Some source code refactoring, no real changes.

AMDiS/src/AMDiS_fwd.h

@@ -33,6 +33,8 @@ namespace AMDiS {
   class CoarseningManager;
   class DiagonalPreconditioner; 
   class DOFAdmin; 
+  class DOFContainer;
+  class DOFIndexedBase;
   class DOFMatrix;
   class Element;
   class ElementMatrix;
@@ -63,6 +65,7 @@ namespace AMDiS {
   class RefinementManager;
   class RobinBC;
   class SystemVector;
+  class VertexInfo;
   class VertexVector;
 
   template<typename ReturnType, typename ArgumentType> class AbstractFunction;

AMDiS/src/AbstractFunction.h

@@ -23,7 +23,6 @@
 #define AMDIS_ABSTRACTFUNCTION_H
 
 #include "Global.h"
-#include "MemoryManager.h"
 
 namespace AMDiS {
 

AMDiS/src/AdaptInfo.h

@@ -22,7 +22,6 @@
 #ifndef AMDIS_ADAPTINFO_H
 #define AMDIS_ADAPTINFO_H
 
-#include "MemoryManager.h"
 #include "MatrixVector.h"
 #include "Parameters.h"
 #include "Serializable.h"

AMDiS/src/AdaptInstationary.h

@@ -26,7 +26,6 @@
 #include <ctime>
 #include <queue>
 #include "Flag.h"
-#include "MemoryManager.h"
 #include "AdaptInfo.h"
 #include "AdaptBase.h"
 #include "AMDiS_fwd.h"

AMDiS/src/AdaptStationary.h

@@ -31,7 +31,6 @@
 
 #include <string>
 #include "Flag.h"
-#include "MemoryManager.h"
 #include "AdaptInfo.h"
 #include "AdaptBase.h"
 #include "AMDiS_fwd.h"

AMDiS/src/Assembler.h

@@ -32,7 +32,6 @@
 
 #include <vector>
 #include "FixVec.h"
-#include "MemoryManager.h"
 #include "ZeroOrderAssembler.h"
 #include "FirstOrderAssembler.h"
 #include "SecondOrderAssembler.h"

AMDiS/src/Boundary.h

@@ -24,7 +24,6 @@
 
 #include <map>
 #include "Global.h"
-#include "MemoryManager.h"
 
 namespace AMDiS {
 

AMDiS/src/CoarseningManager1d.h

@@ -23,14 +23,9 @@
 #define AMDIS_COARSENINGMANAGER_1D_H
 
 #include "CoarseningManager.h"
-#include "MemoryManager.h"
 
 namespace AMDiS {
 
-  // ============================================================================
-  // ===== class CoarseningManager1d ============================================
-  // ============================================================================
-
   /** \ingroup Adaption 
    * \brief
    * Implements a CoarseningManager for 1-dimensional meshes.
@@ -38,17 +33,13 @@ namespace AMDiS {
   class CoarseningManager1d : public CoarseningManager
   {
   public:
-    MEMORY_MANAGED(CoarseningManager1d);
+    /// Calls base class constructor and checks dimension of mesh. 
+    CoarseningManager1d() 
+      : CoarseningManager() 
+    {}
 
-    /** \brief
-     * Calls base class constructor and checks dimension of mesh. 
-     */
-    CoarseningManager1d() : CoarseningManager() {};
-
-    /** \brief
-     * destructor
-     */
-    virtual ~CoarseningManager1d() {};
+    /// destructor
+    virtual ~CoarseningManager1d() {}
 
     /** \brief
      * Overloads CoarseningManager::coarsenMesh. In 1d a simple recursive
@@ -57,18 +48,14 @@ namespace AMDiS {
     Flag coarsenMesh(Mesh *aMesh);
 
   protected:
-    /** \brief
-     * Not needed in this sub class
-     */
+    /// Not needed in this sub class
     int coarsenFunction(ElInfo *) {
       FUNCNAME("CoarseningManager1d::coarsenFunction");
       ERROR_EXIT("not used for dim = 1");
       return 0;
-    };
+    }
   
