Mesh.cc

#include <algorithm>
#include <set>
#include <map>

#include "time.h"

#include "AdaptStationary.h"
#include "AdaptInstationary.h"
#include "FiniteElemSpace.h"
#include "ElementData.h"
#include "MacroElement.h"
#include "MacroReader.h"
#include "Mesh.h"
#include "Traverse.h"
#include "Parameters.h"
#include "FixVec.h"
#include "DOFVector.h"
#include "CoarseningManager.h"
#include "DOFIterator.h"
#include "VertexVector.h"
#include "MacroWriter.h"
#include "PeriodicMap.h"
#include "Projection.h"
#include "ElInfoStack.h"


namespace AMDiS {

#define TIME_USED(f,s) ((double)((s)-(f))/(double)CLOCKS_PER_SEC)

  //**************************************************************************
  //  flags, which information should be present in the elInfo structure     
  //**************************************************************************

  const Flag Mesh::FILL_NOTHING    = 0X00L;
  const Flag Mesh::FILL_COORDS     = 0X01L;
  const Flag Mesh::FILL_BOUND      = 0X02L;
  const Flag Mesh::FILL_NEIGH      = 0X04L;
  const Flag Mesh::FILL_OPP_COORDS = 0X08L;
  const Flag Mesh::FILL_ORIENTATION= 0X10L;
  const Flag Mesh::FILL_DET        = 0X20L;
  const Flag Mesh::FILL_GRD_LAMBDA = 0X40L;
  const Flag Mesh::FILL_ADD_ALL    = 0X80L;


  const Flag Mesh::FILL_ANY_1D = (0X01L|0X02L|0X04L|0X08L|0x20L|0X40L|0X80L);
  const Flag Mesh::FILL_ANY_2D = (0X01L|0X02L|0X04L|0X08L|0x20L|0X40L|0X80L);
  const Flag Mesh::FILL_ANY_3D = (0X01L|0X02L|0X04L|0X08L|0X10L|0x20L|0X40L|0X80L);

  //**************************************************************************
  //  flags for Mesh traversal                                                
  //**************************************************************************

  const Flag Mesh::CALL_EVERY_EL_PREORDER  = 0X0100L;
  const Flag Mesh::CALL_EVERY_EL_INORDER   = 0X0200L;
  const Flag Mesh::CALL_EVERY_EL_POSTORDER = 0X0400L;
  const Flag Mesh::CALL_LEAF_EL            = 0X0800L;
  const Flag Mesh::CALL_LEAF_EL_LEVEL      = 0X1000L;
  const Flag Mesh::CALL_EL_LEVEL           = 0X2000L;
  const Flag Mesh::CALL_MG_LEVEL           = 0X4000L ; // used in mg methods 


  // const Flag Mesh::USE_PARAMETRIC          = 0X8000L ; // used in mg methods 

  DOFAdmin* Mesh::compressAdmin = NULL;
  Mesh* Mesh::traversePtr = NULL;
  int Mesh::iadmin = 0;
  std::vector<DegreeOfFreedom> Mesh::dof_used;
  const int Mesh::MAX_DOF = 100;
  std::map<DegreeOfFreedom, DegreeOfFreedom*> Mesh::serializedDOFs;

  struct delmem { 
    DegreeOfFreedom* ptr;
    int len;
  };


  Mesh::Mesh(const std::string& aName, int dimension) 
    : name(aName), 
      dim(dimension), 
      nVertices(0),
      nEdges(0),
      nLeaves(0), 
      nElements(0),
      parametric(NULL), 
      preserveCoarseDOFs(false),
      nDOFEl(0),
      nDOF(dimension, DEFAULT_VALUE, 0),
      nNodeEl(0),
      node(dimension, DEFAULT_VALUE, 0),
      elementPrototype(NULL),
      elementDataPrototype(NULL),
      elementIndex(-1),
      initialized(false),
      macroFileInfo(NULL),
      final_lambda(dimension, DEFAULT_VALUE, 0.0)
  {

    FUNCNAME("Mesh::Mesh()");

