Added new operators.

AMDiS/src/AdaptInstationary.cc

@@ -80,7 +80,8 @@ namespace AMDiS {
     // estimate before first adaption
     if (adaptInfo->getTime() <= adaptInfo->getStartTime())
       problemIteration_->oneIteration(adaptInfo, ESTIMATE);
- 
+
+
     // increment time
     adaptInfo->setTime(adaptInfo->getTime() + adaptInfo->getTimestep());
 

AMDiS/src/DOFMatrix.cc

@@ -72,11 +72,13 @@ namespace AMDiS {
   DOFMatrix::~DOFMatrix()
   {
     FUNCNAME("DOFMatrix::~DOFMatrix()");
+
     if (rowFESpace && rowFESpace->getAdmin())
       (const_cast<DOFAdmin*>(rowFESpace->getAdmin()))->removeDOFIndexed(this);
-
-    if (boundaryManager) delete boundaryManager;
-    if (inserter) delete inserter;
+    if (boundaryManager) 
+      delete boundaryManager;
+    if (inserter) 
+      delete inserter;
   }
 
   void DOFMatrix::print() const
@@ -135,11 +137,10 @@ namespace AMDiS {
 
     int non_symmetric = !symmetric();
 
-    if (non_symmetric) {
+    if (non_symmetric)
       MSG("matrix `%s' not symmetric.\n", name.data());
-    } else {
+    else
       MSG("matrix `%s' is symmetric.\n", name.data());
-    }
   }
 
   DOFMatrix& DOFMatrix::operator=(const DOFMatrix& rhs)
@@ -154,12 +155,11 @@ namespace AMDiS {
     if (rhs.inserter == 0 && inserter == 0)
       matrix = rhs.matrix;
 
-    if (rhs.boundaryManager) {
+    if (rhs.boundaryManager)
       boundaryManager = new BoundaryManager(*rhs.boundaryManager);
-    } else {
+    else
       boundaryManager = NULL;
-    }
-
+    
     nRow = rhs.nRow;
     nCol = rhs.nCol;
     elementMatrix.change_dim(nRow, nCol);
@@ -302,9 +302,8 @@ namespace AMDiS {
   {
     FUNCNAME("DOFMatrix::assemble2()");
 
-    if (!op && operators.size() == 0) {
+    if (!op && operators.size() == 0)
       return;
-    }
 
     set_to_zero(elementMatrix);
     
@@ -335,8 +334,7 @@ namespace AMDiS {
   {
     // call the operatos cleanup procedures
     for (std::vector<Operator*>::iterator it = operators.begin();
-	 it != operators.end();
-	 ++it)
+	 it != operators.end(); ++it)
       (*it)->finishAssembling();
   }
 

AMDiS/src/DOFMatrix.h

@@ -382,6 +382,23 @@ namespace AMDiS {
       boundaryManager = bm;
     }
 
+    /// Calculates the average of non zero entries per row in matrix.
+    void calculateNnz()
+    {
+      nnzPerRow = 0;
+
+      if (num_rows(matrix) != 0)
+	nnzPerRow = int(double(matrix.nnz()) / num_rows(matrix) * 1.2); 
+      if (nnzPerRow < 5) 
+	nnzPerRow= 5;      
+    }
+
+    /// Returns \ref nnzPerRow.
+    int getNnz()
+    {
+      return nnzPerRow;
+    }
+
   private:
     template <typename T>
     void s_write(::std::ostream &out, const T& value)
@@ -536,6 +553,13 @@ namespace AMDiS {
      */    
     std::set<int> applyDBCs;
 
+    /* \brief
+     * Number of non zero entries per row (average). For instationary problems this
+     * information may be used in the next timestep to accelerate insertion of
+     * elemnts during assembling.
+     */
+     int nnzPerRow;
+
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
     std::map<DegreeOfFreedom, bool> isRankDOF;
 #endif