-    /** \brief
-     * Needed instead of coarsenFunction in 1d.
-     */
+    /// Needed instead of coarsenFunction in 1d.
     int coarsenRecursive(Line *parent);
   
   };

AMDiS/src/CoarseningManager2d.h

@@ -23,14 +23,9 @@
 #define AMDIS_COARSENINGMANAGER_2D_H
 
 #include "CoarseningManager.h"
-#include "MemoryManager.h"
 
 namespace AMDiS {
 
-  // ============================================================================
-  // ===== class CoarseningManager2d ============================================
-  // ============================================================================
-
   /** \ingroup Adaption  
    * \brief
    * Implements a CoarseningManager for 2-dimensional meshes.
@@ -38,25 +33,17 @@ namespace AMDiS {
   class CoarseningManager2d : public CoarseningManager
   {
   public:
-    MEMORY_MANAGED(CoarseningManager2d);
 
-    /** \brief
-     * Calls base class constructor and checks dimension of mesh. 
-     */
-    CoarseningManager2d() : CoarseningManager() {
-      //     FUNCNAME("CoarseningManager2d::CoarseningManager2d");
-      //     TEST_EXIT(mesh->getDim()==2)("mesh->dim != 2\n");
-    };
+    /// Calls base class constructor and checks dimension of mesh. 
+    CoarseningManager2d() 
+      : CoarseningManager() 
+    {}
 
-    /** \brief
-     * destructor
-     */
-    virtual ~CoarseningManager2d() {};
+    /// destructor
+    virtual ~CoarseningManager2d() {}
 
   protected:
-    /** \brief
-     * Implements CoarseningManager::coarsenFunction
-     */
+    /// Implements CoarseningManager::coarsenFunction
     virtual int coarsenFunction(ElInfo *el_info);
 
     /** \brief

AMDiS/src/CoarseningManager3d.h

@@ -23,14 +23,9 @@
 #define AMDIS_COARSENINGMANAGER_3D_H
 
 #include "CoarseningManager.h"
-#include "MemoryManager.h"
 
 namespace AMDiS {
 
-  // ============================================================================
-  // ===== class CoarseningManager3d ============================================
-  // ============================================================================
-
   /** \ingroup Adaption 
    * \brief
    * Implements a CoarseningManager for 3-dimensional meshes.
@@ -38,22 +33,16 @@ namespace AMDiS {
   class CoarseningManager3d : public CoarseningManager
   {
   public:
-    MEMORY_MANAGED(CoarseningManager3d);
-
-    /** \brief
-     * Calls base class constructor and checks dimension of mesh. 
-     */
-    CoarseningManager3d() : CoarseningManager() {};
+    /// Calls base class constructor and checks dimension of mesh. 
+    CoarseningManager3d() 
+      : CoarseningManager() 
+    {}
 
-    /** \brief
-     * destructor
-     */
-    virtual ~CoarseningManager3d() {};
+    /// destructor
+    virtual ~CoarseningManager3d() {}
 
   protected:
-    /** \brief
-     * Implements CoarseningManager::coarsenFunction
-     */
+    /// Implements CoarseningManager::coarsenFunction
     int coarsenFunction(ElInfo *el_info);
 
     /** \brief

AMDiS/src/ConditionalEstimator.h

@@ -30,10 +30,6 @@
 
 namespace AMDiS {
 
-  // ============================================================================
-  // ===== class ConditionalEstimator ==============================================
-  // ============================================================================
-
   /**
    * \ingroup Estimator
    * 
@@ -43,45 +39,21 @@ namespace AMDiS {
   class ConditionalEstimator : public Estimator
   {
   public:
-    MEMORY_MANAGED(ConditionalEstimator);
-
     ConditionalEstimator(Estimator *decorated) 
       : decoratedEstimator_(decorated),
 	elementCount_(0), 
 	row_(decorated ? decorated->getRow() : 0)
-    {};
+    {}
 
