Commit 39e2b3e2 authored by Chris Cantwell's avatar Chris Cantwell
Browse files

Removed references to FldToVtk and FldToTecplot

Restructured FieldConvert and MeshConvert chapters.
parent fb35d080
\chapter{ADRSolver}
\chapter{Advection-Diffusion-Reaction Solver}
%3.4/UserGuide/Tutorial/ADRSolver
%3.4/UserGuide/Examples/ADRSolver/1DAdvection
......@@ -242,8 +242,8 @@ ADRSolver Advection1D.xml
To visualise the output, we can convert it into either TecPlot or VTK formats
\begin{lstlisting}[style=BashInputStyle]
FldToTecplot Advection1D.xml Advection1D.fld
FldToVtk Advection1D.xml Advection1D.fld
FieldConvert Advection1D.xml Advection1D.fld Advection1D.dat
FieldConvert Advection1D.xml Advection1D.fld Advection1D.vtu
\end{lstlisting}
......
......@@ -156,10 +156,11 @@ of the \inltt{ShallowWaterSolver} the code can be executed by:
\subsubsection{Post-proceesing}
After the final time step the solver will write an output file
\inltt{RossbyModon\_Nonlinear\_DG.fld}. We can convert it to tecplot
format by using the \inltt{FldToTecplot} utility. Thus we execute the
format by using the \inltt{FieldConvert} utility. Thus we execute the
following command:
\begin{lstlisting}[style=BashInputStyle]
FldToTecplot RossbyModon_Nonlinear_DG.xml RossbyModon_Nonlinear_DG.fld
FieldConvert RossbyModon_Nonlinear_DG.xml RossbyModon_Nonlinear_DG.fld \
RossbyModon_Nonlinear_DG.dat
\end{lstlisting}
This will generate a file called \inltt{RossbyModon\_Nonlinear\_DG.dat} that
can be loaded directly into tecplot:
......
\section{FieldConvert}
\chapter{FieldConvert}
\label{s:utilities:fieldconvert}
FieldConvert is a utility embedded in \nekpp with the primary
aim of allowing the user to convert the \nekpp output binary files
......@@ -15,11 +15,11 @@ files will be performed.
Almost all of the FieldConvert functionalities can be run in parallel if \nekpp
is compiled using MPI (see the installation documentation for additional
info on how to implement \nekpp using MPI). \footnote{the modules which
does not have parallel support will be specified the related subsection}
does not have parallel support will be specified the related section}
%
%
%
\subsection{Convert .fld / .chk files into Paraview or Tecplot format}
\section{Convert .fld / .chk files into Paraview or Tecplot format}
\label{s:utilities:fieldconvert:sub:convert}
To convert the \nekpp output binary files (.chk and .fld) into a format
which can be read by two common visualisation softwares: Paraview
......@@ -53,7 +53,7 @@ in its compressed format \inltt{test.xml.gz}.
%
%
%
\subsection{Range option \textit{-r}}
\section{Range option \textit{-r}}
The Fieldconvert range option \inltt{-r} allows the user to specify
a sub-range of the mesh (computational domain) by using an
additional flag, \inltt{-r} (which stands for \inltt{r}ange and either
......@@ -86,7 +86,7 @@ to define the $z$ range.
%
%
%
\subsection{FieldConvert modules \textit{-m}}
\section{FieldConvert modules \textit{-m}}
FieldConvert allows the user to manipulate the \nekpp output
binary files (.chk and .fld) by using the flag \inltt{-m} (which
stands for \inltt{m}odule)..
......@@ -122,7 +122,7 @@ In the following we will detail the usage of each module.
%
%
\subsubsection{Smooth the data: \textit{C0Projection} module}
\subsection{Smooth the data: \textit{C0Projection} module}
To smooth the data of a given .fld file one can
use the \inltt{C0Projection} module of FieldConvert
%
......@@ -134,7 +134,7 @@ where the file \inltt{test-C0Proj.fld} can be processed in a similar
way as described in section \ref{s:utilities:fieldconvert:sub:convert}
to visualise either in Tecplot or in Paraview the result.
