Work on pdd and some other small code refactorings.

AMDiS/libtool

@@ -44,7 +44,7 @@ available_tags=" CXX F77"
 
 # ### BEGIN LIBTOOL CONFIG
 
-# Libtool was configured on host p1d062:
+# Libtool was configured on host p2q004:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -6760,7 +6760,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
 # End:
 # ### BEGIN LIBTOOL TAG CONFIG: CXX
 
-# Libtool was configured on host p1d062:
+# Libtool was configured on host p2q004:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -7065,7 +7065,7 @@ include_expsyms=""
 
 # ### BEGIN LIBTOOL TAG CONFIG: F77
 
-# Libtool was configured on host p1d062:
+# Libtool was configured on host p2q004:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"

AMDiS/src/AMDiS.h

@@ -84,7 +84,6 @@
 #include "SystemVector.h"
 #include "TecPlotWriter.h"
 #include "Tetrahedron.h"
-#include "TimedObject.h"
 #include "Traverse.h"
 #include "Triangle.h"
 #include "ValueWriter.h"

AMDiS/src/DOFAdmin.h

@@ -213,7 +213,7 @@ namespace AMDiS {
     /// Sets \ref firstHole
     inline void setFirstHole(int i)
     {
-      TEST_EXIT_DBG(!dofFree[i])("There is no hole!\n");
+      TEST_EXIT_DBG(dofFree[i])("There is no hole!\n");
 
       firstHole = i;
     }

AMDiS/src/DOFMatrix.cc

@@ -216,7 +216,8 @@ namespace AMDiS {
 	  applyDBCs.insert(static_cast<int>(row));
 #endif
 	}
-      } else
+      } else {
+
 	for (int j = 0; j < nCol; j++) {  // for all columns
 	  DegreeOfFreedom col = colIndices[j];
 	  double entry = elMat[i][j];
@@ -224,8 +225,9 @@ namespace AMDiS {
 	  if (add)
 	    ins[row][col] += sign * entry;
 	  else
-	    ins[row][col] = sign * entry;
+	    ins[row][col] = sign * entry;	
 	}   
+      }
     }
   }
 
@@ -250,18 +252,6 @@ namespace AMDiS {
 	(*it)->getElementMatrix(elInfo,	elementMatrix, *factorIt ? **factorIt : 1.0);
 
     addElementMatrix(factor, elementMatrix, bound, elInfo, NULL);   
-
-//     if (MPI::COMM_WORLD.Get_rank() == 0 && elInfo->getElement()->getIndex() == 53) {
-//       std::cout << elementMatrix << std::endl;
-
-//       rowFESpace->getBasisFcts()->getLocalIndicesVec(elInfo->getElement(),
-// 						     rowFESpace->getAdmin(),
-// 						     &rowIndices);
-      
-//       rowIndices.print();
-//       print();
-//     }
-
   }
 
   void DOFMatrix::assemble(double factor, ElInfo *elInfo, const BoundaryType *bound,

AMDiS/src/ParallelDomainProblem.h

@@ -130,6 +130,18 @@ namespace AMDiS {
     /// Removes all macro elements from the mesh that are not part of ranks partition.
     void removeMacroElements();
 
+
+    /** \brief
+     * Creates from a macro mesh a correct local and global DOF index numbering.
+     *
+     * @param[out] rankDOFs      Returns all DOFs from the macro mesh, which are owned
+     *                           by the rank after partitioning the macro mesh.
+     * @param[out] boundaryDOFs  Returns all DOFs from the macro mesh, which lies at
+     *                           an interior boundary of the rank. This object maps
+     *                           each such DOF to the rank that owns this DOF.
+     * @param[out] nRankDOFs     Number of DOFs owned by rank.
+     * @param[out] nOverallDOFs  Number of all DOFs in macro mesh.
+     */
     void createLocalGlobalNumbering(std::vector<const DegreeOfFreedom*>& rankDOFs,
 				    std::map<const DegreeOfFreedom*, int>& boundaryDOFs,
 				    int& nRankDOFs, 
@@ -138,8 +150,7 @@ namespace AMDiS {
     void updateLocalGlobalNumbering(int& nRankDOFs, int& nOverallDOFs);
 
     void addAllDOFs(Element *el, int ithEdge, 
-		    std::vector<const DegreeOfFreedom*>& dofs,
-		    bool addVertices = true);
+		    std::vector<const DegreeOfFreedom*>& dofs);
 
