Added automatically adaption of macro mesh files for parallel computing plus several small changes.

AMDiS/src/DOFAdmin.h

@@ -227,6 +227,12 @@ namespace AMDiS {
     /// Sets \ref nrDOF[i] = v
     void setNumberOfDOFs(int i, int v);
 
+    /// Sets all values of \ref nrDOF
+    void setNumberOfDOFs(DimVec<int> v)
+    {
+      nrDOF = v;
+    }
+
     /// Sets \ref nr0DOF[i] = v
     void setNumberOfPreDOFs(int i, int v);
 

AMDiS/src/DOFVector.cc

@@ -749,9 +749,10 @@ namespace AMDiS {
  
     TEST_EXIT_DBG(quad || quadFast)("neither quad nor quadFast defined\n");
 
-    if (quad && quadFast)
+    if (quad && quadFast) {
       TEST_EXIT_DBG(quad == quadFast->getQuadrature())
       	("quad != quadFast->quadrature\n");
+    }
 
     TEST_EXIT_DBG(!quadFast || quadFast->getBasisFunctions() == feSpace->getBasisFcts())
       ("invalid basis functions");

AMDiS/src/DataCollector.cc

@@ -16,12 +16,18 @@ namespace AMDiS {
       level(l),
       traverseFlag(flag),
       feSpace(fe),
+      nVertices(0),
+      nElements(0),
+      nInterpPoints(0),
+      nConnection(0),
+      elementDataCollected(false),
+      valueDataCollected(false),
+      periodicDataCollected(false),
       writeElem(writeElemFct)
   {
     FUNCNAME("DataCollector::DataCollector()");
 
-    TEST_EXIT(feSpace)("no feSpace\n");
-    TEST_EXIT(values)("no value Vector\n");
+    TEST_EXIT(feSpace)("No finite elem space defined!\n");
    
     // === get mesh  ===    
     mesh = feSpace->getMesh();
@@ -29,36 +35,26 @@ namespace AMDiS {
     // === get admin ===    
     localAdmin = const_cast<DOFAdmin*>(feSpace->getAdmin());
     // === create vertex info vector ===
-    vertexInfos = new DOFVector< std::list<VertexInfo> >(feSpace, "vertex infos");
+    vertexInfos = new DOFVector<std::list<VertexInfo> >(feSpace, "vertex infos");
 
     interpPointInd = new DOFVector<int>(feSpace, "interpolation point indices");
     interpPointCoords = new DOFVector< std::list<WorldVector<double> > >(feSpace, "interpolation point coordinates");
     dofCoord = new DOFVector< std::list<WorldVector<double> > >(feSpace, "dof coords");
 
     dim = mesh->getDim();    
-    
     nPreDofs = localAdmin->getNumberOfPreDOFs(VERTEX);
-    nVertices = 0;
-    nElements = 0;
-    nInterpPoints = 0;
-    nConnection = 0;
-
-    elementDataCollected = false;
-    valueDataCollected = false;
-    periodicDataCollected = false;
-
-    vertexCoords = new WorldVector<double>;
   } 
 
+
   DataCollector::~DataCollector()
   {
     delete vertexInfos;
     delete interpPointInd;
     delete interpPointCoords;
     delete dofCoord;
-    delete vertexCoords;
   }
 
+
   void DataCollector::fillAllData()
   {
     if (!elementDataCollected)
@@ -71,6 +67,7 @@ namespace AMDiS {
       startCollectingValueData();
   }
 
+
   void DataCollector::startCollectingElementData()
   {
     FUNCNAME("DataCollector::startCollectingElementData()");
@@ -107,6 +104,7 @@ namespace AMDiS {
     elementDataCollected = true;
   }
 
+
   void DataCollector::startCollectingValueData()
   {
     FUNCNAME("DataCollector::startCollectingValueData()");
@@ -156,6 +154,7 @@ namespace AMDiS {
     valueDataCollected = true;
   }
 
+
   void DataCollector::startCollectingPeriodicData()
   {    
     FUNCNAME("DataCollector::startCollectingPeriodicData()");
@@ -200,6 +199,7 @@ namespace AMDiS {
     periodicDataCollected = true;
   }
 
+
   void DataCollector::addElementData(ElInfo* elInfo)
   {
     FUNCNAME("DataCollector::addElementData()");
@@ -272,10 +272,12 @@ namespace AMDiS {
     elements.push_back(elementInfo);
   }
 
+
   void DataCollector::addValueData(ElInfo *elInfo)
   {
     FUNCNAME("DataCollector::addValueData()");
     
+    WorldVector<double> vertexCoords;
     basisFcts->getLocalIndices(elInfo->getElement(), localAdmin, localDOFs);
 
     // First, traverse all DOFs at the vertices of the element, determine
@@ -286,18 +288,18 @@ namespace AMDiS {
       (*interpPointInd)[dofi] = -2; // mark as vertex
       