AMDiS/src/DOFVector.hh

@@ -970,11 +970,9 @@ namespace AMDiS {
 #ifdef _OPENMP
 #pragma omp parallel for schedule(dynamic, 25000) default(shared) private(i)
 #endif
-      for (i = 0; i < maxI; i++) {
-	if (!admin->isDOFFree(i)) {
+      for (i = 0; i < maxI; i++)
+	if (!admin->isDOFFree(i))
 	  y[i] = alpha * y[i] + x[i];
-	}
-      }
   }
 
   template<typename T>
@@ -984,12 +982,9 @@ namespace AMDiS {
   {
     typename DOFVector<T>::Iterator vIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&v)), USED_DOFS);
     typename DOFVector<T>::Iterator rIterator(dynamic_cast<DOFIndexed<T>*>(&result), USED_DOFS);
-    for(vIterator.reset(), rIterator.reset();
-	!vIterator.end();
-	++vIterator, ++rIterator) 
-      {  
-	*rIterator = scal * (*vIterator);
-      };
+    for (vIterator.reset(), rIterator.reset();
+	 !vIterator.end(); ++vIterator, ++rIterator) 
+      *rIterator = scal * (*vIterator);
 
     return result;
   }
@@ -1001,12 +996,10 @@ namespace AMDiS {
   {
     typename DOFVector<T>::Iterator vIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&v)), USED_DOFS);
     typename DOFVector<T>::Iterator rIterator(dynamic_cast<DOFIndexed<T>*>(&result), USED_DOFS);
-    for(vIterator.reset(), rIterator.reset();
-	!vIterator.end();
-	++vIterator, ++rIterator) 
-      {  
-	*rIterator = (*vIterator) + scal;
-      };
+    for (vIterator.reset(), rIterator.reset();
+	!vIterator.end(); ++vIterator, ++rIterator) 
+      *rIterator = (*vIterator) + scal;
+
     return result;
   }
 
@@ -1018,20 +1011,18 @@ namespace AMDiS {
     typename DOFVector<T>::Iterator v1Iterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&v1)), USED_DOFS);
     typename DOFVector<T>::Iterator v2Iterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&v2)), USED_DOFS);
     typename DOFVector<T>::Iterator rIterator(dynamic_cast<DOFIndexed<T>*>(&result), USED_DOFS);
-    for(v1Iterator.reset(), v2Iterator.reset(), rIterator.reset();
-	!v1Iterator.end();
-	++v1Iterator, ++v2Iterator, ++rIterator) 
-      {  
-	*rIterator = (*v1Iterator) + (*v2Iterator);
-      };
-    return result;
+    for (v1Iterator.reset(), v2Iterator.reset(), rIterator.reset();
+	 !v1Iterator.end(); ++v1Iterator, ++v2Iterator, ++rIterator) 
+      *rIterator = (*v1Iterator) + (*v2Iterator);
 
+    return result;
   }
 
   template<typename T>
   const T *DOFVectorBase<T>::getLocalVector(const Element *el, T *d) const
   {
     static T* localVec = NULL;
+    static int localVecSize = 0;
     const DOFAdmin* admin = feSpace->getAdmin();
 
     T *result;
@@ -1039,8 +1030,14 @@ namespace AMDiS {
     if (d) {
       result = d;
     } else {
-      if(localVec) delete [] localVec;
-      localVec = new T[nBasFcts]; 
+      if (localVec && nBasFcts > localVecSize)  {
+	delete [] localVec;
+	localVec = new T[nBasFcts]; 
+      }
+      if (!localVec)
+	localVec = new T[nBasFcts]; 
+
+      localVecSize = nBasFcts;
       result = localVec;
     }
 

AMDiS/src/FirstOrderAssembler.cc

@@ -47,8 +47,8 @@ namespace AMDiS {
        &standardSubAssemblersGrdPhi);
     
     int myRank = omp_get_thread_num();
-    std::vector<OperatorTerm*> opTerms 
-      = (type == GRD_PSI) ? op->firstOrderGrdPsi[myRank] : op->firstOrderGrdPhi[myRank];
+    std::vector<OperatorTerm*> opTerms = 
+      (type == GRD_PSI) ? op->firstOrderGrdPsi[myRank] : op->firstOrderGrdPhi[myRank];
 
     // check if a assembler is needed at all
     if (opTerms.size() == 0)
@@ -103,15 +103,15 @@ namespace AMDiS {
 
   Stand10::Stand10(Operator *op, Assembler *assembler, Quadrature *quad) 
     : FirstOrderAssembler(op, assembler, quad, false, GRD_PSI)
-  {}
+  {
+    psi = owner->getRowFESpace()->getBasisFcts();
+    phi = owner->getColFESpace()->getBasisFcts();
+  }
 
   void Stand10::calculateElementMatrix(const ElInfo *elInfo, ElementMatrix& mat)
   {
     DimVec<double> grdPsi(dim, DEFAULT_VALUE, 0.0);
 