\subsubsection{Calculate Q-Criterion: \textit{QCriterion} module}
\subsection{Calculate Q-Criterion: \textit{QCriterion} module}
To perform the Q-criterion calculation and obtain an output
data containing the Q-criterion solution, the user can run
%
......@@ -149,7 +149,7 @@ to visualise either in Tecplot or in Paraview the result.
%
%
\subsubsection{Sum two .fld files: \textit{addFld} module}
\subsection{Sum two .fld files: \textit{addFld} module}
To sum two .fld files one can use the \inltt{addFld} module of FieldConvert
%
\begin{lstlisting}[style=BashInputStyle]
......@@ -168,7 +168,7 @@ it either in Tecplot or in Paraview the result.
%
%
%
\subsubsection{Concatenate two files: \textit{concatenate} module}
\subsection{Concatenate two files: \textit{concatenate} module}
To concatenate \inltt{file1.fld} and \inltt{file2.fld} into \inltt{file-conc.fld}
one can run the following command
%
......@@ -182,7 +182,7 @@ to visualise either in Tecplot or in Paraview the result.
%
%
%
\subsubsection{Equi-spaced output of data: \textit{equispacedoutput} module}
\subsection{Equi-spaced output of data: \textit{equispacedoutput} module}
This module interpolates the output data to an truly equispaced set of
points (not equispaced along the collapsed coordinate
system). Therefore a tetrahedron is represented by a tetrahedral
......@@ -200,7 +200,7 @@ tetrahedrons and prisms. It also only is currently used in tecplot
output.
\end{notebox}
\subsubsection{Extract a boundary region: \textit{extract} module}
\subsection{Extract a boundary region: \textit{extract} module}
The boundary region of a domain can be extracted from the output
data using the following command line
%
......@@ -239,7 +239,7 @@ a Paraview output.
%
%
%
\subsubsection{Compute the gradient of a field: \textit{gradient} module}
\subsection{Compute the gradient of a field: \textit{gradient} module}
To compute the spatial gradients of all fields one can run the following command
%
\begin{lstlisting}[style=BashInputStyle]
......@@ -253,7 +253,7 @@ to visualise either in Tecplot or in Paraview the result.
%
%
%
\subsubsection{Interpolate one field to another: \textit{interpfield} module}
\subsection{Interpolate one field to another: \textit{interpfield} module}
To interpolate one field to another, one can use the following command:
%
\begin{lstlisting}[style=BashInputStyle]
......@@ -278,7 +278,7 @@ faster.
%
%
%
\subsubsection{Interpolate scattered point data to a field: \textit{interppointdatatofld} module}
\subsection{Interpolate scattered point data to a field: \textit{interppointdatatofld} module}
\label{s:utilities:fieldconvert:sub:interppointdatatofld}
To interpolate discrete point data to a field, use the interppointdatatofld module:
%
......@@ -329,7 +329,7 @@ The Inverse Distance implementation has no such requirement.
%
%
%
\subsubsection{Interpolate a field to a series of points: \textit{interppoints} module}
\subsection{Interpolate a field to a series of points: \textit{interppoints} module}
You can interpolate one field to a series of given points using the following command:
\begin{lstlisting}[style=BashInputStyle]
FieldConvert -m interppoints:fromxml=file1.xml:fromfld=file1.fld \
......@@ -381,7 +381,7 @@ This module does not run in parallel.
%
%
%
\subsubsection{Isoncontour extraction: \textit{iscontour} module}
\subsection{Isoncontour extraction: \textit{iscontour} module}
Extract an isocontour from a field file. This option automatically
take the field to an equispaced distribution of points connected by
......@@ -426,7 +426,7 @@ Currently this option is only set up for triangles, quadrilaterals,
%
%
\subsubsection{Show high frequency energy of the Jacobian: \textit{jacobianenergy} module}
\subsection{Show high frequency energy of the Jacobian: \textit{jacobianenergy} module}
\begin{lstlisting}[style=BashInputStyle]
FieldConvert -m jacobianenergy file.xml file.fld jacenergy.fld
......@@ -443,7 +443,7 @@ to visualise it either in Tecplot or in Paraview the result.
