diff --git a/doc/handbook/0_dumux-handbook.tex b/doc/handbook/0_dumux-handbook.tex
index 2a942326544ae93992954917166de085865346de..e23d630f07cd788825ca6aa284a6694c846e84f4 100644
--- a/doc/handbook/0_dumux-handbook.tex
+++ b/doc/handbook/0_dumux-handbook.tex
@@ -39,7 +39,7 @@
% Dune and Dumux logo
\newcommand{\Dune}{{DUNE}\xspace}
\newcommand{\Dumux}{\texorpdfstring{Du\-Mu$^\text{x}$\xspace}{DuMuX\xspace}}
-\newcommand{\DumuxVersion}{2.10}
+\newcommand{\DumuxVersion}{2.11c}
\definecolor{dumuxYellow}{HTML}{E19417}
\definecolor{dumuxBlue}{HTML}{0C73CF}
@@ -142,7 +142,6 @@ in deeper modifications of underlying \Dumux models, classes, functions, etc.
\input{5_spatialdiscretizations}
\input{5_stepsofasimulation}
\input{5_propertysystem}
-\input{5_fluidframework}
\input{5_grids}
\bibliographystyle{plain}
diff --git a/doc/handbook/4_structure.tex b/doc/handbook/4_structure.tex
index d685f33b095b25db4dc1a47cfa17b98b9df9ee8b..66d97a6c83b610a53490f2e7461b9e3385dfe1d5 100644
--- a/doc/handbook/4_structure.tex
+++ b/doc/handbook/4_structure.tex
@@ -3,65 +3,18 @@
\Dumux has the following folder structure, which is similar to other \Dune modules.
\begin{itemize}
-\item \texttt{bin}: contains binaries, e.g. used for the automatic testing
+\item \texttt{bin}: binaries, e.g. used for the automatic testing, postprocessing, installation
\item \texttt{cmake}: the configuration options for building \Dumux
-\item \texttt{doc}: contains the Doxygen documentation (\texttt{doc/doxygen/html/index.html}),
- this handbook, and various logos
+\item \texttt{doc}: files necessary for the Doxygen documentation and this handbook, and various logos
\item \texttt{dumux}: the main folder, containing the source files, see \ref{fig:dumux-structure}
for a visualized structure. For more information on the models have a look at the
Doxygen documentation.
- \begin{itemize}
- \item \texttt{common}: general methods shared by all models,
- like the \texttt{start.hh} or the time manager
-
- \item \texttt{freeflow}: single-phase free-flow models. All models are discretized
- fully implicitly using the box-method.
-
- \item \texttt{geomechanics}: models for solving rock mechanics and flow.
-
- \item \texttt{implicit}: contains the general methods shared
- by all implicit models, together with specilized methods
- for the two discretization types \texttt{box} and \texttt{cellcentered}.
- The \texttt{adaptive} folder contains methods for grid adaption.
- The specialized model files can be found
- at \texttt{porousmediumflow/model of interest/implicit/},
- \texttt{freeflow/model of interest/}, or \texttt{geomechanics/model of interest/}.
-
- \item \texttt{io}: additional in-/output possibilities like restart files,
- gnuplot-interface and a VTKWriter.
-
- \item \texttt{linear}: contains linear solver backends.
-
- \item \texttt{material}: all material parameters and constitutive equations.
- Properties of a pure chemical (pseudo)substance (e.g. water, air) are located
- in \texttt{components}. The fluidsystems collect information from the \texttt{components} and
- \texttt{binarycoefficients} (like Henry coefficients), and combines them with fluid phase characteristics
- (e.g. viscosity, density).
- The folder \texttt{spatialparams} contains all spatially dependend variables, like permeability and porosity.
- The class in \texttt{implicitspatialparameters.hh} provides spatial averaging routines.
- Constitutive relations are found in \texttt{fluidmatrixinteractions}.
-
- \item \texttt{multidomain}: coupling handling and coupling conditions for connecting
- different model types in different subdomains.
-
- \item \texttt{nonlinear}: Newton's method.
-
- \item \texttt{parallel}: helper files for parallel simulations.
-
- \item \texttt{porousmediumflow}: contains all models for porous media setups.
-
- \item \texttt{sequential}: contains the general methods shared
- by all sequential models. The specialized model files can be found
- at \texttt{porousmediumflow/model of interest/sequential/}.
-\end{itemize}
-
\item \texttt{test}: tests for each numerical model and some functionality.
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{*.input}.
+ \texttt{*.cc}, the problem definition \texttt{*problem.hh}, and an input file \texttt{*.input}.
+ If necessary, spatially dependent parameters are defined in \texttt{*spatialparameters.hh}.
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}.
\end{itemize}
@@ -102,27 +55,30 @@
[.\node[draw=dumuxYellow, ultra thick] {dumux};
[.\node[FirstLevel] {common};
\node[ThirdLevel] {
- Common files of the implicit (box and cell centered) models and the
- sequential models: time integration, start routine, the property
- system, ...};
+ Common files of the implicit and the sequential models:
+ time integration, start routine \texttt{start.hh}, the property system, ...};
]
[.\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[ThirdLevel] {Single-phase free flow models using Navier-Stokes
+ and algebraic turbulence models.
