From 6c44a579918d64d17fdcfd99a3901ee6c5669fd3 Mon Sep 17 00:00:00 2001
From: Gabi Seitz <gabriele.seitz@iws.uni-stuttgart.de>
Date: Tue, 8 Sep 2015 15:28:33 +0000
Subject: [PATCH] [handbook] deleted chapter "discussion" and smoothed away
some odds and ends
git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15454 2fb0f335-1f38-0410-981e-8018bf24f1b0
---
doc/handbook/0_discussion.tex | 72 ---------------------------
doc/handbook/0_dumux-handbook.tex | 3 +-
doc/handbook/2_detailedinstall.tex | 1 -
doc/handbook/3_tutorialcoupled.tex | 6 +--
doc/handbook/3_tutorialdecoupled.tex | 4 +-
doc/handbook/4_externaltools.tex | 4 +-
doc/handbook/4_structure.tex | 2 +-
doc/handbook/5_grids.tex | 13 ++---
doc/handbook/5_models.tex | 5 +-
doc/handbook/5_stepsofasimulation.tex | 35 ++++---------
doc/handbook/CMakeLists.txt | 1 -
11 files changed, 28 insertions(+), 118 deletions(-)
delete mode 100644 doc/handbook/0_discussion.tex
diff --git a/doc/handbook/0_discussion.tex b/doc/handbook/0_discussion.tex
deleted file mode 100644
index 53ee896f66..0000000000
--- a/doc/handbook/0_discussion.tex
+++ /dev/null
@@ -1,72 +0,0 @@
-\chapter*{Discussion about the new handbook}
-\section*{Beschlossene ToDos}
-\begin{itemize}
- \item[x] steps of dumux simulations - flow chart/Grafik (Gaby + Thomas)
- \item[x] Fluidstate/Fluidsystem -$>$ Abstrakte Klassen einführen für doxygen (Natalie)
- \item Modelle raus, Liste rein (Christoph, Beatrix)
- \item[x] Neues Gitterkapitel (Natalie)
- \begin{itemize}
- \item[x] gmesh (Timo)
- \item[x] petrel (Alex)
- \item[x] artgridcreator (Nicolas)
- \item[x] dgf (kurz kommentieren)
- \item[x] icemcfd (nicolas)
- \end{itemize}
- \item Newton etwas ausfuhrlicher und Dumux spezifischer, schematische
- Skizze der Matrix (Christoph)
- \item Rechtschreibung - pdf in word öffnen (?)
- \item[x] Updated folder structure figure in Chapter \ref{sc_structure}
- \item[x] How to change compiler (4.6.2)
-\end{itemize}
-\todo[inline]{An manchen stellen haben wir noch Problemen mit bad boxen, vor allem
- wenn \textbackslash texttt\{\} benutzt wird}
-
-% \section*{Offene Fragen}
-% \begin{itemize}
-% \item Was kann ins Wiki ausgelagert werden?
-% \item Was kann ins doxygen ausgelagert werden?
-% \item Alles was (nicht?) LH2 spezifische raus?
-% \item Fur listOfProperties und listOfFeatures auf doxygen verweisen! (kommt
-% unter doxygen main pages)
-% \item Modelbeschreibungen rausschmeißen?
-% \item bennenung der ausgelagerten tex dateien mit kapitelnummer (nur eine nummer)
-% beginnend
-% \item Neue Kapitel/Abschnitte
-% \begin{itemize}
-% \item Wie kann ich Gitter erstellen (externe tools), /einlesen (dune), wo
-% kann ich bei dune nachschauen. Welche Dateien werden uberhaupt unterstutzt?
-% in Kap 5 (jemanden finden, der sich auskennt Alex, Timo, Bernd)
-% \end{itemize}
-% \item Tutorials:
-% \begin{itemize}
-% \item Noch aktuell, noch funktioniert?
