Better solution to create element matrices for assembling on different meshes.

AMDiS/bin/Makefile.am

@@ -16,7 +16,6 @@ if USE_PARALLEL_AMDIS
   $(PARALLEL_DIR)/MeshStructure_ED.h \
   $(PARALLEL_DIR)/ParallelError.h $(PARALLEL_DIR)/ParallelError.hh \
   $(PARALLEL_DIR)/ParallelProblem.h $(PARALLEL_DIR)/ParallelProblem.cc \
-  $(PARALLEL_DIR)/ParallelDomainProblem.h $(PARALLEL_DIR)/ParallelDomainProblem.cc \
   $(PARALLEL_DIR)/ParMetisPartitioner.h $(PARALLEL_DIR)/ParMetisPartitioner.cc \
   $(PARALLEL_DIR)/PartitionElementData.h
   PARALLEL_INCLUDES = -I/work/home7/witkowsk/local/include \

AMDiS/src/Assembler.cc

@@ -109,22 +109,35 @@ namespace AMDiS {
   
     ElementMatrix& mat = rememberElMat ? elementMatrix : userMat;
 
-    TEST_EXIT(zeroOrderAssembler)("Not yet implemented for not zero order assembler!\n");
-
-    if (secondOrderAssembler)
+    if (secondOrderAssembler) {
       secondOrderAssembler->calculateElementMatrix(smallElInfo, mat);
-    if (firstOrderAssemblerGrdPsi)
+
+      ElementMatrix m(nRow, nRow);
+      smallElInfo->getSubElemCoordsMat_so(m, rowFESpace->getBasisFcts()->getDegree());
+      ElementMatrix tmpMat(nRow, nRow);
+      tmpMat = m * mat;
+      mat = tmpMat;
+    }
+
+    if (firstOrderAssemblerGrdPsi) {
+      ERROR_EXIT("Not yet implemented for not zero order assembler!\n");
       firstOrderAssemblerGrdPsi->calculateElementMatrix(smallElInfo, mat);
-    if (firstOrderAssemblerGrdPhi)
+    }
+
+    if (firstOrderAssemblerGrdPhi) {
+      ERROR_EXIT("Not yet implemented for not zero order assembler!\n");
       firstOrderAssemblerGrdPhi->calculateElementMatrix(smallElInfo, mat);
-    if (zeroOrderAssembler)
-      zeroOrderAssembler->calculateElementMatrix(smallElInfo, mat);
+    }
 
-    const mtl::dense2D<double>& m = smallElInfo->getSubElemCoordsMat();
-    ElementMatrix tmpMat(nRow, nRow);
-    tmpMat = m * mat;
-    mat = tmpMat;
+    if (zeroOrderAssembler) {
+      zeroOrderAssembler->calculateElementMatrix(smallElInfo, mat);
 
+      ElementMatrix m(nRow, nRow);
+      smallElInfo->getSubElemCoordsMat(m, rowFESpace->getBasisFcts()->getDegree());
+      ElementMatrix tmpMat(nRow, nRow);
+      tmpMat = m * mat;
+      mat = tmpMat;
+    }
 
     if (rememberElMat)
       userMat += factor * elementMatrix;
@@ -240,23 +253,20 @@ namespace AMDiS {
     FUNCNAME("Assembler::matVecAssemble()");
 
     Element *el = elInfo->getElement(); 
-    const BasisFunction *basFcts = rowFESpace->getBasisFcts();
-    int nBasFcts = basFcts->getNumber();
-    double *uhOldLoc = new double[nBasFcts];
+    double *uhOldLoc = new double[nRow];
 
     operat->uhOld->getLocalVector(el, uhOldLoc);
     
     if (el != lastMatEl)
       calculateElementMatrix(elInfo, elementMatrix);
     
-    for (int i = 0; i < nBasFcts; i++) {
+    for (int i = 0; i < nRow; i++) {
       double val = 0.0;
-      for (int j = 0; j < nBasFcts; j++) {
+      for (int j = 0; j < nRow; j++) {
 	val += elementMatrix[i][j] * uhOldLoc[j];
       }
       vec[i] += val;
-    }
-    
+    }   
 
     delete [] uhOldLoc;
   }
@@ -283,7 +293,8 @@ namespace AMDiS {
 
     operat->uhOld->getLocalVector(auxEl, uhOldLoc);
 
-    const mtl::dense2D<double>& m = smallElInfo->getSubElemCoordsMat();
+    mtl::dense2D<double> m(nRow, nRow);
+    smallElInfo->getSubElemCoordsMat(m, rowFESpace->getBasisFcts()->getDegree());
 
     for (int i = 0; i < nBasFcts; i++) {
       uhOldLoc2[i] = 0.0;
@@ -306,7 +317,6 @@ namespace AMDiS {
       vec[i] += val;
     }
     