+ All models are discretized with the box-method.};
]
]
[.\node[FirstLevel] {geomechanics};
[.\node[SecondLevel] {\emph{models}};
- \node[ThirdLevel] {Specific model definition for coupled flow and geomechnics simulations.};
+ \node[ThirdLevel] {Specific model files for coupling flow and rock mechanisms.};
]
]
[.\node[FirstLevel] {implicit};
% [.\node[SecondLevel] {\emph{models}};
\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.};
+ assembling in localjacobian.hh, evaluation of partial derivative
+ in localresidual.hh, base classes for model and problem definition.};
% ]
+ [.\node[SecondLevel] {adaptive};
+ \node[ThirdLevel] {Contains the methods for grid adaption.};
+ ]
[.\node[SecondLevel] {box};
\node[ThirdLevel] {Specific files for the gerenal fully implicit boxmethod:
assembler, dual mesh geometry in fvelementgeometry.hh,
@@ -133,10 +89,13 @@
mesh geometry in fvelementgeometry.hh, base classes for model and
problem definition.};
]
+ [.\node[SecondLevel] {cornerpoint};
+ \node[ThirdLevel] {Files need for handling cornerpoint grids.};
+ ]
]
[.\node[FirstLevel] {io};
- \node[ThirdLevel] {Additional in-/output possibilities like restart files, gnuplot-interface
- and a VTKWriter extension. Grid Creator files.};
+ \node[ThirdLevel] {Additional in-/output possibilities like restart files, gnuplot-interface,
+ VTKWriter extensions and files for grid generation.};
]
[.\node[FirstLevel] {linear};
\node[ThirdLevel] {Linear solver backend.};
@@ -146,13 +105,15 @@
\node[ThirdLevel] {Binary coefficients (like binary diffusion coefficients) and those
needed for the constitutive relationships (e.g. Henry coefficient)};
]
+ [.\node[SecondLevel] {chemistry};
+ \node[ThirdLevel] {Files needed to account for, e.g. electrochemical processes as in a fuel cell.};
+ ]
[.\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
+ \node[ThirdLevel] {Constraint solvers to make sure that the resulting fluid state is consistent with a
given set of thermodynamic equations.};
]
[.\node[SecondLevel] {eos};
@@ -161,16 +122,16 @@
and density.};
]
[.\node[SecondLevel] {fluidmatrixint.};
- \node[ThirdLevel] {Constitutive relationships (e.g. capillary pressure - saturation - curve};
+ \node[ThirdLevel] {Constitutive relationships (e.g. capillary pressures, relative permeabilities};
]
[.\node[SecondLevel] {fluidstates};
- \node[ThirdLevel] {Fluid states are responsible for representing the complete thermodynamic
+ \node[ThirdLevel] {Fluid states are responsible for caching the 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[SecondLevel] {spatialparams};
\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.};
@@ -178,8 +139,8 @@
]
[.\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[ThirdLevel] {Localoperators, which implement the coupling and communication
+ between models in different subdomains, and model specific properties.};
]
[.\node[SecondLevel] {common};
\node[ThirdLevel] {The multidomain wrappers, generic functions, and properties.};
@@ -192,22 +153,16 @@
\node[ThirdLevel] {Newton's method.};
]
[.\node[FirstLevel] {parallel};
- \node[ThirdLevel] {Files for parallel programming.};
- ]
+ \node[ThirdLevel] {Helper files for parallel simulations.};
+ ]
[.\node[FirstLevel] {porousmediumflow};
[.\node[SecondLevel] {\emph{models}};
\node[ThirdLevel] {Specific model definition for porous medium flow simulations,
- in both \emph{implicit} or \emph{sequential} formulation:
+ in both \texttt{implicit} or \texttt{sequential} formulation:
implementation of equations,
model specific properties and indices.};
]
]
- [.\node[FirstLevel] {sequential};
-% [.\node[SecondLevel] {\emph{models}};
- \node[ThirdLevel] {
- General model definitions for the sequential formulation.};
-% ]
- ]
]
\end{tikzpicture}
\caption{Structure of the directory \texttt{dumux} containing the \Dumux source files.}
diff --git a/doc/handbook/5_fluidframework.tex b/doc/handbook/5_fluidframework.tex
deleted file mode 100644
index 2a242f22e897168c4e747205508f4502069a6c67..0000000000000000000000000000000000000000
--- a/doc/handbook/5_fluidframework.tex
+++ /dev/null
@@ -1,6 +0,0 @@
-\section{Material and Fluid Framework}
-\label{sec:fluidframework}
-
-Detailed explanations for the \Dumux material and fluid framework can be found in the Doxygen documentation via \texttt{Modules -> Material and Fluid Framework}.
-
-
diff --git a/doc/handbook/CMakeLists.txt b/doc/handbook/CMakeLists.txt
index c639c9fc34faa153faec412321b738a9d52f7204..f2f89dcb575b7b07f9ee84414275c978b9f7da04 100644
--- a/doc/handbook/CMakeLists.txt
+++ b/doc/handbook/CMakeLists.txt
@@ -18,7 +18,6 @@ set(TEX_INPUTS
4_restartsimulations.tex
4_structure.tex
5_stepsofasimulation.tex
- 5_fluidframework.tex
5_grids.tex
5_models.tex
5_propertysystem.tex