Updated MeshConvert references to NekMesh and also added in an ARCHIVE option...

Updated MeshConvert references to NekMesh and also added in an ARCHIVE option to the cylinder case since this seemed to be missing

flow-stability/bfs/flow-stability-bfs.tex

@@ -76,7 +76,7 @@ elements.
 \item Folder \texttt{base}
 \begin{itemize}
 \item \texttt{bfs-Base.xml} - \nektar session file, generated with the
-\texttt{\$NEK/MeshConvert} utility, for computing the base flow.
+\texttt{\$NEK/NekMesh} utility, for computing the base flow.
 \item \texttt{bfs-Base.fld} - \nektar field file that contains the base flow,
 generated using \\\texttt{bfs-Base.xml}.
 \end{itemize}
@@ -84,7 +84,7 @@ generated using \\\texttt{bfs-Base.xml}.
 \item Folder \texttt{stability}
 \begin{itemize}
 \item \texttt{bfs\_tg.xml} - \nektar session file, generated with
-\texttt{\$NEK/MeshConvert}, for performing the transient growth analysis.
+\texttt{\$NEK/NekMesh}, for performing the transient growth analysis.
 \item \texttt{bfs\_tg.bse} - \nektar field file that contains the base flow. 
 It is the same as the \texttt{.fld} file present in the folder \texttt{Base}.
 \end{itemize}

flow-stability/channel/flow-stability-channel.tex

@@ -131,20 +131,20 @@ and elements.
 \item Folder \texttt{base}
 \begin{itemize}
 \item \texttt{Channel-Base.xml} - \nektar session file, generated 
-with the \texttt{\$NEK/MeshConvert} utility, for computing the base flow.
+with the \texttt{\$NEK/NekMesh} utility, for computing the base flow.
 \end{itemize}
 
 \item Folder \texttt{stability/VCS}
 \begin{itemize}
 \item \texttt{Channel-VCS.xml} - \nektar session file, generated with
-\texttt{\$NEK/MeshConvert}, for performing the stability analysis.
+\texttt{\$NEK/NekMesh}, for performing the stability analysis.
 \item \texttt{Channel-VCS.rst} - \nektar field file that contains a set of initial 
 conditions closer to the solution in order to achieve faster convergence. 
 \end{itemize}
 \item Folder \texttt{stability/Coupled}
 \begin{itemize}
 \item \texttt{Channel-Coupled.xml} - \nektar session file, generated 
-with \texttt{\$NEK/MeshConvert}, for performing the stability analysis.
+with \texttt{\$NEK/NekMesh}, for performing the stability analysis.
 \end{itemize}
 \item Folder \texttt{stability3D}
 \begin{itemize}
@@ -161,9 +161,9 @@ coupled 3D stability analysis at $Re=15000$.
 The first step is to generate a mesh that is readable by \nektar. 
 The files necessary in this section can be found in \texttt{\$NEKTUTORIAL/geometry/}.
 To achieve this task we use \gmsh in conjunction with the \nektar pre-processing utility 
-called \texttt{\$NEK/MeshConvert}. Specifically, we first generate the mesh in figure 
+called \texttt{\$NEK/NekMesh}. Specifically, we first generate the mesh in figure 
 \ref{Channel_mesh} using \gmsh and successively we convert it into a suitable \nektar 
-format using \texttt{\$NEK/MeshConvert}.
+format using \texttt{\$NEK/NekMesh}.
  
