Commit 807bbd38 authored by Spencer Sherwin's avatar Spencer Sherwin

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
parent 11ca4edd
......@@ -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}
......
......@@ -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
......
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