Parallel type changes.

AMDiS/src/AMDiS_fwd.h

@@ -97,6 +97,10 @@ namespace AMDiS {
   class VertexInfo;
   class VertexVector;
 
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+  class FeSpaceDofMap;
+#endif
+
   struct BoundaryObject;
   struct AtomicBoundary;
 

AMDiS/src/DOFMatrix.cc

@@ -26,6 +26,9 @@
 #include "BoundaryManager.h"
 #include "Assembler.h"
 #include "Serializer.h"
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+#include "parallel/ParallelDofMapping.h"
+#endif
 
 namespace AMDiS {
 
@@ -233,11 +236,12 @@ namespace AMDiS {
 
       if (condition && condition->isDirichlet()) {	
 	if (condition->applyBoundaryCondition()) {
+
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-	  if ((*rankDofs)[rowIndices[i]]) 
-	    applyDBCs.insert(static_cast<int>(row));
+ 	  if (dofMap->isRankDof(rowIndices[i])) 
+ 	    applyDBCs.insert(static_cast<int>(row));
 #else
-	  applyDBCs.insert(static_cast<int>(row));
+ 	  applyDBCs.insert(static_cast<int>(row));
 #endif
 	}
       } else {
@@ -514,4 +518,10 @@ namespace AMDiS {
     inserter = new inserter_type(matrix, nnz_per_row);
   }
 
+
+  void DOFMatrix::setDofMap(FeSpaceDofMap& m)
+  {
+    dofMap = &m; 
+  }
+
 }

AMDiS/src/DOFMatrix.h

@@ -39,6 +39,8 @@
 
 namespace AMDiS {
 
+  using namespace std;
+
   /** \ingroup DOFAdministration
    * \brief
    * A DOFMatrix is a sparse matrix representation for matrices that work
@@ -65,18 +67,17 @@ namespace AMDiS {
     /// Symbolic constant for an unused matrix entry
     static const int UNUSED_ENTRY = -1;
     
-    /** \brief
-     * Symbolic constant for an unused entry which is not followed by any
-     * used entry in this row
-     */
+    /// Symbolic constant for an unused entry which is not followed by any
+    /// used entry in this row
     static const int NO_MORE_ENTRIES = -2;
 
   public:    
     DOFMatrix();
 
     /// Constructs a DOFMatrix with name n and the given row and olumn FeSpaces.
-    DOFMatrix(const FiniteElemSpace* rowFeSpace, const FiniteElemSpace* colFeSpace,
-	      std::string n = "");
+    DOFMatrix(const FiniteElemSpace* rowFeSpace, 
+	      const FiniteElemSpace* colFeSpace,
+	      string n = "");
 
     /// Copy-Constructor
     DOFMatrix(const DOFMatrix& rhs);
@@ -102,15 +103,15 @@ namespace AMDiS {
     }
 
     // Only to get rid of the abstract functions, I hope they are not used
-    std::vector<bool>::iterator begin() 
+    vector<bool>::iterator begin() 
     {
-      ERROR_EXIT("Shouldn't be used, only fake."); std::vector<bool> v; 
+      ERROR_EXIT("Shouldn't be used, only fake."); vector<bool> v; 
       return v.begin();
     }
     
-    std::vector<bool>::iterator end() 
+    vector<bool>::iterator end() 
     {
-      ERROR_EXIT("Shouldn't be used, only fake."); std::vector<bool> v; 
+      ERROR_EXIT("Shouldn't be used, only fake."); vector<bool> v; 
       return v.end();
     }
     
@@ -128,7 +129,7 @@ namespace AMDiS {
     }
  
     /// DOFMatrix does not need to be compressed before assembling, when using MTL4.
-    void compressDOFIndexed(int first, int last, std::vector<DegreeOfFreedom> &newDOF) 
+    void compressDOFIndexed(int first, int last, vector<DegreeOfFreedom> &newDOF) 
     {}
 
     /// Implements DOFIndexedBase::freeDOFContent()
@@ -152,39 +153,38 @@ namespace AMDiS {
     /// Multiplication with a scalar.
     void scal(double s);
 
-    /** \brief
-     * Adds an operator to the DOFMatrix. A factor, that is multipled
-     * to the operator, and a multilier factor for the estimator may be
-     * also given.
-     */
-    void addOperator(Operator *op, double* factor = NULL, double* estFactor = NULL);
+    /// Adds an operator to the DOFMatrix. A factor, that is multipled to the 
+    /// operator, and a multilier factor for the estimator may be also given.
+    void addOperator(Operator *op, 
+		     double* factor = NULL, 
+		     double* estFactor = NULL);
 
