Merge branch 'feature/handbook-structure' into 'feature/improve-handbook'

[handbook] Update structure and folder setup

See merge request !1339

doc/handbook/4_newfoldersetup.tex

@@ -13,12 +13,15 @@ the build system there is a new one.
 \end{enumerate}
 
 \paragraph{Adding new Test Programs}
-\noindent To add a test use the \texttt{add\_dumux\_test} macro.
-The command has four arguments:
-\begin{enumerate}[1)]
-  \item name of test (has to be unique)
-  \item name of executable
-  \item source file (*.cc)
-  \item command to be executed as test - either the executable or a
-        some helper script with arguments
-\end{enumerate}
+\noindent To add a test use the \texttt{add\_dune\_test} macro within the \texttt{CMakeList.txt} file.
+The macro can be used with a variable amount of arguments. A simple call could look like this:
+
+\begin{lstlisting}[style=DumuxCode]
+dune_add_test(NAME my_test
+               SOURCES mainfile.cc
+               CMD_ARGS my_test params.input)
+\end{lstlisting}
+
+Here, we create an exectuable called \texttt{my\_test} from a source file \texttt{mainfile.cc}.
+The name of the test will also be \texttt{my\_test} (has to be unique). The last argument specifies a command - here, we just run the executbable \texttt{my\_test} with an input file \texttt{params.input}. For more advanced uses of
+the \texttt{add\_dune\_test} macro, have a look at the \texttt{test} directory. A complete documentation is given \href{https://www.dune-project.org/sphinx/core-2.5/}{here}

doc/handbook/4_parameterfiles.tex

@@ -5,9 +5,7 @@ A list of all available parameters is provided in the Doxygen documentation: \te
 
 After having run the example application from section \ref{quick-start-guide} you will
 get the following output at the end of the simulation run
-\footnote{If you did not get the output, restart the application the following way:
-\texttt{./test{\_}2p{\_}incompressible{\_}tpfa test{\_}2p.input -PrintParameters true},
-this will print the parameters once your simulation is finished}:
+\footnote{If you did not get the output, add \texttt{Parameters::print();} to your main file.}:
 \begin{lstlisting}[style=Bash]
 # Runtime-specified parameters used:
 [ Grid ]
@@ -24,8 +22,9 @@ DtInitial = "250"
 TEnd = "3000"
 
 # Default parameters used:
-[ Implicit ]
+[ Assembly ]
 NumericDifferenceMethod = "1"
+[ Flux ]
 UpwindWeight = "1.0"
 [ LinearSolver ]
 MaxIterations = "250"
@@ -64,20 +63,37 @@ A number of things can be learned:
 
 
 \subsection{Parameter Values}
-If you want to get the value of a parameter please use:
+To get the value of an input parameter please use:
 \begin{lstlisting}[name=propsyscars,style=DumuxCode]
-paramname_ = getParam<TYPE>("GROUPNAME.PARAMNAME");
+static const TYPE paramname = getParam<TYPE>("GROUPNAME.PARAMNAME");
 \end{lstlisting}
 
 If you also want to set a default value for a parameter, just add it like this:
 
 \begin{lstlisting}[name=propsyscars,style=DumuxCode]
-paramname_ = getParam<TYPE>("GROUPNAME.PARAMNAME", default);
+static const TYPE paramname = getParam<TYPE>("GROUPNAME.PARAMNAME", default);
 \end{lstlisting}
 
-For further information you can also look at the \Dumux tutorial, especially exercise 1. 
+As this function call is relatively expensive, the respective variables should always be \texttt{static} (e.g., if used in a loop). When dealing with multiple group names, e.g., in the context of coupled models, the fowolling methods might be more convenient:
+
+\begin{lstlisting}[name=propsyscars,style=DumuxCode]
+auto modelParamGroup0 = "Model0";
+static const TYPE paramname0 = getParamFromGroup<TYPE>(modelParamGroup0, "GROUPNAME.PARAMNAME");
+auto modelParamGroup1 = "Model1";
+static const TYPE paramname1 = getParamFromGroup<TYPE>(modelParamGroup1, "GROUPNAME.PARAMNAME");
+\end{lstlisting}
+
+The \texttt{FVProblem} class provides a convenience function \texttt{paramGroup()}.\\
+
+The parameters can then be specified in the input file:
+
+\begin{lstlisting}[style=Bash]
+[ Model0.Grid ]
+File = file0.dgf
+[ Model1.Grid ]
+File = file1.dgf
+\end{lstlisting}
+
+
+For further details, please have a look at the \Dumux tutorial, especially exercise 1.
 
