From aada7b245a51aca5fb3ffce44ac0cf5f0c718fbb Mon Sep 17 00:00:00 2001 From: Thomas Fetzer Date: Wed, 25 May 2016 11:12:37 +0200 Subject: [PATCH 1/3] [doc][*.opts] Update documentation of gstat * in handbook and doxygen * add hint in the opts file --- debug.opts | 12 +++--- doc/handbook/4_externaltools.tex | 37 ++++++++++++++----- .../spatialparams/gstatrandomfield.hh | 13 +++++-- optim.opts | 13 ++++--- 4 files changed, 50 insertions(+), 25 deletions(-) diff --git a/debug.opts b/debug.opts index 338c71c009..925e0ffb07 100644 --- a/debug.opts +++ b/debug.opts @@ -16,13 +16,15 @@ GXX_OPTS=" \ -fstrict-overflow \ -g" -USE_CMAKE=yes - +# configure flags CMAKE_FLAGS="\ -DCMAKE_CXX_FLAGS=\"$GXX_WARNING_OPTS $GXX_OPTS\" \ " -# for CO2 and CO2ni tests +# optional configure flags +# for the CO2 and CO2ni tests enable the experimental grid extension +# and make sure the module dune-alugrid is present # -DDUNE_GRID_EXPERIMENTAL_GRID_EXTENSIONS=TRUE \ -# need to be set in the configure flags -# and the module dune-alugrid must be present + +# for using gstat +# -DGSTAT_ROOT=gstat_installation_path \ diff --git a/doc/handbook/4_externaltools.tex b/doc/handbook/4_externaltools.tex index ba942f9284..1ef274c4ce 100644 --- a/doc/handbook/4_externaltools.tex +++ b/doc/handbook/4_externaltools.tex @@ -1,6 +1,17 @@ \section{External Tools} \label{sc_externaltools} +\subsection{Eclipse} +There is an Eclipse style file which can be used for \Dumux. +\begin{enumerate} + \item open in eclipse: \texttt{Window} $\rightarrow$ \texttt{Preferences} $\rightarrow$ + \texttt{C/C++} $\rightarrow$ \texttt{Code Style} $\rightarrow$ \texttt{Formatter} + \item press the \texttt{Import} button + \item choose the file \texttt{eclipse\_profile.xml} from your dumux-devel directory + \item make sure that that now \Dumux is chosen in \texttt{Select a profile} +\end{enumerate} + + \subsection{Git} Git is a version control tool which we use. The basic Git commands are: @@ -17,15 +28,20 @@ The basic Git commands are: a commit \end{itemize} -\subsection{Eclipse} -There is an Eclipse style file which can be used for \Dumux. -\begin{enumerate} - \item open in eclipse: \texttt{Window} $\rightarrow$ \texttt{Preferences} $\rightarrow$ - \texttt{C/C++} $\rightarrow$ \texttt{Code Style} $\rightarrow$ \texttt{Formatter} - \item press the \texttt{Import} button - \item choose the file \texttt{eclipse\_profile.xml} from your dumux-devel directory - \item make sure that that now \Dumux is chosen in \texttt{Select a profile} -\end{enumerate} + +\subsection{Gnuplot} +A gnuplot interface is available to plot or visualize results during a simulation run. +This is achieved with the help of the class provided in \texttt{io/gnuplotinterface.hh}. +Have a look at tests including this header for examples how to use this interface. + + +\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.sh} from your \Dumux root +directory or donwload, 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{Kate} For kate there is syntax highlighting style for \Dumux input files. Simply @@ -33,11 +49,12 @@ copy the file \texttt{dumux-devel/dumux\-InputFiles.xml} to the \texttt{syntax} your kate configuration directory (e.g. \texttt{HOME/.kde4/share/apps\-/katepart/syntax/dumuxInputFiles.xml}). + \subsection{ParaView} \paragraph{Reload Button:} There are scripts to reload \texttt{*.pvd} or series of {\texttt{*.vtu} files since ParaView 4.2. The scripts can be found -\href{http://markmail.org/message/exxynsgishbvtngg#query:+page:1+mid:rxlwxs7uqrfgibyv+state:results}{\texttt{under this lin}}. +\href{http://markmail.org/message/exxynsgishbvtngg#query:+page:1+mid:rxlwxs7uqrfgibyv+state:results}{\texttt{under this link}}. Just save the specific code portion in a file and load it via \texttt{Macros} $\rightarrow$ \texttt{Add new macro}. \paragraph{Guide:} diff --git a/dumux/material/spatialparams/gstatrandomfield.hh b/dumux/material/spatialparams/gstatrandomfield.hh index 8f8fe9b010..b34554f784 100644 --- a/dumux/material/spatialparams/gstatrandomfield.hh +++ b/dumux/material/spatialparams/gstatrandomfield.hh @@ -19,6 +19,7 @@ /*! * \file * + * \ingroup