Okay, ab ins Wochenende.

AMDiS/Reinit/src/HL_SignedDistTraverse.cc

@@ -4,7 +4,7 @@
 void HL_SignedDistTraverse::initializeBoundary() 
 {
   FUNCNAME("HL_SignedDistTraverse::initializeBoundary()");
-  
+ 
   // ===== All non-boundary vertices are initialized with "infinity". =====
   sD_DOF->set(inftyValue);
   

AMDiS/src/AdaptInfo.cc

@@ -8,7 +8,7 @@ namespace AMDiS {
 
   void AdaptInfo::setScalContents(int newSize) 
   {
-    int oldSize = scalContents.getSize();
+    int oldSize = static_cast<int>(scalContents.size());
 
     if (newSize > oldSize) { 
       scalContents.resize(newSize);
@@ -42,7 +42,7 @@ namespace AMDiS {
     SerUtil::serialize(out, solverTolerance);
     SerUtil::serialize(out, solverResidual);
 
-    int size = scalContents.getSize();
+    int size = static_cast<int>(scalContents.size());
     SerUtil::serialize(out, size);
     for (int i = 0; i < size; i++) {
       SerUtil::serialize(out, scalContents[i]->est_sum);

AMDiS/src/AdaptInfo.h

@@ -171,8 +171,9 @@ namespace AMDiS {
     }
 
     /// Destructor.
-    virtual ~AdaptInfo() {
-      for (int i = 0;  i < scalContents.getSize(); i++)
+    virtual ~AdaptInfo() 
+    {
+      for (unsigned int i = 0;  i < scalContents.size(); i++)
 	delete scalContents[i];
     }
 
@@ -193,10 +194,10 @@ namespace AMDiS {
     /// Returns whether space tolerance is reached.
     virtual bool spaceToleranceReached() 
     {
-      int size = scalContents.getSize();
-      for (int i = 0; i < size; i++)
-      {
-	std::cout<<"est_sum:"<<scalContents[i]->est_sum<<" spaceTol:"<<scalContents[i]->spaceTolerance<<std::endl;
+      for (unsigned int i = 0; i < scalContents.size(); i++) {
+	std::cout << "est_sum:" <<scalContents[i]->est_sum 
+		  << " spaceTol: " << scalContents[i]->spaceTolerance 
+		  << std::endl;
 	if (!(scalContents[i]->est_sum < scalContents[i]->spaceTolerance))
 	  return false;
       }
@@ -216,8 +217,7 @@ namespace AMDiS {
     /// Returns whether time tolerance is reached.
     virtual bool timeToleranceReached() 
     {
-      int size = scalContents.getSize();
-      for (int i = 0; i < size; i++)
+      for (unsigned int i = 0; i < scalContents.size(); i++)
 	if (!(scalContents[i]->est_t_sum < scalContents[i]->timeTolerance))
 	  return false;
 
@@ -236,8 +236,7 @@ namespace AMDiS {
     /// Returns whether time error is under its lower bound.
     virtual bool timeErrorLow() 
     {
-      int size = scalContents.getSize();
-      for (int i = 0; i < size; i++)
+      for (unsigned int i = 0; i < scalContents.size(); i++)
 	if (!(scalContents[i]->est_t_sum < scalContents[i]->timeErrLow))
 	  return false;
 
@@ -247,7 +246,7 @@ namespace AMDiS {
     /// Print debug information about time error and its bound.
     void printTimeErrorLowInfo() 
     {
-      for (int i = 0; i < scalContents.getSize(); i++)
+      for (unsigned int i = 0; i < scalContents.size(); i++)
 	std::cout << "    Time error estimate = " << scalContents[i]->est_t_sum 
 		  << "    Time error bound = " << scalContents[i]->timeErrLow << "\n";
     }
@@ -387,6 +386,11 @@ namespace AMDiS {
     /// Returns \ref est_sum.
     inline double getEstSum(int index) 
     { 
+      FUNCNAME("AdaptInfo::getEstSum()");
+
+      TEST_EXIT_DBG(static_cast<unsigned int>(index) < scalContents.size())
+	("Wrong index for adaptInfo!\n");
+
       return scalContents[index]->est_sum; 
     }
 