    // set default element prototype
    switch(dim) {
    case 1:
      elementPrototype = NEW Line(this);
      break;
    case 2:
      elementPrototype = NEW Triangle(this);
      break;
    case 3:
      elementPrototype = NEW Tetrahedron(this);
      break;
    default:
      ERROR_EXIT("invalid dimension\n");
    }

    elementPrototype->setIndex(-1);

    elementIndex = 0;
  }

  Mesh::~Mesh()
  {
    Element::deletedDOFs.clear();

    for (std::deque<MacroElement*>::const_iterator it = macroElements.begin();
	 it != macroElements.end();
	 ++it) {
      (*it)->getElement()->deleteElementDOFs();
      DELETE *it;
    }    

    Element::deletedDOFs.clear();

    if (macroFileInfo != NULL) {
      DELETE macroFileInfo;
    }
    if (elementPrototype) {
      DELETE elementPrototype;
    }
    if (elementDataPrototype) {
      DELETE elementDataPrototype;
    }
    
    for (int i = 0; i < static_cast<int>(admin.size()); i++) {
      DELETE admin[i];
    }
  }

  Mesh& Mesh::operator=(const Mesh& m)
  {
    FUNCNAME("Mesh::operator=()");

    if (this == &m)
      return *this;

    TEST_EXIT(dim == m.dim)("operator= works only on meshes with equal dim!\n");

    name = m.name;
    nVertices = m.nVertices;
    nEdges = m.nEdges;
    nLeaves = m.nLeaves;
    nElements = m.nElements;
    nFaces = m.nFaces;
    maxEdgeNeigh = m.maxEdgeNeigh;
    diam = m.diam;
    parametric = NULL;

    preserveCoarseDOFs = m.preserveCoarseDOFs;
    nDOFEl = m.nDOFEl;
    nDOF = m.nDOF;
    nNodeEl = m.nNodeEl;
    node = m.node;
    newDOF = m.newDOF;
    elementIndex = m.elementIndex;
    initialized = m.initialized;
    final_lambda = m.final_lambda;
    
    /* ====================== Create new DOFAdmins ================== */
    admin.resize(m.admin.size());
    for (int i = 0; i < static_cast<int>(admin.size()); i++) {
      admin[i] = NEW DOFAdmin(this);
      *(admin[i]) = *(m.admin[i]);
      admin[i]->setMesh(this);
    }


    /* ====================== Copy macro elements =================== */
  
    // mapIndex[i] is the index of the MacroElement element in the vector
    // macroElements, for which holds: element->getIndex() = i    
    std::map<int, int> mapIndex;

    // We use this map for coping the DOFs of the Elements within the
    // MacroElements objects.
    Mesh::serializedDOFs.clear();

    int insertCounter = 0;

    macroElements.clear();

    // Go through all MacroElements of mesh m, and create for every a new
    // MacroElement in this mesh.
    for (std::deque<MacroElement*>::const_iterator it = m.macroElements.begin();
	 it != m.macroElements.end();
	 ++it, insertCounter++) {

      // Create new MacroElement.
      MacroElement *el = NEW MacroElement(dim);

      // Use copy operator to copy all the data to the new MacroElement.
      *el = **it;

      // Make a copy of the Element data, together with all DOFs
      el->setElement((*it)->getElement()->cloneWithDOFs());

      // Insert the new MacroElement in the vector of all MacroElements.
      macroElements.push_back(el);

      // Update the index map.
      mapIndex.insert(std::pair<int, int>(el->getIndex(), insertCounter));
    }

    // Now we have to go through all the new MacroElements, and update the neighbour
    // connections.
    insertCounter = 0;
    for (std::deque<MacroElement*>::const_iterator it = m.macroElements.begin();
	 it != m.macroElements.end();
	 ++it, insertCounter++) {
      // Go through all neighbours.
      for (int i = 0; i < dim; i++) {
	// 1. Get index of the old MacroElement for its i-th neighbour.
	// 2. Because the index in the new MacroElement is the same, search
	//    for the vector index the corresponding element is stored in.
	// 3. Get this element from macroElements, and set it as the i-th
	//    neighbour for the current element.
	macroElements[insertCounter]->
	  setNeighbour(i, macroElements[mapIndex[(*it)->getNeighbour(i)->getIndex()]]);
      }
    }

    // Cleanup
    Mesh::serializedDOFs.clear();

