Commit 3ff6d9ef authored by Johannes Hommel's avatar Johannes Hommel
Browse files

Merge branch 'fix/handbook-2.10' into 'master'

Fix/handbook 2.10

- [x] Should we still mention flyspray?
- [x] Mention implicit box adaptive?
- [x] Remove link to dune user wiki? (-> FS#330)

See merge request !198
parents 2fe531e4 d36609b6
......@@ -39,7 +39,7 @@
% Dune and Dumux logo
\newcommand{\Dune}{{DUNE}\xspace}
\newcommand{\Dumux}{\texorpdfstring{Du\-Mu$^\text{x}$\xspace}{DuMuX\xspace}}
\newcommand{\DumuxVersion}{2.9}
\newcommand{\DumuxVersion}{2.10}
\definecolor{dumuxYellow}{HTML}{E19417}
\definecolor{dumuxBlue}{HTML}{0C73CF}
......
......@@ -41,9 +41,9 @@ After extracting the source code for all relevant \Dune modules, including \Dumu
by the shell-command \texttt{dunecontrol} which is part of the \Dune build system.
\subsection{Prerequisites} \label{sec:prerequisites}
A reasonable recent \Cplusplus compiler (g++ (4.8), clang++ (3.5), or Intels ICC), CMake (version 2.8.12 or newer) and their
A reasonable recent \Cplusplus compiler (g++ (4.9), clang++ (3.5), or Intels ICC), CMake (version 2.8.12 or newer) and their
dependencies are required.
For a list of prerequisite software packages to install see \cite{DUNE-WIKI-PREREQUISITE-SOFTWARE}.
For prerequisite software packages to install see \cite{DUNE-HP}.
The building of included documentation like this handbook requires \LaTeX{} and auxiliary tools
\texttt{bibtex}. One usually chooses a \LaTeX{} distribution like \texttt{texlive} for this purpose.
......@@ -59,7 +59,7 @@ Git clients must be installed to download modules from Git repositories.
\subsection{Obtaining Source Code for \Dune and \Dumux}
As stated above, the \Dumux release and trunk (developer tree) are based on the most recent
\Dune release 2.3, comprising the core modules dune-common, dune-geometry, dune-grid,
\Dune release 2.4, comprising the core modules dune-common, dune-geometry, dune-grid,
dune-istl and dune-localfunctions. For working with \Dumux, these modules are required. The
external module dune-PDELab is recommended and required for several \Dumux features.
......@@ -107,18 +107,17 @@ on the Dune grid interface, act similar.
\paragraph{Obtaining \Dune and \Dumux from software repositories}
Direct access to a software revision control system for downloading code can be of advantage later on.
It is easier to keep up with code changes and to receive important bug fixes.\Dune and \Dumux use
Git for their software repositories. To access them a certain programs are needed which
is referred to here shortly as Git client.
Git for their software repositories. To access them a Git client is needed.
In the technical language of Git \emph{cloning a certain software version} means nothing more then fetching
In the technical language of Git, \emph{cloning a certain software version} means nothing more then fetching
a local copy from the software repository and laying it out in the file system.
In addition to the software some more files for the use of the software revision
In addition to the software, some more files for the use of the software revision
control system itself are created. If you have developer access to \Dumux, it is
also possible to do the opposite, i.\,e. to load up a modified revision of software
into the software repository. This is usually termed as \emph{commit} and \emph{push}.
The installation procedure is done as follows:
Create a {\Dune} root directory, named \texttt{dune} in the lines below.
Create a {\Dune} root directory, named e.g. \texttt{DUNE-ROOT} in the lines below.
Then, enter the previously created directory and check out the desired modules.
As you see below, the check-out uses two different servers for getting the sources,
one for \Dune and one for \Dumux.
