Updated Reinit library to some changes in AMDiS.

AMDiS/Reinit/src/BoundaryElementDist.h

@@ -9,21 +9,17 @@
 using namespace AMDiS;
 
 class BoundaryElementDist {
- public:
-  MEMORY_MANAGED(BoundaryElementDist);
+public:
 
-  /**
-   * Constructor.
-   */
   BoundaryElementDist(ElementLevelSet *elLS_, int dim_)
     : dim(dim_),
-    elLS(elLS_)
+      elLS(elLS_)
   {
     FUNCNAME("BoundaryElementDist::BoundaryElementDist()");
 
     TEST_EXIT(dim == 2 || dim == 3)
       ("function only works for dimension 2 !\n");
-  };
+  }
 
   /**
    * Virtual destructor.

AMDiS/Reinit/src/BoundaryElementEdgeDist.h

@@ -12,16 +12,12 @@ using namespace AMDiS;
 
 class BoundaryElementEdgeDist : public BoundaryElementDist
 {
- public:
-  MEMORY_MANAGED(BoundaryElementEdgeDist);
+public:
 
-  /**
-   * Constructor.
-   */
   BoundaryElementEdgeDist(ElementLevelSet *elLS_,
 			  int dim_)
     : BoundaryElementDist(elLS_, dim_)
-  {};
+  {}
 
   /**
    * Calculates distance from the interface for all vertices of a boundary 

AMDiS/Reinit/src/BoundaryElementLevelSetDist.h

@@ -3,24 +3,18 @@
 
 #include "ElInfo.h"
 #include "FixVec.h"
-
 #include "ElementLevelSet.h"
-
 #include "BoundaryElementDist.h"
 
 using namespace AMDiS;
 
 class BoundaryElementLevelSetDist : public BoundaryElementDist
 {
- public:
-  MEMORY_MANAGED(BoundaryElementLevelSetDist);
+public:
 
-  /**
-   * Constructor.
-   */
   BoundaryElementLevelSetDist(ElementLevelSet *elLS_, int dim_)
     : BoundaryElementDist(elLS_, dim_)
-  {};
+  {}
 
   /**
    * Calculates distance from the interface for all vertices of a boundary 

AMDiS/Reinit/src/BoundaryElementNormalDist.h

@@ -3,24 +3,18 @@
 
 #include "ElInfo.h"
 #include "FixVec.h"
-
 #include "ElementLevelSet.h"
-
 #include "BoundaryElementDist.h"
 
 using namespace AMDiS;
 
 class BoundaryElementNormalDist : public BoundaryElementDist
 {
- public:
-  MEMORY_MANAGED(BoundaryElementNormalDist);
+public:
 
-  /**
-   * Constructor.
-   */
   BoundaryElementNormalDist(ElementLevelSet *elLS_, int dim_)
     : BoundaryElementDist(elLS_, dim_)
-  {};
+  {}
 
   /**
    * Calculates distance from the interface for all vertices of a boundary 

AMDiS/Reinit/src/BoundaryElementTopDist.h

@@ -3,9 +3,7 @@
 
 #include "ElInfo.h"
 #include "FixVec.h"
-
 #include "ElementLevelSet.h"
-
 #include "BoundaryElementDist.h"
 #include "VelocityExt.h"
 
@@ -13,24 +11,16 @@ using namespace AMDiS;
 
 class BoundaryElementTopDist : public BoundaryElementDist
 {
- public:
-  MEMORY_MANAGED(BoundaryElementTopDist);
-
-  /**
-   * Constructor.
-   */
+public:
   BoundaryElementTopDist(ElementLevelSet *elLS_, 
 			 int dim_,
 			 VelocityExt *velExt_ = NULL)
     : BoundaryElementDist(elLS_, dim_),
-    velExt(velExt_)
-  {};
+      velExt(velExt_)
+  {}
 
-  /**
-   * Destructor.
-   */
   ~BoundaryElementTopDist()
-  {};
+  {}
 
   /**
    * Calculates distance from the interface for all vertices of a boundary 

AMDiS/Reinit/src/ElementLevelSet.h

 #ifndef AMDIS_ELEMENTLEVELSET_H
 #define AMDIS_ELEMENTLEVELSET_H
 
+#include "AMDiS_fwd.h"
 #include "ElementFunction.h"
 #include "FixVec.h"
-// #include "MemoryManager.h"
 #include "Parameters.h"
 