-
     delete [] uhOldLoc;
     delete [] uhOldLoc2;
   }

AMDiS/src/DOFIterator.h

@@ -72,14 +72,13 @@ namespace AMDiS {
     virtual void reset() {
       position = 0;
       dofFreeIterator = dofFree->begin();
-      if(dofFreeIterator == dofFree->end()) {
+      if (dofFreeIterator == dofFree->end())
 	return;
-      }
+
       goToBeginOfIteratedObject();
-      if(type != ALL_DOFS) { 
-	if(*dofFreeIterator == (type == USED_DOFS))
+      if (type != ALL_DOFS)
+	if (*dofFreeIterator == (type == USED_DOFS))
 	  operator++();
-      }
     }
 
     /** \brief
@@ -196,14 +195,20 @@ namespace AMDiS {
     virtual void decObjectIterator() {}
 
   protected:
-    DOFAdmin                   *dofAdmin;        /**< DOFAdmin which contains
-						  * the dofFree vector 
-						  */ 
-    int                         position;        /**< current position index */
-    std::vector<bool>          *dofFree;         /**< stores which DOFs are used 
-						    */
-    std::vector<bool>::iterator dofFreeIterator; /**< iterator for dofFree */
-    const DOFIteratorType       type;            /**< type of this iterator */
+    /// DOFAdmin which contains the dofFree vector.
+    DOFAdmin *dofAdmin;
+    
+    /// Current position index.
+    int position;
+
+    /// Stores which DOFs are used.
+    std::vector<bool> *dofFree; 
+
+    /// Iterator for dofFree.
+    std::vector<bool>::iterator dofFreeIterator;
+
+    /// Type of this iterator.
+    const DOFIteratorType type;
   };
 
 

AMDiS/src/DOFVector.cc

 #include <boost/numeric/mtl/mtl.hpp>
-
 #include "DOFVector.h"
 #include "Traverse.h"
 #include "DualTraverse.h"
@@ -314,10 +313,8 @@ namespace AMDiS {
   
     TEST_EXIT_DBG(quad || quadFast)("neither quad nor quadFast defined\n");
 
-    if (quad && quadFast) {
-      TEST_EXIT_DBG(quad == quadFast->getQuadrature())
-      	("quad != quadFast->quadrature\n");
-    }
+    if (quad && quadFast)
+      TEST_EXIT_DBG(quad == quadFast->getQuadrature())("quad != quadFast->quadrature\n");
 
     TEST_EXIT_DBG(!quadFast || quadFast->getBasisFunctions() == feSpace->getBasisFcts())
       ("invalid basis functions");
@@ -335,29 +332,29 @@ namespace AMDiS {
 	delete [] grd;
 
       grd = new WorldVector<double>[nPoints];
-      for (int i = 0; i < nPoints; i++) {
+      for (int i = 0; i < nPoints; i++)
 	grd[i].set(0.0);
-      }
+
       result = grd;
     }
   
     double *localVec = localVectors[myRank];
     getLocalVector(largeElInfo->getElement(), localVec);
-    const mtl::dense2D<double> m = smallElInfo->getSubElemCoordsMat();
+
+    const BasisFunction *basFcts = feSpace->getBasisFcts();    
+    mtl::dense2D<double> m(nBasFcts, nBasFcts);
+    smallElInfo->getSubElemCoordsMat(m, basFcts->getDegree());
 
     DimVec<double> &grd1 = *grdTmp[myRank];
     int parts = Global::getGeo(PARTS, dim);
     const DimVec<WorldVector<double> > &grdLambda = largeElInfo->getGrdLambda();
 
-    
-    const BasisFunction *basFcts = feSpace->getBasisFcts();
     DimVec<double>* grdPhi = grdPhis[myRank];
     DimVec<double> tmp(dim, DEFAULT_VALUE, 0.0);
     
     for (int i = 0; i < nPoints; i++) {
-      for (int j = 0; j < dim + 1; j++) {
+      for (int j = 0; j < dim + 1; j++)
 	grd1[j] = 0.0;
-      }
       
       for (int j = 0; j < nBasFcts; j++) {
 
@@ -368,16 +365,14 @@ namespace AMDiS {
 	  *grdPhi += tmp;
 	}
 
-	for (int k = 0; k < parts; k++) {
+	for (int k = 0; k < parts; k++)
 	  grd1[k] += (*grdPhi)[k] * localVec[j];
-	}
       }
       
       for (int l = 0; l < dow; l++) {
 	result[i][l] = 0.0;
-	for (int k = 0; k < parts; k++) {
+	for (int k = 0; k < parts; k++)
 	  result[i][l] += grdLambda[k][l] * grd1[k];
-	}
       }
     }    
   
