diff --git a/doc/handbook/0_discussion.tex b/doc/handbook/0_discussion.tex
index 1a0ccb31454cdddb6bdcb2f1db62c6c79d5b5128..1a4d30364d21ff1d44f9aa13e4a2e1f1348e3d17 100644
--- a/doc/handbook/0_discussion.tex
+++ b/doc/handbook/0_discussion.tex
@@ -18,6 +18,8 @@ DEADLINE: 01.09.15
\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}
% \section*{Offene Fragen}
diff --git a/doc/handbook/0_dumux-handbook.tex b/doc/handbook/0_dumux-handbook.tex
index a588d41a8be51c1ed2b6c2ebe5b2926365560258..0d8d15098aae0caca7a5cf19a7eeed07329f7a9c 100644
--- a/doc/handbook/0_dumux-handbook.tex
+++ b/doc/handbook/0_dumux-handbook.tex
@@ -24,12 +24,20 @@
\usepackage{textcomp}
\usepackage{theorem}
\usepackage{tikz}
+\usepackage{tikz-qtree}
\usepackage[colorinlistoftodos]{todonotes}
\usepackage{units}
\usepackage{url}
\usepackage{xspace}
\hypersetup{bookmarksdepth=3}
-\usetikzlibrary{arrows,backgrounds,decorations.pathmorphing,patterns,positioning,fit,shapes}
+\usetikzlibrary{arrows}
+\usetikzlibrary{backgrounds}
+\usetikzlibrary{decorations.pathmorphing}
+\usetikzlibrary{fit}
+\usetikzlibrary{patterns}
+\usetikzlibrary{positioning}
+\usetikzlibrary{shapes}
+\usetikzlibrary{trees}
\include{0_listingstyle}
\DeclareGraphicsExtensions{.pdf, .jpg}
diff --git a/doc/handbook/0_listingstyle.tex b/doc/handbook/0_listingstyle.tex
index fc76d8868638fff98d61974713f15f91adeddea3..eb88e52723bef99523da8bdfc3affa8e91012f19 100644
--- a/doc/handbook/0_listingstyle.tex
+++ b/doc/handbook/0_listingstyle.tex
@@ -45,7 +45,8 @@
{e-8}{{\textcolordigits{e-8}}}{2}%
{e-9}{{\textcolordigits{e-9}}}{2},
}
-% for listings of bash code in install.tex
+
+% for listings of bash code
\lstdefinestyle{Bash}{
language=Bash,
backgroundcolor=\color{lightgray},
@@ -61,6 +62,18 @@
aboveskip=\bigskipamount,
belowskip=\bigskipamount
}
+
+% for listings of shell code
+\lstdefinestyle{Shell}{
+ language=sh,
+ numbers=left,
+ numbersep=5pt,
+ numberstyle=\tiny,
+ basicstyle=\ttfamily\scriptsize,
+ stringstyle=\color{BrickRed}\ttfamily\let\textcolor\textcolordummy,
+ commentstyle=\color[gray]{0.35}\ttfamily\it\let\textcolor\textcolordummy,
+}
+
% for listings of DuMuX code
\lstdefinestyle{DumuxCode}{
language=C++,
@@ -75,6 +88,7 @@
commentstyle=\color[gray]{0.35}\ttfamily\it\let\textcolor\textcolordummy,
morecomment=[l][\color{OliveGreen}\let\textcolor\textcolordummy]{\#},
}
+
% for listings of DuMuX parameter files
\lstdefinestyle{DumuxParameterFile}{
language=sh,
diff --git a/doc/handbook/4_developingdumux.tex b/doc/handbook/4_developingdumux.tex
index bf557e2acb8a574e50277665a4cc1b5bf0672339..6d948cb611066d0af503aaa1917653057228df62 100644
--- a/doc/handbook/4_developingdumux.tex
+++ b/doc/handbook/4_developingdumux.tex
@@ -33,11 +33,17 @@ more information.
The options needed to be specified for that are provided using option files like
\texttt{debug.opts} and \texttt{optim.opts}. These two compile \Dune and \Dumux
either for debugging or for fast simulation. Programs compiled with optimization options
-can lead to a speedup of factor up to ten!
+can lead to a speedup of factor up to ten!\\
In contrast programs that are compiled with optimization can hardly be debugged.
-You can modify the files and add third-party dependencies or additional compiler flags.
-
-\todo{Hinweis/Beispiel, wie ein anderer Compiler eingebunden werden kann (Thomas)}
+You can modify the files and change the compiler, the name of the build director,
+add third-party dependencies, add additional compiler flags, ... .