......@@ -126,8 +125,8 @@ The \Dune modules of the stable 2.4 release branch are checked out as described
on the \Dune website \cite{DUNE-DOWNLOAD-GIT}:
\begin{lstlisting}[style=Bash]
$ mkdir DUMUX
$ cd DUMUX
$ mkdir DUNE-ROOT
$ cd DUNE-ROOT
$ git clone -b releases/2.4 https://gitlab.dune-project.org/core/dune-common.git
$ git clone -b releases/2.4 https://gitlab.dune-project.org/core/dune-geometry.git
$ git clone -b releases/2.4 https://gitlab.dune-project.org/core/dune-grid.git
......@@ -137,9 +136,9 @@ $ git clone -b releases/2.3 https://gitlab.dune-project.org/PDELab/dune-typetree
$ git clone -b releases/2.0 https://gitlab.dune-project.org/PDELab/dune-pdelab.git
\end{lstlisting}
The newest and maybe unstable developments are also provided in these repositories and is called \emph{master}.
Please check the \Dune website \cite{DUNE-DOWNLOAD-GIT} for further information. However, the current \Dumux release
is based on the stable 2.4 release and it might not compile without further adaptations using the newest versions of \Dune.
The newest and maybe unstable developments are also provided in these repositories and can be found in the \emph{master} branch.
Please check the \Dune website \cite{DUNE-DOWNLOAD-GIT} for further information. We always try to keep up with the latest developments of \Dune.
However, the current \Dumux release is based on the stable 2.4 release and it might not compile without further adaptations using the newest versions of \Dune.
Furthermore, if you wish to install the optional \Dune Grid-Howto which provides a tutorial
on the Dune grid interface, act similar.
......
......@@ -10,8 +10,8 @@ If not given differently in the input files, this is \texttt{build-cmake} as def
\begin{enumerate}
\item Go to the directory \texttt{build-cmake/test}. There, various test application
folders can be found. Let us consider as example \texttt{implicit/test{\_}box2p}:
\item Enter the folder \texttt{implicit/2p}. Type \texttt{make test{\_}box2p} in order
folders can be found. Let us consider as example \texttt{porousmediumflow/2p/implicit/test{\_}box2p}:
\item Enter the folder \texttt{porousmediumflow/2p/implicit}. Type \texttt{make test{\_}box2p} in order
to compile the application \texttt{test{\_}box2p}. To run the simulation, type\\
\texttt{./test{\_}box2p -parameterFile ./test\_box2p.input}\\
into the console. The parameter \texttt{-parameterFile} specifies that all
......
......@@ -248,7 +248,7 @@ of mixtures such as density or enthalpy are of interest. These
interactions are defined by {\em fluid systems}, which are located in
\verb+dumux/material/fluidsystems+. A more thorough overview of the
\Dumux fluid framework can be found
at \url{http://www.dumux.org/doxygen-stable/html-2.9/modules.php}
at \url{http://www.dumux.org/doxygen-stable/html-2.10/modules.php}
%in chapter~\ref{sec:fluidframework}.
% In this example, a class for the definition of a two-phase system is used. This allows for the choice
......@@ -412,7 +412,7 @@ To do that, you have to select different components via the property system in t
If you want to take a closer look on how the fluid classes are defined and which
substances are already available please browse through the files in the directory
\texttt{/dumux/material/components} and read
the doxygen documentation \url{http://www.dumux.org/doxygen-stable/html-2.9/modules.php}.
the doxygen documentation \url{http://www.dumux.org/doxygen-stable/html-2.10/modules.php}.
%chapter~\ref{sec:fluidframework}.
\item \textbf{Use a Full-Fledged Fluid System} \\
......
......@@ -119,14 +119,14 @@ a problem class is attached to the new type tag, while the grid which
is going to be used is defined in line \ref{tutorial-sequential:set-grid-type} --
in this case an \texttt{YaspGrid} is created. Since there's no uniform mechanism to
allocate grids in \Dune, \Dumux features the concept of grid creators.
In this case the generic \texttt{CubeGridCreator} (line \ref{tutorial-sequential:set-gridcreator}) which creates a
In this case the generic \texttt{CubeGridCreator} which creates a
structured hexahedron grid of a specified size and resolution. For
this grid creator the physical domain of the grid is specified via the
run-time parameters \texttt{Grid.UpperRight} and
\texttt{Grid.Cells}. These parameters can be specified via
the command-line or in a parameter file.
For more information about the \Dune grid interface, the different grid types
that are supported and the generation of different grids consult
that are supported and the generation of different grids, consult chapter \ref{sec:gridhandling} of this document and
the \textit{Dune Grid Interface HOWTO} \cite{DUNE-HP}.