       // get coords of this vertex
-      *vertexCoords = elInfo->getCoord(i);
+      vertexCoords = elInfo->getCoord(i);
 
       // search for coords at this dof
       std::list<WorldVector<double> >::iterator it =
 	  find((*dofCoord)[dofi].begin(),
 	       (*dofCoord)[dofi].end(),
-	       *vertexCoords);
+	       vertexCoords);
       
       // coords not yet in list?
       if (it == (*dofCoord)[dofi].end()) {
 	// add new coords to list
-	(*dofCoord)[dofi].push_back(*vertexCoords);
+	(*dofCoord)[dofi].push_back(vertexCoords);
       }
     }
    
@@ -307,7 +309,7 @@ namespace AMDiS {
     for (int i = mesh->getGeo(VERTEX); i < nBasisFcts; i++) {
       DegreeOfFreedom dofi = localDOFs[i];
 
-      elInfo->coordToWorld(*basisFcts->getCoords(i), *vertexCoords);
+      elInfo->coordToWorld(*basisFcts->getCoords(i), vertexCoords);
       
       if ((*interpPointInd)[dofi] == -1) {
 	// mark as interpolation point
@@ -318,16 +320,17 @@ namespace AMDiS {
 	std::list<WorldVector<double> >::iterator it =
 		find((*interpPointCoords)[dofi].begin(), 
 		     (*interpPointCoords)[dofi].end(),
-		     *vertexCoords);
+		     vertexCoords);
 	
 	if (it == (*interpPointCoords)[dofi].end()) {
-	  (*interpPointCoords)[dofi].push_back(*vertexCoords); 
+	  (*interpPointCoords)[dofi].push_back(vertexCoords); 
 	  nInterpPoints++;
 	}
       }      
     }  
   }
 
+
   void DataCollector::addInterpData(ElInfo *elInfo)
   {
     FUNCNAME("DataCollector::addInterpData()");
@@ -341,6 +344,7 @@ namespace AMDiS {
     interpPoints.push_back(elemInterpPoints); 
   }
 
+
   void DataCollector::addPeriodicData(ElInfo *elInfo) 
   {
     FUNCNAME("DataCollector::addPeriodicData");
@@ -401,6 +405,7 @@ namespace AMDiS {
     }
   }
 
+
   std::list<ElementInfo>* DataCollector::getElementInfos()
   {        
     if (!elementDataCollected)
@@ -409,6 +414,7 @@ namespace AMDiS {
     return &elements;
   }
 
+
   DOFVector< std::list<VertexInfo> >* DataCollector::getVertexInfos()
   {
     if (!elementDataCollected)
@@ -417,6 +423,7 @@ namespace AMDiS {
     return vertexInfos;
   }
 
+
   std::list<PeriodicInfo>* DataCollector::getPeriodicInfos()
   {
     if (!periodicDataCollected)
@@ -425,6 +432,7 @@ namespace AMDiS {
     return &periodicInfos;
   }
 
+
   int DataCollector::getNumberVertices()
   {
     if (!elementDataCollected)
@@ -433,6 +441,7 @@ namespace AMDiS {
     return nVertices;
   }
 
+
   int DataCollector::getNumberElements()
   {
     if (!elementDataCollected)
@@ -441,6 +450,7 @@ namespace AMDiS {
     return nElements;
   }
 
+
   int DataCollector::getNumberInterpPoints()
   {
     if (!valueDataCollected)
@@ -449,6 +459,7 @@ namespace AMDiS {
     return nInterpPoints;
   }
 
+  
   int DataCollector::getNumberConnections()
   {
     if (!periodicDataCollected)
@@ -457,15 +468,6 @@ namespace AMDiS {
     return nConnection;
   }
 
-  const FiniteElemSpace* DataCollector::getFeSpace()
-  {
-    return feSpace;
-  }
-
-  Mesh* DataCollector::getMesh()
-  {
-    return mesh;
-  }
 
   DOFVector<double>* DataCollector::getValues()
   {
@@ -475,6 +477,7 @@ namespace AMDiS {
     return values;
   }
 
+
   DOFVector< std::list<WorldVector<double> > >* DataCollector::getDofCoords()
   {
     if (!valueDataCollected)
@@ -483,6 +486,7 @@ namespace AMDiS {
     return dofCoord;
   }
 
+
   DOFVector<int>* DataCollector::getInterpPointInd()
   {
     if (!valueDataCollected)
@@ -491,6 +495,7 @@ namespace AMDiS {
     return interpPointInd;
   }
 
+
   DOFVector< std::list<WorldVector<double> > >* DataCollector::getInterpPointCoords()
   {
     if (!valueDataCollected)
@@ -499,6 +504,7 @@ namespace AMDiS {
     return interpPointCoords;
   }
 
+
   std::vector< std::vector<int> >* DataCollector::getInterpPoints()
   {
     if (!valueDataCollected)