+\begin{lstlisting}[style=Shell]
+BUILDDIR=build-clang
+CMAKE_FLAGS="\
+ -DCMAKE_C_COMPILER=/usr/bin/clang \
+ -DCMAKE_CXX_COMPILER=/usr/bin/clang++ \
+ -DUG_DIR=./externals/ug-3.12.1"
+\end{lstlisting}
\paragraph{Dunecontrol for selected modules}
A complete build using \texttt{dunecontrol} takes some time. In many cases not all modules need to be re-built.
diff --git a/doc/handbook/4_structure.tex b/doc/handbook/4_structure.tex
index 417dac550e3090a4ac51698c6bb25d09547843e6..83c9ce1206a4575d87628466067afc727e33de1f 100644
--- a/doc/handbook/4_structure.tex
+++ b/doc/handbook/4_structure.tex
@@ -63,125 +63,153 @@
\item \texttt{tutorial}: contains the tutorials described in Chapter \ref{chp:tutorial}.
\end{itemize}
-% \begin{figure}
-\begin{sidewaysfigure}
-\begin{tikzpicture}[>=latex,inner xsep=0.15cm,rounded corners]
-\node [minimum height=0.7cm,draw,inner xsep=0.94cm,rotate=90,thick] (d) at(-2,0) {dumux};
-\node [minimum height=0.7cm,draw,inner xsep=1.03cm,thick] (lin) at(0.5,0) {linear};
-\node [minimum height=0.7cm,draw,inner xsep=1.32cm,thick] (io) at(0.5,1) {io};
-
-\node [minimum height=0.7cm,draw,inner xsep=0.87cm,thick] (imp) at(0.5,3.5) {implicit};
- \node [minimum height=0.7cm,draw,inner xsep=0.88cm,thick] (c1) at(4.2,2) {common};
- \node [minimum height=0.7cm,draw,inner xsep=0.54cm,thick] (cell) at(4.2,3) {cell centered};
- \node [minimum height=0.7cm,draw,inner xsep=1.28cm,thick] (box) at(4.2,4) {box};
- \node [minimum height=0.7cm,draw,inner xsep=0.33cm,thick] (spec1) at(4.2,5) {specific models};
-
-\node [minimum height=0.7cm,draw,inner xsep=0.82cm,thick] (free) at(0.5,6) {free flow};
- \node [minimum height=0.7cm,draw,inner xsep=0.33cm,thick] (spec2) at(4.2,6) {specific models};
-
-\node [minimum height=0.7cm,draw,inner xsep=0.7cm,thick] (dec) at(0.5,7.5) {decoupled};
- \node [minimum height=0.7cm,draw,inner xsep=0.88cm,thick] (c2) at(4.2,7) {common};
- \node [minimum height=0.7cm,draw,inner xsep=0.33cm,thick] (spec3) at(4.2,8) {specific models};
-
-\node [minimum height=0.7cm,draw,inner xsep=0.82cm,thick] (c3) at(0.5,9) {common};
-
-\node [minimum height=0.7cm,draw,inner xsep=0.82cm,thick] (m) at(0.5,-4.5) {material};
- \node [minimum height=0.7cm,draw,thick] (bin) at(4.2,-1) {binarycoefficients};
- \node [minimum height=0.7cm,draw,inner xsep=0.6cm,thick] (comp) at(4.2,-2) {components};
- \node [minimum height=0.7cm,draw,inner xsep=0.2cm,thick] (con) at(4.2,-3) {constraintsolvers};
- \node [minimum height=0.7cm,draw,inner xsep=1.34cm,thick] (eos) at(4.2,-4) {eos};
- \node [inner ysep=0.05cm,draw,text width=2cm,align=center,inner xsep=0.59cm,thick] (fi) at(4.2,-5) {fluidmatrix-\\[-16pt]interactions};
- \node [minimum height=0.7cm,draw,inner xsep=0.73cm,thick] (fstate) at(4.2,-6) {fluidstates};
- \node [minimum height=0.7cm,draw,inner xsep=0.56cm,thick] (fsys) at(4.2,-7) {fluidsystems};
- \node [minimum height=0.7cm,draw,inner xsep=0.11cm,thick] (s) at(4.2,-8) {spatialparameters};
-
-\node [minimum height=0.7cm,draw,inner xsep=0.74cm,thick] (non) at(0.5,-9) {nonlinear};
-\node [minimum height=0.7cm,draw,inner xsep=0.9cm,thick] (para) at(0.5,-10) {parallel};
-
-\draw (d)--(lin);
-\draw (-1.4,0)--(-1.4,9)--(c3);
-\draw (-1.4,0)--(-1.4,-10)--(para);
-\draw (-1.4,7.5)--(dec);
-\draw (-1.4,6)--(free);
-\draw (-1.4,3.5)--(imp);
-\draw (-1.4,1)--(io);
-\draw (-1.4,-4.5)--(m);
-\draw (-1.4,-9)--(non);
-
-\draw (dec)--(2.4,7.5);
-\draw (spec3)--(2.4,8)--(2.4,7)--(c2);
-\draw (free)--(spec2);
-\draw (imp)--(2.4,3.5);
-\draw (spec1)--(2.4,5)--(2.4,2)--(c1);
-\draw (box)--(2.4,4);
-\draw (cell)--(2.4,3);
-\draw (m)--(2.4,-4.5);