@@ -399,6 +403,11 @@ namespace AMDiS {
     /// Returns \ref est_max.
     inline double getEstMax(int index) 
     { 
+      FUNCNAME("AdaptInfo::getEstSum()");
+
+      TEST_EXIT_DBG(static_cast<unsigned int>(index) < scalContents.size())
+	("Wrong index for adaptInfo!\n");
+
       return scalContents[index]->est_max; 
     }
 
@@ -586,7 +595,7 @@ namespace AMDiS {
 
     inline int getSize() 
     { 
-      return scalContents.getSize(); 
+      return scalContents.size(); 
     }
 
     inline void setSolverIterations(int it) 
@@ -728,7 +737,7 @@ namespace AMDiS {
     double solverResidual;
 
     /// Scalar adapt infos.
-    Vector<ScalContent*> scalContents;
+    std::vector<ScalContent*> scalContents;
 
     /// Is true, if the adaptive procedure was deserialized from a file.
     bool isDeserialized_;

AMDiS/src/Assembler.cc

@@ -135,12 +135,12 @@ namespace AMDiS {
       ElementMatrix &m = 
 	smallElInfo->getSubElemCoordsMat(rowFESpace->getBasisFcts()->getDegree());
 
-      if (smallElInfo == colElInfo) 
+      if (smallElInfo == colElInfo)
 	tmpMat = m * mat;	
       else
-	tmpMat = mat * trans(m);
-
-      mat = tmpMat;     
+  	tmpMat = mat * trans(m);
+      
+      mat = tmpMat;
     }
 
     if (rememberElMat && &userMat != &elementMatrix)

AMDiS/src/DOFAdmin.cc

@@ -246,14 +246,14 @@ namespace AMDiS {
     ERROR("container not in list\n");
   }
 
+
   void DOFAdmin::compress(std::vector<DegreeOfFreedom> &new_dof)
   {
     FUNCNAME("DOFAdmin::compress()");
 
     // nothing to do ?
-    if (size < 1) return;
-    if (usedCount < 1) return;
-    if (holeCount < 1) return;
+    if (size < 1 || usedCount < 1 || holeCount < 1) 
+      return;
 
     // vector to mark used dofs
     for (int i = 0; i < size; i++)
@@ -289,7 +289,7 @@ namespace AMDiS {
     // get index of first changed dof
     int first = last;
     for (int i = 0; i<size; i++) {
-      if ((new_dof[i] < i) && (new_dof[i] >= 0)) {
+      if (new_dof[i] < i && new_dof[i] >= 0) {
 	first = i;
 	break;
       }
@@ -307,6 +307,7 @@ namespace AMDiS {
       (*dc)->compressDOFContainer(n, new_dof);
   }
 
+
   void DOFAdmin::setNumberOfDOFs(int i, int v) 
   { 
     FUNCNAME("DOFAdmin::setNumberOfDOFs()");

AMDiS/src/DOFMatrix.cc

@@ -345,6 +345,7 @@ namespace AMDiS {
     addElementMatrix(elementMatrix, bound, mainElInfo, NULL);       
   }
 
+
   void DOFMatrix::finishAssembling()
   {
     // call the operatos cleanup procedures
@@ -353,6 +354,7 @@ namespace AMDiS {
       (*it)->finishAssembling();
   }
 
+
   // Should work as before
   Flag DOFMatrix::getAssembleFlag()
   {
@@ -364,6 +366,7 @@ namespace AMDiS {
     return fillFlag;
   }
 
+
   void DOFMatrix::axpy(double a, const DOFMatrix& x, const DOFMatrix& y)
   {
     matrix+= a * x.matrix + y.matrix;
@@ -375,6 +378,7 @@ namespace AMDiS {
     matrix*= b;
   }
 
+
   void DOFMatrix::addOperator(Operator *op, double* factor, double* estFactor) 
   { 
     operators.push_back(op);
@@ -382,6 +386,7 @@ namespace AMDiS {
     operatorEstFactor.push_back(estFactor);
   }
 
+
   void DOFMatrix::serialize(std::ostream &out)
   {
     using namespace mtl; 