-namespace AMDiS {
-    class Element;
-    class ElInfo;
-    class Mesh;
-}
-
 using namespace AMDiS;
 using namespace std;
 
@@ -58,26 +52,21 @@ using namespace std;
 class ElementLevelSet
 {
  public:
-  MEMORY_MANAGED(ElementLevelSet);
-
-  /**
-   * Constructor.
-   */
   ElementLevelSet(const char *name_,
 		  ElementFunction<double> *lSFct_,
 		  Mesh *mesh_) 
     : name(name_),
-    elInfo(NULL),
-    lastEl(NULL),
-    level_set_domain(LEVEL_SET_UNDEFINED),
-    numIntersecPoints(0),
-    elStatus(LEVEL_SET_UNDEFINED),
-    numElVertexInterior(0),
-    numElVertexBoundary(0),
-    numElVertexExterior(0),
-    LS_VAL_TOL(1.e-8),
-    LS_VAL_MIN(1.e-8),
-    SP_BARY_TOL(1.e-7)
+      elInfo(NULL),
+      lastEl(NULL),
+      level_set_domain(LEVEL_SET_UNDEFINED),
+      numIntersecPoints(0),
+      elStatus(LEVEL_SET_UNDEFINED),
+      numElVertexInterior(0),
+      numElVertexBoundary(0),
+      numElVertexExterior(0),
+      LS_VAL_TOL(1.e-8),
+      LS_VAL_MIN(1.e-8),
+      SP_BARY_TOL(1.e-7)
   {
     FUNCNAME("ElementLevelSet::ElementLevelSet()");
 
@@ -108,11 +97,8 @@ class ElementLevelSet
       TEST_EXIT(LS_VAL_MIN > 0)("illegal LS_VAL_MIN\n");
       TEST_EXIT(SP_BARY_TOL > 0)("illegal SP_BARY_TOL\n");
     }
-  };
+  }
 
-  /**
-   * Destructor.
-   */
   ~ElementLevelSet()
   {
     if (elVertexStatusVec)
@@ -121,7 +107,7 @@ class ElementLevelSet
       delete [] elVertexLevelSetVec;
     if (elIntersecPoints)
       DELETE elIntersecPoints;
-  };
+  }
 
   /**
    * Calculates LevelSet-status of element and its intersection points 

AMDiS/Reinit/src/ElementUpdate.h

@@ -2,28 +2,18 @@
 #define ELEMENTUPDATE_H
 
 #include "FixVec.h"
-// #include "MemoryManager.h"
-
 #include "VelocityExt.h"
 
 using namespace AMDiS;
 
 class ElementUpdate
 {
- public:
-  MEMORY_MANAGED(ElementUpdate);
-
-  /**
-   * Constructor.
-   */
+public:
   ElementUpdate(VelocityExt *velExt_)
     : velExt(velExt_)
-  {};
+  {}
 
-  /**
-   * Virtual destructor.
-   */
-  virtual ~ElementUpdate() {};
+  virtual ~ElementUpdate() {}
 
   /**
    * Pure virtual function.

AMDiS/Reinit/src/ElementUpdate_2d.h

@@ -2,8 +2,6 @@
 #define ELEMENTUPDATE_2D_H
 
 #include "FixVec.h"
-// #include "MemoryManager.h"
-
 #include "ElementUpdate.h"
 #include "VelocityExt.h"
 
@@ -11,15 +9,10 @@ using namespace AMDiS;
 
 class ElementUpdate_2d : public ElementUpdate
 {
- public:
-  MEMORY_MANAGED(ElementUpdate_2d);
-
-  /**
-   * Constructor.
-   */
+public:
   ElementUpdate_2d(VelocityExt *velExt_ = NULL)
     : ElementUpdate(velExt_)
-  {};
+  {}
 
   /**
    * Realization of ElementUpdate::calcElementUpdate.