-    inline std::vector<double*>::iterator getOperatorFactorBegin() 
+    inline vector<double*>::iterator getOperatorFactorBegin() 
     {
       return operatorFactor.begin();
     }
 
-    inline std::vector<double*>::iterator getOperatorFactorEnd() 
+    inline vector<double*>::iterator getOperatorFactorEnd() 
     {
       return operatorFactor.end();
     }
 
-    inline std::vector<double*>::iterator getOperatorEstFactorBegin() 
+    inline vector<double*>::iterator getOperatorEstFactorBegin() 
     {
       return operatorEstFactor.begin();
     }
 
-    inline std::vector<double*>::iterator getOperatorEstFactorEnd() 
+    inline vector<double*>::iterator getOperatorEstFactorEnd() 
     {
       return operatorEstFactor.end();
     }
 
-    inline std::vector<Operator*>::iterator getOperatorsBegin() 
+    inline vector<Operator*>::iterator getOperatorsBegin() 
     {
       return operators.begin();
     }
 
-    inline std::vector<Operator*>::iterator getOperatorsEnd() 
+    inline vector<Operator*>::iterator getOperatorsEnd() 
     {
       return operators.end();
     }
@@ -237,11 +237,9 @@ namespace AMDiS {
 			  ElInfo* rowElInfo,
 			  ElInfo* colElInfo);
 
-    /* \brief
-     * That function must be called after the matrix assembling has been finished. 
-     * This makes it possible to start some cleanup or matrix data compressing 
-     * procedures.
-     */
+    /// That function must be called after the matrix assembling has been 
+    /// finished. This makes it possible to start some cleanup or matrix 
+    /// data compressing procedures.
     void finishAssembling();
 
     /** \brief
@@ -252,10 +250,8 @@ namespace AMDiS {
      */
     void startInsertion(int nnz_per_row = 10);
 
-    /** \brief
-     * Finishes insertion. For compressed matrix types, this is where the 
-     * compression happens.
-     */
+    /// Finishes insertion. For compressed matrix types, this is where the
+    /// compression happens.
     void finishInsertion()
     {
       FUNCNAME("DOFMatrix::finishInsertion()");
@@ -266,10 +262,8 @@ namespace AMDiS {
       inserter= 0;
     }
 
-    /** \brief
-     * Returns whether restriction should be performed after coarsening
-     * (false by default)
-     */
+    /// Returns whether restriction should be performed after coarsening
+    /// (false by default)
     virtual bool coarseRestrict() 
     {
       return false;
@@ -299,17 +293,15 @@ namespace AMDiS {
       return num_rows(matrix);
     }
 
-    /** \brief
-     * Returns the number of used rows (equal to number of used DOFs in
-     * the row FE space).
-     */
+    /// Returns the number of used rows (equal to number of used DOFs in
+    /// the row FE space).
     inline int getUsedSize() const 
     {
       return rowFeSpace->getAdmin()->getUsedSize();
     }
 
     /// Returns \ref name
-    inline std::string getName() const 
+    inline string getName() const 
     { 
       return name; 
     }
@@ -326,10 +318,8 @@ namespace AMDiS {
     /// Changes col at logical indices a,b to c 
     void changeColOfEntry(DegreeOfFreedom a, DegreeOfFreedom b, DegreeOfFreedom c);
 
-    /** \brief
-     * Creates an entry with logical indices irow, icol if there is no entry
-     * yet. Than sign * entry is added to the value at this logical indices
-     */
+    /// Creates an entry with logical indices irow, icol if there is no entry
+    /// yet. Than sign * entry is added to the value at this logical indices
     void addSparseDOFEntry(double sign,
 			   int irow, int jcol, double entry,
 			   bool add = true);
@@ -350,17 +340,17 @@ namespace AMDiS {
 
     bool symmetric();
 
-    inline std::vector<Operator*>& getOperators() 
+    inline vector<Operator*>& getOperators() 
     { 
       return operators; 
     }
     
-    inline std::vector<double*>& getOperatorFactor() 
+    inline vector<double*>& getOperatorFactor() 
     { 
       return operatorFactor; 
     }
 