    /* ================== Things will be done when required ============ */
      
    TEST_EXIT(elementDataPrototype == NULL)("TODO\n");
    TEST_EXIT(m.parametric == NULL)("TODO\n");
    TEST_EXIT(periodicAssociations.size() == 0)("TODO\n");

    return *this;
  }

  void Mesh::addMacroElement(MacroElement* m) {
    macroElements.push_back(m); 
    m->setIndex(macroElements.size());
  }

  int Mesh::traverse(int level, Flag flag, 
		     int (*el_fct)(ElInfo*))
  {
    FUNCNAME("Mesh::traverse()");

    std::deque<MacroElement*>::iterator mel;
    ElInfoStack elInfoStack(this);
    ElInfo* elinfo = elInfoStack.getNextElement();
    Traverse tinfo(this, flag, level, el_fct);
    int sum = 0;
  
    elinfo->setFillFlag(flag);
  
    if (flag.isSet(Mesh::CALL_LEAF_EL_LEVEL) || 
	flag.isSet(Mesh::CALL_EL_LEVEL)      || 
	flag.isSet(Mesh::CALL_MG_LEVEL)) {
      TEST(level >= 0)("invalid level: %d\n", level);
    }
  
    for (mel = macroElements.begin(); mel != macroElements.end(); mel++) {
      elinfo->fillMacroInfo(*mel);
      sum += tinfo.recursive(&elInfoStack);
    }

    elInfoStack.getBackElement();
    
    return (flag.isSet(Mesh::FILL_ADD_ALL)) ? sum : 0;
  }



  void Mesh::addDOFAdmin(DOFAdmin *localAdmin)
  {    
    FUNCNAME("Mesh::addDOFAdmin()");

    localAdmin->setMesh(this);

    std::vector<DOFAdmin*>::iterator dai = std::find(admin.begin(),admin.end(),localAdmin);

    if (dai!= admin.end()) {
      ERROR("admin %s is already associated to mesh %s\n",
	    localAdmin->getName().c_str(), this->getName().c_str());
    }

    // ===== adding dofs to already existing elements ============================ 
    
    // If adding DOFAdmins to already initilized meshes is required, see older
    // AMDiS version (revision < 244) at the same code position.
    TEST_EXIT(!initialized)("Adding DOFAdmins to initilized meshes does not work!\n");


    admin.push_back(localAdmin);

    nDOFEl = 0;

    localAdmin->setNumberOfPreDOFs(VERTEX,nDOF[VERTEX]);
    nDOF[VERTEX] += localAdmin->getNumberOfDOFs(VERTEX);
    nDOFEl += getGeo(VERTEX) * nDOF[VERTEX];

    if (dim > 1) {
      localAdmin->setNumberOfPreDOFs(EDGE,nDOF[EDGE]);
      nDOF[EDGE] += localAdmin->getNumberOfDOFs(EDGE);
      nDOFEl += getGeo(EDGE) * nDOF[EDGE];
    }

    localAdmin->setNumberOfPreDOFs(CENTER,nDOF[CENTER]);
    nDOF[CENTER]  += localAdmin->getNumberOfDOFs(CENTER);
    nDOFEl += nDOF[CENTER];

    TEST_EXIT_DBG(nDOF[VERTEX] > 0)("no vertex dofs\n");

    node[VERTEX] = 0;
    nNodeEl = getGeo(VERTEX);

    if (dim > 1) {
      node[EDGE] = nNodeEl;
      if (nDOF[EDGE] > 0) 
	nNodeEl += getGeo(EDGE);
    }

    if (dim == 3) {
      localAdmin->setNumberOfPreDOFs(FACE,nDOF[FACE]);
      nDOF[FACE] += localAdmin->getNumberOfDOFs(FACE);
      nDOFEl += getGeo(FACE) * nDOF[FACE];
      node[FACE] = nNodeEl;
      if (nDOF[FACE] > 0) 
	nNodeEl += getGeo(FACE);
    }

    node[CENTER] = nNodeEl;
    if (nDOF[CENTER] > 0) {
      nNodeEl += 1;
    }
  }


  /****************************************************************************/
  /*  dofCompress: remove holes in dof vectors                                */
  /****************************************************************************/

  void Mesh::dofCompress()
  {
    FUNCNAME("Mesh::dofCompress()");
    int size;
    Flag fill_flag;

    for (iadmin = 0; iadmin < static_cast<int>(admin.size()); iadmin++) {
      compressAdmin = admin[iadmin];