 \begin{tutorialtask}
 Convert the $Gmsh$ geometry provided into the XML \nektar format and with two periodic 
@@ -171,12 +171,12 @@ boundaries
 \begin{itemize}
 \item \texttt{Channel.msh} can be generated using $Gmsh$ by running the following command:
 \tutorialcommand{gmsh -2 Channel.geo}
-\item \texttt{Channel.xml} can be generated using the \texttt{\$NEK/MeshConvert} pre-processing 
+\item \texttt{Channel.xml} can be generated using the \texttt{\$NEK/NekMesh} pre-processing 
 tool:
-\tutorialcommand{\$NEK/MeshConvert Channel.msh Channel.xml}
+\tutorialcommand{\$NEK/NekMesh Channel.msh Channel.xml}
 \item \texttt{Channel-al.xml} can be generated using the module 
-\texttt{peralign} available with the pre-processing tool \texttt{\$NEK/MeshConvert}:
-\tutorialcommand{\$NEK/MeshConvert -m peralign:surf1=2:surf2=3:dir=x Channel.xml Channel-al.xml}
+\texttt{peralign} available with the pre-processing tool \texttt{\$NEK/NekMesh}:
+\tutorialcommand{\$NEK/NekMesh -m peralign:surf1=2:surf2=3:dir=x Channel.xml Channel-al.xml}
 where \texttt{surf1} and \texttt{surf2} correspond to the periodic physical surface 
 IDs specified in \textit{Gmsh} (in our case the inflow has a physical ID=2 while the outflow 
 has a physical ID=3) and \texttt{dir} is the periodicity direction (i.e. the direction normal 
@@ -227,7 +227,7 @@ task. The expansion type and order is specified in the \texttt{EXPANSIONS} secti
 An expansion basis is applied to a geometry \textit{composite}, where by 
 \textit{composite} we mean a collection of mesh entities (specifically here, 
 a collection of mesh elements), specified in the \texttt{GEOMETRY} section. 
-A default entry is always included by the \texttt{\$NEK/MeshConvert} utility. In this 
+A default entry is always included by the \texttt{\$NEK/NekMesh} utility. In this 
 case the composite \texttt{C[0]} refers to the set of all elements. The \texttt{FIELDS} 
 attribute specifies the fields for which this expansion should be used. The \texttt{TYPE} 
 attribute specifies the kind of the polynomial basis functions to be used in the expansion. 

flow-stability/cylinder/CMakeLists.txt

 ADD_NEKTAR_TUTORIAL(PDF HTML TARGET flow-stability-cylinder
     HTML_BREAK_LEVEL 2
     BASE flow-stability-cylinder
-    STYLING_FILE styling.cfg)
-
+    STYLING_FILE styling.cfg
+    ARCHIVE flow-stability-cylinder)
+    
 # Add tests only if we are building from within the Nektar++ tree
 IF (DEFINED NEKTAR_BUILD_TESTS)
     ADD_NEKTAR_TUTORIAL_TEST(IncNavierStokesSolver flow-stability-cylinder-base)

flow-stability/cylinder/flow-stability-cylinder.tex

@@ -75,21 +75,21 @@ elements.
 \item Folder \texttt{base}
 \begin{itemize}
 \item \texttt{Cylinder-Base.xml} - \nektar session file, generated with the
-\texttt{\$NEK/MeshConvert} utility, for computing the base flow.
+\texttt{\$NEK/NekMesh} utility, for computing the base flow.
 \item \texttt{Cylinder-Base.fld} - \nektar field file that contains the base flow,
 generated using \\\texttt{Cylinder-Base.xml}.
 \end{itemize}
 
 \item Folder \texttt{stability/Direct}
 \begin{itemize}
-\item \texttt{Cylinder\_Direct.xml} - \nektar session file, generated with \texttt{\$NEK/MeshConvert}.
+\item \texttt{Cylinder\_Direct.xml} - \nektar session file, generated with \texttt{\$NEK/NekMesh}.
 \item \texttt{Cylinder\_Direct.bse} - \nektar field file that contains the base flow. 
 \item \texttt{Cylinder\_Direct.rst} - \nektar field file that contains the initial conditions.
 \end{itemize}
 
 \item Folder \texttt{stability/Adjoint}
 \begin{itemize}
-\item \texttt{Cylinder\_Adjoint.xml} - \nektar session file, generated with \texttt{\$NEK/MeshConvert}.
+\item \texttt{Cylinder\_Adjoint.xml} - \nektar session file, generated with \texttt{\$NEK/NekMesh}.
 \item \texttt{Cylinder\_Adjoint.bse} - \nektar field file that contains the base flow. 
 \item \texttt{Cylinder\_Adjoint.rst} - \nektar field file that contains the initial conditions.
 \end{itemize}
@@ -121,7 +121,7 @@ variations in the size of the elements should be avoided.}
 \chapter{Computation of the base flow} 
 \texttt{Cylinder-Base.xml} can be found inside the \texttt{\$NEKTUTORIAL/base} 
 folder. 
-This is the \nektar file generated using \texttt{\$NEK/MeshConvert} and augmented 
+This is the \nektar file generated using \texttt{\$NEK/NekMesh} and augmented 
 with all the configuration settings that are required. In this case, CFL conditions 
 can be particularly restrictive and the time step must be set around $8 \times 
 10^{-4}$. We will be using Reynolds number $Re=42$ for this study.