code is now included using \snippet. Apparently this looks better with the new Doxygen version. The HTML_EXTRA_STYLESHEET is now used rather then the HTML_STYLESHEET in order to include used-defined styles for the same reason

tutorials/tutorial2.cpp

@@ -24,7 +24,7 @@
 /// \f${\bf u}\f$ denotes the velocity and \f$p\f$ the pressure. The permeability tensor is
 /// given by \f$K\f$ and \f$\mu\f$ denotes the viscosity.
 ///
-/// We solve the flow equations for a cartesian grid and we set the source term
+/// We solve the flow equations for a Cartesian grid and we set the source term
 /// \f$q\f$ be zero except at the left-lower and right-upper corner, where it is equal
 /// with opposite sign (inflow equal to outflow).
 
@@ -49,28 +49,33 @@
 #include <opm/core/simulator/WellState.hpp>
 
 /// \page tutorial2
-/// \section commentedcode2 Program walkthrough.
-/// \code
+/// \section commentedcode2 Program walk-through.
+/// 
+
 int main()
 {
-    /// \endcode
+    
     /// \page tutorial2
-    /// We construct a cartesian grid
-    /// \code
+    /// We construct a Cartesian grid
+    /// \snippet tutorial2.cpp cartesian grid
+    /// \internal [cartesian grid]
     int dim = 3;
     int nx = 40;
     int ny = 40;
     int nz = 1;
     Opm::GridManager grid(nx, ny, nz);
-    /// \endcode
+    /// \internal [cartesian grid]
+    /// \endinternal
     /// \page tutorial2
     /// \details We access the unstructured grid  through
     /// the pointer given by \c grid.c_grid(). For more  details on the
     /// UnstructuredGrid data structure, see  grid.h.
-    /// \code
+    /// \snippet tutorial2.cpp access grid
+    /// \internal [access grid]
     int num_cells = grid.c_grid()->number_of_cells;
     int num_faces = grid.c_grid()->number_of_faces;
-    /// \endcode
+    /// \internal [access grid]
+    /// endinternal
 
 
     /// \page tutorial2
@@ -80,90 +85,107 @@ int main()
     /// The <opm/core/utility/Units.hpp> header contains support
     /// for common units and prefixes, in the namespaces Opm::unit
     /// and Opm::prefix.
-    /// \code
+    /// \snippet tutorial2.cpp fluid
+    /// \internal [fluid]
     using namespace Opm::unit;
     using namespace Opm::prefix;
     int num_phases = 1;
     std::vector<double> mu(num_phases, 1.0*centi*Poise);
     std::vector<double> rho(num_phases, 1000.0*kilogram/cubic(meter));
-    /// \endcode
+    /// \internal [fluid]
+    /// \endinternal
     /// \page tutorial2
     /// \details
     /// We define a permeability equal to 100 mD.
-    /// \code
+    /// \snippet tutorial2.cpp perm
+    /// \internal [perm]
     double k = 100.0*milli*darcy;
-    /// \endcode
-    /// \page tutorial2
-    /// \details
+    /// \internal [perm]
+    /// \endinternal
 
     /// \page tutorial2
     /// \details
     /// We set up a simple property object for a single-phase situation.
-    /// \code
+    /// \snippet tutorial2.cpp single-phase property
+    /// \internal [single-phase property]
     Opm::IncompPropertiesBasic props(1, Opm::SaturationPropsBasic::Constant, rho,
                                      mu, 1.0, k, dim, num_cells);
-    /// \endcode
+    /// \internal [single-phase property]
+    /// /endinternal
 
     /// \page tutorial2
     /// \details
     /// We take UMFPACK as the linear solver for the pressure solver
     /// (this library has therefore to be installed).
-    /// \code
+    /// \snippet tutorial2.cpp linsolver
+    /// \internal [linsolver] 
     Opm::LinearSolverUmfpack linsolver;
-    /// \endcode
-    /// \page tutorial2
+    /// \internal [linsolver] 
+    /// \endinternal
 
-    /// \endcode
     /// \page tutorial2
     /// We define the source term.
-    /// \code
+    /// \snippet tutorial2.cpp source
+    /// \internal [source]
     std::vector<double> src(num_cells, 0.0);
     src[0] = 100.;
     src[num_cells-1] = -100.;
-    /// \endcode
+    /// \internal [source]
+    /// \endinternal
+    
     /// \page tutorial2
     /// \details We set up the boundary conditions.
     /// By default, we obtain no-flow boundary conditions.
-    /// \code
+    /// \snippet tutorial2.cpp boundary
+    /// \internal [boundary]
     Opm::FlowBCManager bcs;
-    /// \endcode
+    /// \internal [boundary]
+    /// \endinternal
 
     /// We set up a pressure solver for the incompressible problem,
     /// using the two-point flux approximation discretization.  The
     /// null pointers correspond to arguments for gravity, wells and
     /// boundary conditions, which are all defaulted (to zero gravity,
     /// no wells, and no-flow boundaries).
-    /// \code
+    /// \snippet tutorial2.cpp tpfa
+    /// \internal [tpfa]
     Opm::IncompTpfa psolver(*grid.c_grid(), props, linsolver, NULL, NULL, src, NULL);
-
+    /// \internal [tpfa]
+    /// \endinternal
+    
     /// \page tutorial2
     /// We declare the state object, that will contain the pressure and face
     /// flux vectors we are going to compute.  The well state
     /// object is needed for interface compatibility with the
     /// <CODE>solve()</CODE> method of class
     /// <CODE>Opm::IncompTPFA</CODE>.
-    /// \code
+    /// \snippet tutorial2.cpp state
+    /// \internal [state]
     Opm::TwophaseState state;
     state.pressure().resize(num_cells, 0.0);
     state.faceflux().resize(num_faces, 0.0);
     state.saturation().resize(num_cells, 1.0);
     Opm::WellState well_state;
-    /// \endcode
+    /// \internal [state]
+    /// \endinternal
 
     /// \page tutorial2
     /// We call the pressure solver.
     /// The first (timestep) argument does not matter for this
     /// incompressible case.
-    /// \code
+    /// \snippet tutorial2.cpp pressure solver
+    /// \internal [pressure solver]
     psolver.solve(1.0*day, state, well_state);
-    /// \endcode
+    /// \internal [pressure solver]
+    /// \endinternal
 
     /// \page tutorial2
     /// We write the results to a file in VTK format.
     /// The data vectors added to the Opm::DataMap must
     /// contain cell data. They may be a scalar per cell
     /// (pressure) or a vector per cell (cell_velocity).
-    /// \code
+    /// \snippet tutorial2.cpp write output
+    /// \internal [write output]
     std::ofstream vtkfile("tutorial2.vtu");
     Opm::DataMap dm;
     dm["pressure"] = &state.pressure();
@@ -171,8 +193,10 @@ int main()
     Opm::estimateCellVelocity(*grid.c_grid(), state.faceflux(), cell_velocity);
     dm["velocity"] = &cell_velocity;
     Opm::writeVtkData(*grid.c_grid(), dm, vtkfile);
+    /// \internal [write output]
+    /// \endinternal
 }
-/// \endcode
+
 /// \page tutorial2
 /// We read the vtu output file in \a Paraview and obtain the following pressure
 /// distribution. \image html tutorial2.png
@@ -181,3 +205,8 @@ int main()
 /// \page tutorial2
 /// \section completecode2 Complete source code:
 /// \include tutorial2.cpp
+
+/// \page tutorial2
+/// \details
+/// \section pythonscript2 python script to generate figures: 
+/// \snippet generate_doc_figures.py tutorial2