-% \item Welche Features, Modelle brauchten auch ein Tutorial? Wie konnen wir
-% den Einstieg leicht machen und fur uns den Aufwand gering halten?
-% \item Verweis auf lecture fur realistischere Anwendungen
-% \end{itemize}
-% \end{itemize}
-
-\section*{Erledigt}
-\begin{itemize}
- \item[x] Kapitel 4 weiter aufräumen (Christoph+Thomas)
- \begin{itemize}
- \item[x] Tips und Tricks weiter integrieren
- \item[x] Reihenfolge der Unterkapitel
- \end{itemize}
- \item[x] Kapitel 5 weiter aufräumen (Christoph+Thomas)
- \begin{itemize}
- \item[x] Reihenfolge der Unterkapitel
- \item[x] \Dumux aus den Uberschriften in Kap 5 rausnehmen
- \end{itemize}
- \item[x] release manager tasks + tutorials anschauen/testen (Thomas)
- \item[x] Hinweis auf tests, lecture und feature list am Ende von Tutorial
- (Gaby)
- \item[x] Doxygen (main page - link auf modules, featureList und parameterList)
- (Kilian)
- \item[x] Wiki
- \begin{itemize}
- \item[x] behandla, Mailing list (LH2), external Modules, lectures, tests
- teilweise schon erledigt -$>$ Rest (Vishal)
- \item[x] Infos fur neue Doktoranden (Christoph)
- \end{itemize}
-\end{itemize}
diff --git a/doc/handbook/0_dumux-handbook.tex b/doc/handbook/0_dumux-handbook.tex
index 7986e62ec9..7e277dbfed 100644
--- a/doc/handbook/0_dumux-handbook.tex
+++ b/doc/handbook/0_dumux-handbook.tex
@@ -108,9 +108,8 @@ Universit\"at Stuttgart, Paffenwaldring 61, D-70569 Stuttgart, Germany}\\
\newpage
\pdfbookmark[1]{List of ToDos}{List of ToDos}
% \makeatletter\let\chapter\@undefined\makeatother
-\listoftodos
+%\listoftodos
-\input{0_discussion}
\chapter{Introduction}
\input{1_introduction}
diff --git a/doc/handbook/2_detailedinstall.tex b/doc/handbook/2_detailedinstall.tex
index 7879d228c5..7490ec7f04 100644
--- a/doc/handbook/2_detailedinstall.tex
+++ b/doc/handbook/2_detailedinstall.tex
@@ -1,6 +1,5 @@
\section{Detailed Installation Instructions}
\label{install}
-\todo[inline]{Dieses Unterkapitel könnte auch kürzer sein}
In this section about the installation of \Dumux it is assumed that you work with
a Linux or Apple OS X operating system
diff --git a/doc/handbook/3_tutorialcoupled.tex b/doc/handbook/3_tutorialcoupled.tex
index 3e90b0ffd9..6189e49d27 100644
--- a/doc/handbook/3_tutorialcoupled.tex
+++ b/doc/handbook/3_tutorialcoupled.tex
@@ -497,7 +497,7 @@ sizes.
\subsubsection{Exercise 2}
For this exercise you should create a new problem file analogous to
the file \texttt{tutorialproblem\_coupled.hh} (e.g. with the name
-\texttt{ex2\_tutorialproblem\_coupled.hh} and new spatial parameters \texttt{ex2\_tutorialspatialparams\_coupled.hh},
+\texttt{ex2\_tutorialproblem\_coupled.hh} and new spatial parameters \texttt{ex2\_tutorial\allowbreak spatialparams\_coupled.hh},
just like \texttt{tutorialspatialparams\_coupled.hh}.
The new files should contain the definition of new classes with names
@@ -600,8 +600,8 @@ As you have experienced, compilation takes quite some time. Therefore,
via \textit{parameter input files}.