     double estimate(double timestep);
 
     inline int getElementCount() {
       return elementCount_;
-    };
-
-    //   inline double getErrorSum() const { 
-    //     return decoratedEstimator_->getErrorSum(); 
-    //   };
-
-    //   inline void setErrorSum(double sum) {
-    //     decoratedEstimator_->setErrorSum(sum); 
-    //   };
-
-    //   inline double getErrorMax() const {
-    //     return decoratedEstimator_->getErrorMax(); 
-    //   };
-
-    //   inline double getTimeEst() const {
-    //     return decoratedEstimator_->getTimeEst(); 
-    //   };
-
-    //   inline void setErrorMax(double m) {
-    //     decoratedEstimator_->setErrorMax(m); 
-    //   };
-
-    //   inline Norm getErrorNorm() {
-    //     return decoratedEstimator_->getErrorNorm(); 
-    //   };
+    }
 
-    inline Estimator *getDecoratedEstimator() { return decoratedEstimator_; };
+    inline Estimator *getDecoratedEstimator() { 
+      return decoratedEstimator_; 
+    }
 
   protected:
     Estimator *decoratedEstimator_;

AMDiS/src/ConditionalMarker.h

@@ -25,17 +25,12 @@
 #include "mpi.h"
 #include "Marker.h"
 #include "Marker.h"
-#include "MemoryManager.h"
 #include "PartitionElementData.h"
 #include "Traverse.h"
 #include "ElInfo.h"
 
 namespace AMDiS {
 
-  // ===========================================================================
-  // ===== class ESMarker ======================================================
-  // ===========================================================================
-
   /**
    * \ingroup Adaption
    * 
@@ -45,11 +40,7 @@ namespace AMDiS {
   class ConditionalMarker : public Marker
   {
   public:
-    MEMORY_MANAGED(ConditionalMarker);
-
-    /** \brief
-     * Constructor.
-     */
+    /// Constructor.
     ConditionalMarker(const std::string name,
 		      int row,
 		      Marker *decoratedMarker,
@@ -59,18 +50,18 @@ namespace AMDiS {
 	decoratedMarker_(decoratedMarker),
 	globalCoarseGridLevel_(globalCoarseGridLevel),    
 	localCoarseGridLevel_(localCoarseGridLevel)
-    {};
+    {}
 
-    /** \brief
-     * Implementation of MarkScal::initMarking().
-     */
-    virtual void initMarking(AdaptInfo *adaptInfo, Mesh *mesh) {
-      if(decoratedMarker_) 
+    /// Implementation of MarkScal::initMarking().
+    virtual void initMarking(AdaptInfo *adaptInfo, Mesh *mesh) 
+    {
+      if (decoratedMarker_) 
 	decoratedMarker_->initMarking(adaptInfo, mesh);
-    };
+    }
 
-    virtual void finishMarking(AdaptInfo *adaptInfo) {
-      if(decoratedMarker_) {
+    virtual void finishMarking(AdaptInfo *adaptInfo) 
+    {
+      if (decoratedMarker_) {
 	int tmp = decoratedMarker_->getElMarkRefine();
 	MPI::COMM_WORLD.Allreduce(&tmp,
 				  &elMarkRefine,
@@ -85,10 +76,12 @@ namespace AMDiS {
 				  MPI_SUM);
 	decoratedMarker_->finishMarking(adaptInfo);
       }
-    };
+    }
 
-    void markElement(AdaptInfo *adaptInfo, ElInfo *elInfo) {
+    void markElement(AdaptInfo *adaptInfo, ElInfo *elInfo) 
+    {
       FUNCNAME("ConditionalMarker::markElement()");
+
       if (decoratedMarker_) {
 	PartitionElementData *elData = 
 	  dynamic_cast<PartitionElementData*>(elInfo->getElement()->
@@ -110,11 +103,11 @@ namespace AMDiS {
 	  localCoarseGridLevel_ :
 	  globalCoarseGridLevel_;
 