-\draw (bin)--(2.4,-1)--(2.4,-8)--(s);
-\draw (comp)--(2.4,-2);
-\draw (con)--(2.4,-3);
-\draw (eos)--(2.4,-4);
-\draw (fi)--(2.4,-5);
-\draw (fstate)--(2.4,-6);
-\draw (fsys)--(2.4,-7);
-
-\draw [->](c3)--(6.5,9) node [right,text width=12.5cm,align=left]
- {Common files of the implicit (box and cell centered) models and the de-\\[-4pt]
- coupled models: time integration, start routine, the property system, ...};
-\draw [->](spec3)--(6.5,8) node [right,text width=12.5cm,align=left]
- {Specific model definition for the decoupled formulation. In each model \\[-4pt]
- folder are subdirectories for the implicit pressure equation, sorted by \\[-4pt]discretization method, and for the explicit transport.};
-\draw [->](c2)--(6.5,7) node [right,text width=12.5cm,align=left]
- {Base classes and general files for the decoupled formulation.};
-\draw [->](spec2)--(6.5,6) node [right,text width=12.5cm,align=left]
- {Specific model definition for free flow problems using the Strokes \\[-4pt]
- equation: non-isothermal, compositional, one-phase models.};
-\draw [->](spec1)--(6.5,5) node [right,text width=12.5cm,align=left]
- {Model and problem definition: implementation of equations, model spe-\\[-4pt]
- cific properties and indices.};
-\draw [->](box)--(6.5,4) node [right,text width=12.5cm,align=left]
- {Specific files for gerenal fully implicit boxmethod: boxassembler, dual \\[-5pt]
- mesh geometry in boxfvelementgeometry.hh, base classes for model and \\[-5pt]problem definition.};
-\draw [->](cell)--(6.5,3) node [right,text width=12.5cm,align=left]
- {Specific files for fully implicit cell centered method: ccassembler, mesh \\[-5pt]
- geometry in ccfvelementgeometry.hh, base classes for model and problem \\[-5pt]definition.};
-\draw [->](c1)--(6.5,2) node [right,text width=12.5cm,align=left]
- {Common functionality of cell centered and box formulation: assembling \\[-5pt]
- in implicitlocaljacobian.hh, evaluation of partial derivative in \\[-5pt]implicitlocalresidual.hh, base classes for model and problem definition.};
-\draw [->](io)--(6.5,1) node [right,text width=12.5cm,align=left]
- {Additional in-/output possibilities like restart files, gnuplot-interface and a VTKWriter \\[-4pt]
- extension. Grid Creator files.};
-\draw [->](lin)--(6.5,0) node [right,text width=12.5cm,align=left] {Linear solver backend.};
-\draw [->](bin)--(6.5,-1) node [right,text width=12.5cm,align=left]
- {Binary coefficients (like binary diffusion coefficients) and those needed for \\[-4pt]
- the constitutive relationships (e.g. Henry coefficient).};
-\draw [->](comp)--(6.5,-2) node [right,text width=12.5cm,align=left]
- {Properties of a pure chemical substance (e.g. water) \\[-4pt]or pseudo substance (e.g. air).};
-\draw [->](con)--(6.5,-3) node [right,text width=12.5cm,align=left]
- {Constraint solvers specify a well defined set of input variables and make \\[-4pt]
- sure that the resulting fluid state is consistent with a given set of \\[-4pt]thermodynamic equations.};
-\draw [->](eos)--(6.5,-4) node [right,text width=12.5cm,align=left]
- {Equations of state (eos) are auxiliary classes which provide relations \\[-4pt]
- between a fluid phase's temperature, pressure, composition and density.};
-\draw [->](fi)--(6.5,-5) node [right,text width=12.5cm,align=left]
- {Constitutive relationships (e.g. capillary pressure - saturation - curve).};
-\draw [->](fstate)--(6.5,-6) node [right,text width=12.5cm,align=left]
- {Fluid states are responsible for representing the complete thermodynamic \\[-4pt]
- configuration of a system at a given spatial and temporal position.};
