[doc] fix some stuff in handbook and doxygen

Handbook:
- don't use deprecated Latex commands \it and \bf
- use the \Cplusplus macro consistently

Doxygen:
- put FluidStates group to the right hierarchy level
- improve wording

doc/doxygen/modules.txt

@@ -7,7 +7,7 @@
 
 /* ***************** Porousmediaflow ******************/
 /*!
- * \defgroup Porousmediaflow Porousmediumflow (fully implicit if not denoted otherwise)
+ * \defgroup Porousmediaflow Porous-Medium Flow (fully implicit if not denoted otherwise)
  */
     /*!
      * \ingroup Porousmediaflow
@@ -112,19 +112,19 @@
      */
     /*!
      * \ingroup Porousmediaflow
-     * \defgroup CO2Model CO2 (2-phase, 2-component Darcy flow)
+     * \defgroup CO2Model CO2 (two-phase, two-component Darcy flow)
      *
      * \copydetails Dumux::CO2Model
      */
     /*!
      * \ingroup Porousmediaflow
-     * \defgroup MPNCModel Mpnc (m-phase, n-component Darcy flow)
+     * \defgroup MPNCModel MpNc (m-phase, n-component Darcy flow)
      *
      * \copydetails Dumux::MPNCModel
      */
     /*!
      * \ingroup Porousmediaflow
-     * \defgroup NIModel Nonisothermal (non-isothermal model)
+     * \defgroup NIModel Non-isothermal (energy equation, to be added to an isothermal model)
      *
      * \copydetails Dumux::NIModel
      */
@@ -160,11 +160,11 @@
 
 /* ***************** Freeflow ******************/
 /*!
- * \defgroup Freeflow Freeflow (fully implicit)
+ * \defgroup Freeflow Free Flow (fully implicit)
  */
     /*!
      * \ingroup Freeflow
-     * \defgroup BoxStokesModel Stokes (one-phase Stokes model)
+     * \defgroup BoxStokesModel Stokes (one-phase Stokes flow)
      *
      * \copydetails Dumux::StokesModel
      */
@@ -209,7 +209,7 @@
      */
     /*!
      * \ingroup Multidomain
-     * \defgroup TwoPTwoCStokesTwoCModel 2cstokes2p2c (Stokes2c flow, coupled to two-phase, two-component Darcy flow)
+     * \defgroup TwoPTwoCStokesTwoCModel 2cstokes2p2c (1p2c Stokes flow coupled to 2p2c Darcy flow)
      *
      * # Coupling Conditions
      * \copydetails Dumux::TwoCStokesTwoPTwoCLocalOperator
@@ -222,7 +222,7 @@
      */
     /*!
      * \ingroup Multidomain
-     * \defgroup TwoPTwoCNIStokesTwoCNIModel 2cnistokes2p2cni (Stokes2c flow, coupled to two-phase, two-component Darcy flow, non-isothermal)
+     * \defgroup TwoPTwoCNIStokesTwoCNIModel 2cnistokes2p2cni (1p2cni Stokes flow coupled to 2p2cni Darcy flow)
      *
      * # Coupling Conditions
      * \copydetails Dumux::TwoCNIStokesTwoPTwoCNILocalOperator
@@ -238,7 +238,7 @@
      */
     /*!
      * \ingroup Multidomain
-     * \defgroup TwoPTwoCZeroEqTwoCModel 2czeroeq2p2c (Stokes2c flow with zero-eq turbulence model, coupled to two-phase, two-component Darcy flow)
+     * \defgroup TwoPTwoCZeroEqTwoCModel 2czeroeq2p2c (1p2c Stokes flow with zero-eq turbulence model coupled to 2p2c Darcy flow)
      *
      * # Coupling Conditions
      * \copydetails Dumux::TwoCStokesTwoPTwoCLocalOperator
@@ -251,7 +251,7 @@
      */
     /*!
      * \ingroup Multidomain
-     * \defgroup TwoPTwoCNIZeroEqTwoCNIModel 2cnizeroeq2p2cni (Stokes2c flow with zero-eq turbulence model, coupled to two-phase, two-component Darcy flow, non-isothermal)
+     * \defgroup TwoPTwoCNIZeroEqTwoCNIModel 2cnizeroeq2p2cni (1p2cni Stokes flow with zero-eq turbulence model coupled to 2p2cni Darcy flow)
      *
      * # Coupling Conditions
      * \copydetails Dumux::TwoCNIStokesTwoPTwoCNILocalOperator
@@ -268,7 +268,7 @@
 