@@ -804,7 +799,8 @@ namespace AMDiS {
     double *localVec = localVectors[omp_get_thread_num()];
     getLocalVector(largeElInfo->getElement(), localVec);
 
-    const mtl::dense2D<double> m = smallElInfo->getSubElemCoordsMat();
+    mtl::dense2D<double> m(nBasFcts, nBasFcts);    
+    smallElInfo->getSubElemCoordsMat(m, basFcts->getDegree());
 
     for (int i = 0; i < nPoints; i++) {
       result[i] = 0.0;

AMDiS/src/DOFVector.h

@@ -290,11 +290,11 @@ namespace AMDiS {
       {}
 
       DOFVector<T> *create() { 
-	return NEW DOFVector<T>(feSpace, ""); 
+	return new DOFVector<T>(feSpace, ""); 
       }
 
       void free(DOFVector<T> *vec) { 
-	DELETE vec; 
+	delete vec; 
       }
 
     private:
@@ -493,12 +493,14 @@ namespace AMDiS {
 
     void interpol(DOFVector<T> *v, double factor);
 
+    /// Writes the data of the DOFVector to an output stream.
     void serialize(std::ostream &out) {
       unsigned int size = vec.size();
       out.write(reinterpret_cast<const char*>(&size), sizeof(unsigned int));
       out.write(reinterpret_cast<const char*>(&(vec[0])), size * sizeof(T));
     }
 
+    /// Reads data of an DOFVector from an input stream.
     void deserialize(std::istream &in) {
       unsigned int size;
       in.read(reinterpret_cast<char*>(&size), sizeof(unsigned int));

AMDiS/src/DualTraverse.cc

@@ -170,12 +170,19 @@ namespace AMDiS {
     if (!fillSubElemMat)
       return;
 
-    mtl::dense2D<double>& subCoordsMat = 
-      const_cast<mtl::dense2D<double>&>(elInfoSmall->getSubElemCoordsMat());
+//     mtl::dense2D<double>& subCoordsMat = 
+//       const_cast<mtl::dense2D<double>&>(elInfoSmall->getSubElemCoordsMat());
+//     mtl::dense2D<double>& subCoordsMat_so = 
+//       const_cast<mtl::dense2D<double>&>(elInfoSmall->getSubElemCoordsMat_so());
+
     if (elInfo1 == elInfoSmall) {
-      stack1.getCoordsInElem(elInfo2, basisFcts, subCoordsMat);
+//       stack1.getCoordsInElem(elInfo2, basisFcts, subCoordsMat);
+//       stack1.getCoordsInElem_so(elInfo2, basisFcts, subCoordsMat_so);
+      stack1.fillRefinementPath(*elInfoSmall, *elInfo2);
     } else {
-      stack2.getCoordsInElem(elInfo1, basisFcts, subCoordsMat);
+//       stack2.getCoordsInElem(elInfo1, basisFcts, subCoordsMat);
+//       stack2.getCoordsInElem_so(elInfo1, basisFcts, subCoordsMat_so);
+      stack2.fillRefinementPath(*elInfoSmall, *elInfo1);
     }
   }
 }

AMDiS/src/ElInfo.cc

@@ -29,7 +29,8 @@ namespace AMDiS {
       neighbourCoord_(mesh_->getDim(), NO_INIT),
       oppVertex_(mesh_->getDim(), NO_INIT),
       grdLambda(mesh_->getDim(), NO_INIT),
-      subElemCoordsMat(2, 2)
+      refinementPath(0),
+      refinementPathLength(0)
   {
     projection_.set(NULL);
 
@@ -46,14 +47,12 @@ namespace AMDiS {
 			    WorldVector<double>& w) const
 
   {
-    int dim = l.getSize() - 1;
-
     double c = l[0];
 
     for (int j = 0; j < dimOfWorld; j++)
       w[j] = c * coord_[0][j];
   
-    int vertices = Global::getGeo(VERTEX, dim);
+    int vertices = Global::getGeo(VERTEX, l.getSize() - 1);
 
     for (int i = 1; i < vertices; i++) {
       c = l[i];
@@ -62,10 +61,6 @@ namespace AMDiS {
     }
   }
 
-  /****************************************************************************/
-  /*  compute volume of an element                                            */
-  /****************************************************************************/
-
   double ElInfo::calcDet() const
   {
     testFlag(Mesh::FILL_COORDS);