%
%
\subsubsection{Print L2 and LInf norms: \textit{printfldnorms} module}
\subsection{Print L2 and LInf norms: \textit{printfldnorms} module}
\begin{lstlisting}[style=BashInputStyle]
FieldConvert -m printfldnorms test.xml test.fld
......@@ -455,7 +455,7 @@ This module does not create an output file. The L2 and LInf norms for each field
%
%
\subsubsection{Computes the scalar gradient: \textit{scalargrad} module}
\subsection{Computes the scalar gradient: \textit{scalargrad} module}
The scalar gradient of a field is computed by running:
\begin{lstlisting}[style=BashInputStyle]
FieldConvert -m scalargrad:bnd=0 test.xml test.fld test-scalgrad.fld
......@@ -466,7 +466,7 @@ The option \inltt{bnd} specifies which boundary region to extract. Note this is
%
%
\subsubsection{Scale a given .fld: \textit{scaleinputfld} module}
\subsection{Scale a given .fld: \textit{scaleinputfld} module}
To scale a .fld file by a given scalar quantity, the user can run:
\begin{lstlisting}[style=BashInputStyle]
FieldConvert -m scaleinputfld:scale=value test.xml test.fld test-scal.fld
......@@ -480,7 +480,7 @@ to visualise it either in Tecplot or in Paraview the result.
%
%
%
\subsubsection{Time-averaged shear stress metrics: \textit{shear} module}
\subsection{Time-averaged shear stress metrics: \textit{shear} module}
Time-dependent wall shear stress derived metrics relevant to cardiovascular fluid dynamics research can be computed using this module. They are
\begin{itemize}
......@@ -503,7 +503,7 @@ The input \inltt{.fld} files are the outputs of the \textit{wss} module. If they
%
%
%
\subsubsection{Calculate vorticity: \textit{vorticity} module}
\subsection{Calculate vorticity: \textit{vorticity} module}
To perform the vorticity calculation and obtain an output
data containing the vorticity solution, the user can run
\begin{lstlisting}[style=BashInputStyle]
......@@ -515,7 +515,7 @@ way as described in section \ref{s:utilities:fieldconvert:sub:convert}.
%
%
\subsubsection{Computing the wall shear stress: \textit{wss} module}
\subsection{Computing the wall shear stress: \textit{wss} module}
To obtain the wall shear stres vector and magnitude, the user can run:
\begin{lstlisting}[style=BashInputStyle]
FieldConvert -m wss:bnd=0:addnormals=1 test.xml test.fld test-wss.fld
......@@ -525,7 +525,7 @@ The option \inltt{bnd} specifies which boundary region to extract. Note this is
%
%
\subsubsection{Manipulating meshes with FieldConvert}
\subsection{Manipulating meshes with FieldConvert}
FieldConvert has support for two modules that can be used in conjunction with
the linear elastic solver, as shown in chapter~\ref{s:elasticity}. To do this,
FieldConvert has an XML output module, in addition to the Tecplot and VTK
......@@ -568,7 +568,7 @@ LinearElasticSolver mesh-linear.xml conditions.xml
FieldConvert-g -m deform mesh-linear.xml mesh-linear.fld mesh-deformed.xml
\end{lstlisting}
\subsection{FieldConvert in parallel}
\section{FieldConvert in parallel}
To run FieldConvert in parallel the user needs to compile
\nekpp with MPI support and can employ the following
command
......@@ -585,7 +585,7 @@ within the directory.
%
%
%
\subsection{Processing large files}
\section{Processing large files}
When processing large files it is not always convenient to run in parallel
but process each parallel partition in serial, for example when interpolating
one field to another. To do this we can use the \inltt{--nprocs} and
......
\section{MeshConvert}
\chapter{MeshConvert}
\label{s:utilities:meshconvert}
\newcommand{\mc}{\texttt{MeshConvert}\xspace}
......@@ -16,7 +16,7 @@ There is also some limited support for other output formats. We begin by running
through a basic example to show how a mesh can be converted from the widely-used
mesh-generator \gmsh to the XML file format.
\subsection{Exporting a mesh from \gmsh}
\section{Exporting a mesh from \gmsh}
To demonstrate how \mc works, we will define a simple channel-like 3D geometry.
First, we must define the \gmsh geometry to be used. The \gmsh definition is
......@@ -41,7 +41,7 @@ prismatic mesh and both occurances to generate a tetrahedral mesh. Increasing
the \texttt{Layers} numbers refines the mesh in the radial and azimuthal
direction respectively.
