And moved Reinit library to src and updated makefiles.

AMDiS/Reinit/Makefile

-SHELL = /bin/sh
-COMPILE = g++
-DEFS = -DPACKAGE=\"AMDiS\" -DVERSION=\"0.1\" -DHAVE_DLFCN_H=1 
-DEBUG = 0
-AMDIS_DIR = ../
-
-INCLUDES = -I./src -I$(AMDIS_DIR)/src -I$(AMDIS_DIR)/compositeFEM/src -I$(AMDIS_DIR)/lib/mtl4
-
-ifeq ($(strip $(DEBUG)), 0)
-       CPPFLAGS = -O2
-else
-       CPPFLAGS = -g -O0
-endif
-CPPFLAGS +=  -ftemplate-depth-40
-
-VPATH = .:$(AMDIS_DIR)/Reinit/src
-
-LIBOFILES = \
-BoundaryElementDist.o \
-BoundaryElementNormalDist.o \
-BoundaryElementLevelSetDist.o \
-BoundaryElementTopDist.o \
-BoundaryElementEdgeDist.o \
-ElementLevelSet.o \
-ElementUpdate_2d.o \
-ElementUpdate_3d.o \
-HL_SignedDist.o \
-HL_SignedDistTraverse.o \
-VelocityExt.o \
-VelocityExtFromVelocityField.o \
-NormEps.o 
-
-all: libreinit.a
-
-# statische Bibliothek
-libreinit.a: $(LIBOFILES)
-	rm -f lib/libreinit.a
-	ar cq lib/libreinit.a $(LIBOFILES)
-
-.cc.o: $*.cc
-	$(COMPILE) $(DEFS) $(INCLUDES) $(CPPFLAGS) -c -o $*.o $<
-
-clean: 
-	-rm -rf *.o

AMDiS/Reinit/src/HL_SignedDistLevels.cc

-//
-// Software License for AMDiS
-//
-// Copyright (c) 2010 Dresden University of Technology 
-// All rights reserved.
-// Authors: Simon Vey, Thomas Witkowski et al.
-//
-// This file is part of AMDiS
-//
-// See also license.opensource.txt in the distribution.
-
-
-#include "HL_SignedDistLevels.h"
-
-#include "VelocityExtFromVelocityField.h"
-
-void 
-HL_SignedDistLevels::initializeBoundary() 
-{
-  FUNCNAME("HL_SignedDistLevels::initializeBoundary()");
-  
-  TraverseStack stack;
-  FixVec<double, VERTEX> distVec(dim, NO_INIT);
-  int elStatus;
-  const int *elVertStatusVec;
-  int NumVertIntPoints;
-  int ElNum;
-  clock_t time1;
-  clock_t time2;
-  double TIME;
-  
-  //=== transvering Mesh to SMI and add quantities
-  time1 = clock();
-  Mesh_to_SMI_and_quantity();
-  time2 = clock();
-  TIME = TIME_USED(time1, time2);
-  
-  cout <<"Zeit zum Transformieren nach SMI: "<<TIME<<" sec.\n";
-  
-  // ===== All non-boundary vertices are initialized with "infinity". =====
-  sD_DOF->set(inftyValue);
-  
-  // ===== Traverse mesh and initialize boundary elements. =====
-  const int nBasFcts = feSpace->getBasisFcts()->getNumber();
-  DegreeOfFreedom *locInd = GET_MEMORY(DegreeOfFreedom, nBasFcts);
-
-  ElInfo *elInfo;
-  if (velExt && velExtType.isSet(VEL_EXT_FROM_VEL_FIELD)) {
-    elInfo = stack.traverseFirst(feSpace->getMesh(),
-				 -1, 
-				 Mesh::CALL_LEAF_EL | 
-				 Mesh::FILL_BOUND |
-				 Mesh::FILL_COORDS |
-				 Mesh::FILL_GRD_LAMBDA);
-  } 
-  else {
-    elInfo = stack.traverseFirst(feSpace->getMesh(),
-				 -1, 
-				 Mesh::CALL_LEAF_EL | 
-				 Mesh::FILL_BOUND |
-				 Mesh::FILL_COORDS);
-  }
-  while(elInfo) {
-
-    // Set elInfo in case velocity extension from velocity field is used.
-    if (velExt && velExtType.isSet(VEL_EXT_FROM_VEL_FIELD)) {
-      ((VelocityExtFromVelocityField *)velExt)->setElInfo(elInfo);
-    }  
-    
-    // Get local indices of vertices.