     /** \brief
      * This function traverses the whole mesh, i.e. before it is really partitioned,
@@ -220,6 +231,12 @@ namespace AMDiS {
     /// Number of DOFs in the rank mesh.
     int nRankDOFs;
 
+    /** \brief
+     * Set of all interior boundary DOFs in ranks partition. The object maps to
+     * each such DOF to the number of the rank that owns this DOF.
+     */
+    std::map<const DegreeOfFreedom*, int> boundaryDOFs;
+
     /** \brief 
      * Defines the interior boundaries of the domain that result from partitioning
      * the whole mesh. Contains only the boundaries, which are owned by the rank, i.e.,
@@ -240,13 +257,13 @@ namespace AMDiS {
      * This map contains for each rank the list of dofs the current rank must send
      * to exchange solution dofs at the interior boundaries.
      */
-    std::map<int, std::vector<DegreeOfFreedom> > sendDofs;
+    std::map<int, std::vector<const DegreeOfFreedom*> > sendDofs;
 
     /** \brief
      * This map contains for each rank the list of dofs from which the current rank 
      * must receive solution values of dofs at the interior boundaries.
      */
-    std::map<int, std::vector<DegreeOfFreedom> > recvDofs;
+    std::map<int, std::vector<const DegreeOfFreedom*> > recvDofs;
 
     /// Maps local to global dof indices.
     std::map<DegreeOfFreedom, DegreeOfFreedom> mapLocalGlobalDOFs;

AMDiS/src/SurfaceOperator.h

@@ -100,21 +100,14 @@ namespace AMDiS {
     {
       coords_ = coords;
 
-      if (quad2) {
+      if (quad2)
 	quad2->scaleSurfaceQuadrature(coords);
-      }
-
-      if (quad1GrdPsi) {
+      if (quad1GrdPsi)
 	quad1GrdPsi->scaleSurfaceQuadrature(coords);
-      }
-
-      if (quad1GrdPhi) {
+      if (quad1GrdPhi)
 	quad1GrdPhi->scaleSurfaceQuadrature(coords);
-      }
-
-      if (quad0) {
+      if (quad0)
 	quad0->scaleSurfaceQuadrature(coords);
-      }
     }
 
     /** \brief
@@ -126,16 +119,14 @@ namespace AMDiS {
 				  ElementMatrix& userMat, 
 				  double factor = 1.0)
     {
-      int i;
       int dim = rowFESpace->getMesh()->getDim();
       double origDet = elInfo->getDet();
 
       FixVec<WorldVector<double>, VERTEX> worldCoords(dim-1, NO_INIT);
 
       // transform barycentric coords to world coords
-      for(i = 0; i < dim; i++) {
+      for (int i = 0; i < dim; i++)
 	elInfo->coordToWorld(coords_[i], worldCoords[i]);
-      }
 
       // set determinant for world coords of the side
       const_cast<ElInfo*>(elInfo)->setDet(elInfo->calcDet(worldCoords));
@@ -177,9 +168,7 @@ namespace AMDiS {
   protected:
     VectorOfFixVecs<DimVec<double> > coords_;
 
-    /** \brief
-     * Surface quadratures
-     */
+    /// Surface quadratures
     SurfaceQuadrature *quad2;
     SurfaceQuadrature *quad1GrdPsi;
     SurfaceQuadrature *quad1GrdPhi;

AMDiS/src/SurfaceQuadrature.cc

@@ -5,8 +5,6 @@
 
 namespace AMDiS {
 
-  //std::list<SurfaceQuadrature*> SurfaceQuadrature::surfaceQuadratureList;
-
   SurfaceQuadrature::SurfaceQuadrature(Quadrature *quad,
 				       VectorOfFixVecs<DimVec<double> > &coords)
     : Quadrature((quad->getName() + " surface").c_str(),
@@ -18,69 +16,39 @@ namespace AMDiS {
       quad_(quad),
       coords_(coords)
   {
-    int i, j, k;
-
-    // copy coords
-    // coords_ = new DimVec<double>[dim](dim, NO_INIT);
-    //   for(i = 0; i < dim; i++) {
-    //     coords_[i] = coords[i];
-    //   }
-  
     lambda = new VectorOfFixVecs<DimVec<double> >(dim, n_points, NO_INIT);
 