      TEST_EXIT_DBG(compressAdmin)("no admin[%d] in mesh\n", iadmin);
      
      if ((size = compressAdmin->getSize()) < 1) 
	continue;

      if (compressAdmin->getUsedDOFs() < 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;
      }
      
      traverse( -1, fill_flag, newDOFFct1);
      traverse( -1, fill_flag, newDOFFct2);
      
      newDOF.resize(0);
    }   
  }


  DegreeOfFreedom *Mesh::getDOF(GeoIndex position)
  {
    FUNCNAME("Mesh::getDOF()");

    TEST_EXIT_DBG(position >= CENTER && position <= FACE)
      ("unknown position %d\n", position);

    int ndof = getNumberOfDOFs(position);
    if (ndof <= 0) 
      return NULL;

    DegreeOfFreedom *dof = GET_MEMORY(DegreeOfFreedom, ndof);

    for (int i = 0; i < getNumberOfDOFAdmin(); i++) {
      const DOFAdmin *localAdmin = &getDOFAdmin(i);
      TEST_EXIT_DBG(localAdmin)("no admin[%d]\n", i);
      
      int n  = localAdmin->getNumberOfDOFs(position);
      int n0 = localAdmin->getNumberOfPreDOFs(position);
      
      TEST_EXIT_DBG(n + n0 <= ndof)("n=%d, n0=%d too large: ndof=%d\n", n, n0, ndof);
      
      for (int j = 0; j < n; j++) {
	dof[n0 + j] = const_cast<DOFAdmin*>(localAdmin)->getDOFIndex();
      }
    }
  
    return dof;
  }


  DegreeOfFreedom **Mesh::createDOFPtrs()
  {
    FUNCNAME("Mesh::createDOFPtrs()");

    if (nNodeEl <= 0)
      return NULL;

    DegreeOfFreedom **ptrs = GET_MEMORY(DegreeOfFreedom*, nNodeEl);
    for (int i = 0; i < nNodeEl; i++)
      ptrs[i] = NULL;

    return ptrs;
  }

  void Mesh::freeDOFPtrs(DegreeOfFreedom **ptrs)
  {
    FUNCNAME("Mesh::freeDOFPtrs()");

    TEST_EXIT_DBG(ptrs)("ptrs=NULL\n");

    if (nNodeEl <= 0)
      return;
  
    FREE_MEMORY(ptrs, DegreeOfFreedom*, nNodeEl);
  }


  const DOFAdmin *Mesh::createDOFAdmin(const std::string& lname,DimVec<int> lnDOF)
  {
    FUNCNAME("Mesh::createDOFAdmin()");

    DOFAdmin *localAdmin = NEW DOFAdmin(this, lname);

    for (int i = 0; i < dim+1; i++)
      localAdmin->setNumberOfDOFs(i,lnDOF[i]);

    addDOFAdmin(localAdmin);

    return localAdmin;
  }


  const DOFAdmin* Mesh::getVertexAdmin() const
  {
    const DOFAdmin *localAdmin = NULL;

    for (int i = 0; i < static_cast<int>(admin.size()); i++) {
      if (admin[i]->getNumberOfDOFs(VERTEX)) {
	if (!localAdmin)  
	  localAdmin = admin[i];
	else if (admin[i]->getSize() < localAdmin->getSize())
	  localAdmin = admin[i];
      }
    }

    return localAdmin;
  }

  void Mesh::freeDOF(DegreeOfFreedom* dof, GeoIndex position)
  {
    FUNCNAME("Mesh::freeDOF()");

    TEST_EXIT_DBG(position >= CENTER && position <= FACE)
      ("unknown position %d\n",position);

    int ndof = nDOF[position];
    if (ndof) {
      if (!dof) {
	MSG("dof = NULL, but ndof=%d\n", ndof);
	return;
      }
    } else  {
      if (dof) {
	MSG("dof != NULL, but ndof=0\n");
      }
      return;
    }

    TEST_EXIT_DBG(ndof <= MAX_DOF)
      ("ndof too big: ndof=%d, MAX_DOF=%d\n",ndof,MAX_DOF);

    for (int i = 0; i < static_cast<int>(admin.size()); i++) {
      DOFAdmin *localAdmin = admin[i];
      int n = localAdmin->getNumberOfDOFs(position);
      int n0 = localAdmin->getNumberOfPreDOFs(position);
      