-    feSpace->getBasisFcts()->getLocalIndices(
-			     const_cast<Element *>(elInfo->getElement()),
-			     const_cast<DOFAdmin *>(feSpace->getAdmin()),
-			     locInd); 
-    
-    // Get element status.
-    elStatus = elLS->createElementLevelSet(elInfo);
-    
-    //Get some information for creating the first list
-    
-    elVertStatusVec = elLS->getElVertStatusVec();
-    
-    //Beginn creating the first list
-    
-    NumVertIntPoints = elLS->getNumVertIntPoints();
-    ElNum = elInfo->getElement()->getIndex();
-    
-    createFirstList( elStatus, elVertStatusVec, ElNum, NumVertIntPoints);
-
-    //end creating the first list
-    
-    // Is element cut by the interface ?
-    if (elStatus == ElementLevelSet::LEVEL_SET_BOUNDARY) {
-      
-      // Reset element distance vector.
-      for (int i=0; i<=dim; ++i) {
-	distVec[i] = inftyValue;
-      }
-      
-      // Mark all vertices as boundary vertices.
-      for (int i=0; i<=dim; ++i) {
-	(*bound_DOF)[locInd[i]] = 1.0;
-      }
-      
-      // Calculate distance for all vertices.
-      if (bndElDist->calcDistOnBoundaryElement(elInfo, distVec) !=
-	  ElementLevelSet::LEVEL_SET_BOUNDARY) {
-	ERROR_EXIT("error in distance calculation !\n");
-	}
-      else {
-	
-	// If distance is smaller, correct to new distance.
-	for (int i=0; i<=dim; ++i) {
-	  if ((*sD_DOF)[locInd[i]] > distVec[i]) {
-	    (*sD_DOF)[locInd[i]] = distVec[i];
-	    //If distance is corrected, calculate new velocity.
-	    if(velExt != NULL)
-	      {
-		velExt->calcVelocityBoundary(locInd, i);
-	      }
-	  }
-	}
-      }
-    }  // end of: elStatus == ElementLevelSet::LEVEL_SET_BOUNDARY
-    
-    else if (elLS->getNumVertIntPoints() != 0){
-//       // Interface cuts element only in vertices.
-//       elVertStatusVec = elLS->getElVertStatusVec();
-      
-//       for (int i=0; i<=dim; ++i) {
-// 	if (elVertStatusVec[i] == ElementLevelSet::LEVEL_SET_BOUNDARY) {
-// 	  (*bound_DOF)[locInd[i]] = 1.0;
-// 	  (*sD_DOF)[locInd[i]] = 0.0;
-// 	  }
-//       }
-
-      ERROR_EXIT("intersection point is element vertex. should never happen !\n");
-    } 
-    
-    elInfo = stack.traverseNext(elInfo);
-  }  // end of: mesh traverse
-  
-  FREE_MEMORY(locInd, DegreeOfFreedom, nBasFcts);
-  
-  return;
-}
-
-void 
-HL_SignedDistLevels::Mesh_to_SMI_and_quantity()
-{
-  if(!smiAdapter)
-    {
-      smiAdapter = NEW SMIAdapter(1, 1,
-				  const_cast<FiniteElemSpace*>(feSpace),
-				  1, -1);
-    }
-  
-  // cout << "\n\n\tSMI-Adapter angelegt !\n\n";
-  
-  //====== transfer Mesh to SMI ======================
-  
-  smiAdapter->addNeighbourInfo();
-  
-  // cout << "\n\n\tNachbarschafts-Infos in SMI ergaenzt !\n\n";
-  
-  smiAdapter-> transferMeshToSMI();
-  
-  //   cout << "\n\n\tGitter nach SMI geschrieben !\n\n";
-  
-  int smiError = SMI_Begin_write_transaction(1,1);
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_Begin_write_transaction() failed with error %d\n", smiError);
-  
-  int nul = 0;
-  int *null = new int [dim+1];
-  for (int i=0; i<=dim; i++)
-    {
-      null[i] = nul;
-    }
-
-  //which pair of element and node is saved in list
-  smiError = 
-    SMI_Add_quantity(1, 1, 1, SMI_LOC_ELEM, SMI_TYPE_INT, dim+1, null);
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_Add_quantity() failed with error %d\n", smiError);
-
-  //which node is a boundary-node