-	if(elData->getLevel() + elInfo->getElement()->getMark() < minLevel) {
+	if (elData->getLevel() + elInfo->getElement()->getMark() < minLevel) {
 	  elInfo->getElement()->setMark(-(elData->getLevel() - minLevel));
 	}
       }
-    };
+    }
 
   protected:
     Marker *decoratedMarker_;

AMDiS/src/CouplingTimeInterface.h

@@ -22,16 +22,12 @@
 #ifndef AMDIS_COUPLINGTIMEINTERFACE_H
 #define AMDIS_COUPLINGTIMEINTERFACE_H
 
+#include <vector>
 #include "Flag.h"
 #include "ProblemTimeInterface.h"
-#include <vector>
 
 namespace AMDiS {
 
-  // ============================================================================
-  // ===== class CouplingTimeInterface ==========================================
-  // ============================================================================
-
   /**
    * \ingroup Problem 
    *
@@ -40,64 +36,52 @@ namespace AMDiS {
   class CouplingTimeInterface : public ProblemTimeInterface
   {
   public:
-    void addTimeInterface(ProblemTimeInterface *interface) {
+    void addTimeInterface(ProblemTimeInterface *interface) 
+    {
       interfaces_.push_back(interface);
-    };
+    }
 
-    /** \brief
-     * Executes all needed operations when the simulation time changes.
-     */
-    virtual void setTime(AdaptInfo *adaptInfo) {
-      int i, size = static_cast<int>(interfaces_.size());
-      for(i = 0; i < size; i++) {
+    /// Executes all needed operations when the simulation time changes.
+    virtual void setTime(AdaptInfo *adaptInfo) 
+    {
+      int size = static_cast<int>(interfaces_.size());
+      for (int i = 0; i < size; i++)
 	interfaces_[i]->setTime(adaptInfo);
-      }
-    };
+    }
 
-    /** \brief
-     * Called at the beginning of each timestep
-     */
-    virtual void initTimestep(AdaptInfo *adaptInfo) {
-      int i, size = static_cast<int>(interfaces_.size());
-      for(i = 0; i < size; i++) {
+    /// Called at the beginning of each timestep
+    virtual void initTimestep(AdaptInfo *adaptInfo) 
+    {
+      int size = static_cast<int>(interfaces_.size());
+      for (int i = 0; i < size; i++)
 	interfaces_[i]->initTimestep(adaptInfo);
-      }
-    };
+    }
 
-    /** \brief
-     * Called at the end of each timestep.
-     */
-    virtual void closeTimestep(AdaptInfo *adaptInfo) {
+    /// Called at the end of each timestep.
+    virtual void closeTimestep(AdaptInfo *adaptInfo) 
+    {
       int i, size = static_cast<int>(interfaces_.size());
-      for(i = 0; i < size; i++) {
+      for (int i = 0; i < size; i++)
 	interfaces_[i]->closeTimestep(adaptInfo);
-      }
-    };
+    }
 
-    /** \brief
-     * Solves the initial problem.
-     */
-    virtual void solveInitialProblem(AdaptInfo *adaptInfo) {
-      int i, size = static_cast<int>(interfaces_.size());
-      for(i = 0; i < size; i++) {
+    /// Solves the initial problem.
+    virtual void solveInitialProblem(AdaptInfo *adaptInfo) 
+    {
+      int size = static_cast<int>(interfaces_.size());
+      for (int i = 0; i < size; i++)
 	interfaces_[i]->solveInitialProblem(adaptInfo);
-      }
-    };  
+    }
 
-    /** \brief
-     * Solves the initial problem.
-     */
+    /// Solves the initial problem.
     virtual void transferInitialSolution(AdaptInfo *adaptInfo) {
-      int i, size = static_cast<int>(interfaces_.size());
-      for(i = 0; i < size; i++) {
+      int size = static_cast<int>(interfaces_.size());
+      for (int i = 0; i < size; i++)
 	interfaces_[i]->transferInitialSolution(adaptInfo);
-      }
-    };  
+    }
 
   protected:
-    /** \brief
-     * vector of coupled time interfaces
-     */
+    /// vector of coupled time interfaces
     std::vector<ProblemTimeInterface*> interfaces_;
   };
 