-\draw [->](fsys)--(6.5,-7) node [right,text width=12.5cm,align=left]
- {Fluid systems express the thermodynamic relations between quantities.};
-\draw [->](s)--(6.5,-8) node [right,text width=12.5cm,align=left]
- {Base class for all spatially dependent variables, like permeability and \\[-4pt]
- porosity. Includes spatial averaging routines. All other properties are \\[-4pt]
- specified in the specific files of the respective models.};
-\draw [->](non)--(6.5,-9) node [right,text width=12.5cm,align=left]
- {Newton's method.};
-\draw [->](para)--(6.5,-10) node [right,text width=12.5cm,align=left]
- {Files for parallel programming.};
+\begin{figure}
+% \begin{sidewaysfigure}
+\begin{tikzpicture}[scale=0.8,grow'=right,level distance=1.5in,sibling distance=.05in]
+\tikzset{edge from parent/.style={thick, draw=dumuxBlue, edge from parent fork right}}
+\tikzset{every tree node/.style={draw, thick, align=center}}
+\tikzset{frontier/.style={distance from root=6.0in}}
+
+\tikzset{FirstLevel/.style={
+ draw=dumuxYellow,
+ rectangle,
+ align=center,
+ minimum width=1.1in,
+ minimum height=0.2in,
+ text width=1.2in,
+}}
+\tikzset{SecondLevel/.style={
+ draw=dumuxBlue,
+ rectangle,
+ align=center,
+ minimum width=1.1in,
+ minimum height=0.2in,
+ text width=1.2in,
+}}
+
+\tikzset{ThirdLevel/.style={
+ draw=none,
+ align=left,
+ minimum width=4.2in,
+ text width=4.1in,
+ font=\footnotesize
+}}
+
+
+\Tree
+[.\node[draw=dumuxYellow, ultra thick] {dumux};
+ [.\node[FirstLevel] {common};
+ \node[ThirdLevel] {
+ Common files of the implicit (box and cell centered) models and the
+ decoupled models: time integration, start routine, the property
+ system, ...};
+ ]
+ [.\node[FirstLevel] {decoupled};
+ [.\node[SecondLevel] {\emph{models}};
+ \node[ThirdLevel] {
+ Specific model definition for the decoupled formulation. In each model
+ folder are subdirectories for the implicit pressure equation, sorted by
+ discretization method, and for the explicit transport.};
+ ]
+ [.\node[SecondLevel] {common};
+ \node[ThirdLevel] {Base classes and general files for the decoupled formulation.};
+ ]
+ ]
+ [.\node[FirstLevel] {geomechanics};
+ [.\node[SecondLevel] {\emph{models}};
+ \node[ThirdLevel] {Specific model definition for coupled flow and geomechnics simulations.};
+ ]
+ ]
+ [.\node[FirstLevel] {freeflow};
+ [.\node[SecondLevel] {\emph{models}};
+ \node[ThirdLevel] {Specific model definition for free flow problems using the (Navier-) Stokes
+ and algebraic turbulence models.};
+ ]
+ ]
+ [.\node[FirstLevel] {implicit};
+ [.\node[SecondLevel] {\emph{models}};
+ \node[ThirdLevel] {Model and problem definition: implementation of equations,
+ model specific properties and indices.};
+ ]
+ [.\node[SecondLevel] {box};
+ \node[ThirdLevel] {Specific files for gerenal fully implicit boxmethod:
+ boxassembler, dual mesh geometry in boxfvelementgeometry.hh,
+ base classes for model and problem definition.};
+ ]
+ [.\node[SecondLevel] {cellcentered};
+ \node[ThirdLevel] {Specific files for fully implicit cell centered method: ccassembler,
+ mesh geometry in ccfvelementgeometry.hh, base classes for model and
+ problem definition.};
+ ]
+ [.\node[SecondLevel] {common};
+ \node[ThirdLevel] {Common functionality of cell centered and box formulation:
+ assembling in implicitlocaljacobian.hh, evaluation of partial derivative
+ in implicitlocalresidual.hh, base classes for model and problem definition.};
+ ]
+ ]
+ [.\node[FirstLevel] {io};
+ \node[ThirdLevel] {Additional in-/output possibilities like restart files, gnuplot-interface
+ and a VTKWriter extension. Grid Creator files.};
+ ]