In the code, parameters can be read via the macro
-\texttt{GET\_RUNTIME\_PARAM(TypeTag, Scalar,
-MyWonderfulGroup.MyWonderfulParameter);}. In this exercise we will explore the possibilities of the
+\texttt{GET\_RUNTIME\_PARAM(TypeTag, Scalar,
+MyWonderful\allowbreak Group.MyWonderfulParameter);}. In this exercise we will explore the possibilities of the
parameter file. For this we take a look at the file \texttt{ex3\_tutorial\_coupled.input} in the \texttt{solutions\_coupled} folder.
Besides the parameters which you already used in the parameter file above,
there are parameters which can be used to control the
diff --git a/doc/handbook/3_tutorialdecoupled.tex b/doc/handbook/3_tutorialdecoupled.tex
index 0ba993c4c2..02ae0a6527 100644
--- a/doc/handbook/3_tutorialdecoupled.tex
+++ b/doc/handbook/3_tutorialdecoupled.tex
@@ -221,7 +221,7 @@ For more options you can also type \texttt{./tutorial\_decoupled -h}. For the
visualisation with paraview please refer to \ref{quick-start-guide}.\\
As you can see, the simulation creates many output files. To reduce these in order
to perform longer simulations, change the method responsible for output (line
-\ref{tutorial-decoupled:outputinterval} in the file \texttt{tutorialproblem\_decoupled})
+\ref{tutorial-decoupled:outputinterval} in the file \texttt{tutorialproblem\_\allowbreak decoupled})
as to write an output only every 20 time-steps. Compile the main file by typing
\texttt{make tutorial\_decoupled} and run the model. Now, run the simulation for 5e5 seconds.
@@ -311,7 +311,7 @@ feeling of the time-step sizes.
For this exercise you should create a new problem file analogous to
the file \texttt{tutorialproblem\_decoupled.hh} (e.g. with the name
\texttt{ex2\_tutorialproblem\_decoupled.hh} and new spatial parameters
-just like \texttt{tutorialspatialparams\_decoupled.hh}. These files need to
+just like \texttt{tutorial\-spatialparams\_decoupled.hh}. These files need to
be included in the file \texttt{tutorial\_decoupled.cc}.
Each new files should contain the definition of a new class with a
diff --git a/doc/handbook/4_externaltools.tex b/doc/handbook/4_externaltools.tex
index 54bd1e9149..2f7a99fae9 100644
--- a/doc/handbook/4_externaltools.tex
+++ b/doc/handbook/4_externaltools.tex
@@ -42,9 +42,9 @@ There is an eclipse style file which can be used for Dumux.
\subsection{Kate}
For kate there is syntax highlighting style for \Dumux input files. Simply
-copy the file \texttt{dumux-devel/dumuxInputFiles.xml} to the \texttt{syntax} folder in
+copy the file \texttt{dumux-devel/dumux\-InputFiles.xml} to the \texttt{syntax} folder in
your kate configuration directory (e.g.
-\texttt{HOME/.kde4/share/apps/katepart/syntax/dumuxInputFiles.xml}).
+\texttt{HOME/.kde4/share/apps\-/katepart/syntax/dumuxInputFiles.xml}).
\subsection{ParaView}
\paragraph{Reload Button:}
diff --git a/doc/handbook/4_structure.tex b/doc/handbook/4_structure.tex
index 83c9ce1206..f97cac6275 100644
--- a/doc/handbook/4_structure.tex
+++ b/doc/handbook/4_structure.tex
@@ -57,7 +57,7 @@
The structure is equivalent to the dumux folder, the \texttt{references} folder
contains solutions for the automatic testing. Each test program consist of source
\texttt{*.cc}, the problem definition \texttt{*problem.hh}, the definition of the spatially dependent
- parameters \texttt{*spatialparameters.hh} and an input file \texttt{*problem.hh}.
+ parameters \texttt{*spatialparameters.hh} and an input file \texttt{*.input}.