AMDiS/Reinit/src/ElementUpdate_3d.h

@@ -2,8 +2,6 @@
 #define ELEMENTUPDATE_3D_H
 
 #include "FixVec.h"
-// #include "MemoryManager.h"
-
 #include "ElementUpdate.h"
 #include "ElementUpdate_2d.h"
 #include "VelocityExt.h"
@@ -12,25 +10,17 @@ using namespace AMDiS;
 
 class ElementUpdate_3d : public ElementUpdate
 {
- public:
-  MEMORY_MANAGED(ElementUpdate_3d);
-
-  /**
-   * Constructor.
-   */
+public:
   ElementUpdate_3d(VelocityExt *velExt_ = NULL)
     : ElementUpdate(velExt_)
   {
-    elUpdate2d = NEW ElementUpdate_2d(velExt_);
-  };
+    elUpdate2d = new ElementUpdate_2d(velExt_);
+  }
 
-  /**
-   * Destructor.
-   */
   ~ElementUpdate_3d()
   {
-    DELETE elUpdate2d;
-  };
+    delete elUpdate2d;
+  }
 
   /**
    * Realization of ElementUpdate::calcElementUpdate.

AMDiS/Reinit/src/HL_SignedDist.h

@@ -8,11 +8,8 @@
 #include "FileWriter.h"
 #include "FixVec.h"
 #include "Flag.h"
-// #include "MemoryManager.h"
 #include "Parameters.h"
-
 #include "ElementLevelSet.h"
-
 #include "BoundaryElementDist.h"
 #include "BoundaryElementLevelSetDist.h"
 #include "BoundaryElementTopDist.h"
@@ -41,12 +38,7 @@ using namespace AMDiS;
 //////////////////////////////////////////////////////////////////////////////
 class HL_SignedDist
 {
- public:
-  MEMORY_MANAGED(HL_SignedDist);
-
-  /**
-   * Constructor.
-   */
+public:
   HL_SignedDist(const char *name_, 
 		int dim_,
 		bool doVelocityExt = false,
@@ -77,11 +69,11 @@ class HL_SignedDist
     // ===== Create functionality for velocity extension. =====
     if (doVelocityExt) {
       if (velExtType.isSet(VEL_EXT))
-	velExt = NEW VelocityExt(dim);
+	velExt = new VelocityExt(dim);
       else
-	velExt = NEW VelocityExtFromVelocityField(dim);
+	velExt = new VelocityExtFromVelocityField(dim);
     }
-  };
+  }
 
   /**
    * Virtual destructor.
@@ -89,19 +81,19 @@ class HL_SignedDist
   virtual ~HL_SignedDist()
   {
     if (elUpdate)
-      DELETE elUpdate;
+      delete elUpdate;
     if (bndElDist)
-      DELETE bndElDist;
+      delete bndElDist;
 
     if (elLS)
-      DELETE elLS;
+      delete elLS;
     if (phi)
-      DELETE phi;
+      delete phi;
 
     if (bound_DOF)
-      DELETE bound_DOF;
+      delete bound_DOF;
 
-    DELETE velExt;
+    delete velExt;
   };
 
   /**
@@ -251,13 +243,13 @@ class HL_SignedDist
    */
   void printLevelSetFct()
   {
-    FileWriter *fileWriter = NEW FileWriter(
+    FileWriter *fileWriter = new FileWriter(
 			     "SignedDist->level set fct output", 
 			     feSpace->getMesh(),
 			     const_cast<DOFVector<double> *>(lS_DOF));
     fileWriter->writeFiles(adaptInfo, false);
 
-    DELETE fileWriter;
+    delete fileWriter;
   };
 
   /**
@@ -265,13 +257,13 @@ class HL_SignedDist
    */
   void printSignedDistFct()
   {
-    FileWriter *fileWriter = NEW FileWriter(
+    FileWriter *fileWriter = new FileWriter(
 			     "SignedDist->result output", 
 			     feSpace->getMesh(),
 			     sD_DOF);
     fileWriter->writeFiles(adaptInfo, false);
 
-    DELETE fileWriter;
+    delete fileWriter;
   };
 
  protected:
@@ -306,13 +298,12 @@ class HL_SignedDist
    */
   void printBoundInitFct()
   {
-    FileWriter *fileWriter = NEW FileWriter(
-			     "SignedDist->boundary initialization output", 
-			     feSpace->getMesh(),
-			     sD_DOF);
+    FileWriter *fileWriter = new FileWriter("SignedDist->boundary initialization output", 
+					    feSpace->getMesh(),
+					    sD_DOF);
     fileWriter->writeFiles(adaptInfo, false);
 
