major folder restructuring. dorie-rfg remains untouched

* defined top-level headers for easy file includes
* moved previous header files into 'solver' subfolder
* moved Simulation headers and implementations into 'interface' subfolder
* moved library instantiations into 'impl' subfolder

dune/CMakeLists.txt

 add_subdirectory(dorie)
-add_subdirectory(dorie-rfg)
-add_subdirectory(interface EXCLUDE_FROM_ALL)
\ No newline at end of file
+add_subdirectory(dorie-rfg)
\ No newline at end of file

dune/dorie/CMakeLists.txt

+add_subdirectory("impl")
+add_subdirectory("interface")
\ No newline at end of file

dune/dorie/dorie.hh

-#ifndef DORIE_HH
-#define DORIE_HH
-
-//#pragma GCC system_header
+#ifndef DUNE_DORIE_HH
+#define DUNE_DORIE_HH
 
 #ifdef HAVE_CONFIG_H
 #include "config.h"
 #endif
 
-#include <math.h>
 #include <iostream>
 #include <vector>
 #include <map>
@@ -22,47 +19,39 @@
 #include <unistd.h>
 #include <hdf5.h>
 
-#include <dune/grid/uggrid.hh>
-
+#include <dune/common/fvector.hh>
+#include <dune/common/fmatrix.hh>
+#include <dune/common/ios_state.hh>
 #include <dune/common/parallel/mpihelper.hh>
 #include <dune/common/exceptions.hh>
-#include <dune/common/fvector.hh>
 #include <dune/common/timer.hh>
 #include <dune/common/parametertreeparser.hh>
-#include <dune/common/std/memory.hh>
+
+#include <dune/grid/uggrid.hh>
+#include <dune/grid/yaspgrid.hh>
 #include <dune/grid/io/file/vtk/vtksequencewriter.hh>
 #include <dune/grid/io/file/gmshreader.hh>
-
 #include <dune/grid/utility/structuredgridfactory.hh>
-#include <dune/istl/bvector.hh>
-#include <dune/istl/operators.hh>
-#include <dune/istl/solvers.hh>
-#include <dune/istl/preconditioners.hh>
-#include <dune/istl/io.hh>
-#include <dune/istl/superlu.hh>
-#include <dune/istl/owneroverlapcopy.hh>
-#include <dune/pdelab/newton/newton.hh>
+
+#include <dune/geometry/type.hh>
+
+#include <dune/pdelab/adaptivity/adaptivity.hh>
+#include <dune/pdelab/backend/istl.hh>
+#include <dune/pdelab/backend/interface.hh>
 #include <dune/pdelab/common/function.hh>
-#include <dune/pdelab/common/vtkexport.hh>
-#include <dune/pdelab/finiteelementmap/qkfem.hh>
-#include <dune/pdelab/finiteelementmap/p0fem.hh>
-#include <dune/pdelab/finiteelementmap/pkfem.hh>
-#include <dune/pdelab/finiteelementmap/qkdg.hh>
+#include <dune/pdelab/constraints/p0.hh>
+#include <dune/pdelab/constraints/p0ghost.hh>
 #include <dune/pdelab/constraints/common/constraints.hh>
-#include <dune/pdelab/constraints/conforming.hh>
+#include <dune/pdelab/finiteelementmap/qkdg.hh>
+#include <dune/pdelab/finiteelementmap/pkfem.hh>
 #include <dune/pdelab/gridfunctionspace/gridfunctionspace.hh>
-#include <dune/pdelab/gridfunctionspace/gridfunctionspaceutilities.hh>
-#include <dune/pdelab/gridfunctionspace/genericdatahandle.hh>
-#include <dune/pdelab/gridfunctionspace/interpolate.hh>
-#include <dune/pdelab/gridfunctionspace/vtk.hh>
-#include <dune/pdelab/gridfunctionspace/subspace.hh>
 #include <dune/pdelab/gridoperator/gridoperator.hh>
 #include <dune/pdelab/gridoperator/onestep.hh>
-
-#include <dune/pdelab/backend/istl.hh>
-#include <dune/pdelab/backend/interface.hh>
-#include <dune/pdelab/stationary/linearproblem.hh>
 #include <dune/pdelab/instationary/onestep.hh>
-#include <dune/pdelab/adaptivity/adaptivity.hh>
+#include <dune/pdelab/newton/newton.hh>
+#include <dune/pdelab/stationary/linearproblem.hh>
+
+#include <dune/dorie/solver.hh>
+#include <dune/dorie/interface.hh>
 