      TEST_EXIT_DBG(n + n0 <= ndof)("n=%d, n0=%d too large: ndof=%d\n", n, n0, ndof);
      
      for (int j = 0; j < n; j++)
	localAdmin->freeDOFIndex(dof[n0 + j]);
    }

    FREE_MEMORY(dof, DegreeOfFreedom, ndof);
  }

  void Mesh::freeElement(Element* el)
  {
    freeDOFPtrs(const_cast<DegreeOfFreedom**>(el->getDOF()));
    DELETE el;
  }


  Element* Mesh::createNewElement(Element *parent)
  {
    FUNCNAME("Mesh::createNewElement()");

    TEST_EXIT_DBG(elementPrototype)("no element prototype\n");

    Element *el = parent ? parent->clone() : elementPrototype->clone();
  
    if (!parent && elementDataPrototype) {
      el->setElementData(elementDataPrototype->clone()); 
    } else {
      el->setElementData(NULL); // must be done in ElementData::refineElementData()
    }

    return el;
  }


  ElInfo* Mesh::createNewElInfo()
  {
    switch(dim) {
    case 1:
      return NEW ElInfo1d(this);
      break;
    case 2:
      return NEW ElInfo2d(this);
      break;
    case 3:
      return NEW ElInfo3d(this);
      break;
    default:
      ERROR_EXIT("invalid dim\n");
      return NULL;
    };
  }



  bool Mesh::findElInfoAtPoint(const WorldVector<double>& xy,
			       ElInfo *el_info,
			       DimVec<double>& bary,
			       const MacroElement *start_mel,
			       const WorldVector<double> *xy0,
			       double *sp)
  {
    static const MacroElement *mel = NULL;
    DimVec<double> lambda(dim, NO_INIT);
    ElInfo *mel_info = NULL;

    mel_info = createNewElInfo();

    if (start_mel != NULL)
      mel = start_mel;
    else
      if ((mel == NULL) || (mel->getElement()->getMesh() != this))
	mel = *(macroElements.begin());

    mel_info->setFillFlag(Mesh::FILL_COORDS);
    g_xy = &xy;
    g_xy0 = xy0;
    g_sp = sp;

    mel_info->fillMacroInfo(mel);

    int k;
    while ((k = mel_info->worldToCoord(xy, &lambda)) >= 0) {
      if (mel->getNeighbour(k)) {
	mel = mel->getNeighbour(k);
	mel_info->fillMacroInfo(mel);
	continue;
      }
      break;
    }

    /* now, descend in tree to find leaf element at point */
    bool inside = findElementAtPointRecursive(mel_info, lambda, k, el_info);
    for (int i = 0; i <= dim; i++) {
      bary[i] = final_lambda[i];
    }
  
    DELETE mel_info;

    return inside;
  }

  bool Mesh::findElementAtPoint(const WorldVector<double>&  xy,
				Element **elp, 
				DimVec<double>& bary,
				const MacroElement *start_mel,
				const WorldVector<double> *xy0,
				double *sp)
  {
    ElInfo *el_info = createNewElInfo();
    int val = findElInfoAtPoint(xy, el_info, bary, start_mel, xy0, sp);

    *elp = el_info->getElement();

    DELETE el_info;

    return val;
  }



  bool Mesh::findElementAtPointRecursive(ElInfo *el_info,
					 const DimVec<double>& lambda,
					 int outside,
					 ElInfo* final_el_info)
  {
    FUNCNAME("Mesh::findElementAtPointRecursive()");
    Element *el = el_info->getElement();
    DimVec<double> c_lambda(dim, NO_INIT);
    int inside;
    int ichild, c_outside;

    if (el->isLeaf()) {
      *final_el_info = *el_info;
      if (outside < 0) {
	for (int i = 0; i <= dim; i++) {
	  final_lambda[i] = lambda[i];
	}

	return true;
      }  else {  /* outside */
	if (g_xy0) { /* find boundary point of [xy0, xy] */
	  el_info->worldToCoord(*(g_xy0), &c_lambda);
	  double s = lambda[outside] / (lambda[outside] - c_lambda[outside]);
	  for (int i = 0; i <= dim; i++) {
	    final_lambda[i] = s * c_lambda[i] + (1.0-s) * lambda[i];
	  }
	  if (g_sp) {
	    *(g_sp) = s;
	  }
	  if (dim == 3) 
	    MSG("outside finest level on el %d: s=%.3e\n", el->getIndex(), s);

