Added documentation for precompilation using NEKTAR_USE_CCM option and the...

Added documentation for precompilation using NEKTAR_USE_CCM option and the options to directly read ccm files from Star. There is also an additional option in ProcessJac called removecurveifsingular

docs/user-guide/installation/source.tex

@@ -517,10 +517,22 @@ Components of the \nekpp package can be selected using the following options:
     Enabled compilation of the 'X' solver.
 \end{itemize}
 
-A number of ThirdParty libraries are required by \nekpp. There are also
-optional libraries which provide additional functionality. These can be selected
-using the following options:
+A number of ThirdParty libraries are required by \nekpp. There are
+also optional libraries which provide additional functionality. These
+can be selected using the following options:
 \begin{itemize}
+    \item \inlsh{NEKTAR\_USE\_ACCELERATE\_FRAMEWORK}
+      
+    Use the Mac Osx accelerate framework for BLAS and LAPACK
+    methods. This option should only be required under in a Mac OSX
+    environment.
+
+    \item \inlsh{NEKTAR\_USE\_ARPACK}
+    
+    Build \nekpp with support for ARPACK. This provides routines used for
+    linear stability analyses. Alternative Arnoldi algorithms are also
+    implemented directly in \nekpp.
+    
     \item \inlsh{NEKTAR\_USE\_BLAS\_LAPACK} (Required)
     
     Enables the use of Basic Linear Algebra Subroutines libraries for linear
@@ -532,34 +544,37 @@ using the following options:
     This may not be the implementation offering the highest performance for your
     architecture, but it is the most likely to work without problem.
     
-    \item \inlsh{NEKTAR\_USE\_OPENBLAS}
+    \item \inlsh{NEKTAR\_USE\_CCM}
     
-    Use OpenBLAS for the BLAS library. OpenBLAS is based on the Goto BLAS
-    implementation and generally offers better performance than a non-optimised
-    system BLAS. However, the library must be installed on the system.
+    Use the ccmio library provided with the Star-CCM package for
+    reading ccm files. This option is required as part of MeshConvert
+    if you wish to convert a Star-CCM mesh into the Nektar format. It
+    is possible to read a Tecplot plt file from Star-CCM but this
+    output currently needs to be converted to ascii format using the
+    Tecplot package.
+
+    \item \inlsh{NEKTAR\_USE\_FFTW}
     
+    Build \nekpp with support for FFTW for performing Fast Fourier Transforms
+    (FFTs). This is used only when using domains with homogeneous coordinate
+    directions.
+        
     \item \inlsh{NEKTAR\_USE\_MKL}
     
     Use the Intel MKL library. This is typically available on cluster
     environments and should offer performance tuned for the specific cluster
     environment.
-    
+
     \item \inlsh{NEKTAR\_USE\_MPI} (Recommended)
     
     Build Nektar++ with MPI parallelisation. This allows solvers to be run in
     serial or parallel.
     
-    \item \inlsh{NEKTAR\_USE\_FFTW}
-    
-    Build \nekpp with support for FFTW for performing Fast Fourier Transforms
-    (FFTs). This is used only when using domains with homogeneous coordinate
-    directions.
-    
-    \item \inlsh{NEKTAR\_USE\_ARPACK}
+    \item \inlsh{NEKTAR\_USE\_OPENBLAS}
     
-    Build \nekpp with support for ARPACK. This provides routines used for
-    linear stability analyses. Alternative Arnoldi algorithms are also
-    implemented directly in \nekpp.
+    Use OpenBLAS for the BLAS library. OpenBLAS is based on the Goto BLAS
+    implementation and generally offers better performance than a non-optimised
+    system BLAS. However, the library must be installed on the system.
     
     \item \inlsh{NEKTAR\_USE\_VTK}
     

docs/user-guide/utilities/meshconvert.tex

@@ -213,7 +213,8 @@ where it exists. The table below indicates support currently implemented.
     Nektar++ & \texttt{xml} & \cmark & Fully supported. \\
     PLY & \texttt{ply} & \xmark & Reads only the ASCII format.. \\
     Semtex & \texttt{sem} & \cmark & Reads elements and boundary conditions. In order to read high-order information, run \inltt{meshpr session.sem > session.msh} and place in the same directory as the session file.\\
-    Star-CCM+ & \texttt{dat} & \xmark & Reads mesh only, only support for quads and triangles (2D) and hexes, prisms, tetrahedra (3D).\\
+    Star-CCM+ & \texttt{dat} & \xmark & Star outputs plt file which currently needs to be coverted to ascii using Tecplot. Reads mesh only, only support for quads and triangles (2D) and hexes, prisms, tetrahedra (3D).\\
+    Star-CCM+ & \texttt{ccm} & \xmark & Reads start ccm format. Reads mesh only, only support for quads and triangles (2D) and hexes, prisms, tetrahedra (3D). Requires NEKTAR\_USE\_CCM option to be activated in cmake and then requires ccmio library to be compiled by user.  \\
     VTK & \texttt{vtk} & \xmark & Experimental support. Only ASCII triangular data is supported. \\
     \bottomrule
   \end{tabularx}
@@ -291,6 +292,15 @@ use the \inltt{extract} boolean parameter:
 MeshConvert -m jac:extract Mesh.xml MeshWithNegativeElements.xml
 \end{lstlisting}
 
+To turn off curvature associated with negative jacobians one can try to use the \inltt{removecurveifsingular} boolean parameter: 
+\begin{lstlisting}[style=BashInputStyle]
+MeshConvert -m jac:removecurveifsingular  Mesh.xml output.xml
+\end{lstlisting}
+This option will remove the high order curvature on prismatic faces
+with singular jacobians. This does not guarantee a non-singular mesh
+since it is possible for neighbouring element then to have singular
+jacobians. Multiple calls to the module might help with this scenario.
+
 \subsubsection{Spherigon patches}
 
 Where high-order information is not available (e.g. when using meshes from