+ [.\node[FirstLevel] {linear};
+ \node[ThirdLevel] {Linear solver backend.};
+ ]
+ [.\node[FirstLevel] {material};
+ [.\node[SecondLevel] {binarycoefficients};
+ \node[ThirdLevel] {Binary coefficients (like binary diffusion coefficients) and those
+ needed for the constitutive relationships (e.g. Henry coefficient)};
+ ]
+ [.\node[SecondLevel] {components};
+ \node[ThirdLevel] {Properties of a pure chemical substance (e.g. water)
+ or pseudo substance (e.g. air).};
+ ]
+ [.\node[SecondLevel] {constraintsolvers};
+ \node[ThirdLevel] {Constraint solvers specify a well defined set of input variables
+ and make sure that the resulting fluid state is consistent with a
+ given set of thermodynamic equations.};
+ ]
+ [.\node[SecondLevel] {eos};
+ \node[ThirdLevel] {Equations of state (eos) are auxiliary classes which provide
+ relations between a fluid phase's temperature, pressure, composition
+ and density.};
+ ]
+ [.\node[SecondLevel] {fluidmatrixint.};
+ \node[ThirdLevel] {Constitutive relationships (e.g. capillary pressure - saturation - curve};
+ ]
+ [.\node[SecondLevel] {fluidstates};
+ \node[ThirdLevel] {Fluid states are responsible for representing the complete thermodynamic
+ configuration of a system at a given spatial and temporal position.};
+ ]
+ [.\node[SecondLevel] {fluidsystems};
+ \node[ThirdLevel] {Fluid systems express the thermodynamic relations between quantities.};
+ ]
+ [.\node[SecondLevel] {spatialparameters};
+ \node[ThirdLevel] {Base class for all spatially dependent variables, like permeability and
+ porosity. Includes spatial averaging routines. All other properties are
+ specified in the specific files of the respective models.};
+ ]
+ ]
+ [.\node[FirstLevel] {multidomain};
+ [.\node[SecondLevel] {\emph{models}};
+ \node[ThirdLevel] {Localoperators, which implement the correct coupling and
+ communication between the submodels, and model specific properties.};
+ ]
+ [.\node[SecondLevel] {common};
+ \node[ThirdLevel] {The multidomain wrappers, generic functions, and properties.};
+ ]
+ [.\node[SecondLevel] {couplinglocalres.};
+ \node[ThirdLevel] {The localresiduals extending the baselocalresiduals for coupling.};
+ ]
+ ]
+ [.\node[FirstLevel] {nonlinear};
+ \node[ThirdLevel] {Newton's method.};
+ ]
+ [.\node[FirstLevel] {parallel};
+ \node[ThirdLevel] {Files for parallel programming.};
+ ]
+]
\end{tikzpicture}
-\caption{Structure of the directory \texttt{dumux} containing the \Dumux source files.
- \todo[inline]{Diese Skizze ist NICHT mehr aktuell. Hochkant passt sie wahrscheinlich besser auf die Seite.
- Neue Tikz Templates sollten eingführt werden. Eventuell Grafik/Schrift verkleinern und einpassen.
- Eventuell mit nur relative Platzierung der Boxen mit lower-of ... (Thomas)}}
+\caption{Structure of the directory \texttt{dumux} containing the \Dumux source files.}
\label{fig:dumux-structure}
-\end{sidewaysfigure}
-% \end{figure}
+% \end{sidewaysfigure}
+\end{figure}
diff --git a/doc/handbook/5_propertysystem.tex b/doc/handbook/5_propertysystem.tex
index 2cabe372b5c174943fffdb1833d08ce9980f4ec2..538f9a373b48b29dae823dfffad6eb4ffe7f040e 100644
--- a/doc/handbook/5_propertysystem.tex
+++ b/doc/handbook/5_propertysystem.tex
@@ -1,6 +1,8 @@
\section{Property System}
\label{sec:propertysystem}
-
+\todo[inline]{Irgendwo sollten wir erklären wir Property Werte geholt werden und
+ was der Unterschied zwisch GET\_PROP\_VALUE, GET\_PARAM\_FROM\_GROUP
+ und GET\_RUNTIME\_PARAM\_FROM\_GROUP ist.}
A high level overview over the property system's design and principle ideas
are given, then follows a reference and a self-contained example.