* Bugfixing around SolutionDataStorage

AMDiS/src/DOFAdmin.cc

@@ -53,13 +53,14 @@ namespace AMDiS {
       usedCount = src.usedCount;
       holeCount = src.holeCount;
       sizeUsed = src.sizeUsed;
-      for (int i = 0; i < mesh->getDim(); i++) {
+      for (int i = 0; i <= mesh->getDim(); i++) {
 	nrDOF[i] = src.nrDOF[i];
 	nr0DOF[i] = src.nr0DOF[i];
       }
       dofIndexedList = src.dofIndexedList;
       dofContainerList = src.dofContainerList;
     }
+
     return *this;
   }
   /****************************************************************************/

AMDiS/src/DOFVector.h

@@ -76,32 +76,33 @@ namespace AMDiS {
 	elementVector(NULL),
         boundaryManager(NULL),
         nBasFcts(0)
-    {};
+    {}
     
     DOFVectorBase(const FiniteElemSpace *f, std::string n);
 
     virtual ~DOFVectorBase();
 
-    virtual const T *getLocalVector(const Element *el, T* localVec) const;
+    virtual const T *getLocalVector(const Element *el, 
+				    T* localVec) const;
 
-    const T *getVecAtQPs(const ElInfo         *elInfo, 
-			 const Quadrature     *quad,
+    const T *getVecAtQPs(const ElInfo *elInfo, 
+			 const Quadrature *quad,
 			 const FastQuadrature *quadFast,
-			 T                    *vecAtQPs) const;
+			 T *vecAtQPs) const;
 
-    const WorldVector<T> *getGrdAtQPs(const ElInfo         *elInfo, 
-				      const Quadrature     *quad,
+    const WorldVector<T> *getGrdAtQPs(const ElInfo *elInfo, 
+				      const Quadrature *quad,
 				      const FastQuadrature *quadFast,
-				      WorldVector<T>       *grdAtQPs) const;
+				      WorldVector<T> *grdAtQPs) const;
 
-    const WorldMatrix<T> *getD2AtQPs(const ElInfo         *elInfo, 
-				     const Quadrature     *quad,
+    const WorldMatrix<T> *getD2AtQPs(const ElInfo *elInfo, 
+				     const Quadrature *quad,
 				     const FastQuadrature *quadFast,
-				     WorldMatrix<T>       *d2AtQPs) const;
+				     WorldMatrix<T> *d2AtQPs) const;
 
-    virtual const FiniteElemSpace* getFESpace() const {
+    inline const FiniteElemSpace* getFESpace() const {
       return feSpace;
-    };
+    }
 
     ElementVector *assemble(T factor, ElInfo *elInfo,
 			    const BoundaryType *bound, 
@@ -119,32 +120,32 @@ namespace AMDiS {
       operators.push_back(op);
       operatorFactor.push_back(factor);
       operatorEstFactor.push_back(estFactor);
-    };
+    }
 
     inline std::vector<double*>::iterator getOperatorFactorBegin() {
       return operatorFactor.begin();
-    };
+    }
 
     inline std::vector<double*>::iterator getOperatorFactorEnd() {
       return operatorFactor.end();
-    };
+    }
 
     inline std::vector<double*>::iterator getOperatorEstFactorBegin() {
       return operatorEstFactor.begin();
-    };
+    }
 
     inline std::vector<double*>::iterator getOperatorEstFactorEnd() {
       return operatorEstFactor.end();
-    };
+    }
 
 
     inline std::vector<Operator*>::iterator getOperatorsBegin() {
       return operators.begin();
-    };
+    }
 
     inline std::vector<Operator*>::iterator getOperatorsEnd() {
       return operators.end();
-    };
+    }
 
     Flag getAssembleFlag();
 
@@ -158,30 +159,30 @@ namespace AMDiS {
 
     inline std::vector<Operator*>& getOperators() { 
       return operators; 
-    };
+    }
 
     inline std::vector<double*>& getOperatorFactor() { 
       return operatorFactor; 
-    };
+    }
 
     inline std::vector<double*>& getOperatorEstFactor() { 
       return operatorEstFactor; 
-    };
+    }
 
     /** \brief
      * Returns \ref name
      */
     inline const std::string& getName() const { 
       return name; 
-    }; 
+    } 
 
     inline BoundaryManager* getBoundaryManager() const { 
       return boundaryManager; 
-    };
+    }
 
     inline void setBoundaryManager(BoundaryManager *bm) {
       boundaryManager = bm;
-    };
+    }
 
   protected:
     /** \brief
@@ -285,26 +286,28 @@ namespace AMDiS {
     public:
       Iterator(DOFIndexed<T> *c, DOFIteratorType type)
 	: DOFIterator<T>(c, type)
-      {};   
+      {}
 