For more detailed descriptions of the tests, please have a look at the Doxygen documentation.
\item \texttt{tutorial}: contains the tutorials described in Chapter \ref{chp:tutorial}.
diff --git a/doc/handbook/5_grids.tex b/doc/handbook/5_grids.tex
index 3b5da010e3..cde9d79e71 100644
--- a/doc/handbook/5_grids.tex
+++ b/doc/handbook/5_grids.tex
@@ -18,7 +18,7 @@ complex DGF files, we recommend to write your own scripts, e.g in C++, Matlab or
The DGF format can also used to read in spatial parameters defined on the grid. These parameters can
be defined on nodes as well as on the elements. An example for predefined parameters on a grid is
-the \texttt{test\_boxco2} or \texttt{test\_cco2} in the \texttt{dumux/test/co2} folder.
+the \texttt{test\_boxco2} or \texttt{test\_cco2} in the \texttt{dumux/test/implicit/co2} folder.
\subsubsection{Gmsh Mesh Format}
Gmsh is an open-source flexible grid generator for unstructured finite-element meshes (\cite{GEUZAINE2009}, \url{http://geuz.org/gmsh/}).
@@ -27,8 +27,10 @@ the provided GUI, we refer to the Gmsh documentation (\url{http://geuz.org/gmsh/
The MSH format can contain element and boundary markers defined in the grid. Thus, boundaries can be easily marked as e.g. inflow boundaries
using Gmsh. Further, the format supports higher order elements. They can be used to create boundary parameterization supported by e.g. the grid
-manager \texttt{UGGrid}.
-\todo{Timo: Gmsh in einem Test in stable benutzen. Am besten mit boundaryFlags und boundarySegments.}
+manager \texttt{UGGrid}.
+An example can be found in \texttt{dumux/test\allowbreak/io/gridcreator}.
+
+
\subsection{The default \texttt{GridCreator}}
The default \texttt{GridCreator} is called \texttt{GridCreator} and is automatically avaible in all problems.
@@ -145,8 +147,7 @@ can be found for example in the dissertation of \href{http://elib.uni
-stuttgart.de/opus/frontdoor.php?source_opus=8047&la=de}{Tatomir}, pp. 68.
\subsubsection{ICEM}
-\todo[inline]{Detailierte Beschreibung im Wiki? Links entfernen, die nicht funktionieren. Text überarbeiten. (Natalie)}
For complex geometries a graphical tool to create grids might be appropriate. One possibility to mesh for example CAD
geometry data is the commercial software \href{http://www.ansys.com/Products/Other+Products/ANSYS+ICEM+CFD/}{ANSYS ICEM
-CFD}. A very detailed, but outdated description can be found at the LH2 internal wiki. A more recent best practice guide is available at
-\url{XXX}. At LH2 exists a script which converts the ICEM mesh into the DGF.
+CFD}. A very detailed, but outdated description can be found at the LH2 internal wiki. A more recent best practice guide is available
+in dumux-devel at dumux-devel/util/gridconverters/Documentation\_ICEM\_CFD\_create\_mesh.odt. At LH2 exists a script which converts the ICEM mesh into the DGF.
diff --git a/doc/handbook/5_models.tex b/doc/handbook/5_models.tex
index 673364e66a..a5d540aa8a 100644
--- a/doc/handbook/5_models.tex
+++ b/doc/handbook/5_models.tex
@@ -57,8 +57,7 @@ $D_\alpha^\kappa$ & diffusivity of component $\kappa$ in phase $\alpha$ & $\bold
$\boldsymbol{v}_\alpha$ & velocity (Darcy or free flow)& & \\
\end{tabular}
\caption{Notation list for most of the variables and indices used in \Dumux.}
-\todo[inline]{Diese Liste macht ohne ausführliche Beschreibung der Modelle eigentlich keinen Sinn mehr.