-All applications have a help message which you can read by giving
-\texttt{--help} as a command line argument to the application.
-For further details, please have a look at \texttt{Dune::ParameterTree}
-in the \Dune documentation.

doc/handbook/4_structure.tex

@@ -15,7 +15,6 @@
       \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.
 \end{itemize}
 
 \begin{figure}
@@ -71,20 +70,16 @@
     [.\node[SecondLevel] {properties};
       \node[ThirdLevel] {Base properties for all models.};
     ]
+    [.\node[SecondLevel] {typetraits};
+      \node[ThirdLevel] {Helper classes to query type information on compile-time. };
+    ]
   ]
   [.\node[FirstLevel] {discretization};
-%     [.\node[SecondLevel] {\emph{models}};
-      \node[ThirdLevel] {Common methods for all discretizations: variable caching, advective and diffusive fluxes, upwinding...};
-%     ]
-    [.\node[SecondLevel] {box};
-      \node[ThirdLevel] {Specific files for the box finite volume method:
-                         specifications for advective and diffusive fluxes...};
-    ]
-    [.\node[SecondLevel] {cellcentered};
-      \node[ThirdLevel] {Specific files for cell centered finite volume methods.};
-    ]
-    [.\node[SecondLevel] {staggered};
-      \node[ThirdLevel] {Specific files for staggered finite volume method.};
+      \node[ThirdLevel] {Common methods for all discretizations (box, cell-centered TPFA/MPFA, staggered grid): variable caching, advective and diffusive fluxes, ...};
+  ]
+  [.\node[FirstLevel] {flux};
+    [\node[ThirdLevel] {
+            Collection of classes used to calculate advective and diffusive fluxes.};
     ]
   ]
   [.\node[FirstLevel] {freeflow};
@@ -93,6 +88,11 @@
                          and eddy-viscosity based Reynolds-averaged Navier-Stokes turbulence models.};
     ]
   ]
+  [.\node[FirstLevel] {geomechanics};
+    [.\node[SecondLevel] {\emph{models}};
+      \node[ThirdLevel] {Elastic and poro-elastic geomechanics models.};
+    ]
+  ]
   [.\node[FirstLevel] {io};
     \node[ThirdLevel] {Additional in-/output possibilities like restart files, gnuplot-interface,
                        VTKWriter extensions and files for grid generation.};
@@ -126,28 +126,35 @@
     ]
     [.\node[SecondLevel] {fluidstates};
       \node[ThirdLevel] {Fluid states are responsible for caching the thermodynamic
-                         configuration of a system at a given spatial and temporal position.};
+                         configuration of a fluid system at a given spatial and temporal position.};
     ]
     [.\node[SecondLevel] {fluidsystems};
       \node[ThirdLevel] {Fluid systems express the thermodynamic relations between quantities.};
     ]
+    [.\node[SecondLevel] {solidstates};
+      \node[ThirdLevel] {Solid states are responsible for caching the thermodynamic
+                         configuration of a solid system at a given spatial and temporal position.};
+    ]
+    [.\node[SecondLevel] {solidsystems};
+      \node[ThirdLevel] {Solid systems express the thermodynamic properties of a solid.};
+    ]
     [.\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.};
     ]
   ]
-  [.\node[FirstLevel] {mixeddimension};
+  [.\node[FirstLevel] {multidomain};
     \node[ThirdLevel] {
-          Coupled model with different dimensions.};
+          Common infrastructure to couple multiple domains, models or physics.};
     [.\node[SecondLevel] {embedded};
-      \node[ThirdLevel] {Embedded mixed dimension method.};
+      \node[ThirdLevel] {Embedding of a lower-dimensional model into a higher-dimensional one};
     ]
     [.\node[SecondLevel] {facet};
-      \node[ThirdLevel] {Facet mixed dimension method.};
+      \node[ThirdLevel] {Mixed-dimensional coupling at facets.};
     ]
-    [.\node[SecondLevel] {glue};
-      \node[ThirdLevel] {Grid glue backend.};
+    [.\node[SecondLevel] {boundary};
+      \node[ThirdLevel] {Coupling at the domain boundaries.};
     ]
   ]
   [.\node[FirstLevel] {nonlinear};