 /* ***************** Fully Implicit ******************/
 /*!
- * \defgroup ImplicitModel Fully Implicit Scheme
+ * \defgroup ImplicitModel Fully-Coupled Fully-Implicit Scheme
  */
     /*!
      * \ingroup ImplicitModel
@@ -280,11 +280,11 @@
      */
          /*!
          * \ingroup Discretizations
-         * \defgroup CCModel Fully implicit cell-centered discretization
+         * \defgroup CCModel Fully-implicit cell-centered discretization
          */
          /*!
          * \ingroup Discretizations
-         * \defgroup BoxModel Fully implicit box discretization
+         * \defgroup BoxModel Fully-implicit box discretization
          */
     /*!
      * \ingroup ImplicitModel
@@ -317,7 +317,7 @@
 
 /* ***************** Sequential ******************/
 /*!
- * \defgroup Sequential Sequential Scheme (Implicit Pressure Explicit Transport)
+ * \defgroup Sequential Sequential Scheme (Implicit Pressure, Explicit Transport)
  */
     /*!
      * \ingroup Sequential
@@ -405,7 +405,8 @@
      * pressure, composition and density. Since these classes are only used
      * internally in fluid systems, their programming interface is
      * currently ad-hoc.
-     *
+     */
+    /*!
      * \ingroup Material
      * \defgroup FluidStates Fluid States
      * Fluid states are responsible for representing the

doc/handbook/0_dumux-handbook.tex

@@ -46,7 +46,7 @@
 % sytles
 \newcommand{\nextline}{\par\phantom{a}\vspace*{0.1\textwidth}}
 \newcommand{\snakeline}{\uwave{\mbox{}}}
-\DeclareRobustCommand\Cplusplus{\texorpdfstring{C\nolinebreak[4]\hspace{-.05em}\raisebox{.4ex}{\tiny\bf ++}\xspace}{C++}}
+\DeclareRobustCommand\Cplusplus{\texorpdfstring{C\nolinebreak[4]\hspace{-.05em}\raisebox{.4ex}{\tiny\bfseries ++}\xspace}{C++}}
 
 % notation
 \newcommand{\porosity}{\phi}
@@ -67,7 +67,7 @@
 \theoremheaderfont{\sffamily\bfseries}
 \newtheorem{lst}{Listing}
 
-\DeclareMathOperator{\grad}{\bf grad}
+\DeclareMathOperator{\grad}{\mathbf{grad}}
 \DeclareMathOperator{\curl}{curl}
 \DeclareMathOperator{\Div}{div}
 

doc/handbook/0_listingstyle.tex

@@ -71,7 +71,7 @@
  numberstyle=\tiny,
  basicstyle=\ttfamily\scriptsize,
  stringstyle=\color{BrickRed}\ttfamily\let\textcolor\textcolordummy,
- commentstyle=\color[gray]{0.35}\ttfamily\it\let\textcolor\textcolordummy,
+ commentstyle=\color[gray]{0.35}\ttfamily\itshape\let\textcolor\textcolordummy,
 }
 