     // for each integration point
-    for(i=0; i < n_points; i++) {
+    for (int i = 0; i < n_points; i++) {
       // get coords of quadrature point in dim-1
       DimVec<double> origin = quad->getLambda(i);
 
-      for(j=0; j < dim+1; j++)
+      for (int j = 0; j < dim + 1; j++)
 	(*lambda)[i][j] = 0.0;
 
-      for(j = 0; j < dim; j++) {
-	for(k = 0; k < dim+1; k++) {
+      for (int j = 0; j < dim; j++)
+	for (int k = 0; k < dim + 1; k++)
 	  (*lambda)[i][k] += origin[j] * coords_[j][k];
-	}
-      }
-    
-      //     // create barycentric coords for dim
-      //     if(dim > 1) {
-      //       for (j = 0; j < side; j++)
-      // 	(*lambda)[i][j] = origin[j];
-
-      //       (*lambda)[i][side] = 0.0;
-      
-      //       for (j = side+1; j <= dim; j++)
-      // 	(*lambda)[i][j] = origin[j-1];
-      //     } else {
-      //       (*lambda)[i][side] = 1.0;
-      //       (*lambda)[i][1-side] = 0.0;
-      //     }
     }
   }
 
-  void
-  SurfaceQuadrature::scaleSurfaceQuadrature(VectorOfFixVecs<DimVec<double> >&coords)
+  void SurfaceQuadrature::scaleSurfaceQuadrature(VectorOfFixVecs<DimVec<double> >&coords)
   {
-    int i, j, k;
-
     // copy coords
-    for(i = 0; i < dim; i++) {
+    for (int i = 0; i < dim; i++)
       coords_[i] = coords[i];
-    }
   
     // for each integration point
-    for(i=0; i < n_points; i++) {
+    for (int i = 0; i < n_points; i++) {
       // get coords of quadrature point in dim-1
       DimVec<double> origin = quad_->getLambda(i);
 
-      for(j=0; j < dim+1; j++)
+      for (int j = 0; j < dim + 1; j++)
 	(*lambda)[i][j] = 0.0;
 
-      for(j = 0; j < dim; j++) {
-	for(k = 0; k < dim+1; k++) {
+      for (int j = 0; j < dim; j++)
+	for (int k = 0; k < dim+1; k++)
 	  (*lambda)[i][k] += origin[j] * coords_[j][k];
-	}
-      }
     }
   }
 

AMDiS/src/SurfaceQuadrature.h

@@ -39,36 +39,21 @@ namespace AMDiS {
   class SurfaceQuadrature : public Quadrature
   {
   public:
-    /** \brief
-     * Constructs a SurfaceQuadrature based on a standard Quadrature of dim-1.
-     */
+    /// Constructs a SurfaceQuadrature based on a standard Quadrature of dim-1.
     SurfaceQuadrature(Quadrature *quad, VectorOfFixVecs<DimVec<double> >& coords);
 
-    /** \brief
-     * Destructor.
-     */
+    /// Destructor.
     ~SurfaceQuadrature()
     {}
 
-    /** \brief
-     * Adapts SurfaceQuadrature to \ref coords.
-     */
+    /// Adapts SurfaceQuadrature to \ref coords.
     void scaleSurfaceQuadrature(VectorOfFixVecs<DimVec<double> > &coords);
 
   protected:
-    /** \brief
-     * Pointer to the original quadrature
-     */
+    /// Pointer to the original quadrature
     Quadrature *quad_;
 
     VectorOfFixVecs<DimVec<double> > coords_;
-
-    /** \brief
-     * List of all existing surface quadratures. Used by 
-     * \ref provideSurfaceQuadrature(). If the needed quadrature is not in the
-     * list, a new list entry is created.
-     */
-    //static std::list<SurfaceQuadrature*> surfaceQuadratureList;
   };
 