-    DELETE fileWriter;
+    delete fileWriter;
   };
 
  public:

AMDiS/Reinit/src/HL_SignedDistBornemann.h

 #ifndef HL_SIGNEDDISTBORNEMANN
 #define HL_SIGNEDDISTBORNEMANN
 
+#include <queue>
+#include <time.h>
 #include "ElInfo.h"
 #include "FixVec.h"
-// #include "MemoryManager.h"
 #include "Traverse.h"
-#include <queue>
-#include <time.h>
-
 #include "ElementLevelSet.h"
-
 #include "BoundaryElementDist.h"
-/* #include "BoundaryElementTopDist.h" */
-/* #include "BoundaryElementEdgeDist.h" */
-/* #include "BoundaryElementNormalDist.h" */
 #include "ElementUpdate.h"
 #include "ElementUpdate_2d.h"
 #include "ElementUpdate_3d.h"
@@ -32,25 +26,20 @@ typedef struct
 
 class HL_SignedDistBornemann : public HL_SignedDist
 {
- public:
-  MEMORY_MANAGED(HL_SignedDistBornemann);
-
-  /**
-   * Constructor.
-   */
+public:
   HL_SignedDistBornemann(const char *name_,int dim_)
     : HL_SignedDist(name_, dim_),
-    smiAdapter(NULL)
+      smiAdapter(NULL)
   {
     FUNCNAME("HL_SignedDistBornemann::HL_SignedDistBornemann");
 
     // ===== Read parameters from init file. =====
-    GET_PARAMETER(0,name + "->tolerance", "%f", &tol);
-    GET_PARAMETER(0,name + "->count_how_often_saved_in_list", "%d", &count_in_list);
-    GET_PARAMETER(0,name + "->save_in_list->the ..th", "%d", &print_in_list);
+    GET_PARAMETER(0, name + "->tolerance", "%f", &tol);
+    GET_PARAMETER(0, name + "->count_how_often_saved_in_list", "%d", &count_in_list);
+    GET_PARAMETER(0, name + "->save_in_list->the ..th", "%d", &print_in_list);
 
     TEST_EXIT(tol > 0)("illegal tolerance !\n");
-  };
+  }
 
  protected:
   /**

AMDiS/Reinit/src/HL_SignedDistLevels.h

 #ifndef HL_SIGNEDDISTLEVELS
 #define HL_SIGNEDDISTLEVELS
 
-#include "ElInfo.h"
-#include "FixVec.h"
-// #include "MemoryManager.h"
-#include "Traverse.h"
 #include <queue>
 #include <vector>
 #include <time.h>
-
+#include "ElInfo.h"
+#include "FixVec.h"
+#include "Traverse.h"
 #include "ElementLevelSet.h"
-
 #include "BoundaryElementDist.h"
 #include "ElementUpdate.h"
 #include "ElementUpdate_2d.h"
 #include "ElementUpdate_3d.h"
 #include "HL_SignedDist.h"
 #include "VelocityExt.h"
-
 #include "SMIAdapter.h"
 #include "smi.h"
 
@@ -31,31 +27,26 @@ typedef struct
 
 class HL_SignedDistLevels : public HL_SignedDist
 {
- public:
-  MEMORY_MANAGED(HL_SignedDistLevels);
-
-  /**
-   * Constructor.
-   */
+public:
   HL_SignedDistLevels(const char *name_, 
 		      int dim_,
 		      bool doVelocityExt = false,
 		      Flag velExtType_ = VEL_EXT)
     : HL_SignedDist(name_, dim_, doVelocityExt, velExtType_),
-    smiAdapter(NULL)
+      smiAdapter(NULL)
   {
-    FUNCNAME("HL_SignedDistLevels::HL_SignedDistLevels");
+    FUNCNAME("HL_SignedDistLevels::HL_SignedDistLevels()");
 