-    inline std::vector<double*>& getOperatorEstFactor() 
+    inline vector<double*>& getOperatorEstFactor() 
     { 
       return operatorEstFactor; 
     }
@@ -399,65 +389,53 @@ namespace AMDiS {
     }
 
     /// Writes the matrix to an output stream.
-    void serialize(std::ostream &out);
+    void serialize(ostream &out);
 
     /// Reads a matrix from an input stream.
-    void deserialize(std::istream &in);
+    void deserialize(istream &in);
 
     ///
     int memsize();
 
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-    void setRankDofs(std::map<DegreeOfFreedom, bool>& dofmap)
-    {
-      rankDofs = &dofmap;
-    }
+    void setDofMap(FeSpaceDofMap& m);
 #endif
 
   protected:
-    /** \brief
-     * Pointer to a FiniteElemSpace with information about corresponding row DOFs
-     * and basis functions
-     */
+    /// Pointer to a FiniteElemSpace with information about corresponding row DOFs
+    /// and basis functions
     const FiniteElemSpace *rowFeSpace;
 
-    /** \brief
-     * Pointer to a FiniteElemSpace with information about corresponding 
-     * column DOFs and basis functions
-     */
+    /// Pointer to a FiniteElemSpace with information about corresponding 
+    /// column DOFs and basis functions
     const FiniteElemSpace *colFeSpace;
 
     /// Name of the DOFMatrix
-    std::string name;
+    string name;
 
-    /// Sparse matrix, type is a template parameter by default compressed2D<double>
+    /// Sparse matrix, type is a template parameter by 
+    /// default compressed2D<double>
     base_matrix_type matrix;
 
     /// Used while mesh traversal
     static DOFMatrix *traversePtr;
   
-    /** \brief
-     * Pointers to all operators of the equation systems. Are used in the
-     * assembling process.
-     */
-    std::vector<Operator*> operators;
+    /// Pointers to all operators of the equation systems. Are used in the
+    /// assembling process.
+    vector<Operator*> operators;
     
-    /** \brief
-     * Defines for each operator a factor which is used to scal the element
-     * matrix after the assembling process of the operator.
-     */
-    std::vector<double*> operatorFactor;
+    /// Defines for each operator a factor which is used to scal the element
+    /// matrix after the assembling process of the operator.
+    vector<double*> operatorFactor;
 
     ///
-    std::vector<double*> operatorEstFactor;
+    vector<double*> operatorEstFactor;
 
     ///
     BoundaryManager *boundaryManager;
 
-    /** \brief
-     * If false, the matrix is a diagonal matrix within a matrix of DOF matrices.
-     * Otherwise the value is true, and the matrix is an off-diagonal matrix.
-     */
+    /// If false, the matrix is a diagonal matrix within a matrix of DOF matrices.
+    /// Otherwise the value is true, and the matrix is an off-diagonal matrix.
     bool coupleMatrix;
 
     /// Temporary variable used in assemble()
@@ -470,10 +448,10 @@ namespace AMDiS {
     int nCol;
 
     /// Maps local row indices of an element to global matrix indices.
-    std::vector<DegreeOfFreedom> rowIndices;
+    vector<DegreeOfFreedom> rowIndices;
 
     /// Maps local col indices of an element to global matrix indices.
-    std::vector<DegreeOfFreedom> colIndices;
+    vector<DegreeOfFreedom> colIndices;
 
     /* \brief
      * A set of row indices. When assembling the DOF matrix, all rows, that
@@ -492,10 +470,10 @@ namespace AMDiS {
      int nnzPerRow;
 
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-     /// Stores for the DOFs of the row FE spaces whether they are owned by the
-     /// rank or not. This is used to ensure that Dirichlet BC is handled
-     /// correctly in parallel computations.
-     std::map<DegreeOfFreedom, bool> *rankDofs;
+     /// Is used in parallel computations to check whether specific DOFs in the
+     /// row FE spaces are owned by the rank or not. This is used to ensure that 
+     /// Dirichlet BC is handled correctly in parallel computations.
+     FeSpaceDofMap *dofMap;
 #endif
 
