[patches] adapt patches for the 2.9 release

Dumux 2.9 depends on Dune >= 2.4. Delete obsolete patch for
dune-grid, update the one for dune-istl. Adapt README.

patches/README

@@ -5,18 +5,9 @@
 
 - If the AMGBackend should be used without SuperLU as coarse grid solver, it can
   be benefitial to decrease the corresponding tolerance. To do so, apply the
-  patch istl-2.3.0.patch in your directory containing
-  dune-istl 2.3.0, e.g.:
-  patch -p1 <../dumux/patches/istl-2.3.0.patch
-
-- If UG has been installed for parallel usage, and you want to run a Dumux
-  multidomain model, you have to patch dune-grid. The patch will introduce
-  geometries for edges and faces in UG, which need to be present, otherwise the
-  compiler will complain. Apply the patch grid-2.3.1.patch in your directory
-  containing dune-grid 2.3.1 by, e.g.:
-  patch -p1 <../dumux/patches/grid-2.3.1.patch
-  If you want to use Dune 2.4, the missing functionality is already included,
-  so the patch is not needed.
+  patch istl-2.4.1.patch in your directory containing
+  dune-istl 2.4.1, e.g.:
+  patch -p1 <../dumux/patches/istl-2.4.1.patch
 
 - If dune-cornerpoint has to be used for, e.g., employing the CpGridCreator,
   and Opm is compiled from source, it might be necessary to patch opm-parser:

patches/grid-2.3.1.patch

-diff --git a/dune/grid/uggrid/uggridentity.hh b/dune/grid/uggrid/uggridentity.hh
-index 4e71316..acadd5d 100644
---- a/dune/grid/uggrid/uggridentity.hh
-+++ b/dune/grid/uggrid/uggridentity.hh
-@@ -223,6 +223,8 @@ namespace Dune {
-     friend class UGGridEntitySeed<codim, GridImp>;
-     typedef typename GridImp::ctype UGCtype;
- 
-+    typedef typename GridImp::Traits::template Codim<codim>::GeometryImpl GeometryImpl;
-+
-   public:
- 
-     typedef typename GridImp::template Codim<codim>::Geometry Geometry;
-@@ -271,6 +273,9 @@ namespace Dune {
-     //!< Default codim 1 Faces and codim == dim Vertices
-     template<int cc> int count () const;
- 
-+    //! geometry of this entity
-+    Geometry geometry () const { return Geometry( *geo_ ); }
-+
-     /** \brief Get the seed corresponding to this entity */
-     EntitySeed seed () const { return EntitySeed( *this ); }
- 
-@@ -290,6 +295,20 @@ namespace Dune {
-     /** \brief Set edge object to a UG edge object */
-     void setToTarget(typename UG_NS<dim>::template Entity<codim>::T* target, const GridImp* gridImp) {
-       target_ = target;
-+
-+      // obtain the corner coordinates from UG
-+      UGCtype* cornerCoords[2*dim];
-+      UG_NS<dim>::Corner_Coordinates(target_, cornerCoords);
-+
-+      // convert to the type required by MultiLinearGeometry
-+      std::vector<FieldVector<UGCtype, dim> > geometryCoords(2);
-+      for(size_t i = 0; i < 2; i++)
-+        for (size_t j = 0; j < dim; j++)
-+            geometryCoords[i][j] = cornerCoords[i][j];
-+
-+      geo_ = Dune::make_shared<GeometryImpl>(type(), geometryCoords);
-+
-+      gridImp_ = gridImp;
-     }
-   public:
-     /** \brief Set edge object to a UG edge object using the center element and the side number
-@@ -305,7 +324,14 @@ namespace Dune {
-     }
- 
-   protected:
-+    Dune::shared_ptr<GeometryImpl> geo_;
-+
-     typename UG_NS<dim>::template Entity<codim>::T* target_;
-+
-+    /** \brief gridImp Not actually used, only the codim-0 specialization needs it
-+     * But code is simpler if we just keep it everywhere.
-+     */
-+    const GridImp* gridImp_;
-   };
- 
-   /*! \brief Specialization for edge in 2D
-@@ -332,9 +358,14 @@ namespace Dune {
-   class UGFaceEntity
-   {
-     enum {codim = 1};
-+    typedef typename GridImp::ctype UGCtype;
-+
-+    typedef typename GridImp::Traits::template Codim<codim>::GeometryImpl GeometryImpl;
- 
-   public:
- 
-+    typedef typename GridImp::template Codim<codim>::Geometry Geometry;
-+
-     /** \brief Return the entity type identifier */
-     GeometryType type() const
-     {
-@@ -403,12 +434,30 @@ namespace Dune {
-     }
- #endif
- 
-+    //! geometry of this entity
-+    Geometry geometry () const { return Geometry( *geo_ ); }
-+
-     /** \brief Set to a UG side vector object
-         \param target The UG side vector to point to
-         \param gridImp Dummy argument, only for consistency with codim-0 entities
-      */
-     void setToTarget(typename UG_NS<dim>::template Entity<codim>::T* target, const GridImp* gridImp) {
-       target_ = target;
-+
-+      // obtain the corner coordinates from UG
-+      UGCtype* cornerCoords[4*dim];
-+      UG_NS<dim>::Corner_Coordinates(target_, cornerCoords);
-+
-+      // convert to the type required by MultiLinearGeometry
-+      size_t numCorners = type().isTriangle() ? 3 : 4;
-+      std::vector<FieldVector<UGCtype, dim> > geometryCoords(numCorners);
-+      for(size_t i = 0; i < numCorners; i++)
-+        for (size_t j = 0; j < dim; j++)
-+            geometryCoords[i][j] = cornerCoords[i][j];
-+
-+      geo_ = Dune::make_shared<GeometryImpl>(type(), geometryCoords);
-+
-+      gridImp_ = gridImp;
-     }
- 
-     typename UG_NS<dim>::template Entity<codim>::T* getTarget() const
-@@ -416,9 +465,16 @@ namespace Dune {
-       return target_;
-     }
- 
-+protected:
-+    Dune::shared_ptr<GeometryImpl> geo_;
-+
-     /** \brief The UG object (a side vector) that represents this face */
-     typename UG_NS<dim>::template Entity<codim>::T* target_;
- 
-+    /** \brief gridImp Not actually used, only the codim-0 specialization needs it
-+     * But code is simpler if we just keep it everywhere.
-+     */
-+    const GridImp* gridImp_;
-   };
- 
-   /*! \brief Specialization for faces in 3D
-diff --git a/dune/grid/uggrid/uggridgeometry.hh b/dune/grid/uggrid/uggridgeometry.hh
-index 26a2f88..079906d 100644
---- a/dune/grid/uggrid/uggridgeometry.hh
-+++ b/dune/grid/uggrid/uggridgeometry.hh
-@@ -159,6 +159,26 @@ namespace Dune {
- 
-   /****************************************************************/
-   /*                                                              */
-+  /*       Specialization for edges in 3d                         */
-+  /*                                                              */
-+  /****************************************************************/
-+
-+  template<class GridImp>
-+  class UGGridGeometry<1, 3, GridImp> :
-+    public CachedMultiLinearGeometry<typename GridImp::ctype, 1, 3>
-+  {
-+  public:
-+
-+    /** \brief Constructor from a given geometry type and a vector of corner coordinates */
-+    UGGridGeometry(const GeometryType& type, const std::vector<FieldVector<typename GridImp::ctype,3> >& coordinates)
-+      : CachedMultiLinearGeometry<typename GridImp::ctype, 1, 3>(type, coordinates)
-+    {}
-+
-+  };
-+
-+
-+  /****************************************************************/
-+  /*                                                              */
-   /*       Specialization for faces in 2d                         */
-   /*                                                              */
-   /****************************************************************/
-diff --git a/dune/grid/uggrid/ugwrapper.hh b/dune/grid/uggrid/ugwrapper.hh
-index ac6fd06..57202f1 100644
---- a/dune/grid/uggrid/ugwrapper.hh
-+++ b/dune/grid/uggrid/ugwrapper.hh
-@@ -393,7 +393,7 @@ namespace Dune {
-       return FIRSTELEMENT(grid);
-     }
- 
--    /** \brief Returns pointers to the coordinate arrays of an UG element */
-+    /** \brief Returns pointers to the coordinate arrays of a UG element */
-     static void Corner_Coordinates(const UG_NS< UG_DIM >::Element* theElement, double* x[]) {
-       using UG_NAMESPACE ::NODE;
-       using UG_NAMESPACE ::TRIANGLE;
-@@ -407,11 +407,29 @@ namespace Dune {
-       CORNER_COORDINATES(theElement, n, x);
-     }
- 
--    /** \brief Returns pointers to the coordinate arrays of an UG node */
-+    /** \brief Returns pointers to the coordinate arrays of a UG node */
-     static void Corner_Coordinates(const UG_NS< UG_DIM >::Node* theNode, double* x[]) {
-       x[0] = theNode->myvertex->iv.x;
-     }
- 
-+    /** \brief Returns pointers to the coordinate arrays of a UG edge */
-+    static void Corner_Coordinates(const UG_NS< UG_DIM >::Edge* theEdge, double* x[]) {
-+      x[0] = theEdge->links[0].nbnode->myvertex->iv.x;
-+      x[1] = theEdge->links[1].nbnode->myvertex->iv.x;
-+    }
-+
-+    /** \brief Returns pointers to the coordinate arrays of a UG vector */
-+    static void Corner_Coordinates(const UG_NS< UG_DIM >::Vector* theVector, double* x[]) {
-+      typename UG_NS< UG_DIM >::Element* center;
-+      unsigned int side;
-+      UG_NS< UG_DIM >::GetElementAndSideFromSideVector(theVector, center, side);
-+      for (unsigned i = 0; i < Corners_Of_Side(center, side); i++)
-+      {
-+        unsigned idxInElem = Corner_Of_Side(center, side, i);
-+        x[i] = Corner(center, idxInElem)->myvertex->iv.x;
-+      }
-+    }
-+
-     static int GlobalToLocal(int n, const double** cornerCoords,
-                              const double* EvalPoint, double* localCoord) {
-       if (UG_DIM==2)

patches/istl-2.3.0.patch → patches/istl-2.4.1.patch

 diff --git a/dune/istl/paamg/amg.hh b/dune/istl/paamg/amg.hh
-index a224b2b..ee48857 100644
+index 56b1d8d..d672756 100644
 --- a/dune/istl/paamg/amg.hh
 +++ b/dune/istl/paamg/amg.hh
-@@ -527,13 +527,13 @@ namespace Dune
+@@ -526,13 +526,13 @@ namespace Dune
                // We are still participating on this level
                solver_.reset(new BiCGSTABSolver<X>(const_cast<M&>(matrices_->matrices().coarsest().getRedistributed()),
                                                    *scalarProduct_,