AMDiS/src/DataCollector.h

@@ -43,7 +43,7 @@ namespace AMDiS {
   public:
     /// Constructor
     DataCollector(const FiniteElemSpace *feSpace,
-		  DOFVector<double> *values,
+		  DOFVector<double> *values = NULL,
 		  int level = -1,
 		  Flag traverseFlag = Mesh::CALL_LEAF_EL,
 		  bool (*writeElem)(ElInfo*) = NULL);
@@ -60,7 +60,10 @@ namespace AMDiS {
     DOFVector< std::list<VertexInfo> >* getVertexInfos();
 
     /// Returns the finite element space of the problem.
-    const FiniteElemSpace* getFeSpace();
+    const FiniteElemSpace* getFeSpace()
+    {
+      return feSpace;
+    }
 
     /// Returns vector with value information.
     DOFVector<double>* getValues();
@@ -93,7 +96,10 @@ namespace AMDiS {
     int getNumberConnections();
       
     /// Returns the mesh of the problem.
-    Mesh* getMesh();
+    Mesh* getMesh()
+    {
+      return mesh;
+    }
 
     void setMesh(Mesh *m) 
     {
@@ -165,16 +171,16 @@ namespace AMDiS {
     DOFVector<int> *interpPointInd;
 
     /// Stores for each simplex the interpolation points.
-    std::vector< std::vector<int> > interpPoints;
+    std::vector<std::vector<int> > interpPoints;
 
     /** \brief
      * Stores for each DOF a list of its coordinates. If there are now periodic
      * boundaries than there is also only one coordinate per DOF.
      */
-    DOFVector< std::list<WorldVector<double> > > *interpPointCoords;
+    DOFVector<std::list<WorldVector<double> > > *interpPointCoords;
 
     /// list of coords for each dof
-    DOFVector< std::list<WorldVector<double> > > *dofCoord;
+    DOFVector<std::list<WorldVector<double> > > *dofCoord;
 
     /// List that stores an ElementInfo for each element.
     std::list<ElementInfo> elements;
@@ -183,7 +189,7 @@ namespace AMDiS {
     std::list<PeriodicInfo> periodicInfos;
 
     /// Stores a list of vertex infos for each dof.
-    DOFVector< std::list<VertexInfo> > *vertexInfos;
+    DOFVector<std::list<VertexInfo> > *vertexInfos;
 
     /** \brief
      * periodicConnections[i][j] stores whether the connection at side j of 

AMDiS/src/FileWriter.cc

@@ -158,6 +158,7 @@ namespace AMDiS {
     }
   }
 
+
   void FileWriter::writeFiles(AdaptInfo *adaptInfo,
 			      bool force,
 			      int level,
@@ -170,7 +171,7 @@ namespace AMDiS {
       return;
 
     // Containers, which store the data to be written;
-    std::vector< DataCollector* > dataCollectors(solutionVecs.size());
+    std::vector<DataCollector* > dataCollectors(solutionVecs.size());
 
     if (writeElem) {
       for (int i = 0; i < static_cast<int>(dataCollectors.size()); i++)

AMDiS/src/FiniteElemSpace.cc

@@ -20,7 +20,8 @@ namespace AMDiS {
   {
     FUNCNAME("FiniteElemSpace::FiniteElemSpace()");
 
-    TEST_EXIT(mesh)("no Mesh\n");
+    TEST_EXIT(mesh)("No mesh!\n");
+    TEST_EXIT(basFcts)("No basis functions!\n");
    
     if (!admin) {
       const DOFAdmin *admin_local = NULL;

AMDiS/src/FirstOrderTerm.cc

@@ -62,7 +62,7 @@ namespace AMDiS {
 			 const ElementVector& uhAtQP,
 			 const WorldVector<double> *grdUhAtQP,
 			 const WorldMatrix<double> *D2UhAtQP,
-			 double *result,
+			 ElementVector& result,
 			 double fac) 
   {
     int dow = Global::getGeo(WORLD);
@@ -101,7 +101,7 @@ namespace AMDiS {
 			    const ElementVector& uhAtQP,
 			    const WorldVector<double> *grdUhAtQP,
 			    const WorldMatrix<double> *D2UhAtQP,
-			    double *result,
+			    ElementVector& result,
 			    double f) 
   {
     int dow = Global::getGeo(WORLD);
@@ -112,6 +112,7 @@ namespace AMDiS {
 	double resultQP = 0.0;
 	for (int i = 0; i < dow; i++)
 	  resultQP += grdUhAtQP[iq][i];	
+
 	result[iq] += f * factor * resultQP;
       }
     }
@@ -139,7 +140,7 @@ namespace AMDiS {
 			       const ElementVector& uhAtQP,
 			       const WorldVector<double> *grdUhAtQP,
 			       const WorldMatrix<double> *D2UhAtQP,
-			       double *result,
+			       ElementVector& result,
 			       double f) 
   {