     /// Inserter object: implemented as pointer, allocated and deallocated as needed

AMDiS/src/DOFVector.h

@@ -42,9 +42,14 @@
 #include "BasisFunction.h"
 #include "FiniteElemSpace.h"
 #include "SurfaceQuadrature.h"
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+#include "parallel/ParallelDofMapping.h"
+#endif
 
 namespace AMDiS {
 
+  using namespace std;
+
   template<typename T> 
   class DOFVectorBase : public DOFIndexed<T>
   {
@@ -57,25 +62,21 @@ namespace AMDiS {
         nBasFcts(0)
     {
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-      rankDofs = NULL;
+      dofMap = NULL;
 #endif
     }
     
-    DOFVectorBase(const FiniteElemSpace *f, std::string n);
+    DOFVectorBase(const FiniteElemSpace *f, string n);
 
     virtual ~DOFVectorBase();
 
-    /** \brief 
-     * For the given element, this function returns an array of all DOFs of this
-     * DOFVector that are defined on this element.
-     */
+    /// For the given element, this function returns an array of all DOFs of 
+    /// this DOFVector that are defined on this element.
     virtual void getLocalVector(const Element *el, 
 				mtl::dense_vector<T>& localVec) const;
 
-    /** \brief
-     * Evaluates the DOF vector at a set of quadrature points defined on the 
-     * given element.
-     */
+    /// Evaluates the DOF vector at a set of quadrature points defined on the 
+    /// given element.
     void getVecAtQPs(const ElInfo *elInfo, 
 		     const Quadrature *quad,
 		     const FastQuadrature *quadFast,
@@ -87,10 +88,8 @@ namespace AMDiS {
 		     const FastQuadrature *quadFast,
 		     mtl::dense_vector<T>& vecAtQPs) const;
 
-    /** \brief
-     * Evaluates the gradient of a DOF vector at a set of quadrature points defined on the
-     * given element.
-     */
+    /// Evaluates the gradient of a DOF vector at a set of quadrature points
+    /// defined on the given element.
     void getGrdAtQPs( const ElInfo *elInfo,
 		      const Quadrature *quad,
 		      const FastQuadrature *quadFast,
@@ -102,10 +101,8 @@ namespace AMDiS {
 		      const FastQuadrature *quadFast,
 		      mtl::dense_vector<typename GradientType<T>::type> &grdAtQPs) const;
 
-    /** \brief
-     * Evaluates the comp'th component of the derivative of a DOF vector at a set of quadrature points defined on the
-     * given element.
-     */
+    /// Evaluates the comp'th component of the derivative of a DOF vector at a
+    /// set of quadrature points defined on the given element.
     void getDerivativeAtQPs( const ElInfo *elInfo,
 		      const Quadrature *quad,
 		      const FastQuadrature *quadFast,
@@ -119,10 +116,8 @@ namespace AMDiS {
 		      int comp,
 		      mtl::dense_vector<T> &derivativeAtQPs) const;
 
-    /** \brief
-     * Evaluates the jacobian of a DOF vector at a set of quadrature points defined on the
-     * given element.
-     */
+    /// Evaluates the jacobian of a DOF vector at a set of quadrature points
+    ///  defined on the given element.
     void getD2AtQPs(const ElInfo *elInfo,
 		    const Quadrature *quad,
 		    const FastQuadrature *quadFast,
@@ -134,10 +129,8 @@ namespace AMDiS {
       return feSpace;
     }
 
-    /** \brief
-     * Assembles the element vector for the given ellement and adds the
-     * element matrix to the current DOF vector.
-     */ 
+    /// Assembles the element vector for the given ellement and adds the
+    /// element matrix to the current DOF vector.
     void assemble(T factor, ElInfo *elInfo,			    
 		  const BoundaryType *bound, 
 		  Operator *op = NULL);
@@ -154,11 +147,9 @@ namespace AMDiS {
 			  ElInfo *elInfo,
 			  bool add = true); 
 
-    /* \brief
-     * That function must be called after the matrix assembling has been finished. 
-     * This makes it possible to start some cleanup or matrix data compressing 
-     * procedures.
-     */
+    /// That function must be called after the matrix assembling has been
+    /// finished. This makes it possible to start some cleanup or matrix
+    /// data compressing procedures.
     void finishAssembling();
  
     inline void addOperator(Operator* op, 
@@ -170,33 +161,33 @@ namespace AMDiS {
       operatorEstFactor.push_back(estFactor);
     }
 
-    inline std::vector<double*>::iterator getOperatorFactorBegin() 
+    inline vector<double*>::iterator getOperatorFactorBegin()