AMDiS/src/DOFVector.cc

@@ -829,6 +829,7 @@ namespace AMDiS {
       addElementVector(factor, this->elementVector, bound, elInfo);
   }
 
+
   template<>
   void DOFVectorBase<double>::assemble2(double factor, 
 					ElInfo *mainElInfo, ElInfo *auxElInfo,

AMDiS/src/Element.cc

@@ -260,7 +260,7 @@ namespace AMDiS {
 
   void Element::newDOFFct2(const DOFAdmin* admin)
   {
-    int i, j, k, n0, nd0;
+    int j, k, n0, nd0;
     DegreeOfFreedom  *ldof;
     int vertices = mesh->getGeo(VERTEX);
     int edges = mesh->getGeo(EDGE); 
@@ -270,7 +270,7 @@ namespace AMDiS {
     if (nd) {
       nd0 = admin->getNumberOfPreDOFs(VERTEX);
       n0 = admin->getMesh()->getNode(VERTEX);
-      for (i = 0; i < vertices; i++) {
+      for (int i = 0; i < vertices; i++) {
 	CHANGE_DOFS_2(this);
       }
     }
@@ -280,7 +280,7 @@ namespace AMDiS {
       if (nd) {
 	nd0 = admin->getNumberOfPreDOFs(EDGE);
 	n0 = admin->getMesh()->getNode(EDGE);
-	for (i = 0; i < edges; i++) {
+	for (int i = 0; i < edges; i++) {
 	  CHANGE_DOFS_2(this);
 	}
       }
@@ -291,7 +291,7 @@ namespace AMDiS {
       if (nd) {
 	nd0 = admin->getNumberOfPreDOFs(FACE);
 	n0 = admin->getMesh()->getNode(FACE);
-	for (i = 0; i < faces; i++) {
+	for (int i = 0; i < faces; i++) {
 	  CHANGE_DOFS_2(this);
 	}
       }
@@ -302,7 +302,7 @@ namespace AMDiS {
       nd0 = admin->getNumberOfPreDOFs(CENTER);
       n0 = admin->getMesh()->getNode(CENTER);
       // only one center
-      i = 0;   
+      int i = 0;   
       CHANGE_DOFS_2(this);
     }
   }

AMDiS/src/Marker.cc

@@ -35,7 +35,7 @@ namespace AMDiS {
   {
     FUNCNAME("Marker::initMarking()");
 
-    TEST_EXIT(adaptInfo)("No AdaptInfo object!\n");
+    TEST_EXIT_DBG(adaptInfo)("No AdaptInfo object!\n");
 
     elMarkRefine = 0;
     elMarkCoarsen = 0;
@@ -70,8 +70,12 @@ namespace AMDiS {
 
   Flag Marker::markMesh(AdaptInfo *adaptInfo, Mesh *mesh) 
   {
+    FUNCNAME("Marker::markMesh()");
+
+    TEST_EXIT_DBG(mesh)("No mesh!\n");
+
     initMarking(adaptInfo, mesh);
-    
+   
     if (!adaptInfo->isCoarseningAllowed(row == -1 ? 0 : row) && 
 	!adaptInfo->isRefinementAllowed(row == -1 ? 0 : row))
       return 0;    
@@ -100,7 +104,7 @@ namespace AMDiS {
     FUNCNAME("ESMarker::initMarking()");
     
     Marker::initMarking(adaptInfo, mesh);
-    
+   
     double ESThetaP = pow(ESTheta, p);
     double ESThetaCP = pow(ESThetaC, p);
     

AMDiS/src/Mesh.cc

@@ -63,7 +63,6 @@ namespace AMDiS {
 
   // const Flag Mesh::USE_PARAMETRIC          = 0X8000L ; // used in mg methods 
 
-  DOFAdmin* Mesh::compressAdmin = NULL;
   std::vector<DegreeOfFreedom> Mesh::dof_used;
   const int Mesh::MAX_DOF = 100;
   std::map<std::pair<DegreeOfFreedom, int>, DegreeOfFreedom*> Mesh::serializedDOFs;
@@ -432,46 +431,39 @@ namespace AMDiS {
       nNodeEl += 1;
   }
 