Next, we select the material of the simulation: In the case of a pure two-phase
......@@ -408,7 +408,7 @@ As you have experienced, compilation takes quite some time. Therefore, \Dumux
provides a simple method to read in parameters (such as simulation end time or
modelling parameters) via \texttt{Paramter Input Files}. The tests in the Test-folder
\texttt{/test/} already use this system.\\
If you look at the Application in \texttt{/test/implicit/2p/}, you see that
If you look at the Application in \texttt{/test/porousmediumflow/2p/sequential/}, you see that
the main file looks rather empty: The parameter file \texttt{test\_box2p.input}
is read by a standard start procedure, which is called in the main function.
This should be adapted for your problem at hand. The program run has to be
......
......@@ -2,10 +2,15 @@
\label{sc_developingdumux}
\subsection{Communicate with \Dumux Developers}
\paragraph{GitLab Issues}
The bug-tracking system \emph{GitLab Issues} offers the possibility to report bugs or
discuss new development requests. Feel free to register (if you don't have a \emph{Git} account alreay) and to constribute
at \url{https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/issues}.
\paragraph{Flyspray}
The bug-tracking system \emph{Flyspray} offers the possibility to report bugs or
discuss new development requests. Feel free to register and to constribute
at \url{http://www.dumux.org/flyspray/}.
The bug-tracking system \emph{Flyspray} has been replaced by \emph{GitLab Issues} and will not
be used anymore.
\paragraph{Automatic Testing Dashboard}
The automatic testing using \emph{BuildBot} helps to constantly check the
......
......@@ -18,7 +18,7 @@ complex DGF files, we recommend to write your own scripts, e.g in \Cplusplus, Ma
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/implicit/co2} folder.
the \texttt{test\_boxco2} or \texttt{test\_cco2} in the \texttt{dumux/test/porousmediumflow/co2/implicit/} 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/}).
......
......@@ -127,7 +127,7 @@ $\boldsymbol{v}_\alpha$ & velocity (Darcy or free flow)& & \\
\subsection{Available Models}
We distinguish fully-implicit and sequential models. A list of all available models can be found
in the Doxygen documentation at
\url{http://www.dumux.org/doxygen-stable/html-2.9/modules.php}.
\url{http://www.dumux.org/doxygen-stable/html-2.10/modules.php}.
The documentation includes a detailed description for every model.
\subsubsection{Fully-Implicit Models}
......@@ -138,6 +138,11 @@ method as temporal discretization. The fully-implicit models are located in
subdirectories of \texttt{dumux/freeflow}, \texttt{dumux/geomechanics},
and \texttt{dumux/porousmediumflow}.
Grid adaption is available for both discretization schemes, box and cc. The \texttt{adaptionhelper}-method has to be adjusted to the respective model.
Note that the current implementation only ensures mass conservation for incompressible fluids.
In general, the spatial parameters, especially the porosity, have to be assigned on
the coarsest level of discretization.
\subsubsection{Sequential Models}
The basic idea of the sequential models is to reformulate the
equations of multi-phase flow into one equation for
......
......@@ -1498,22 +1498,6 @@ doi ={10.1039/TF9615701200}
key = {DUNE-INST}
}
@MISC{DUNE-MAIN-WIKI,
title = {{{DUNE} Main Wiki: \url{http://users.dune-project.org/projects/main-wiki/wiki/}}},
key = {DUNE-MAIN-WIKI}
}
@MISC{DUNE-USER-WIKI,
title = {{{DUNE} User Wiki: \url{http://users.dune-project.org/}}},
key = {DUNE-USER-WIKI}
}
@MISC{DUNE-WIKI-PREREQUISITE-SOFTWARE,
title = {{{DUNE} user wiki, prerequisite software packages:
\url{http://users.dune-project.org/projects/main-wiki/wiki/Installation_prerequisite_software}}},
key = {DUNE-WIKI-PREREQUISITE-SOFTWARE}
}
@MISC{FENICS-HP,
title = {{The {FEniCS} Project: \url{http://www.fenicsproject.org/}}},
key = {FENICS}
......
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