 }

AMDiS/src/SurfaceRegion_ED.h

@@ -31,7 +31,7 @@ namespace AMDiS {
   {
   public:
     inline bool isOfType(int typeID) const {
-      if(typeID == SURFACE_REGION) 
+      if (typeID == SURFACE_REGION) 
 	return true;
       return false;
     }
@@ -39,7 +39,8 @@ namespace AMDiS {
     class Creator : public CreatorInterface<ElementData>
     {
     public:
-      ElementData* create() {
+      ElementData* create() 
+      {
 	return new SurfaceRegion_ED;
       }
     };
@@ -61,7 +62,7 @@ namespace AMDiS {
       SurfaceRegion_ED *surfaceRegion;
 
       sideOfChild = parent->getSideOfChild(0, side_, elType);
-      if(sideOfChild >= 0) {
+      if (sideOfChild >= 0) {
 	surfaceRegion = new SurfaceRegion_ED(child1->getElementData());
 	surfaceRegion->setSide(sideOfChild);
 	surfaceRegion->setRegion(region_);
@@ -69,7 +70,7 @@ namespace AMDiS {
       }    
 
       sideOfChild = parent->getSideOfChild(1, side_, elType);
-      if(sideOfChild >= 0) {
+      if (sideOfChild >= 0) {
 	surfaceRegion = new SurfaceRegion_ED(child2->getElementData());
 	surfaceRegion->side_ = sideOfChild;
 	surfaceRegion->region_ = region_;
@@ -77,41 +78,60 @@ namespace AMDiS {
       }
 
       return false;
-    };
+    }
 
-    ElementData *clone() const { 
+    ElementData *clone() const 
+    { 
       SurfaceRegion_ED *newObj = new SurfaceRegion_ED;
       newObj->side_ = side_;
       newObj->region_ = region_;
       newObj->decorated_ = ElementData::clone();
       return newObj; 
-    };
+    }
 
-    inline std::string getTypeName() const { return "SurfaceRegion_ED"; };
+    inline std::string getTypeName() const 
+    { 
+      return "SurfaceRegion_ED"; 
+    }
 
-    inline const int getTypeID() const { return SURFACE_REGION; };
+    inline const int getTypeID() const 
+    { 
+      return SURFACE_REGION; 
+    }
 
     void serialize(std::ostream& out) 
     {
       ElementData::serialize(out);
       out.write(reinterpret_cast<const char*>(&side_), sizeof(int));
       out.write(reinterpret_cast<const char*>(&region_), sizeof(int));
-    };
+    }
 
     void deserialize(std::istream& in) 
     {
       ElementData::deserialize(in);
       in.read(reinterpret_cast<char*>(&side_), sizeof(int));
       in.read(reinterpret_cast<char*>(&region_), sizeof(int));
-    };
+    }
 
-    inline void setSide(int side) { side_ = side; };
+    inline void setSide(int side) 
+    { 
+      side_ = side; 
+    }
 
-    inline int getSide() const { return side_; };
+    inline int getSide() const 
+    { 
+      return side_; 
+    }
 
-    inline void setRegion(int region) { region_ = region; };
+    inline void setRegion(int region) 
+    { 
+      region_ = region; 
+    }
 
-    inline int getRegion() const { return region_; };
+    inline int getRegion() const 
+    { 
+      return region_; 
+    }
 
   protected:
     int side_;

AMDiS/src/SystemVector.h

@@ -30,22 +30,15 @@
 
 namespace AMDiS {
 
-  /** \brief
-   * A system vector is a vector of dof vectors used for vector valued
-   * problems.
-   */
+  /// A system vector is a vector of dof vectors used for vector valued problems.
   class SystemVector : public Serializable
   {
   public:
-    /** \brief
-     * Creator. 
-     */
+    /// Creator. 
     class Creator 
       : public CreatorInterface<SystemVector> {
     public:
-      /** \brief
-       * Creators constructor.
-       */
+      /// Creators constructor.
       Creator(const std::string &name_,
 	      std::vector<FiniteElemSpace*> feSpace_, 
 	      int size_) 
@@ -54,15 +47,12 @@ namespace AMDiS {
 	  size(size_) 
       {}
 
-      /** \brief
-       * Destructor
-       */
+      /// Destructor
       virtual ~Creator() {}
 
-      /** \brief
-       * Implementation of CreatorInterface::create().
-       */
-      SystemVector *create() { 
+      /// Implementation of CreatorInterface::create().
+      SystemVector *create() 
+      { 
 	char number[10];
 	std::string numberedName;
 	SystemVector *result = new SystemVector(name, feSpace, size);
@@ -74,10 +64,9 @@ namespace AMDiS {
 	return result; 
       }
 