     // ===== Read parameters from init file. =====
-    GET_PARAMETER(0,name + "->tolerance", "%f", &tol);
-    GET_PARAMETER(0,name + "->count_how_often_saved_in_list", "%d", &count_in_list);
-    GET_PARAMETER(0,name + "->save_in_list->the ..th", "%d", &print_in_list);
-    GET_PARAMETER(0,name + "->save_in_list->after the ..th traversing of the list", "%d", &print_in_list_2);
-    GET_PARAMETER(0,name + "->print_level", "%d", &chosen_level);
-    GET_PARAMETER(0,name + "->print_level_yes_no", "%d", &print_level);
+    GET_PARAMETER(0, name + "->tolerance", "%f", &tol);
+    GET_PARAMETER(0, name + "->count_how_often_saved_in_list", "%d", &count_in_list);
+    GET_PARAMETER(0, name + "->save_in_list->the ..th", "%d", &print_in_list);
+    GET_PARAMETER(0, name + "->save_in_list->after the ..th traversing of the list", "%d", &print_in_list_2);
+    GET_PARAMETER(0, name + "->print_level", "%d", &chosen_level);
+    GET_PARAMETER(0, name + "->print_level_yes_no", "%d", &print_level);
 
     TEST_EXIT(tol > 0)("illegal tolerance !\n");
-  };
+  }
 
  protected:
   /**

AMDiS/Reinit/src/HL_SignedDistTraverse.cc

 #include "HL_SignedDistTraverse.h"
-
 #include "VelocityExtFromVelocityField.h"
 
-void 
-HL_SignedDistTraverse::initializeBoundary() 
+void HL_SignedDistTraverse::initializeBoundary() 
 {
   FUNCNAME("HL_SignedDistTraverse::initializeBoundary()");
   
@@ -16,7 +14,7 @@ HL_SignedDistTraverse::initializeBoundary()
   int elStatus;
   
   const int nBasFcts = feSpace->getBasisFcts()->getNumber();
-  DegreeOfFreedom *locInd = GET_MEMORY(DegreeOfFreedom, nBasFcts);
+  DegreeOfFreedom *locInd = new DegreeOfFreedom[nBasFcts];
   
   ElInfo *elInfo;
   if (velExt && velExtType.isSet(VEL_EXT_FROM_VEL_FIELD)) {
@@ -26,8 +24,7 @@ HL_SignedDistTraverse::initializeBoundary()
 				 Mesh::FILL_BOUND |
 				 Mesh::FILL_COORDS |
 				 Mesh::FILL_GRD_LAMBDA);
-  } 
-  else {
+  } else {
     elInfo = stack.traverseFirst(feSpace->getMesh(),
 				 -1, 
 				 Mesh::CALL_LEAF_EL | 
@@ -94,9 +91,7 @@ HL_SignedDistTraverse::initializeBoundary()
     elInfo = stack.traverseNext(elInfo);
   }  // end of: mesh traverse
   
-  FREE_MEMORY(locInd, DegreeOfFreedom, nBasFcts);
-  
-  return;
+  delete [] locInd;
 }
 
 void 
@@ -165,7 +160,7 @@ HL_SignedDistTraverse::HL_elementUpdate(ElInfo *elInfo)
   
   // ===== Get global indices of vertices of element. =====
   const int nBasFcts = feSpace->getBasisFcts()->getNumber();
-  DegreeOfFreedom *locInd = GET_MEMORY(DegreeOfFreedom, nBasFcts);
+  DegreeOfFreedom *locInd = new DegreeOfFreedom[nBasFcts];
   
   feSpace->getBasisFcts()->getLocalIndices(
 			   const_cast<Element *>(elInfo->getElement()),
@@ -203,13 +198,12 @@ HL_SignedDistTraverse::HL_elementUpdate(ElInfo *elInfo)
     }
   }
   
-  FREE_MEMORY(locInd, DegreeOfFreedom, nBasFcts);
+  delete [] locInd;
 }
 
-double 
-HL_SignedDistTraverse::calcElementUpdate(ElInfo *elInfo, 
-					 int nXh,
-					 const DegreeOfFreedom *locInd) 
+double HL_SignedDistTraverse::calcElementUpdate(ElInfo *elInfo, 
+						int nXh,
+						const DegreeOfFreedom *locInd) 
 {
   double update;
   FixVec<WorldVector<double> *, VERTEX> elVert(dim, NO_INIT);
@@ -257,8 +251,7 @@ HL_SignedDistTraverse::calcElementUpdate(ElInfo *elInfo,
   return update;
 }
 
-bool 
-HL_SignedDistTraverse::checkTol()
+bool HL_SignedDistTraverse::checkTol()