-#endif // DORIE_HH
+#endif // DUNE_DORIE_HH

dune/interface/CMakeLists.txt → dune/dorie/impl/CMakeLists.txt

-add_executable("sim" sim.cc)
-
 dune_add_library(simulations OBJECT 
 	sim_ug_2_1.cc
 	sim_ug_2_2.cc
@@ -12,6 +10,4 @@ dune_add_library(simulations OBJECT
 	sim_yasp_2_3.cc
 	sim_yasp_3_1.cc
 	sim_yasp_3_2.cc
-	sim_yasp_3_3.cc)
-dune_target_link_libraries(sim doriesim)
-#target_link_dune_default_libraries("sim")
\ No newline at end of file
+	sim_yasp_3_3.cc)
\ No newline at end of file

dune/interface/simulation.hh → dune/dorie/impl/impl.hh

-#ifndef DUNE_DORIE_SIMULATION_HH
-#define DUNE_DORIE_SIMULATION_HH
-
-#include "simulation_base.hh"
-#include "adaptivity.hh"
-#include "output.hh"
+#ifndef DUNE_DORIE_IMPL_HH
+#define DUNE_DORIE_IMPL_HH
 
 namespace Dune{
 namespace Dorie{
 
-template<typename Traits>
-class AdaptiveSimulation : 
-	public AdaptivityHandler<Traits>,
-	public OutputWriter<Traits>
-{
-private:
-	using Grid = typename Traits::Grid;
-
-public:
-	/// Set up the simulation. Call base class constructors
-	AdaptiveSimulation (Dune::MPIHelper& _helper, std::shared_ptr<Grid> _grid, Dune::ParameterTree& _inifile);
-
-	/// Perform the simulation.
-	/** Compute a time step, adapt the grid locally, and write the VTK output
-	 */
-	void run () override;
-};
-
-template<typename Traits>
-class SimpleSimulation : 
-	public OutputWriter<Traits>
-{
-private:
-	using Grid = typename Traits::Grid;
-
-public:
-	/// Set up the simulation. Call base class constructors
-	SimpleSimulation (Dune::MPIHelper& _helper, std::shared_ptr<Grid> _grid, Dune::ParameterTree& _inifile);
-
-	/// Perform the simulation.
-	/** Compute a time step, adapt the grid locally, and write the VTK output
-	 */
-	void run () override;
-};
-
-// forward declare templates
-template<int dim>
-using YaspGrid = Dune::YaspGrid<dim>;
-
+// --- Forward declare templates ---
 extern template class AdaptiveSimulation<BaseTraits<Dune::UGGrid,Dune::GeometryType::BasicType::cube,2,1>>;
 extern template class AdaptiveSimulation<BaseTraits<Dune::UGGrid,Dune::GeometryType::BasicType::cube,2,2>>;
 extern template class AdaptiveSimulation<BaseTraits<Dune::UGGrid,Dune::GeometryType::BasicType::cube,2,3>>;
@@ -61,9 +19,7 @@ extern template class SimpleSimulation<BaseTraits<YaspGrid,Dune::GeometryType::B
 extern template class SimpleSimulation<BaseTraits<YaspGrid,Dune::GeometryType::BasicType::cube,3,2>>;
 extern template class SimpleSimulation<BaseTraits<YaspGrid,Dune::GeometryType::BasicType::cube,3,3>>;
 
+}
+}
 
-} // namespace Dorie
-} // namespace Dune
-
-
-#endif // DUNE_DORIE_SIMULATION_HH
\ No newline at end of file
+#endif // DUNE_DORIE_IMPL_HH