 % for listings of DuMuX code
@@ -85,7 +85,7 @@
   basicstyle=\ttfamily\scriptsize,
   keywordstyle=\color{dumuxBlue}\ttfamily\let\textcolor\textcolordummy,
   stringstyle=\color{BrickRed}\ttfamily\let\textcolor\textcolordummy,
-  commentstyle=\color[gray]{0.35}\ttfamily\it\let\textcolor\textcolordummy,
+  commentstyle=\color[gray]{0.35}\ttfamily\itshape\let\textcolor\textcolordummy,
   emph={NEW_TYPE_TAG, NEW_PROP_TAG, UNSET_PROP, TTAG, PTAG,
        SET_PROP, GET_PROP, GET_PROP_VALUE, GET_PROP_TYPE,
        SET_BOOL_PROP, SET_STRING_PROP, SET_SCALAR_PROP, SET_TYPE_PROP, SET_INT_PROP,
@@ -103,6 +103,6 @@
  numberstyle=\tiny,
  basicstyle=\ttfamily\scriptsize,
  stringstyle=\color{BrickRed}\ttfamily\let\textcolor\textcolordummy,
- commentstyle=\color[gray]{0.35}\ttfamily\it\let\textcolor\textcolordummy,
+ commentstyle=\color[gray]{0.35}\ttfamily\itshape\let\textcolor\textcolordummy,
  morecomment=[l][\color{dumuxBlue}\let\textcolor\textcolordummy]{[},
 }

doc/handbook/2_detailedinstall.tex

@@ -41,7 +41,7 @@ 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 C++ 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++ (4.8), 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}.
 

doc/handbook/4_assemblinglinearsystem.tex

@@ -15,8 +15,8 @@ example:
   \phi \frac{\partial \varrho_\alpha S_\alpha}{\partial t}
  -
  \text{div} \left(
- \varrho_\alpha \frac{k_{r\alpha}}{\mu_\alpha} \mbox{\bf K}
- \left(\grad\, p_\alpha - \varrho_{\alpha} \mbox{\bf g} \right)
+ \varrho_\alpha \frac{k_{r\alpha}}{\mu_\alpha} \mathbf{K}
+ \left(\grad\, p_\alpha - \varrho_{\alpha} \mathbf{g} \right)
  \right) - q_\alpha} _
 {=: \, \textbf{r}(\textbf{u})}
 = 0

doc/handbook/4_guidelines.tex

@@ -40,7 +40,7 @@ of the code we have the following naming conventions:
   \item \emph{Self-Explaining}: in general abbreviations should be avoided (write saturation in stead of S)
   \item \emph{Abbreviations}: If and only if a single letter that represents an
          abbreviation or index is followed by a single letter (abbreviation or index),
-         CamelCase is {\bf not} used. An inner-word underscore is only permitted if
+         CamelCase is \textbf{not} used. An inner-word underscore is only permitted if
          it symbolizes a fraction line. Afterwards, we continue with lower case, i.e.
          the common rules apply to both enumerator and denominator. Examples:
   \begin{itemize}

doc/handbook/5_grids.tex

@@ -14,7 +14,7 @@ and briefly mention how to customize and deal with common other grid formats.
 Most of our \Dumux tests and tutorials use the Dune Grid Format (DGF) to read in grids. A detailed description
 of the DGF format and some examples can be found in the \Dune doxygen documentation
 \textbf{(Modules $\rightarrow$ I/O $\rightarrow$ Dune Grid Format (DGF)}). To generate larger or more
-complex DGF files, we recommend to write your own scripts, e.g in C++, Matlab or Python.
+complex DGF files, we recommend to write your own scripts, e.g in \Cplusplus, Matlab or Python.
 
 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
@@ -92,7 +92,7 @@ CellType = Cube # or Simplex
 For all available parameters see the Doxygen documentation.
 
 \subsection{Other grid formats and customized grid creators}
-Other grid formats than DGF and MSH have to be converted to DGF or MSH to be read into \Dumux. A second possiblity (advanced C++) is to write your own
+Other grid formats than DGF and MSH have to be converted to DGF or MSH to be read into \Dumux. A second possiblity (advanced \Cplusplus) is to write your own
 \texttt{GridCreator}. For examples have a look at the \texttt{CubeGridCreator} for a simple and the \texttt{ArtGridCreator} for a more complex example.
 It follows a (non-comprehensive) list of hints for some other common grid formats.