+
   void Mesh::dofCompress()
   {
     FUNCNAME("Mesh::dofCompress()");
-    Flag fill_flag;
 
-    for (int iadmin = 0; iadmin < static_cast<int>(admin.size()); iadmin++) {
-      compressAdmin = admin[iadmin];
+    for (unsigned int iadmin = 0; iadmin < admin.size(); iadmin++) {
+      DOFAdmin* compressAdmin = admin[iadmin];
 
       TEST_EXIT_DBG(compressAdmin)("no admin[%d] in mesh\n", iadmin);
       
       int size = compressAdmin->getSize();
-      if (size < 1) 
-	continue;
-
-      if (compressAdmin->getUsedDOFs() < 1)    
+      if (size < 1 || 
+	  compressAdmin->getUsedDOFs() < 1 || 
+	  compressAdmin->getHoleCount() < 1)    
 	continue;
 
-      if (compressAdmin->getHoleCount() < 1)    
-	continue;
-  
       newDOF.resize(size);
       
       compressAdmin->compress(newDOF);
-      
-      if (preserveCoarseDOFs)
-	fill_flag = Mesh::CALL_EVERY_EL_PREORDER | Mesh::FILL_NOTHING;
-      else
-	fill_flag = Mesh::CALL_LEAF_EL | Mesh::FILL_NOTHING;
-      
-      
+
+      Flag fill_flag = (preserveCoarseDOFs ?  
+			Mesh::CALL_EVERY_EL_PREORDER | Mesh::FILL_NOTHING :
+			Mesh::CALL_LEAF_EL | Mesh::FILL_NOTHING);          
       TraverseStack stack;
       ElInfo *elInfo = stack.traverseFirst(this, -1, fill_flag);
       while (elInfo) {
-	newDOFFct1(elInfo);
+	elInfo->getElement()->newDOFFct1(compressAdmin);
 	elInfo = stack.traverseNext(elInfo);
       }
 
       elInfo = stack.traverseFirst(this, -1, fill_flag);
       while (elInfo) {
-	newDOFFct2(elInfo);
+	elInfo->getElement()->newDOFFct2(compressAdmin);
 	elInfo = stack.traverseNext(elInfo);
       }
 
@@ -941,18 +933,6 @@ namespace AMDiS {
     diam[i] = w; 
   }
 
-  int Mesh::newDOFFct1(ElInfo* ei) 
-  {
-    ei->getElement()->newDOFFct1(compressAdmin);
-    return 0;
-  }
-
-  int Mesh::newDOFFct2(ElInfo* ei) 
-  {
-    ei->getElement()->newDOFFct2(compressAdmin);
-    return 0;
-  }
-
   void Mesh::serialize(std::ostream &out)
   {
     serializedDOFs.clear();

AMDiS/src/Mesh.h

@@ -68,17 +68,6 @@ namespace AMDiS {
     /// Assignment operator
     Mesh& operator=(const Mesh&);
 
-    /** \name static methods used while mesh traversal 
-     * \{
-     */
-
-    /// Used while dof compress
-    static int newDOFFct1(ElInfo* e);
-
-    /// Used while dof compress
-    static int newDOFFct2(ElInfo* e);
-    /** \} */
-
     /** \name getting methods
      * \{
      */
@@ -765,9 +754,6 @@ namespace AMDiS {
     /// Needed during DOF compression (\ref DOFAdmin::compress).
     std::vector<DegreeOfFreedom> newDOF;
 
-    /// Needed during DOF compression (\ref DOFAdmin::compress).
-    static DOFAdmin *compressAdmin;
-
     /// Used by check functions
     static std::vector<DegreeOfFreedom> dof_used;
 

AMDiS/src/ProblemVec.cc

@@ -564,16 +564,21 @@ namespace AMDiS {
     // here is reached already because of time adaption
     allowFirstRefinement();
 
+    TEST_EXIT_DBG(static_cast<unsigned int>(nComponents == marker.size()))
+      ("Wrong number of markers!\n");
+
     Flag markFlag = 0;
-    for (int i = 0; i < nComponents; i++)
+    for (int i = 0; i < nComponents; i++)