dune/interface/sim_ug_2_1.cc → dune/dorie/impl/sim_ug_2_1.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
-#include "adaptivity.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_ug_2_2.cc → dune/dorie/impl/sim_ug_2_2.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
-#include "adaptivity.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_ug_2_3.cc → dune/dorie/impl/sim_ug_2_3.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
-#include "adaptivity.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_ug_3_1.cc → dune/dorie/impl/sim_ug_3_1.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
-#include "adaptivity.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_ug_3_2.cc → dune/dorie/impl/sim_ug_3_2.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
-#include "adaptivity.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_ug_3_3.cc → dune/dorie/impl/sim_ug_3_3.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
-#include "adaptivity.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_yasp_2_1.cc → dune/dorie/impl/sim_yasp_2_1.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_yasp_2_2.cc → dune/dorie/impl/sim_yasp_2_2.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_yasp_2_3.cc → dune/dorie/impl/sim_yasp_2_3.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_yasp_3_1.cc → dune/dorie/impl/sim_yasp_3_1.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_yasp_3_2.cc → dune/dorie/impl/sim_yasp_3_2.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/interface/sim_yasp_3_3.cc → dune/dorie/impl/sim_yasp_3_3.cc

-#include "dorie.hh"
-#include "simulation.cc"
-#include "output.cc"
-#include "simulation_base.cc"
+#include <dune/dorie/dorie.hh>
+#include <dune/dorie/impl/impl.hh>
+#include <dune/dorie/interface_sources.hh>
 
 namespace Dune{
 namespace Dorie{

dune/dorie/interface.hh

+#ifndef DUNE_DORIE_INTERFACE_HH
+#define DUNE_DORIE_INTERFACE_HH
+
+#include <dune/dorie/interface/util.hh>
+#include <dune/dorie/interface/simulation_base.hh>
+#include <dune/dorie/interface/adaptivity.hh>
+#include <dune/dorie/interface/output.hh>
+#include <dune/dorie/interface/simulation.hh>
+
+#endif // DUNE_DORIE_INTERFACE_HH

dune/dorie/interface/CMakeLists.txt

+add_executable("sim" sim.cc)
+dune_target_link_libraries(sim doriesim)
\ No newline at end of file

dune/interface/adaptivity.hh → dune/dorie/interface/adaptivity.hh

 #ifndef DUNE_DORIE_ADAPTIVITY_HH
 #define DUNE_DORIE_ADAPTIVITY_HH
 
-#include "simulation_base.hh"
-
 namespace Dune{
 namespace Dorie{
 

dune/interface/output.hh → dune/dorie/interface/output.hh

 #ifndef DUNE_DORIE_OUTPUT_WRITER_HH
 #define DUNE_DORIE_OUTPUT_WRITER_HH
 
-#include "simulation_base.hh"
-
 namespace Dune{
 namespace Dorie{
 

dune/interface/sim.cc → dune/dorie/interface/sim.cc

-#include "simulation_base.hh"
-#include "adaptivity.hh"
-#include "output.hh"
-#include "simulation.hh"
-
-//template<int dim>
-//using YaspGrid = Dune::YaspGrid<dim>;
+#include <dune/dorie/dorie.hh>
 
 int main(int argc, char **argv)
 {

dune/dorie/interface/simulation.hh

+#ifndef DUNE_DORIE_SIMULATION_HH
+#define DUNE_DORIE_SIMULATION_HH
+
+namespace Dune{
+namespace Dorie{
+
+template<typename Traits>
+class AdaptiveSimulation : 
+	public AdaptivityHandler<Traits>,
+	public OutputWriter<Traits>
+{
+private:
+	using Grid = typename Traits::Grid;
+
+public:
+	/// Set up the simulation. Call base class constructors
+	AdaptiveSimulation (Dune::MPIHelper& _helper, std::shared_ptr<Grid> _grid, Dune::ParameterTree& _inifile);
+
+	/// Perform the simulation.
+	/** Compute a time step, adapt the grid locally, and write the VTK output
+	 */
+	void run () override;
+};
+
+template<typename Traits>
+class SimpleSimulation : 
+	public OutputWriter<Traits>
+{
+private:
+	using Grid = typename Traits::Grid;
+
+public:
+	/// Set up the simulation. Call base class constructors
+	SimpleSimulation (Dune::MPIHelper& _helper, std::shared_ptr<Grid> _grid, Dune::ParameterTree& _inifile);
+
+	/// Perform the simulation.
+	/** Compute a time step, adapt the grid locally, and write the VTK output
+	 */
+	void run () override;
+};
+
+
+} // namespace Dorie
+} // namespace Dune
+
+
+#endif // DUNE_DORIE_SIMULATION_HH
\ No newline at end of file