	  return false;  /* ??? */
	} else {
	  return false;
	}
      }
    }

    ElInfo *c_el_info = createNewElInfo();

    if (dim == 1) {
      if (lambda[0] >= lambda[1]) {
	c_el_info->fillElInfo(0, el_info);
	if (outside >= 0) {
	  outside = el_info->worldToCoord(*(g_xy), &c_lambda);
	  if (outside >= 0) ERROR("point outside domain\n");
	} else {
	  c_lambda[0] = lambda[0] - lambda[1];
	  c_lambda[1] = 2.0 * lambda[1];
	}
      } else {
	c_el_info->fillElInfo(1, el_info);
	if (outside >= 0)  {
	  outside = el_info->worldToCoord(*(g_xy), &c_lambda);
	  if (outside >= 0) ERROR("point outside domain\n");
	} else {
	  c_lambda[1] = lambda[1] - lambda[0];
	  c_lambda[0] = 2.0 * lambda[0];
	}
      }
    } /* DIM == 1 */

    if (dim == 2) {
      if (lambda[0] >= lambda[1]) {
	c_el_info->fillElInfo(0, el_info);
	if (el->isNewCoordSet()) {
	  outside = c_el_info->worldToCoord(*(g_xy), &c_lambda);
	  if (outside >= 0) {
	    ERROR("outside curved boundary child 0\n");
	  }
	} else {
	  c_lambda[0] = lambda[2];
	  c_lambda[1] = lambda[0] - lambda[1];
	  c_lambda[2] = 2.0 * lambda[1];
	}
      } else {
	c_el_info->fillElInfo(1, el_info);
	if (el->isNewCoordSet()) {
	  outside = c_el_info->worldToCoord(*(g_xy), &c_lambda);
	  if (outside >= 0) {
	    ERROR("outside curved boundary child 1\n");
	  }
	} else {
	  c_lambda[0] = lambda[1] - lambda[0];
	  c_lambda[1] = lambda[2];
	  c_lambda[2] = 2.0 * lambda[0];
	}
      }
    } /* DIM == 2 */

    if (dim == 3) {
      if (el->isNewCoordSet()) {
	if (lambda[0] >= lambda[1])
	  ichild = 0;
	else
	  ichild = 1;
	c_el_info->fillElInfo(ichild, el_info);
	c_outside = c_el_info->worldToCoord(*(g_xy), &c_lambda);

	if (c_outside>=0) {  /* test is other child is better... */
	  DimVec<double> c_lambda2(dim, NO_INIT);
	  int c_outside2;
	  ElInfo *c_el_info2 = createNewElInfo();

	  c_el_info2->fillElInfo(1-ichild, el_info);
	  c_outside2 = c_el_info2->worldToCoord(*(g_xy), &c_lambda2);

	  MSG("new_coord CHILD %d: outside=%d, lambda=(%.2f %.2f %.2f %.2f)\n",
	      ichild, c_outside, c_lambda[0],c_lambda[1],c_lambda[2],c_lambda[3]);
	  MSG("new_coord CHILD %d: outside=%d, lambda=(%.2f %.2f %.2f %.2f)\n",
	      1-ichild, c_outside2, c_lambda2[0],c_lambda2[1],c_lambda2[2],
	      c_lambda2[3]);

	  if ((c_outside2 < 0) || (c_lambda2[c_outside2] > c_lambda[c_outside])) {
	    for (int i = 0; i <= dim; i++) {
	      c_lambda[i] = c_lambda2[i];
	    }
	    c_outside = c_outside2;
	    *c_el_info = *c_el_info2;
	    ichild = 1 - ichild;
	  }
	  DELETE c_el_info2;
	}
	outside = c_outside;
      } else {  /* no new_coord */
	if (lambda[0] >= lambda[1]) {
	  c_el_info->fillElInfo(0, el_info);
	  c_lambda[0] = lambda[0] - lambda[1];
	  c_lambda[1] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
							getType()][0][1]];
	  c_lambda[2] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
							getType()][0][2]];
	  c_lambda[3] = 2.0 * lambda[1];
	} else {
	  c_el_info->fillElInfo(1, el_info);
	  c_lambda[0] = lambda[1] - lambda[0];
	  c_lambda[1] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
							getType()][1][1]];
	  c_lambda[2] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
							getType()][1][2]];
	  c_lambda[3] = 2.0 * lambda[0];
	}
      }
    }  /* DIM == 3 */

    inside = findElementAtPointRecursive(c_el_info, c_lambda, outside, 
					 final_el_info);
    DELETE c_el_info;

    return inside; 
  }


  void Mesh::setDiameter(const WorldVector<double>& w) 
  { 
    diam = w; 
  }

  void Mesh::setDiameter(int i, double w) 
  { 
    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();