-      /** \brief
-       * Implementation of CreatorInterface::free().
-       */ 
-      void free(SystemVector *vec) { 
+      /// Implementation of CreatorInterface::free().
+      void free(SystemVector *vec) 
+      { 
 	for (int i = 0; i < size; i++) {
 	  delete vec->getDOFVector(i);
 	  vec->setDOFVector(i, NULL);
@@ -86,26 +75,18 @@ namespace AMDiS {
       }
 
     private:
-      /** \brief
-       * Name of the system vector
-       */
+      /// Name of the system vector
       std::string name;
 
-      /** \brief
-       * Finite element space used for creation.
-       */
+      /// Finite element space used for creation.
       std::vector<FiniteElemSpace*> feSpace;
 
-      /** \brief
-       * Number of component vectors to be created
-       */
+      /// Number of component vectors to be created
       int size;
     };
 
   public:
-    /** \brief
-     * Constructor.
-     */
+    /// Constructor.
     SystemVector(const std::string& name_,
 		 std::vector<FiniteElemSpace*> feSpace_, 
 		 int size)
@@ -117,92 +98,80 @@ namespace AMDiS {
       vectors.set(NULL);
     }
 
-    /** \brief
-     * Copy Constructor.
-     */
+    /// Copy Constructor.
     SystemVector(const SystemVector& rhs)
       : name(rhs.name),
 	feSpace(rhs.feSpace),
 	vectors(rhs.vectors.getSize())
       
     {
-      for (int i = 0; i < vectors.getSize(); i++) {
+      for (int i = 0; i < vectors.getSize(); i++)
 	vectors[i] = new DOFVector<double>(*rhs.vectors[i]);
-      }
     }
 
     ~SystemVector() 
     {
-      for (int i = 0; i < vectors.getSize(); i++) {
+      for (int i = 0; i < vectors.getSize(); i++)
 	delete vectors[i];
-      }
     }
 
     void createNewDOFVectors(std::string name)
     {     
-      for (int i = 0; i < vectors.getSize(); i++) {
+      for (int i = 0; i < vectors.getSize(); i++)
 	vectors[i] = new DOFVector<double>(feSpace[i], "tmp");
-      }
     }
 
-    /** \brief
-     * Sets \ref vectors[index] = vec.
-     */ 
-    inline void setDOFVector(int index, DOFVector<double> *vec) {
+    /// Sets \ref vectors[index] = vec.
+    inline void setDOFVector(int index, DOFVector<double> *vec) 
+    {
       TEST_EXIT_DBG(index < vectors.getSize())("invalid index\n");
       vectors[index] = vec;
     }
 
-    /** \brief
-     * Returns \ref vectors[index].
-     */
-    inline DOFVector<double> *getDOFVector(int index) {      
+    /// Returns \ref vectors[index].
+    inline DOFVector<double> *getDOFVector(int index) 
+    {
       TEST_EXIT_DBG(index < vectors.getSize())("invalid index\n");
       return vectors[index];
     }
 
-    /** \brief
-     * Returns \ref vectors[index].
-     */
-    inline const DOFVector<double> *getDOFVector(int index) const {
+    /// Returns \ref vectors[index].
+    inline const DOFVector<double> *getDOFVector(int index) const 
+    {
       TEST_EXIT_DBG(index < vectors.getSize())("invalid index\n");
       return vectors[index];
     }
 
-    /** \brief
-     * Returns sum of used vector sizes.
-     */
-    inline int getUsedSize() const {
+    /// Returns sum of used vector sizes.
+    inline int getUsedSize() const 
+    {
       int totalSize = 0;
       int size = vectors.getSize();
-      for (int i = 0; i < size; i++) {
+      for (int i = 0; i < size; i++)
 	totalSize += vectors[i]->getUsedSize();
-      }
       return totalSize;
     }
 
-    /** \brief
-     * Returns number of contained vectors.
-     */
-    inline int getNumVectors() const { 
+    /// Returns number of contained vectors.
+    inline int getNumVectors() const 
+    { 
       return vectors.getSize(); 
     }