dune/interface/simulation_base.hh → dune/dorie/interface/simulation_base.hh

 #ifndef DUNE_DORIE_SIMULATION_BASE_HH
 #define DUNE_DORIE_SIMULATION_BASE_HH
 
-#include "util.hh"
-
 namespace Dune{
 namespace Dorie{
 

dune/interface/util.hh → dune/dorie/interface/util.hh

@@ -4,6 +4,13 @@
 namespace Dune{
 namespace Dorie{
 
+/// Declare template for usage in the Traits template
+/** It looks stupid, but YaspGrid has a second template parameter
+ *  which is deduced automatically this way.
+ */
+template<int dim>
+using YaspGrid = Dune::YaspGrid<dim>;
+
 /// Return the estimation of entries per matrix row for the spatial GridOperator.
 /** This supposedly decreases matrix assembly time.
  *  The values are empirical. The actual matrix statistics can be displayed

dune/dorie/interface_sources.hh

+#ifndef DUNE_DORIE_INTERFACE_SRC_HH
+#define DUNE_DORIE_INTERFACE_SRC_HH
+
+#include <dune/dorie/interface/simulation_base.cc>
+#include <dune/dorie/interface/adaptivity.cc>
+#include <dune/dorie/interface/output.cc>
+#include <dune/dorie/interface/simulation.cc>
+
+#endif // DUNE_DORIE_INTERFACE_SRC_HH

dune/dorie/solver_prep.hh

-#ifndef DUNE_DORIE_SOLVER_PREP_HH
-#define DUNE_DORIE_SOLVER_PREP_HH
-
-/// Define Grid Function Spaces for a simplex grid and call the Richards Solver Routine
-/**
- *  \tparam RF Solution data type
- *  \tparam k Finite element order
- *  \param grid Shared pointer to the grid
- *  \param gv GridView
- *  \param inifile Parameter file reader
- */
-template<typename RF, int k, typename GridType, typename GV>
-void RichardsSolverSimplex (GridType grid, GV& gv, Dune::ParameterTree& inifile, Dune::MPIHelper& helper)
-{
-	typedef typename GV::Grid::ctype DF;
-	enum { dim = GV::dimension };
-
-	// Create GFS for solving the problem
-	typedef Dune::PDELab::PkLocalFiniteElementMap<GV,DF,RF,k> FEM;
-	typedef Dune::PDELab::GridFunctionSpace<GV,FEM,
-											Dune::PDELab::NoConstraints,
-											Dune::PDELab::istl::VectorBackend<Dune::PDELab::istl::Blocking::fixed> >
-											GFS;
-	FEM fem(gv);
-	GFS gfs(gv,fem);
-
-	// Create GFS for adaptivity
-	typedef Dune::PDELab::P0LocalFiniteElementMap<DF,RF,dim> AFEM;
-	typedef Dune::PDELab::GridFunctionSpace<GV,AFEM,
-											Dune::PDELab::NoConstraints,
-											Dune::PDELab::istl::VectorBackend<Dune::PDELab::istl::Blocking::fixed> >
-											AGFS;
-	AFEM afem(Dune::GeometryType(Dune::GeometryType::simplex,dim));
-
-	typedef Dune::Dorie::Traits<GFS,AGFS> T;
-
-	RichardsSolver<T>(grid,gv,gfs,afem,inifile,helper);
-}
-
-
-/// Define Grid Function Spaces for a rectangular grid and call the Richards Solver Routine
-/**
- *  \tparam RF Solution data type
- *  \tparam k Finite element order
- *  \param grid Shared pointer to the grid
- *  \param gv GridView
- *  \param inifile Parameter file reader
- */
-template<typename RF, int k, typename GridType, typename GV>
-void RichardsSolverRectangular (GridType grid, GV& gv, Dune::ParameterTree& inifile, Dune::MPIHelper& helper)
-{
-	typedef typename GV::Grid::ctype DF;
-	enum { dim = GV::dimension };
-
-	// Create GFS for solving the problem
-	typedef Dune::PDELab::QkDGLocalFiniteElementMap<DF,RF,k,dim> FEM;
-	typedef Dune::PDELab::GridFunctionSpace<GV,FEM,
-											Dune::PDELab::NoConstraints,
-											Dune::PDELab::istl::VectorBackend<Dune::PDELab::istl::Blocking::fixed,
-												Dune::QkStuff::QkSize<k,dim>::value> >
-											GFS;
-	FEM fem;
-	GFS gfs(gv,fem);
-
-	// Create GFS for adaptivity
-	typedef Dune::PDELab::QkDGLocalFiniteElementMap<DF,RF,0,dim> AFEM;
-	typedef Dune::PDELab::GridFunctionSpace<GV,AFEM,
-											Dune::PDELab::NoConstraints,
-											Dune::PDELab::istl::VectorBackend<Dune::PDELab::istl::Blocking::fixed,
-												Dune::QkStuff::QkSize<0,dim>::value> >
-											AGFS;
-	AFEM afem;
-
-	typedef Dune::Dorie::Traits<GFS,AGFS> T;
-
-	RichardsSolver<T>(grid,gv,gfs,afem,inifile,helper);
-}
-
-#endif