- Sollen wir sie auch irgendwie auf das doxygen packen?}
+
\end{table}
\begin{figure}
@@ -123,6 +122,8 @@ $\boldsymbol{v}_\alpha$ & velocity (Darcy or free flow)& & \\
\label{fig:phaseMassEnergyTransfer}
\end{figure}
+
+
\subsection{Available Models}
We distinguish fully-implicit and decoupled models. A list of all available models can be found
in the Doxygen documentation at
diff --git a/doc/handbook/5_stepsofasimulation.tex b/doc/handbook/5_stepsofasimulation.tex
index 43c86f4f15..0e4e0b743a 100644
--- a/doc/handbook/5_stepsofasimulation.tex
+++ b/doc/handbook/5_stepsofasimulation.tex
@@ -1,34 +1,17 @@
\section{Steps of a \Dumux Simulation}
\label{flow}
-\todo[inline]{Hier könnte man den Text auch etwas abspecken}
-This chapter is supposed to show how things are ``handed around'' in \Dumux. This
+
+This chapter is supposed to show how things are ``handed around'' in \Dumux. It
is not a comprehenisve guide through the modeling framework of \Dumux, but
hopefully it will help getting to grips with it.
In Section \ref{content} the structure of \Dumux is shown from a \emph{content}
point of view.
-Section \ref{implementation} is written from the point of view of the \emph{implementation}.
-These two approaches are linked by the circled numbers (like \textbf{\textcircled{\ref{init}}})
-in the flowchart of Section \ref{implementation} corresponding to the enumeration
-of the list of Section \ref{content}. This is supposed to demonstrate at which point
-of the program-flow you are content- and implementation-wise.
-
-Section \ref{implementation} is structured by \fbox{boxes} and
-$\overrightarrow{\textnormal{arrows}}$. Boxes stand for more or less important
-points in the programm. They may may be reckoned ``step stones''. Likewise, the
-arrows connect the boxes. If important things happen in between, it is written
-under the arrows.
-
-\fbox{Plain boxes} stand for generic parts of the program. \fbox{\fbox{double}}
-$\lbrace\lbrace$boundings$\rbrace\rbrace$ stand for the implementation specific
-part of the program, like \verb+2p, 2p2c...+. This will be the most important
-part for most users. \uwave{snakelike lines} tell you that this part is specific
-to the components considered.
-
-For keeping things simple, the program flow of a \verb+2p+ model is shown.
-There are extensive comments regarding the formating in the tex file: so feel free,
-to enhance this description.
+Section \ref{implementation} however is written from the point of view of the \emph{implementation}.
+The same coloration in the flowcharts of both sections refers to the same level of calculation. For keeping things
+simple, the program flow of a \verb+2p+ model is shown in section \ref{implementation}. There are extensive comments
+regarding the formating in the tex file: so feel free, to enhance this description.
\subsection{Structure -- by Content}
@@ -38,9 +21,9 @@ to enhance this description.
This list shows the algorithmic outline of a typical \Dumux run. Each item stands
for a characteristic step within the modeling framework.
-\clearpage
-In Figure \ref{fig:algorithm}, the algorithmic representations of both approaches
-down to the element level are illustrated.
+%\clearpage
+In Figure \ref{fig:algorithm}, the algorithmic representations of both approaches, the coupled fully
+implicit and the decoupled semi-implicit one are illustrated down to the element level.
\begin{figure}[hbt]
\begin{tabular}{ l | l }
diff --git a/doc/handbook/CMakeLists.txt b/doc/handbook/CMakeLists.txt
index 20665ea68b..0be836e891 100644
--- a/doc/handbook/CMakeLists.txt
+++ b/doc/handbook/CMakeLists.txt
@@ -1,6 +1,5 @@
set(TEX_INPUTS
0_dumux-handbook.tex
- 0_discussion.tex
0_listingstyle.tex
1_introduction.tex
2_detailedinstall.tex
--
GitLab