-  smiError = SMI_Add_quantity(1, 1, 2, SMI_LOC_NODE, SMI_TYPE_INT, 1, &nul);
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_Add_quantity() failed with error %d\n", smiError);
-
-  //saves the number of tried updates
-  smiError = SMI_Add_quantity(1, 1, 3, SMI_LOC_NODE, SMI_TYPE_INT, 1, &nul);
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_Add_quantity() failed with error %d\n", smiError);
-
-  //saves the number of updates
-  smiError = SMI_Add_quantity(1, 1, 4, SMI_LOC_NODE, SMI_TYPE_INT, 1, &nul);
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_Add_quantity() failed with error %d\n", smiError);
-
-  //how often a node is saved in the second list
-  smiError = SMI_Add_quantity(1, 1, 5, SMI_LOC_NODE, SMI_TYPE_INT, 1, &nul);
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_Add_quantity() failed with error %d\n", smiError);
-
-  //saves the level of an element
-  smiError = SMI_Add_quantity(1, 1, 6, SMI_LOC_ELEM, SMI_TYPE_INT, 1, 
-			      &inftyValue);
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_Add_quantity() failed with error %d\n", smiError);
-
-  // cout << "\n\n\tQuantities in SMI ergaenzt !\n\n";
-
-  delete [] null;
-}
-
-void 
-HL_SignedDistLevels::createFirstList(const int elStatus, 
-				     const int *elVertStatusVec, 
-				     int ElNum, 
-				     const int NumVertIntPoints)
-{
-  int *sv = new int[dim+1];
-  int *nodeIndices;
-  int nul = 0;
-  int smiError;
-  
-  if (elStatus == ElementLevelSet::LEVEL_SET_BOUNDARY)
-    {
-      List_Element.push(ElNum);
-
-      smiError = 
-	SMI_Set_quantity_values(1, 1, 6, SMI_TYPE_INT, 1, 1, &ElNum, &nul);
-      TEST_EXIT(smiError == SMI_OK)
-	("SMI_Set_quantity_values() failed with error %d\n", smiError);
-
-      //saving which nodes are boundary-nodes
-      for (int i=0; i<=dim; i++)
-	{
-	  sv[i] = 1;
-	}
-
-      smiError =
-	SMI_Get_elems(1, 1, 1, const_cast<DegreeOfFreedom*>(&ElNum),
-		      NULL, &nodeIndices, NULL, NULL);
-      TEST_EXIT(smiError == SMI_OK)
-	("SMI_Get_elems() failed with error %d\n", smiError);
-      
-      smiError = 
-	SMI_Set_quantity_values(1, 1, 2, SMI_TYPE_INT, 1, 3, nodeIndices, sv);
-      TEST_EXIT(smiError == SMI_OK)
-	("SMI_Set_quantity_values() failed with error %d\n", smiError);
-    }
-  //if the elemet isn't a boundary-element, but the interface cuts the FE in two nodes
-//   else if (NumVertIntPoints == dim)
-//     {
-//       List_Element.push( ElNum );           
-
-//       smiError = 
-// 	SMI_Set_quantity_values(1, 1, 6, SMI_TYPE_INT, 1, 1, &ElNum, &nul);
-//       TEST_EXIT(smiError == SMI_OK)
-// 	("SMI_Set_quantity_values() failed with error %d\n", smiError);
-      
-//       //saving which nodes are boundary-nodes
-//       for (int i=0; i<=dim; i++)
-// 	{
-// 	  if(elVertStatusVec[i] == ElementLevelSet::LEVEL_SET_BOUNDARY)
-// 	    {
-// 	      sv[i] = 1;
-// 	    }
-// 	  else
-// 	    {
-// 	      sv[i] = 0;
-// 	    }
-
-// 	  smiError = 
-// 	    SMI_Get_elems(1, 1, 1, const_cast<DegreeOfFreedom*>(&ElNum),
-// 			  NULL, &nodeIndices, NULL, NULL);
-// 	  TEST_EXIT(smiError == SMI_OK)
-// 	    ("SMI_Get_elems() failed with error %d\n", smiError);
-
-// 	  smiError = 
-// 	    SMI_Set_quantity_values(1, 1, 2, SMI_TYPE_INT, 1, 3,
-// 				    nodeIndices, sv);
-// 	  TEST_EXIT(smiError == SMI_OK)
-// 	    ("SMI_Set_quantity_values() failed with error %d\n", smiError);
-// 	}