    // write name
    out << name << "\n";

    // write dim
    out.write(reinterpret_cast<const char*>(&dim), sizeof(int));

    // write nVertices
    out.write(reinterpret_cast<const char*>(&nVertices), sizeof(int));

    // write nEdges
    out.write(reinterpret_cast<const char*>(&nEdges), sizeof(int));

    // write nLeaves
    out.write(reinterpret_cast<const char*>(&nLeaves), sizeof(int));

    // write nElements
    out.write(reinterpret_cast<const char*>(&nElements), sizeof(int));

    // write nFaces
    out.write(reinterpret_cast<const char*>(&nFaces), sizeof(int));

    // write maxEdgeNeigh
    out.write(reinterpret_cast<const char*>(&maxEdgeNeigh), sizeof(int));

    // write diam
    diam.serialize(out);

    // write preserveCoarseDOFs
    out.write(reinterpret_cast<const char*>(&preserveCoarseDOFs), sizeof(bool));

    // write nDOFEl
    out.write(reinterpret_cast<const char*>(&nDOFEl), sizeof(int));

    // write nDOF
    nDOF.serialize(out);

    // write nNodeEl
    out.write(reinterpret_cast<const char*>(&nNodeEl), sizeof(int));

    // write node
    node.serialize(out);

    // write admins
    int i, size = static_cast<int>(admin.size());
    out.write(reinterpret_cast<const char*>(&size), sizeof(int));
    for (i = 0; i < size; i++) {
      admin[i]->serialize(out);
    }

    // write macroElements
    size = static_cast<int>(macroElements.size());
    out.write(reinterpret_cast<const char*>(&size), sizeof(int));
    for (i = 0; i < size; i++) {
      macroElements[i]->serialize(out);
    }

    // write elementIndex
    out.write(reinterpret_cast<const char*>(&elementIndex), sizeof(int));

    // write initialized
    out.write(reinterpret_cast<const char*>(&initialized), sizeof(bool));

    serializedDOFs.clear();
  }

  void Mesh::deserialize(std::istream &in)
  {
    serializedDOFs.clear();

    // read name
    in >> name;
    in.get();

    // read dim
    int oldVal = dim;
    in.read(reinterpret_cast<char*>(&dim), sizeof(int));
    TEST_EXIT_DBG((oldVal == 0) || (dim == oldVal))("invalid dimension\n");

    // read nVertices
    in.read(reinterpret_cast<char*>(&nVertices), sizeof(int));

    // read nEdges
    in.read(reinterpret_cast<char*>(&nEdges), sizeof(int));

    // read nLeaves
    in.read(reinterpret_cast<char*>(&nLeaves), sizeof(int));

    // read nElements
    in.read(reinterpret_cast<char*>(&nElements), sizeof(int));

    // read nFaces
    in.read(reinterpret_cast<char*>(&nFaces), sizeof(int));

    // read maxEdgeNeigh
    in.read(reinterpret_cast<char*>(&maxEdgeNeigh), sizeof(int));

    // diam
    diam.deserialize(in);

    // read preserveCoarseDOFs
    in.read(reinterpret_cast<char*>(&preserveCoarseDOFs), sizeof(bool));

    // read nDOFEl
    oldVal = nDOFEl;
    in.read(reinterpret_cast<char*>(&nDOFEl), sizeof(int));
    TEST_EXIT_DBG((oldVal == 0) || (nDOFEl == oldVal))("invalid nDOFEl\n");

    // read nDOF
    nDOF.deserialize(in);

    // read nNodeEl
    oldVal = nNodeEl;
    in.read(reinterpret_cast<char*>(&nNodeEl), sizeof(int));
    TEST_EXIT_DBG((oldVal == 0) || (nNodeEl == oldVal))("invalid nNodeEl\n");

    // read node
    node.deserialize(in);