       Iterator(DOFAdmin *admin, DOFIndexed<T> *c, DOFIteratorType type)
 	: DOFIterator<T>(admin, c, type)
-      {};   
+      {}
     };
 
     class Creator : public CreatorInterface<DOFVector<T> > {
     public:
       MEMORY_MANAGED(Creator);
 
-      Creator(FiniteElemSpace *feSpace_) : feSpace(feSpace_) {};
+      Creator(FiniteElemSpace *feSpace_) 
+        : feSpace(feSpace_) 
+      {}
 
       DOFVector<T> *create() { 
 	return NEW DOFVector<T>(feSpace, ""); 
-      };
+      }
 
       void free(DOFVector<T> *vec) { 
 	DELETE vec; 
-      };
+      }
 
     private:
       FiniteElemSpace *feSpace;
@@ -351,14 +354,14 @@ namespace AMDiS {
      */
     typename std::vector<T>::iterator begin() { 
       return vec.begin(); 
-    };
+    }
 
     /** \brief
      * Returns iterator to the end of \ref vec
      */
     typename std::vector<T>::iterator end() { 
       return vec.end(); 
-    };
+    }
   
     /** \brief
      * Used by DOFAdmin to compress this DOFVector. Implementation of
@@ -469,7 +472,7 @@ namespace AMDiS {
      */
     inline double L2Norm(Quadrature* q = NULL) const {
       return sqrt(L2NormSquare());
-    };
+    }
 
     /** \brief
      * Calculates square of L2 norm of this DOFVector
@@ -481,7 +484,7 @@ namespace AMDiS {
      */
     inline double H1Norm(Quadrature* q = NULL) const {
       return sqrt(H1NormSquare());
-    };  
+    }; 
 
     /** \brief
      * Calculates square of H1 norm of this DOFVector
@@ -575,6 +578,9 @@ namespace AMDiS {
      */
     void print() const; 
 
+    /** \brief
+     *
+     */
     int calcMemoryUsage() const;
 
     /** \brief
@@ -692,11 +698,11 @@ namespace AMDiS {
 
   inline double min(const DOFVector<double>& v) {
     return v.min();
-  }; 
+  } 
 
   inline double max(const DOFVector<double>& v) {
     return v.max();
-  }; 
+  }
 
   // ===========================================================================
   // ===== class DOFVectorDOF ==================================================
@@ -720,14 +726,14 @@ namespace AMDiS {
       : DOFVector<DegreeOfFreedom>(feSpace_, name_)
     {
       feSpace->getAdmin()->addDOFContainer(this);
-    };
+    }
   
     /** \brief
      * Deregisters itself at DOFAdmin.
      */
     ~DOFVectorDOF() {
       feSpace->getAdmin()->removeDOFContainer(this);
-    };
+    }
 
     /** \brief
      * Implements DOFContainer::operator[]() by calling 
@@ -735,14 +741,14 @@ namespace AMDiS {
      */
     DegreeOfFreedom& operator[](DegreeOfFreedom i) {
       return DOFVector<DegreeOfFreedom>::operator[](i);
-    };
+    }
 
     /** \brief
      * Implements DOFIndexedBase::getSize()
      */
     int getSize() const {
       return DOFVector<DegreeOfFreedom>::getSize();
-    };
+    }
 
     /** \brief
      * Implements DOFIndexedBase::resize()
@@ -765,22 +771,22 @@ namespace AMDiS {
   template<typename T>
   double norm(DOFVector<T> *vec) {
     return vec->nrm2();
-  };
+  }
 
   template<typename T>
   double L2Norm(DOFVector<T> *vec) {
     return vec->L2Norm();
-  };
+  }
 
   template<typename T>
   double H1Norm(DOFVector<T> *vec) {
     return vec->H1Norm();
-  };
+  }
 
   template<typename T>
   void print(DOFVector<T> *vec) {
     vec->print();
-  };
+  }
 
   // point wise multiplication
   template<typename T>
@@ -834,7 +840,9 @@ namespace AMDiS {
   void xpay(double a,const DOFVector<T>& x,DOFVector<T>& y);
 
   template<typename T>
-  inline void scal(T a, DOFVector<T>& y) {y*=a;};
+  inline void scal(T a, DOFVector<T>& y) {
+    y *= a;
+  }
 
   template<typename T>
   inline const DOFVector<T>& mult(double scal,
@@ -861,21 +869,19 @@ namespace AMDiS {
 
 
   template<typename T>
-  inline void set(DOFVector<T>& vec, T d) 
-  {
+  inline void set(DOFVector<T>& vec, T d) {
     vec.set(d);
-  };
+  }
 
   template<typename T>
-  inline void setValue(DOFVector<T>& vec, T d) 
-  {
+  inline void setValue(DOFVector<T>& vec, T d) {
     vec.set(d);
-  };
+  }
 
   template<typename T>
   inline int size(DOFVector<T> *vec) {
     return vec->getUsedSize();
-  };
+  }
 