\subsection{Defining physical surfaces and volumes}
\section{Defining physical surfaces and volumes}
\begin{figure}
\begin{center}
......@@ -90,7 +90,7 @@ gmsh -3 -order 6 test.geo
will generate a sixth-order mesh. Note that you will need to use a current
version of \gmsh in order to do this, most likely from subversion.
\subsection{Converting the MSH to Nektar++ format}
\section{Converting the MSH to Nektar++ format}
Assuming that you have compiled \nekpp according to the compilation
instructions, run the command
%
......@@ -129,7 +129,7 @@ the element. Whilst a resulting simulation may run, the results may not be valid
because of this problem, or excessively large amounts of time may be needed to
solve the resulting linear system.
\subsection{MeshConvert modules}
\section{MeshConvert modules}
\mc is designed to provide a pipeline approach to mesh generation. To do this,
we break up tasks into three different types. Each task is called a
......@@ -197,7 +197,7 @@ line argument:
modules by \inltt{out:}.
\end{notebox}
\subsubsection{Input modules}
\subsection{Input modules}
Input and output modules use file extension names to determine the correct
module to use. Not every module is capable of reading high-order information,
......@@ -246,7 +246,7 @@ The resulting file therefore has two composites of IDs \inltt{150} and
\inltt{151} respectively, containing the triangular and quadrilateral elements
of the original mesh.
\subsubsection{Output modules}
\subsection{Output modules}
The following output formats are supported:
......@@ -269,7 +269,7 @@ meshes since robustness is not guaranteed.
In the rest of these subsections, we discuss the various processing modules
available within \mc.
\subsubsection{Negative Jacobian detection}
\subsection{Negative Jacobian detection}
To detect elements with negative Jacobian determinant, use the \inltt{jac}
module:
......@@ -301,7 +301,7 @@ 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}
\subsection{Spherigon patches}
Where high-order information is not available (e.g. when using meshes from
imaging software), various techniques can be used to apply a smoothing to the
......@@ -355,7 +355,7 @@ the surface elements producing leading edge closer to the underlying geometry:
\end{center}
\end{figure}
\subsubsection{Periodic boundary condition alignment}
\subsection{Periodic boundary condition alignment}
When using periodic boundary conditions, the order of the elements within the
boundary composite determines which element edges are periodic with the
......@@ -396,7 +396,7 @@ MeshConvert -m peralign:surf1=11:surf2=12:dir=y:orient input.dat output.xml
\inltt{peralign} module before the \inltt{spherigon} module.
\end{notebox}
\subsubsection{Boundary layer splitting}
\subsection{Boundary layer splitting}
Often it is the case that one can generate a coarse boundary layer grid of a
mesh. \mc has a method for splitting prismatic and hexahedral elements into
......@@ -454,7 +454,7 @@ of 2 and 7 integration points per element use the following command:
self-intersecting.
\end{notebox}
\subsubsection{High-order cylinder generation}
\subsection{High-order cylinder generation}
Generating accurate high-order curved geometries in \gmsh is quite challenging.
This module processes an existing linear cylindrical mesh, with axis aligned
......@@ -480,7 +480,7 @@ The module parameters are:
are not self-intersecting.
\end{notebox}
\subsubsection{Surface extraction}
\subsection{Surface extraction}
Often one wants to visualise a particular surface of a 3D mesh. \mc supports
extraction of two-dimensional surfaces which can be converted using
......@@ -496,7 +496,7 @@ To extract a surface use the command:
where the integers are surface IDs to be extracted.
\subsubsection{Boundary identification}
\subsection{Boundary identification}
Some mesh formats lack the ability to identify boundaries of the domain they
discretise. \mc has a rudimentary boundary identification routine for conformal
......@@ -508,7 +508,7 @@ module:
MeshConvert -m detect volume.xml volumeWithBoundaryComposite.xml
\end{lstlisting}
\subsubsection{Scalar function curvature}
\subsection{Scalar function curvature}
This module imposes curvature on a surface given a scalar function
$z=f(x,y)$. For example, if on surface 1 we wish to apply a surface defined by a
......
\chapter{Utilities for Pre- and Post-Processing}
\input{meshconvert}
\input{fieldconvert}
\ No newline at end of file
\input{fieldconvert}
\input{other}
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