AMDiS/src/CreatorInterface.h

@@ -50,16 +50,14 @@ namespace AMDiS {
      */
     virtual BaseClass* create() = 0;
 
-    virtual BaseClass* create(const DOFMatrix::base_matrix_type& A) { return 0; }
+    virtual BaseClass* create(const DOFMatrix::base_matrix_type& A) { 
+      return 0; 
+    }
 
-    /** \brief
-     * Can be implemented by sub classes.
-     */
+    /// Can be implemented by sub classes.
     virtual void free(BaseClass *) {}
 
-    /** \brief
-     * 
-     */
+    ///
     virtual bool isNullCreator() { 
       return false; 
     }
@@ -72,16 +70,12 @@ namespace AMDiS {
   template<typename BaseClass>
   class NullCreator : public CreatorInterface<BaseClass>
   {
-    /** \brief
-     * Creates no object.
-     */
-    BaseClass* create() { 
+    /// Creates no object.
+    BaseClass* create() {
       return NULL; 
     }
 
-    /** \brief
-     * 
-     */
+    ///
     virtual bool isNullCreator() { 
       return true; 
     }

AMDiS/src/CylinderProject.h

@@ -24,10 +24,6 @@
 
 namespace AMDiS {
 
-  // ==============================================================================
-  // ===== class CylinderProject ==================================================
-  // ==============================================================================
-
   /** \brief
    * Projects world coordinates to the surface of a cylinder with given center, 
    * radius and direction. Can be used as boundary or volume projection.
@@ -35,9 +31,7 @@ namespace AMDiS {
   class CylinderProject : public Projection
   {
   public:
-    /** \brief
-     * Constructor.
-     */ 
+    /// Constructor.
     CylinderProject(int id,
 		    ProjectionType type,
 		    WorldVector<double> &c,
@@ -50,17 +44,14 @@ namespace AMDiS {
     {
       double norm = sqrt(direction_*direction_);
       direction_ *= 1.0 / norm;
-    };
+    }
 
-    /** \brief
-     * Destructor.
-     */
-    virtual ~CylinderProject() {};
+    /// Destructor.
+    virtual ~CylinderProject() {}
 
-    /** \brief
-     * Implementation of Projection::project();
-     */
-    void project(WorldVector<double> &x) {
+    /// Implementation of Projection::project();
+    void project(WorldVector<double> &x) 
+    {
       x -= center_;
       WorldVector<double> v1 = direction_; v1 *= (x*direction_);
       WorldVector<double> v2 = x; v2 -= v1;
@@ -69,22 +60,16 @@ namespace AMDiS {
       v2 *= 1.0 / norm;
       x = v2; x *= radius_; x += v1;
       x += center_;
-    };
+    }
 
   protected:
-    /** \brief
-     * Center of the cylinder.
-     */
+    /// Center of the cylinder.
     WorldVector<double> center_;
 
-    /** \brief
-     * Direction of the cylinder.
-     */
+    /// Direction of the cylinder.
     WorldVector<double> direction_;
 
-    /** \brief
-     * Radius of the cylinder.
-     */
+    /// Radius of the cylinder.
     double radius_;
   };
 

AMDiS/src/DOFAdmin.h

@@ -28,27 +28,17 @@
 #ifndef AMDIS_DOFADMIN_H
 #define AMDIS_DOFADMIN_H
 
+#include <vector>
+#include <memory>
+#include <list>
 #include "Global.h"
 #include "FixVec.h"
-#include "MemoryManager.h"
 #include "Serializable.h"
 #include "OpenMP.h"
-#include <vector>
-#include <memory>
-#include <list>
+#include "AMDiS_fwd.h"
 
 namespace AMDiS {
 
-  class Mesh;
-  class FiniteElemSpace;