-//     }
-  
-  delete [] sv;
-}
-  
-void 
-HL_SignedDistLevels::HL_updateIteration()
-{
-  int numNodes;
-  int *nodeIndices;
-  int max_q3 = 0;
-  int max_q4 = 0;
-  int sum_q3 = 0;
-  int sum_q4 = 0;
-  clock_t time1;
-  clock_t time2;
-  double TIME;
-  int control;
-  
-  int smiError = 
-    SMI_Get_all_nodes(1, 1, const_cast<DegreeOfFreedom*>(&numNodes),
-		      &nodeIndices);
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_Get_all_nodes() failed with error %d\n", smiError);
-
-  int *values_q3 = new int [numNodes];
-  int *values_q4 = new int [numNodes];
-  
-  GET_PARAMETER(0,"SignedDist->count updates", "%d", &count_updates);
-  
-  time1 = clock();
-  control = traverseListElement();
-  time2 = clock();
-  TIME = TIME_USED(time1, time2);
-  
-  cout<<"Zeit zum durchlaufen der ersten (Elementen-) Liste: "<<TIME<<" sec.\n\n";
-  if(control == 1)
-    {
-      createLevels ();
-    }
-  
-  /////////////////////////////////
-  
-  
-  //print chosen level in a file
-  if (print_level == 1)
-    {
-      DOFVector<double> *level_DOF = NEW DOFVector<double>(sD_DOF->getFeSpace(), 
-							   "level_DOF");
-      
-      int numElems;
-      int *elemIndices;
-      int *NodeIndices;
-      
-      smiError = SMI_Get_all_elems(1, 1, &numElems, &elemIndices);
-      TEST_EXIT(smiError == SMI_OK)
-	("SMI_Get_all_elems() failed with error %d\n", smiError);
-      
-      int *value_q6 = new int [numElems];
-      
-      smiError =
-	SMI_Get_quantity_values(1, 1, 6, SMI_TYPE_INT, 1, numElems,
-				elemIndices, value_q6);
-      TEST_EXIT(smiError == SMI_OK)
-	("SMI_Get_quantity_values() failed with error %d\n", smiError);
-      
-      for(int i=0; i<numElems; i++)
-	{	  
-	  smiError = 
-	    SMI_Get_elems(1, 1, 1, &elemIndices[i], NULL, &NodeIndices, 
-			  NULL, NULL);
-	  TEST_EXIT(smiError == SMI_OK)
-	    ("SMI_Get_elems() failed with error %d\n", smiError);
-
-	  for(int j=0; j<=dim; j++)
-	    {
-	      (*level_DOF)[NodeIndices[j]] = -1;
-	    }
-	}
-      for(int i=0; i<numElems; i++)
-	{	  
-	  smiError = 
-	    SMI_Get_elems(1, 1, 1, &elemIndices[i], NULL, &NodeIndices, 
-			  NULL, NULL);
-	  TEST_EXIT(smiError == SMI_OK)
-	    ("SMI_Get_elems() failed with error %d\n", smiError);
-
-	  if (value_q6[i] == chosen_level)
-	    {
-	      for(int j=0; j<dim+1; j++)
-		{
-		  (*level_DOF)[NodeIndices[j]] = 0;
-		}
-	    }
-	}
-      
-      FileWriter *levelFileWriter = 
-	NEW FileWriter("level->output",
-		       level_DOF->getFeSpace()->getMesh(),
-		       level_DOF);
-      levelFileWriter->writeFiles (adaptInfo, false);
-      
-      DELETE levelFileWriter;
-    }
-  
-  //end of the part for printing chosen levels
-  
-  
-  time1 = clock();
-  traversingListLevel_ ( sD_DOF );
-  time2 = clock();
-  TIME = TIME_USED(time1,time2);
-  
-  cout<<"Zeit zum Durchlaufen der zweiten  Liste (Liste von Listen): "<<TIME<<" sec.\n\n";
-  
-  std::string smiOutFile;
-  GET_PARAMETER(0, "SignedDist->count updates->output->filename", &smiOutFile);
-  cout << "count updates Ausgabe-Datei:  " << smiOutFile.c_str() << "\n\n";
-  
-  ofstream out (smiOutFile.c_str());
-  
-  smiError = 
-    SMI_Get_quantity_values(1, 1, 3, SMI_TYPE_INT, 1, numNodes, nodeIndices,
-			    values_q3);
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_Get_quantity_values() failed with error %d\n", smiError);
-
-  smiError =