   WorldVector<DOFVector<double>*> *transform(DOFVector<WorldVector<double> > *vec,
 					     WorldVector<DOFVector<double>*> *result);

AMDiS/src/DataCollector.cc

@@ -23,7 +23,6 @@ namespace AMDiS {
 
     // === get admin ===    
     localAdmin_ = const_cast<DOFAdmin*>(feSpace->getAdmin());
-
     // === create vertex info vector ===
     vertexInfos_ = NEW DOFVector< std::list<VertexInfo> >(feSpace, "vertex infos");
     interpPointInd_ = NEW DOFVector<int>(feSpace, "interpolation point indices");
@@ -100,8 +99,9 @@ namespace AMDiS {
     // Traverse elements to create element information
     elInfo = stack.traverseFirst(mesh_, level_, flag);
     while (elInfo) {
-      if (!writeElem_ || writeElem_(elInfo))
+      if (!writeElem_ || writeElem_(elInfo)) {
 	addElementData(elInfo);
+      }
       elInfo = stack.traverseNext(elInfo);
     }
 
@@ -124,7 +124,7 @@ namespace AMDiS {
     basisFcts_ = const_cast<BasisFunction*>(feSpace_->getBasisFcts());
     nBasisFcts_ = basisFcts_->getNumber();
     localDOFs_ = GET_MEMORY(DegreeOfFreedom, nBasisFcts_);
-    
+  
     TraverseStack stack;
 
     // Traverse elements to add value information and to mark
@@ -133,8 +133,9 @@ namespace AMDiS {
 					 level_, 
 					 traverseFlag_ | Mesh::FILL_COORDS);
     while (elInfo) {
-      if (!writeElem_ || writeElem_(elInfo))
+      if (!writeElem_ || writeElem_(elInfo)) {
 	addValueData(elInfo);
+      }
       elInfo = stack.traverseNext(elInfo);
     }
 
@@ -158,7 +159,7 @@ namespace AMDiS {
 	elInfo = stack.traverseNext(elInfo);
       }
     }
-    
+   
     FREE_MEMORY(localDOFs_, DegreeOfFreedom, nBasisFcts_);
     valueDataCollected_ = true;
     
@@ -231,12 +232,10 @@ namespace AMDiS {
     } else {
       elementInfo.elementRegion = -1;
     }
-    
+   
     // read surface regions to element info
     ed = elInfo->getElement()->getElementData(SURFACE_REGION);
-    
     elementInfo.surfaceRegions.set(-1);
-    
     while (ed) {
       SurfaceRegion_ED *sr = dynamic_cast<SurfaceRegion_ED*>(ed);
       elementInfo.surfaceRegions[sr->getSide()] = sr->getRegion();
@@ -250,7 +249,7 @@ namespace AMDiS {
       
       // get dof index of this vertex
       vertexDOF = dof[i][nPreDofs_];
-      
+     
       // search for coords at this dof
       std::list<VertexInfo>::iterator it =
 	  find((*vertexInfos_)[vertexDOF].begin(),
@@ -280,6 +279,7 @@ namespace AMDiS {
 	outputIndices_[elInfo->getNeighbour(i)->getIndex()] :
 	-1;
     }
+
     
     if (dim_ == 3) {
       elementInfo.type = (dynamic_cast<ElInfo3d*>(elInfo)->getType());
@@ -294,12 +294,11 @@ namespace AMDiS {
   int DataCollector::addValueData(ElInfo *elInfo)
   {
     FUNCNAME("DataCollector::addValueData()");
-
+    
     basisFcts_->getLocalIndices(elInfo->getElement(), localAdmin_, localDOFs_);
-    //    WorldVector<double> vertexCoords;
 
     // First, traverse all DOFs at the vertices of the element, determine
-    // their coordinates and add them to the corresponding entry in dofCoords_.      
+    // their coordinates and add them to the corresponding entry in dofCoords_.
     for (int i = 0; i < mesh_->getGeo(VERTEX); i++) {
       DegreeOfFreedom dofi = localDOFs_[i];
 
@@ -307,7 +306,7 @@ namespace AMDiS {
       
       // get coords of this vertex
       *vertexCoords = elInfo->getCoord(i);