dune/interface/dorie.hh

-#ifndef DORIE_HH
-#define DORIE_HH
-
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
-
-#include <iostream>
-#include <vector>
-#include <map>
-#include <string>
-#include <stdlib.h>
-#include <fstream>
-#include <cmath>
-#include <memory>
-#include <utility>
-#include <sys/stat.h>
-#include <sys/types.h>
-#include <unistd.h>
-#include <hdf5.h>
-
-#include <dune/common/fvector.hh>
-#include <dune/common/fmatrix.hh>
-#include <dune/common/ios_state.hh>
-#include <dune/common/parallel/mpihelper.hh>
-#include <dune/common/exceptions.hh>
-#include <dune/common/timer.hh>
-#include <dune/common/parametertreeparser.hh>
-
-#include <dune/grid/uggrid.hh>
-#include <dune/grid/yaspgrid.hh>
-#include <dune/grid/io/file/vtk/vtksequencewriter.hh>
-#include <dune/grid/io/file/gmshreader.hh>
-#include <dune/grid/utility/structuredgridfactory.hh>
-
-#include <dune/geometry/type.hh>
-
-#include <dune/pdelab/adaptivity/adaptivity.hh>
-#include <dune/pdelab/backend/istl.hh>
-#include <dune/pdelab/backend/interface.hh>
-#include <dune/pdelab/common/function.hh>
-#include <dune/pdelab/constraints/p0.hh>
-#include <dune/pdelab/constraints/p0ghost.hh>
-#include <dune/pdelab/constraints/common/constraints.hh>
-#include <dune/pdelab/finiteelementmap/qkdg.hh>
-#include <dune/pdelab/finiteelementmap/pkfem.hh>
-#include <dune/pdelab/gridfunctionspace/gridfunctionspace.hh>
-#include <dune/pdelab/gridoperator/gridoperator.hh>
-#include <dune/pdelab/gridoperator/onestep.hh>
-#include <dune/pdelab/instationary/onestep.hh>
-#include <dune/pdelab/newton/newton.hh>
-#include <dune/pdelab/stationary/linearproblem.hh>
-
-#include <dune/dorie/util_typedefs.hh>
-#include <dune/dorie/util_vtk_adapters.hh>
-#include <dune/dorie/util_grid_creator.hh>
-#include <dune/dorie/util_boundary_condition.hh>
-#include <dune/dorie/util_controller.hh>
-#include <dune/dorie/util_adaptivity.hh>
-#include <dune/dorie/util_h5tools.hh>
-#include <dune/dorie/richards_initial.hh>
-#include <dune/dorie/richards_boundary.hh>
-#include <dune/dorie/richards_source.hh>
-#include <dune/dorie/util_interpolator.hh>
-#include <dune/dorie/param_base.hh>
-#include <dune/dorie/param_van_genuchten.hh>
-#include <dune/dorie/param_factory.hh>
-#include <dune/dorie/operator_DG.hh>
-#include <dune/dorie/operator_error_indicator.hh>
-#include <dune/dorie/dune_implicitonestep.hh>
-
-#include "util.hh"
-#include "simulation_base.hh"
-#include "adaptivity.hh"
-#include "output.hh"
-#include "simulation.hh"
-
-#endif // DORIE_HH

src/dorie.cc

 // -*- tab-width: 2; indent-tabs-mode: nil -*-
 
-#include <dune/interface/dorie.hh> // System and DUNE Headers
+#include <dune/dorie/dorie.hh> // System and DUNE Headers
 
 //===============================================================
 // Main program with grid setup