SpatialParameters * \brief Creating random fields using gstat */ #ifndef DUMUX_GSTAT_RANDOM_FIELD_HH @@ -33,13 +34,16 @@ namespace Dumux { /*! + * \ingroup SpatialParameters * \brief Creating random fields using gstat * * gstat is an open source software tool which can (among other things) generate - * geostatistical random fields (see www.gstat.org). + * geostatistical random fields (see http://www.gstat.org). * - * To use this class, unpack and install the zipped gstat tarball from the website - * or use the script installexternal.sh provided with dumux. + * To use this class, execute the installexternal.sh from your DuMuX root + * directory or donwload, unpack and install the tarball from the gstat-website. + * Then rerun cmake (in the second case set GSTAT_ROOT in your input file to the + * path where gstat is installed). */ template class GstatRandomField @@ -55,7 +59,8 @@ public: // Add field types if you want to implement e.g. tensor permeabilities. enum FieldType { scalar, log10 }; - /*!\brief Constructor. + /*! + * \brief Constructor. * * Creates a new field with random variables, if desired. * Otherwise creates a data field from already available data. diff --git a/optim.opts b/optim.opts index bb7499ca78..937f720422 100644 --- a/optim.opts +++ b/optim.opts @@ -19,14 +19,15 @@ GXX_OPTS=" \ -march=native \ -DNDEBUG=1" -USE_CMAKE=yes - -# configure flags +# configure flags CMAKE_FLAGS=" \ -DCMAKE_CXX_FLAGS=\"$GXX_WARNING_OPTS $GXX_OPTS\" \ " -# for CO2 and CO2ni tests +# optional configure flags +# for the CO2 and CO2ni tests enable the experimental grid extension +# and make sure the module dune-alugrid is present # -DDUNE_GRID_EXPERIMENTAL_GRID_EXTENSIONS=TRUE \ -# need to be set in the CMake flags -# and the module dune-alugrid must be present + +# for using gstat +# -DGSTAT_ROOT=gstat_installation_path \ -- GitLab From 8871172cdc7142bd296051426e4c821060dd775d Mon Sep 17 00:00:00 2001 From: Kissinger Date: Wed, 25 May 2016 16:44:28 +0200 Subject: [PATCH 2/3] [Handbook] Small typo --- doc/handbook/4_externaltools.tex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/handbook/4_externaltools.tex b/doc/handbook/4_externaltools.tex index 1ef274c4ce..5d2233cb23 100644 --- a/doc/handbook/4_externaltools.tex +++ b/doc/handbook/4_externaltools.tex @@ -8,7 +8,7 @@ There is an Eclipse style file which can be used for \Dumux. \texttt{C/C++} $\rightarrow$ \texttt{Code Style} $\rightarrow$ \texttt{Formatter} \item press the \texttt{Import} button \item choose the file \texttt{eclipse\_profile.xml} from your dumux-devel directory - \item make sure that that now \Dumux is chosen in \texttt{Select a profile} + \item make sure that now \Dumux is chosen in \texttt{Select a profile} \end{enumerate} -- GitLab From 4ac7982282bd4a8a2beb9186b4a792845c008552 Mon Sep 17 00:00:00 2001 From: Kissinger Date: Wed, 25 May 2016 17:03:56 +0200 Subject: [PATCH 3/3] [Doxygen] Some typos in doxygen in gstat header --- dumux/material/spatialparams/gstatrandomfield.hh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dumux/material/spatialparams/gstatrandomfield.hh b/dumux/material/spatialparams/gstatrandomfield.hh index b34554f784..33289d2097 100644 --- a/dumux/material/spatialparams/gstatrandomfield.hh +++ b/dumux/material/spatialparams/gstatrandomfield.hh @@ -65,12 +65,12 @@ public: * Creates a new field with random variables, if desired. * Otherwise creates a data field from already available data. * - * For the a rand field generation three files are necessary. + * For the random field generation three files are necessary. * A \a gstatControlFile in which all commands and in/output files for gstat are specified. * A \a gstatInputFile contains all coordinates (cell centers) of the grid, so that * gstat can perform its random realization. The filename must be same as in the gstatControlFile. * A \a gstatOutputFile in which gstat writes the random values to this file. - * The filename must be same as in the gstatControlFile. + * The filename must be the same as in the gstatControlFile. * * \param gridView the used gridView * \param gstatControlFile name of control file for gstat -- GitLab