    // read admins
    int i, size;
    in.read(reinterpret_cast<char*>(&size), sizeof(int));
    admin.resize(size, NULL);
    for (i = 0; i < size; i++) {
      if (!admin[i]) {
	admin[i] = NEW DOFAdmin(this);
      }
      admin[i]->deserialize(in);
    }

    // read macroElements
    in.read(reinterpret_cast<char*>(&size), sizeof(int));

    std::vector< std::vector<int> > neighbourIndices(size);

    for (i = 0; i < static_cast<int>(macroElements.size()); i++) {
      if (macroElements[i]) {
	DELETE macroElements[i];
      }
    }
    macroElements.resize(size);
    for(i = 0; i < size; i++) {
      macroElements[i] = NEW MacroElement(dim);
      macroElements[i]->writeNeighboursTo(&(neighbourIndices[i]));
      macroElements[i]->deserialize(in);
    }

    // read elementIndex
    in.read(reinterpret_cast<char*>(&elementIndex), sizeof(int));

    // read initialized
    in.read(reinterpret_cast<char*>(&initialized), sizeof(bool));

    // set neighbour pointer in macro elements
    int j, neighs = getGeo(NEIGH);
    for(i = 0; i < static_cast<int>(macroElements.size()); i++) {
      for(j = 0; j < neighs; j++) {
	int index = neighbourIndices[i][j];
	if(index != -1) {
	  macroElements[i]->setNeighbour(j, macroElements[index]);
	} else {
	  macroElements[i]->setNeighbour(j, NULL);
	}
      }
    }

    // set mesh pointer in elements
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(this, -1, CALL_EVERY_EL_PREORDER);
    while(elInfo) {
      elInfo->getElement()->setMesh(this);
      elInfo = stack.traverseNext(elInfo);
    }

    serializedDOFs.clear();
  }

  void Mesh::initialize() 
  {
    std::string macroFilename("");
    std::string valueFilename("");
    std::string periodicFile("");
    int check = 1;

    GET_PARAMETER(0, name + "->macro file name",  &macroFilename);
    GET_PARAMETER(0, name + "->value file name",  &valueFilename);
    GET_PARAMETER(0, name + "->periodic file", &periodicFile);
    GET_PARAMETER(0, name + "->check", "%d", &check);
    GET_PARAMETER(0, name + "->preserve coarse dofs", "%d", &preserveCoarseDOFs);

    if (macroFilename.length()) {
      macroFileInfo = MacroReader::readMacro(macroFilename.c_str(), this,
					     periodicFile == "" ? NULL : periodicFile.c_str(),
					     check);

      // If there is no value file which should be written, we can delete
      // the information of the macro file.
      if (!valueFilename.length()) {
	clearMacroFileInfo();
      }
    }

    initialized = true;
  }

  bool Mesh::associated(DegreeOfFreedom dof1, DegreeOfFreedom dof2) {
    std::map<BoundaryType, VertexVector*>::iterator it;
    std::map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
    for (it = periodicAssociations.begin(); it != end; ++it) {
      if ((*(it->second))[dof1] == dof2)
	return true;
    }
    return false;
  }

  bool Mesh::indirectlyAssociated(DegreeOfFreedom dof1, DegreeOfFreedom dof2) {
    std::vector<DegreeOfFreedom> associatedToDOF1;
    std::map<BoundaryType, VertexVector*>::iterator it;
    std::map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
    DegreeOfFreedom dof, assDOF;

    associatedToDOF1.push_back(dof1);
    for (it = periodicAssociations.begin(); it != end; ++it) {
      int size = static_cast<int>(associatedToDOF1.size());
      for (int i = 0; i < size; i++) {
	dof = associatedToDOF1[i];
	assDOF = (*(it->second))[dof];
	if (assDOF == dof2) {
	  return true;
	} else {
	  if (assDOF != dof) 
	    associatedToDOF1.push_back(assDOF);
	}
      }
    }
    return false;
  }

  void Mesh::clearMacroFileInfo()
  {
    macroFileInfo->clear(getNumberOfEdges(),
			 getNumberOfVertices());
    DELETE macroFileInfo;
    macroFileInfo = NULL;
  }

  int Mesh::calcMemoryUsage()
  {
    int result = sizeof(Mesh);

    for (int i = 0; i < static_cast<int>(macroElements.size()); i++) {
      result += macroElements[i]->calcMemoryUsage();
    }
    
    return result;
  }
}