-    SMI_Get_quantity_values(1, 1, 4, SMI_TYPE_INT, 1, numNodes, nodeIndices,
-			    values_q4);  
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_Get_quantity_values() failed with error %d\n", smiError);
-  
-  for (int i=0; i<numNodes; i++)
-    {
-      out<<nodeIndices[i]<<" "<<values_q3[i]<<" "<<values_q4[i]<<"\n";
-      
-      if(max_q3 < values_q3[i])
-	{
-	  max_q3 = values_q3[i];
-	}
-      if(max_q4 < values_q4[i])
-	{
-	  max_q4 = values_q4[i];
-	}
-      sum_q3 = sum_q3 + values_q3[i];
-      sum_q4 = sum_q4 + values_q4[i];
-    }
-  
-  out<<"\n\n maximale Anzahl an versuchten Updates auf einem Knoten: "<<max_q3<<"\n maximale Anzahl an durchgefuehrten Updates auf einem Knoten:  "<<max_q4<<"\n";
-  out<<"\n Summe aller versuchten Updates: "<<sum_q3<<"\n Summe aller durchgefuehrten updates: "<<sum_q4<<"\n";
-  
-  out<<"Anzahl an Knoten: "<<numNodes<<"\n";
-  
-  out.close();
-  
-  smiError = SMI_End_write_transaction(1, 1);
-  TEST_EXIT(smiError == SMI_OK)
-    ("SMI_End_write_transaction() failed with error %d\n", smiError);
-  
-  return;
-}
- 
-int 
-HL_SignedDistLevels::traverseListElement()
-{
-  int Element;
-  
-  bool neighboursExist;
-  bool neighbourInNewListSet = false;
-  
-  while (List_Element.size() != 0)
-    {
-      Element = List_Element.front();
-      
-      neighboursExist =  collectNeighbours_setLevels (Element, 0, &neighbourInNewListSet);
-      
-      List_Element.pop();
-    }
-  
-  //within the function "collectNeighbours_setLevels" the new pairs are saved in the list "level"
-  //this list will be one entry of the list "Level_"
-  if (neighbourInNewListSet)
-    {
-      Level_.push_back (Level);
-    }
-  
-  while (Level.size() != 0)
-    {
-      Level.pop();
-    }
-  if (!neighbourInNewListSet)
-    {
-      return 0;
-    }
-  else
-    {
-      return 1;
-    }
-  
-}
-
-void 
-HL_SignedDistLevels::createLevels ()
-{
-  bool neighbourExists = true;
-  bool stop = false;
-  Vert_Struct vertStruct;
-  int i = 0;
-  bool elementInNextListSet = true;
-  int value_q2;
-  int smiError;
-  
-  while(elementInNextListSet)
-    {
-      stop = false;
-      neighbourExists = false;
-      elementInNextListSet = false;
-      
-      while(Level_[i].size() != 0) 
-	{
-	  vertStruct =  Level_[i].front();
-	  
-	  neighbourExists = collectNeighbours_setLevels (vertStruct.ElNum, i+1, &elementInNextListSet);
-	  
-	  smiError = 
-	    SMI_Get_quantity_values(1, 1, 2, SMI_TYPE_INT, 1, 1, 
-				    &vertStruct.VertNum, &value_q2);
-	  TEST_EXIT(smiError == SMI_OK)
-	    ("SMI_Get_quantity_values() failed with error %d\n", smiError);
-
-	  if(value_q2 == 0)
-	    {
-	      helpLevel.push (vertStruct);
-	    }
-	  Level_[i].pop();
-	}
-      
-      Level_[i] = helpLevel;
-      while (helpLevel.size() != 0)
-	{
-	  helpLevel.pop();
-	}
-      
-      if(elementInNextListSet)
-	{
-	  Level_.push_back (Level);
-	}
-      
-      while (Level.size() != 0)
-	{
-	  Level.pop();
-	}
-      i++;
-    }
-}
-
-bool 
-HL_SignedDistLevels::collectNeighbours_setLevels (const int Element,
-						  const int currentIndex,
-						  bool *elementInNewListSet)
-{
-  Vert_Struct vertStruct;
-  
-  int *neighbour=new int[dim+1];
-  int *oppVertices=new int[dim+1];
-  int *value = new int [dim+1];
-  int saved_level;
-  int value_q5;
-  int *nodeIndices;
-  int *nodeIndicesOfElem;
-  int smiError;
-