter        name="aggregation: type"                type="string"   value="uncoupled"/>
   <Parameter        name="aggregation: drop tol"            type="double"   value="0.01"/>
   <Parameter        name="aggregation: drop scheme"         type="string"   value="distance laplacian"/>
-  <Parameter        name="aggregation: phase2a include root" type="bool"   value="false"/>
 
   <Parameter        name="repartition: enable"              type="bool"     value="true"/>
   <Parameter        name="repartition: min rows per proc"   type="int"      value="1000"/>

include/user_functions/RecMixFracAuxFunction.h

@@ -0,0 +1,40 @@
+/*------------------------------------------------------------------------*/
+/*  Copyright 2014 Sandia Corporation.                                    */
+/*  This software is released under the license detailed                  */
+/*  in the file, LICENSE, which is located in the top-level Nalu          */
+/*  directory structure                                                   */
+/*------------------------------------------------------------------------*/
+
+#ifndef RecMixFracAuxFunction_h
+#define RecMixFracAuxFunction_h
+
+#include <AuxFunction.h>
+
+#include <vector>
+
+namespace sierra{
+namespace nalu{
+
+class RecMixFracAuxFunction : public AuxFunction
+{
+public:
+
+  RecMixFracAuxFunction();
+
+  virtual ~RecMixFracAuxFunction() {}
+  
+  virtual void do_evaluate(
+    const double * coords,
+    const double time,
+    const unsigned spatialDimension,
+    const unsigned numPoints,
+    double * fieldPtr,
+    const unsigned fieldSize,
+    const unsigned beginPos,
+    const unsigned endPos) const;  
+};
+
+} // namespace nalu
+} // namespace Sierra
+
+#endif

reg_tests/CTestList.cmake

@@ -182,4 +182,6 @@ if(ENABLE_LABORATORY_TESTS)
   add_test_l(2d_quad9_couette 4)
   add_test_l(3d_hex8_open_jet 8)
   add_test_l(3d_tet4_pipe 8)
+  add_test_l(3d_hex8_dam_break 8)
+  add_test_l(2d_quad9_helium 8)
 endif(ENABLE_LABORATORY_TESTS)

reg_tests/test_files/laboratory/2d_quad4_channel/write_up/2d_quad4_channel_laboratory.pdf

@@ -17,7 +17,7 @@ \section{Introduction}
 This case provides a description for two-dimensional channel flow
 with constant properties, and a constant pressure gradient.
 
-\section{Theory}
+\section{Domain}
 The two-dimensional geometry for this tutorial is captured in 
 Figure~\ref{fig:geom} where the rectangular domain is defined by the 
 height, $H$, and length, $L$. The streamwise and vertical velocity are 
@@ -39,6 +39,7 @@ \section{Theory}
   \label{fig:geom}
 \end{figure}
 
+\section{Theory}
 The variable-density low-Mach equation set is defined by the continuity and momentum equation,
 
 \begin{align}
@@ -154,7 +155,7 @@ \section{Discussion Points}
 	\item Ensure that derivation of Equation~\ref{eq:uMax} is clear.
 	\item Ensure that derivation of Equation~\ref{eq:balance} and the expression
            $\frac{dP}{dx} = 2\tau_w$ is clear.
-	\item Explore the mesh and input file associated with this case.
+	\item Explore the mesh and input file specifications associated with this case.
 	\item In Figure~\ref{fig:results}, it is noted that the difference between
           the analytical and simulation result is zero. When you run the two mesh resolutions provided, 
           does this finding hold? Why is this?

reg_tests/test_files/laboratory/2d_quad4_channel/write_up/2d_quad4_channel_laboratory.tex

@@ -17,7 +17,7 @@ \section{Introduction}
 This case provides a description for two-dimensional Couette flow
 with constant properties, and a zero pressure gradient.
 
-\section{Theory}
+\section{Domain}
 The two-dimensional geometry for this tutorial is captured in 
 Figure~\ref{fig:geom} where the rectangular domain is defined by the 
 height, $H$, and length, $L$. The streamwise and vertical velocity are 
@@ -39,6 +39,7 @@ \section{Theory}
   \label{fig:geom}
 \end{figure}
 
+\section{Theory}
 The variable-density low-Mach equation set is defined by the continuity and momentum equation,
 
 \begin{align}
@@ -113,13 +114,13 @@ \subsection{Simulation Specification and Results}
 provided above.
 
 \begin{figure}[!htbp]
-  \subfloat[]
   \centering
+  \subfloat[]
   {
    \includegraphics[height=1.2in]{images/2d_quad9_couette_results_early.png}
   }
-  \subfloat[]
   \centering
+  \subfloat[]
   {
    \includegraphics[height=1.2in]{images/2d_quad9_couette_results_late.png}
   }
@@ -134,7 +135,7 @@ \section{Discussion Points}
 
 \begin{itemize}
 	\item Ensure that derivation of Equation~\ref{eq:simpleEqWithoutK} is clear.
-	\item Explore the mesh and input file associated with this case.
+	\item Explore the mesh and input file specifications associated with this case.
 	\item In Figure~\ref{fig:results}, the flow results demonstrate a linear profile, as 
           expected. Based on past experience with a linear basis, comment on the usage of a quadratic
           basis.