AMDiS/src/ElInfo.h

@@ -205,13 +205,11 @@ namespace AMDiS {
       return parametric_; 
     }
 
-    /** \brief
-     * Returns the element transformation matrix \ref subElemCoordsMat .
-     * This value is set only during dual traverse.
-     */
-    inline const mtl::dense2D<double>& getSubElemCoordsMat() const {
-      return subElemCoordsMat;
-    }
+    virtual void getSubElemCoordsMat(mtl::dense2D<double>& mat,
+				     int basisFctsDegree) const {}
+
+    virtual void getSubElemCoordsMat_so(mtl::dense2D<double>& mat,
+					int basisFctsDegree) const {}
 
     /** \} */ 
 
@@ -279,14 +277,18 @@ namespace AMDiS {
       parametric_ = param; 
     }
 
-    /** \brief
-     * Sets the element transformation matrix \ref subElemCoordsMat .
-     * This value is used only during dual traverse.
-     */
-//     inline void setSubElemCoordsMat(DimMat<double> *mat) {
-//       subElemCoordsMat = mat;
-//     }
-  
+    /// Set \ref refinementPath
+    inline void setRefinementPath(unsigned long rPath)
+    {
+      refinementPath = rPath;
+    } 
+
+    /// Set \ref refinementPathLength
+    inline void setRefinementPathLength(int length)
+    {
+      refinementPathLength = length;
+    }
+
     /** \} */
 
 
@@ -372,14 +374,6 @@ namespace AMDiS {
       return(0.0);
     }
 
-    virtual void getRefSimplexCoords(const BasisFunction *basisFcts,
-				     mtl::dense2D<double>& coords) const = 0;
-
-    virtual void getSubElementCoords(const BasisFunction *basisFcts,
-				     int iChild,
-				     mtl::dense2D<double>& coords) const = 0;
-
-
   protected:
     /// Pointer to the current mesh
     Mesh *mesh_;
@@ -471,6 +465,10 @@ namespace AMDiS {
     /// Stores the world dimension.
     int dimOfWorld;
 
+    unsigned long refinementPath;
+
+    int refinementPathLength;
+
     /** \brief
      * This is a transformation matrix used during dual traverse. It is set, if
      * the current element is the smaller element of an element pair in the traverse.
@@ -480,6 +478,8 @@ namespace AMDiS {
      */
     mtl::dense2D<double> subElemCoordsMat;
 
+    mtl::dense2D<double> subElemCoordsMat_so;
+
   public:
     /** \brief 
      * child_vertex[el_type][child][i] = father's local vertex index of new 

AMDiS/src/ElInfo1d.cc

@@ -40,6 +40,10 @@ namespace AMDiS {
 					     {1.0, 0.75, 0.0},
 					     {0.0, 0.375, 1.0}};
   mtl::dense2D<double> ElInfo1d::mat_d2_right(mat_d2_right_val);
+
+  double ElInfo1d::test1_val[2][2] = {{1.0, 0.0},
+				      {0.0, 1.0}};
+  mtl::dense2D<double> ElInfo1d::test2_val(test1_val);
   
 
   void ElInfo1d::fillMacroInfo(const MacroElement * mel)
@@ -122,11 +126,10 @@ namespace AMDiS {
 
     if (adet2 < 1.0E-15) {
       MSG("det*det = %lf\n", adet2);
-      for (int i = 0; i <= 1; i++)
-	grd_lam[i] = 0.0;
+      grd_lam[0] = grd_lam[1] = 0.0;
     } else {
       grd_lam[1] = e * (1.0 / adet2);
-      grd_lam[0] = grd_lam[1] * (-1.0);
+      grd_lam[0] = grd_lam[1] * -1.0;
     }
 
     return sqrt(adet2);
@@ -296,48 +299,52 @@ namespace AMDiS {
     }   
   }
 
-  void ElInfo1d::getRefSimplexCoords(const BasisFunction *basisFcts,
-				     mtl::dense2D<double>& coords) const
+  void ElInfo1d::getSubElemCoordsMat(mtl::dense2D<double>& mat, int basisFctsDegree) const
   {
-    FUNCNAME("ElInfo1d::getRefSimplexCoords()");
-
-    switch (basisFcts->getDegree()) {
+    switch (basisFctsDegree) {
     case 1:
-      coords = mat_d1;
+      mat = mat_d1;
+
+      for (int i = 0; i < refinementPathLength; i++) {
+	if (refinementPath & (1 << i)) 
+	  mat *= mat_d1_left;
+	else 
+	  mat *= mat_d1_right;
+      }
+
       break;
+      
     case 2: