[doxygen] Move external tools section from handbook to doxygen

doc/doxygen/pages/input-output.md

@@ -198,14 +198,50 @@ The example above is taken from `test/porousmediumflow/1pnc/implicit/1p2c/noniso
 There is support for reading data and grids from VTK files, see Dumux::VTKReader.
 
 ## Gnuplot interface
-DuMux provides a small interface to GNUPlot, which can be used to plot results and generate
-image files (e.g., png). To use the gnuplot, gnuplot has to be installed.
-For more information see Dumux::GnuplotInterface.
+DuMux provides a small interface to [Gnuplot](http://www.gnuplot.info/),
+which can be used to plot results and generate
+image files (e.g. `.png`). To use the gnuplot, gnuplot has to be installed.
+The following is a brief introduction. For the class documentation, see Dumux::GnuplotInterface.
+
+A Gnuplot interface is available to plot or visualize results during a simulation run.
+To use the gnuplot interface you have to make some modifications in your file, e.g., your main file.
+
+First, you have to include the corresponding header file for the gnuplot interface.
+
+```cpp
+#include <dumux/io/gnuplotinterface.hh
+```
+
+Second, you have to create an instance of the class
+Dumux::GnuplotInterface (e.g. called `gnuplot`).
+
+```cpp
+Dumux::GnuplotInterface<double> gnuplot;
+```
+
+As an example, to plot the mole fraction of nitrogen (`y`) over time (`x`),
+extract the variables after each time step in the time loop.
+The actual plotting is done using the method of the Gnuplot interface:
+
+```cpp
+gnuplot.resetPlot();                         // reset the plot
+gnuplot.setXRange(0.0, 72000.0);             // specify xmin and xmax
+gnuplot.setYRange(0.0, 1.0);                 // specify ymin and ymax
+gnuplot.setXlabel("time [s]");               // set xlabel
+gnuplot.setYlabel("mole fraction mol/mol");  // set ylabel
+// set x-values, y-values, the name of the data file and the Gnuplot options
+gnuplot.addDataSetToPlot(x, y, "N2.dat", options);
+gnuplot.plot("mole_fraction_N2");            // set the name of the output file
+```
+
+It is also possible to add several data sets to one plot by calling Dumux::GnuplotInterface::addDataSetToPlot more than once.
+For more information have a look into a test including the gnuplot interface header file, the class documentation
+of Dumux::GnuplotInterface, or the header file itself `dumux/io/gnuplotinterface.hh`.
 
 ## Container I/O
 DuMux supports writing to file from and reading
 into some STL containers like `std::vector<double>` or `std::vector<Dune::FieldVector>`.
-If you want to read and write simple vectors, have a look at the header dumux/io/container.hh.
+If you want to read and write simple vectors, have a look at the header `dumux/io/container.hh`.
 
 ## Matrix and Vector I/O
 

doc/handbook/0_dumux-handbook.tex

@@ -127,7 +127,6 @@ concepts (\ref{sc_linearsystem}).
 \input{5_newfoldersetup}
 \input{5_restartsimulations}
 \input{5_developingdumux}
-\input{5_externaltools}
 \input{5_scripts}
 \input{5_assemblinglinearsystem}
 

doc/handbook/5_externaltools.tex

-% SPDX-FileCopyrightInfo: Copyright © DuMux Project contributors, see AUTHORS.md in root folder
-% SPDX-License-Identifier: CC-BY-4.0
-
-\section{External Tools}
-\label{sc_externaltools}
-
-\subsection{Git}
-Git is a version control tool which we use.
-The basic Git commands are:
-\begin{itemize}
-  \item \texttt{git checkout}: receive a specified branch from the repository
-  \item \texttt{git clone}: clone a repository; creates a local copy
-  \item \texttt{git diff}: to see the actual changes compared to your last commit
-  \item \texttt{git pull}: pull changes from the repository; synchronizes the
-  repository with your local copy
-  \item \texttt{git push}: push committed changes to the repository;  synchronizes
-  your local copy with the repository
-  \item \texttt{git status}: to check which files/folders have been changed
-  \item \texttt{git gui}: graphical user interface, helps selecting changes for
-  a commit
-\end{itemize}
-
-
-\subsection{Gnuplot}
-\label{gnuplot}
-A gnuplot interface is available to plot or visualize results during a simulation run.
-This is achieved with the help of the \texttt{Dumux::GnuplotInterface} class provided in \texttt{io/gnuplotinterface.hh}.
-
-To use the gnuplot interface you have to make some modifications in your file, e.g., your main file.
-
-First, you have to include the corresponding header file for the gnuplot interface.
-\begin{lstlisting}[style=DumuxCode]
-#include <dumux/io/gnuplotinterface.hh
-\end{lstlisting}
-
-Second, you have to define an instance of the class \texttt{Dumux::GnuplotInterface} (e.g. called \texttt{gnuplot}).
-\begin{lstlisting}[style=DumuxCode]
-Dumux::GnuplotInterface<double> gnuplot;
-\end{lstlisting}
-
-As an example, to plot the mole fraction of nitrogen (\texttt{y}) over time (\texttt{x}),
-extract the variables after each time step in the time loop.
-The actual plotting is done using the method of the gnuplot interface:
-
-\begin{lstlisting}[style=DumuxCode]
-gnuplot.resetPlot();                             // reset the plot
-gnuplot.setXRange(0.0, 72000.0);                 // specify xmin and xmax
-gnuplot.setYRange(0.0, 1.0);                     // specify ymin and ymax
-gnuplot.setXlabel("time [s]");                   // set xlabel
-gnuplot.setYlabel("mole fraction mol/mol");  // set ylabel
-
-// set x-values, y-values, the name of the data file and the Gnuplot options
-gnuplot.addDataSetToPlot(x, y, "N2.dat", options);
-
-gnuplot.plot("mole_fraction_N2");                // set the name of the output file
-\end{lstlisting}
-
-It is also possible to add several data sets to one plot by calling \texttt{addDataSetToPlot()} more than once.
-For more information have a look into a test including the gnuplot interface header file, the doxygen documentation
-of \texttt{Dumux::GnuplotInterface}, or the header file itself (\texttt{dumux/io/gnuplotinterface.hh}).
-
-
-\subsection{Gstat}
-Gstat is an open source software tool which generates geostatistical random fields (see \url{www.gstat.org}).
-In order to use gstat, execute the \texttt{bin/installexternal.py} from your \Dumux root
-directory or download, unpack and install the tarball from the gstat-website.
-Then, rerun cmake (in the second case set \texttt{GSTAT\_ROOT} in your input file to the
-path where gstat is installed).
-
-
-\subsection{ParaView} \label{ssec:paraview}
-To visualize the simulation data you have produced using \Dumux, we recommend using \href{https://www.paraview.org/}{Paraview}. 
-This open-source software supports \Dumux~'s standard data formats, and can be operated either with a GUI or with batching tools. 
\ No newline at end of file