-    const BasisFunction *psi = owner->getRowFESpace()->getBasisFcts();
-    const BasisFunction *phi = owner->getColFESpace()->getBasisFcts();
-
     int nPoints = quadrature->getNumPoints();
     int myRank = omp_get_thread_num();
     VectorOfFixVecs<DimVec<double> > &Lb = tmpLb[myRank];
@@ -132,7 +132,7 @@ namespace AMDiS {
       for (int i = 0; i < nRow; i++) {
 	(*(psi->getGrdPhi(i)))(quadrature->getLambda(iq), grdPsi);
 	for (int j = 0; j < nCol; j++)
-	  mat[i][j] += quadrature->getWeight(iq) * (Lb[iq] * grdPsi) * phival[j];	
+	  mat[i][j] += quadrature->getWeight(iq) * phival[j] * (Lb[iq] * grdPsi);
       }
     }
   }
@@ -140,7 +140,6 @@ namespace AMDiS {
   void Stand10::calculateElementVector(const ElInfo *elInfo, ElementVector& vec)
   {
     DimVec<double> grdPsi(dim, DEFAULT_VALUE, 0.0);
-    const BasisFunction *psi = owner->getRowFESpace()->getBasisFcts();
     int nPoints = quadrature->getNumPoints();
     int myRank = omp_get_thread_num();
     VectorOfFixVecs<DimVec<double> > &Lb = tmpLb[myRank];
@@ -189,13 +188,11 @@ namespace AMDiS {
     VectorOfFixVecs<DimVec<double> > &Lb = tmpLb[myRank];
     Lb.resize(nPoints);
 
-    for (int iq = 0; iq < nPoints; iq++) {
+    for (int iq = 0; iq < nPoints; iq++)
       Lb[iq].set(0.0);
-    }
 
-    for (int i = 0; i < static_cast<int>(terms[myRank].size()); i++) {
+    for (int i = 0; i < static_cast<int>(terms[myRank].size()); i++)
       (static_cast<FirstOrderTerm*>((terms[myRank][i])))->getLb(elInfo, nPoints, Lb);
-    }
   
     for (int iq = 0; iq < nPoints; iq++) {
       Lb[iq] *= elInfo->getDet();
@@ -203,10 +200,9 @@ namespace AMDiS {
       const double *phi = phiFast->getPhi(iq);
       grdPsi = psiFast->getGradient(iq);
 
-      for (int i = 0; i < nRow; i++) {
+      for (int i = 0; i < nRow; i++)
 	for (int j = 0; j < nCol; j++)
 	  mat[i][j] += quadrature->getWeight(iq) * (Lb[iq] * (*grdPsi)[i]) * phi[j];
-      }
     }
   }
 
@@ -232,21 +228,17 @@ namespace AMDiS {
     VectorOfFixVecs<DimVec<double> > &Lb = tmpLb[myRank];
     Lb.resize(nPoints);
 
-    for (int iq = 0; iq < nPoints; iq++) {
-      Lb[iq].set(0.0);
-    }
-    for (int i = 0; i < static_cast<int>(terms[myRank].size()); i++) {
+    for (int iq = 0; iq < nPoints; iq++)
+      Lb[iq].set(0.0);    
+    for (int i = 0; i < static_cast<int>(terms[myRank].size()); i++)
       (static_cast<FirstOrderTerm*>((terms[myRank][i])))->getLb(elInfo, nPoints, Lb);
-    }
   
     for (int iq = 0; iq < nPoints; iq++) {
-
       Lb[iq] *= elInfo->getDet();
       grdPsi = psiFast->getGradient(iq);
 
-      for (int i = 0; i < nRow; i++) {
+      for (int i = 0; i < nRow; i++)
 	vec[i] += quadrature->getWeight(iq) * (Lb[iq] * (*grdPsi)[i]);
-      }
     }
   }
 
@@ -305,13 +297,13 @@ namespace AMDiS {
     VectorOfFixVecs<DimVec<double> > 
       grdPhi(assembler->getRowFESpace()->getMesh()->getDim(), nCol, NO_INIT);
     tmpGrdPhi.resize(omp_get_overall_max_threads(), grdPhi);
+
+    psi = owner->getRowFESpace()->getBasisFcts();
+    phi = owner->getColFESpace()->getBasisFcts();
   }
 
   void Stand01::calculateElementMatrix(const ElInfo *elInfo, ElementMatrix& mat)
   {
-    const BasisFunction *psi = owner->getRowFESpace()->getBasisFcts();
-    const BasisFunction *phi = owner->getColFESpace()->getBasisFcts();
-
     int nPoints = quadrature->getNumPoints();
     int myRank = omp_get_thread_num();
     VectorOfFixVecs<DimVec<double> >& Lb = tmpLb[myRank];
@@ -320,6 +312,7 @@ namespace AMDiS {
 
     for (int iq = 0; iq < nPoints; iq++)
       Lb[iq].set(0.0);
+
     for (int i = 0; i < static_cast<int>(terms[myRank].size()); i++)
       (static_cast<FirstOrderTerm*>((terms[myRank][i])))->getLb(elInfo, nPoints, Lb);
   
@@ -332,7 +325,7 @@ namespace AMDiS {
       for (int i = 0; i < nRow; i++) {
 	double psival = (*(psi->getPhi(i)))(quadrature->getLambda(iq));
 	for (int j = 0; j < nCol; j++)
-	  mat[i][j] += quadrature->getWeight(iq) * ((Lb[iq] * psival) * grdPhi[j]);
+	  mat[i][j] += quadrature->getWeight(iq) * psival * (Lb[iq] * grdPhi[j]);
       }
     } 
   }

AMDiS/src/FirstOrderAssembler.h

@@ -78,6 +78,9 @@ namespace AMDiS {
 
     /// Implements SubAssembler::calculateElementVector().
     void calculateElementVector(const ElInfo *, ElementVector&);
+
+  protected:
+    const BasisFunction *psi, *phi;
   };
 
 
@@ -104,6 +107,8 @@ namespace AMDiS {
 
   protected:
     std::vector<VectorOfFixVecs<DimVec<double> > > tmpGrdPhi;
+
+    const BasisFunction *psi, *phi;
   };
 
 

AMDiS/src/FixVec.h

@@ -233,17 +233,20 @@ namespace AMDiS {
     }
 
     /// Returns the \ref size of this VectorOfFixVecs
-    inline int getSize() const { 
+    inline int getSize() const 
+    { 
       return size;
     }
 
     /// Returns \ref dim
-    inline int getDim() const {
+    inline int getDim() const 
+    {
       return dim;
     }
 
     /// Returns the size of the contained FixVecs
-    inline int getSizeOfFixVec() const { 
+    inline int getSizeOfFixVec() const 
+    { 
       return vec[0]->getSize(); 
     }
 
@@ -515,7 +518,8 @@ namespace AMDiS {
   /// creates and inits and double array
   double *createAndInitArray(int size, ...); 
 
-  inline WorldVector<double> operator*(const WorldVector<double>& v, double d) {
+  inline WorldVector<double> operator*(const WorldVector<double>& v, double d) 
+  {
     WorldVector<double> result = v;
     result *= d;
     return result;

AMDiS/src/FixVec.hh

@@ -8,9 +8,8 @@ namespace AMDiS {
 	 thisIt != this->end();
 	 thisIt++) {
       *thisIt = 0;
-      for (T* vIt = v.begin(); vIt != v.end(); vIt++, mIt++) {
+      for (T* vIt = v.begin(); vIt != v.end(); vIt++, mIt++)
 	*thisIt += *vIt * *mIt;
-      }
     }
   }
 
@@ -19,9 +18,8 @@ namespace AMDiS {
   {
     double erg = 0.0;
 
-    for (int i = 0; i < a.getSize() ; i++) {
+    for (int i = 0; i < a.getSize() ; i++)
       erg = erg + ((a[i] - b[i]) * (a[i] - b[i]));
-    }
 
     return sqrt(erg);
   }
@@ -39,9 +37,8 @@ namespace AMDiS {
 	 thisIt++) {
       *thisIt = 0;
       
-      for (T* vIt = v.begin(); vIt != v.end(); vIt++, mIt++) {
-	*thisIt += *vIt * *mIt;
-      }
+      for (T* vIt = v.begin(); vIt != v.end(); vIt++, mIt++) 
+	*thisIt += *vIt * *mIt;      
     }
   }
 
@@ -70,9 +67,8 @@ namespace AMDiS {