// Gmsh - Copyright (C) 1997-2013 C. Geuzaine, J.-F. Remacle
//
// See the LICENSE.txt file for license information. Please report all
// bugs and problems to the public mailing list <gmsh@geuz.org>.

#include <limits>
#include <stdlib.h>
#include <sstream>
#include <stack>
#include "GmshConfig.h"
#include "GmshMessage.h"
#include "GModel.h"
#include "GModelFactory.h"
#include "GFaceCompound.h"
#include "GEdgeCompound.h"
#include "MPoint.h"
#include "MLine.h"
#include "MTriangle.h"
#include "MQuadrangle.h"
#include "MTetrahedron.h"
#include "MHexahedron.h"
#include "MPrism.h"
#include "MPyramid.h"
#include "MElementCut.h"
#include "MElementOctree.h"
#include "discreteRegion.h"
#include "discreteFace.h"
#include "discreteEdge.h"
#include "discreteVertex.h"
#include "gmshSurface.h"
#include "Geo.h"
#include "SmoothData.h"
#include "Context.h"
#include "OS.h"
#include "GEdgeLoop.h"
#include "MVertexPositionSet.h"
#include "OpenFile.h"
#include "CreateFile.h"
#include "Options.h"
#include "meshGEdge.h"
#include "meshGFace.h"
#include "meshGRegion.h"

#if defined(HAVE_MESH)
#include "Field.h"
#include "Generator.h"
#include "meshGFaceOptimize.h"
#include "meshPartition.h"
#include "HighOrder.h"
#include "meshMetric.h"
#include "meshGRegionMMG3D.h"
#include "meshGFaceBamg.h"
#endif

#if defined(HAVE_KBIPACK)
#include "Homology.h"
#endif

std::vector<GModel*> GModel::list;
int GModel::_current = -1;

GModel::GModel(std::string name)
  : _maxVertexNum(0), _maxElementNum(0),
    _checkPointedMaxVertexNum(0), _checkPointedMaxElementNum(0),
    _name(name), _visible(1), _octree(0), _geo_internals(0),
    _occ_internals(0), _acis_internals(0), _fm_internals(0),
    _factory(0), _fields(0), _currentMeshEntity(0), normals(0)
{
  partitionSize[0] = 0; partitionSize[1] = 0;

  // hide all other models
  for(unsigned int i = 0; i < list.size(); i++)
    list[i]->setVisibility(0);

  // push new one into the list
  list.push_back(this);

  // at the moment we always create (at least an empty) GEO model
  _createGEOInternals();

#if defined(HAVE_OCC)
  setFactory("OpenCASCADE");
#else
  setFactory("Gmsh");
#endif

#if defined(HAVE_MESH)
  _fields = new FieldManager();
#endif
}

GModel::~GModel()
{
  std::vector<GModel*>::iterator it = std::find(list.begin(), list.end(), this);
  if(it != list.end()) list.erase(it);

  if(getVisibility()){
    // if no other model is visible, make the last one visible
    bool othervisible = false;
    for(unsigned int i = 0; i < list.size(); i++){
      if(list[i]->getVisibility()) othervisible = true;
    }
    if(!othervisible && list.size())
      list.back()->setVisibility(1);
  }

  destroy();
  _deleteGEOInternals();
  _deleteOCCInternals();
#if defined(HAVE_MESH)
  delete _fields;
#endif
  if(_factory)
    delete _factory;
}

GModel *GModel::current(int index)
{
  if(list.empty()){
    Msg::Info("No current model available: creating one");
    new GModel();
  }
  if(index >= 0) _current = index;
  if(_current < 0 || _current >= (int)list.size()) return list.back();
  return list[_current];
}

int GModel::setCurrent(GModel *m)
{
  for (unsigned int i = 0; i < list.size(); i++){
    if (list[i] == m){
      _current = i;
      break;
    }
  }
  return _current;
}

void GModel::setFactory(std::string name)
{
  if(_factory) delete _factory;
  if(name == "OpenCASCADE"){
#if defined(HAVE_OCC)
    _factory = new OCCFactory();
#else
    Msg::Error("Missing OpenCASCADE support: using Gmsh GEO factory instead");
    _factory = new GeoFactory();
#endif
  }
  else{
    _factory = new GeoFactory();
  }
}

GModel *GModel::findByName(const std::string &name, const std::string &fileName)
{
  // return last mesh with given name
  for(int i = list.size() - 1; i >= 0; i--)
    if(list[i]->getName() == name &&
       (fileName.empty() || !list[i]->hasFileName(fileName))) return list[i];
  return 0;
}

void GModel::destroy()
{
  _name.clear();
  _fileNames.clear();

  _maxVertexNum = _maxElementNum = 0;
  _checkPointedMaxVertexNum = _checkPointedMaxElementNum = 0;

  for(riter it = firstRegion(); it != lastRegion(); ++it)
    delete *it;
  regions.clear();

  std::vector<GFace*> to_keep;
  for(fiter it = firstFace(); it != lastFace(); ++it){
    // projection faces are persistent
    if((*it)->getNativeType() == GEntity::UnknownModel &&
       (*it)->geomType() == GEntity::ProjectionFace)
      to_keep.push_back(*it);
    else
      delete *it;
  }
  faces.clear();
  faces.insert(to_keep.begin(), to_keep.end());

  for(eiter it = firstEdge(); it != lastEdge(); ++it)
    delete *it;
  edges.clear();

  for(viter it = firstVertex(); it != lastVertex(); ++it)
    delete *it;
  vertices.clear();

  destroyMeshCaches();

  if(normals) delete normals;
  normals = 0;

#if defined(HAVE_MESH)
  _fields->reset();
#endif
  gmshSurface::reset();
}

void GModel::destroyMeshCaches()
{
  _vertexVectorCache.clear();
  _vertexMapCache.clear();
  _elementVectorCache.clear();
  _elementMapCache.clear();
  _elementIndexCache.clear();
  delete _octree;
  _octree = 0;
}

void GModel::deleteMesh()
{
  for(riter it = firstRegion(); it != lastRegion();++it)
    (*it)->deleteMesh();
  for(fiter it = firstFace(); it != lastFace();++it)
    (*it)->deleteMesh();
  for(eiter it = firstEdge(); it != lastEdge();++it)
    (*it)->deleteMesh();
  for(viter it = firstVertex(); it != lastVertex();++it)
    (*it)->deleteMesh();
  destroyMeshCaches();
}

bool GModel::empty() const
{
  return vertices.empty() && edges.empty() && faces.empty() && regions.empty();
}

std::vector<GRegion*> GModel::bindingsGetRegions()
{
  return std::vector<GRegion*> (regions.begin(), regions.end());
}

std::vector<GFace*> GModel::bindingsGetFaces()
{
  return std::vector<GFace*> (faces.begin(), faces.end());
}

std::vector<GEdge*> GModel::bindingsGetEdges()
{
  return std::vector<GEdge*> (edges.begin(), edges.end());
}

std::vector<GVertex*> GModel::bindingsGetVertices()
{
  return std::vector<GVertex*> (vertices.begin(), vertices.end());
}

GRegion *GModel::getRegionByTag(int n) const
{
  GEntity tmp((GModel*)this, n);
  std::set<GRegion*, GEntityLessThan>::const_iterator it = regions.find((GRegion*)&tmp);
  if(it != regions.end())
    return *it;
  else
    return 0;
}

GFace *GModel::getFaceByTag(int n) const
{
  GEntity tmp((GModel*)this, n);
  std::set<GFace*, GEntityLessThan>::const_iterator it = faces.find((GFace*)&tmp);
  if(it != faces.end())
    return *it;
  else
    return 0;
}

GEdge *GModel::getEdgeByTag(int n) const
{
  GEntity tmp((GModel*)this, n);
  std::set<GEdge*, GEntityLessThan>::const_iterator it = edges.find((GEdge*)&tmp);
  if(it != edges.end())
    return *it;
  else
    return 0;
}

GVertex *GModel::getVertexByTag(int n) const
{
  GEntity tmp((GModel*)this, n);
  std::set<GVertex*, GEntityLessThan>::const_iterator it = vertices.find((GVertex*)&tmp);
  if(it != vertices.end())
    return *it;
  else
    return 0;
}

std::vector<int> GModel::getEdgesByStringTag(const std::string tag)
{
  std::vector<int> nums;
  std::map<int, std::vector<GEntity*> > physicalGroups[4];
  getPhysicalGroups(physicalGroups);
  std::vector<GEntity*> allEdges = physicalGroups[1][this->getPhysicalNumber(1,tag)];
  for ( std::vector<GEntity*>::iterator it = allEdges.begin(); it != allEdges.end(); it++){
    GEntity *ge = *it;
    nums.push_back(ge->tag());
  }

  return nums;
}

void GModel::remove(GRegion *r)
{
  riter it = std::find(firstRegion(), lastRegion(), r);
  if(it != (riter)regions.end()) regions.erase(it);
}

void GModel::remove(GFace *f)
{
  fiter it = std::find(firstFace(), lastFace(), f);
  if(it != faces.end()) faces.erase(it);
}

void GModel::remove(GEdge *e)
{
  eiter it = std::find(firstEdge(), lastEdge(), e);
  if(it != edges.end()) edges.erase(it);
}

void GModel::remove(GVertex *v)
{
  viter it = std::find(firstVertex(), lastVertex(), v);
  if(it != vertices.end()) vertices.erase(it);
}

void GModel::snapVertices()
{
  viter vit = firstVertex();

  double tol = CTX::instance()->geom.tolerance;

  while (vit != lastVertex()){
    std::list<GEdge*> edges = (*vit)->edges();
    for (std::list<GEdge*>::iterator it = edges.begin(); it != edges.end(); ++it){
      Range<double> parb = (*it)->parBounds(0);
      double t;
      if ((*it)->getBeginVertex() == *vit){
        t = parb.low();
      }
      else if ((*it)->getEndVertex() == *vit){
        t = parb.high();
      }
      else{
        Msg::Error("Weird vertex: impossible to snap");
        break;
      }
      GPoint gp = (*it)->point(t);
      double d = sqrt((gp.x() - (*vit)->x()) * (gp.x() - (*vit)->x()) +
                      (gp.y() - (*vit)->y()) * (gp.y() - (*vit)->y()) +
                      (gp.z() - (*vit)->z()) * (gp.z() - (*vit)->z()));
      if (d > tol){
        (*vit)->setPosition(gp);
        Msg::Info("Snapping geometry vertex %d to curve control point (dist = %g)",
                  (*vit)->tag(), d);
      }
    }
    vit++;
  }
}

void GModel::getEntities(std::vector<GEntity*> &entities) const
{
  entities.clear();
  entities.insert(entities.end(), vertices.begin(), vertices.end());
  entities.insert(entities.end(), edges.begin(), edges.end());
  entities.insert(entities.end(), faces.begin(), faces.end());
  entities.insert(entities.end(), regions.begin(), regions.end());
}

int GModel::getMaxElementaryNumber(int dim)
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  int num = 0;
  for(unsigned int i = 0; i < entities.size(); i++)
    if(dim < 0 || entities[i]->dim() == dim)
      num = std::max(num, std::abs(entities[i]->tag()));
  return num;
}

bool GModel::noPhysicalGroups()
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  for(unsigned int i = 0; i < entities.size(); i++)
    if(entities[i]->physicals.size()) return false;
  return true;
}

void GModel::getPhysicalGroups(std::map<int, std::vector<GEntity*> > groups[4])
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  for(unsigned int i = 0; i < entities.size(); i++){
    std::map<int, std::vector<GEntity*> > &group(groups[entities[i]->dim()]);
    for(unsigned int j = 0; j < entities[i]->physicals.size(); j++){
      // physicals can be stored with negative signs when the entity
      // should be "reversed"
      int p = std::abs(entities[i]->physicals[j]);
      if(std::find(group[p].begin(), group[p].end(), entities[i]) == group[p].end())
        group[p].push_back(entities[i]);
    }
  }
}

void GModel::deletePhysicalGroups()
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  for(unsigned int i = 0; i < entities.size(); i++)
    entities[i]->physicals.clear();
}

void GModel::deletePhysicalGroup(int dim, int num)
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  for(unsigned int i = 0; i < entities.size(); i++){
    if(dim == entities[i]->dim()){
      std::vector<int> p;
      for(unsigned int j = 0; j < entities[i]->physicals.size(); j++)
        if(entities[i]->physicals[j] != num)
          p.push_back(entities[i]->physicals[j]);
      entities[i]->physicals = p;
    }
  }
}

int GModel::getMaxPhysicalNumber(int dim)
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  int num = 0;
  for(unsigned int i = 0; i < entities.size(); i++)
    if(entities[i]->dim() == dim)
      for(unsigned int j = 0; j < entities[i]->physicals.size(); j++)
        num = std::max(num, std::abs(entities[i]->physicals[j]));
  return num;
}

int GModel::setPhysicalName(std::string name, int dim, int number)
{
  // check if the name is already used
  piter it = physicalNames.begin();
  while(it != physicalNames.end()){
    if(name == it->second && dim == it->first.first) return it->first.second;
    ++it;
  }
  // if no number is given, find the next available one
  if(!number) number = getMaxPhysicalNumber(dim) + 1;
  physicalNames[std::pair<int, int>(dim, number)] = name;
  return number;
}

std::string GModel::getPhysicalName(int dim, int number)
{
  //Emi debug here
  // printf("getPhysName size %d \n", physicalNames.size());
  // std::map<std::pair<int, int>, std::string>::iterator itt = physicalNames.begin();
  // for (; itt != physicalNames.end(); itt++){
  //   printf("name %s \n", itt->second.c_str());
  //   printf("par (%d,%d) \n", itt->first.first, itt->first.second);
  // }

  std::map<std::pair<int, int>, std::string>::iterator it =
    physicalNames.find(std::pair<int, int>(dim, number));
  if(it != physicalNames.end()) return it->second;
  return "";
}

int GModel::getPhysicalNumber(const int &dim, const std::string &name)
{
  for(piter physIt = firstPhysicalName(); physIt != lastPhysicalName(); ++physIt)
    if(dim == physIt->first.first && name == physIt->second)
      return physIt->first.second;
  Msg::Warning("No physical group found with the name '%s'", name.c_str());
  return -1;
}

int GModel::getDim() const
{
  if(getNumRegions() > 0) return 3;
  if(getNumFaces() > 0) return 2;
  if(getNumEdges() > 0) return 1;
  if(getNumVertices() > 0) return 0;
  Msg::Warning("The model is empty, dim = -1");
  return -1;
}

std::string GModel::getElementaryName(int dim, int number)
{
  std::map<std::pair<int, int>, std::string>::iterator it =
    elementaryNames.find(std::pair<int, int>(dim, number));
  if(it != elementaryNames.end()) return it->second;
  return "";
}

void GModel::setSelection(int val)
{
  std::vector<GEntity*> entities;
  getEntities(entities);

  for(unsigned int i = 0; i < entities.size(); i++){
    entities[i]->setSelection(val);
    // reset selection in elements (stored in the visibility flag to
    // save space)
    if(val == 0){
      for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++)
        if(entities[i]->getMeshElement(j)->getVisibility() == 2)
          entities[i]->getMeshElement(j)->setVisibility(1);
    }
  }
}

SBoundingBox3d GModel::bounds(bool aroundVisible)
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  // using the mesh vertices for now; should use entities[i]->bounds() instead
  SBoundingBox3d bb;
  for(unsigned int i = 0; i < entities.size(); i++)
    if(!aroundVisible || entities[i]->getVisibility()){
      if(entities[i]->dim() == 0)
        bb += static_cast<GVertex*>(entities[i])->xyz();
      else
        for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++)
          bb += entities[i]->mesh_vertices[j]->point();
    }
  return bb;
}

int GModel::mesh(int dimension)
{
#if defined(HAVE_MESH)
  GenerateMesh(this, dimension);
  return true;
#else
  Msg::Error("Mesh module not compiled");
  return false;
#endif
}

int GModel::adaptMesh(std::vector<int> technique,
                      std::vector<simpleFunction<double>* > f,
                      std::vector<std::vector<double> > parameters,
                      int niter, bool meshAll)
{
#if defined(HAVE_MESH)

  // copy context (in order to allow multiple calls)
  CTX _backup = *(CTX::instance());

  if (getNumMeshElements() == 0) mesh(getDim());
  int nbElemsOld = getNumMeshElements();
  int nbElems;

  FieldManager *fields = getFields();
  fields->reset();

  int ITER = 0;
  if (meshAll){

    while(1){
      Msg::Info("-- adaptMesh (allDim) ITER =%d ", ITER);

      fields->reset();
      meshMetric *metric = new meshMetric(this);
      for (unsigned int imetric = 0; imetric < technique.size(); imetric++){
        metric->addMetric(technique[imetric], f[imetric], parameters[imetric]);
      }
      fields->setBackgroundField(metric);

      opt_mesh_lc_integration_precision(0, GMSH_SET, 1.e-4);
      opt_mesh_algo2d(0, GMSH_SET, 7.0); //bamg
      opt_mesh_algo3d(0, GMSH_SET, 7.0); //mmg3d
      opt_mesh_lc_from_points(0, GMSH_SET, 0.0); //do not mesh lines with lc

      std::for_each(firstRegion(), lastRegion(), deMeshGRegion());
      std::for_each(firstFace(), lastFace(), deMeshGFace());
      std::for_each(firstEdge(), lastEdge(), deMeshGEdge());

      GenerateMesh(this, getDim());
      nbElems = getNumMeshElements();

      char name[256];
      sprintf(name, "meshAdapt-%d.msh", ITER);
      writeMSH(name);
      //metric->exportInfo(name);

      if (ITER++ >= niter)  break;
      if (ITER > 3 && fabs((double)(nbElems - nbElemsOld)) < 0.01 * nbElemsOld) break;

      nbElemsOld = nbElems;
    }
  }
  //adapt only upper most dimension
  else{

    while(1) {
      Msg::Info("-- adaptMesh ITER =%d ", ITER);
      std::vector<MElement*> elements;

      if (getDim() == 2){
        for (fiter fit = firstFace(); fit != lastFace(); ++fit){
          if ((*fit)->quadrangles.size())return -1;
          for (unsigned i=0;i<(*fit)->triangles.size();i++){
            elements.push_back((*fit)->triangles[i]);
          }
        }
      }
      else if (getDim() == 3){
        for (riter rit = firstRegion(); rit != lastRegion(); ++rit){
          if ((*rit)->hexahedra.size())return -1;
          for (unsigned i=0;i<(*rit)->tetrahedra.size();i++){
            elements.push_back((*rit)->tetrahedra[i]);
          }
        }
      }

      if (elements.size() == 0) return -1;

      fields->reset();
      meshMetric *metric = new meshMetric(this);
      for (unsigned int imetric = 0; imetric < technique.size(); imetric++){
        metric->addMetric(technique[imetric], f[imetric], parameters[imetric]);
      }
      fields->setBackgroundField(metric);

      if (getDim() == 2){
        for (fiter fit = firstFace(); fit != lastFace(); ++fit){
          if((*fit)->geomType() != GEntity::DiscreteSurface){
            meshGFaceBamg(*fit);
            laplaceSmoothing(*fit,CTX::instance()->mesh.nbSmoothing);
          }
          if(_octree) delete _octree;
          _octree = 0;
        }
      }
      else if (getDim() == 3){
        for (riter rit = firstRegion(); rit != lastRegion(); ++rit){
          refineMeshMMG(*rit);
          if(_octree) delete _octree;
          _octree = 0;
        }
      }

      char name[256];
      sprintf(name, "meshAdapt-%d.msh", ITER);
      writeMSH(name);

      nbElems = getNumMeshElements();
      if (++ITER >= niter) break;
      if (ITER > 3 && fabs((double)(nbElems - nbElemsOld)) < 0.01 * nbElemsOld) break;

      nbElemsOld = nbElems;
    }
  }

  fields->reset();
  // copy context (in order to allow multiple calls)
  *(CTX::instance()) = _backup ;


  return 0;
#else
  Msg::Error("Mesh module not compiled");
  return -1;
#endif
}

int GModel::refineMesh(int linear)
{
#if defined(HAVE_MESH)
  RefineMesh(this, linear);
  return true;
#else
  Msg::Error("Mesh module not compiled");
  return false;
#endif
}

int GModel::setOrderN(int order, int linear, int incomplete)
{
#if defined(HAVE_MESH)
  SetOrderN(this, order, linear, incomplete);
  return true;
#else
  Msg::Error("Mesh module not compiled");
  return false;
#endif
}

int GModel::getMeshStatus(bool countDiscrete)
{
  for(riter it = firstRegion(); it != lastRegion(); ++it)
    if((countDiscrete || ((*it)->geomType() != GEntity::DiscreteVolume &&
                          (*it)->meshAttributes.method != MESH_NONE)) &&
       ((*it)->tetrahedra.size() ||(*it)->hexahedra.size() ||
        (*it)->prisms.size() || (*it)->pyramids.size() ||
        (*it)->polyhedra.size())) return 3;
  for(fiter it = firstFace(); it != lastFace(); ++it)
    if((countDiscrete || ((*it)->geomType() != GEntity::DiscreteSurface &&
                          (*it)->meshAttributes.method != MESH_NONE)) &&
       ((*it)->triangles.size() || (*it)->quadrangles.size() ||
        (*it)->polygons.size())) return 2;
  for(eiter it = firstEdge(); it != lastEdge(); ++it)
    if((countDiscrete || ((*it)->geomType() != GEntity::DiscreteCurve &&
                          (*it)->meshAttributes.method != MESH_NONE)) &&
       (*it)->lines.size()) return 1;
  for(viter it = firstVertex(); it != lastVertex(); ++it)
    if((*it)->mesh_vertices.size()) return 0;
  return -1;
}

int GModel::getNumMeshVertices() const
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  unsigned int n = 0;
  for(unsigned int i = 0; i < entities.size(); i++)
    n += entities[i]->mesh_vertices.size();
  return n;
}

int GModel::getNumMeshElements()
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  unsigned int n = 0;
  for(unsigned int i = 0; i < entities.size(); i++)
    n += entities[i]->getNumMeshElements();
  return n;
}

int GModel::getNumMeshParentElements()
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  unsigned int n = 0;
  for(unsigned int i = 0; i < entities.size(); i++)
    n += entities[i]->getNumMeshParentElements();
  return n;
}

int GModel::getNumMeshElements(unsigned c[5])
{
  c[0] = 0; c[1] = 0; c[2] = 0; c[3] = 0; c[4] = 0;
  for(riter it = firstRegion(); it != lastRegion(); ++it)
    (*it)->getNumMeshElements(c);
  if(c[0] + c[1] + c[2] + c[3] + c[4]) return 3;
  for(fiter it = firstFace(); it != lastFace(); ++it)
    (*it)->getNumMeshElements(c);
  if(c[0] + c[1] + c[2]) return 2;
  for(eiter it = firstEdge(); it != lastEdge(); ++it)
    (*it)->getNumMeshElements(c);
  if(c[0]) return 1;
  return 0;
}

MElement *GModel::getMeshElementByCoord(SPoint3 &p, int dim, bool strict)
{
  if(!_octree){
    Msg::Debug("Rebuilding mesh element octree");
    _octree = new MElementOctree(this);
  }
  return _octree->find(p.x(), p.y(), p.z(), dim, strict);
}

std::vector<MElement*> GModel::getMeshElementsByCoord(SPoint3 &p, int dim, bool strict)
{
  if(!_octree){
    Msg::Debug("Rebuilding mesh element octree");
    _octree = new MElementOctree(this);
  }
  return _octree->findAll(p.x(), p.y(), p.z(), dim, strict);
}

MVertex *GModel::getMeshVertexByTag(int n)
{
  if(_vertexVectorCache.empty() && _vertexMapCache.empty()){
    Msg::Debug("Rebuilding mesh vertex cache");
    _vertexVectorCache.clear();
    _vertexMapCache.clear();
    bool dense = (getNumMeshVertices() == _maxVertexNum);
    std::vector<GEntity*> entities;
    getEntities(entities);
    if(dense){
      Msg::Debug("Good: we have a dense vertex numbering in the cache");
      // numbering starts at 1
      _vertexVectorCache.resize(_maxVertexNum + 1);
      for(unsigned int i = 0; i < entities.size(); i++)
        for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++)
          _vertexVectorCache[entities[i]->mesh_vertices[j]->getNum()] =
            entities[i]->mesh_vertices[j];
    }
    else{
      for(unsigned int i = 0; i < entities.size(); i++)
        for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++)
          _vertexMapCache[entities[i]->mesh_vertices[j]->getNum()] =
            entities[i]->mesh_vertices[j];
    }
  }

  if(n < (int)_vertexVectorCache.size())
    return _vertexVectorCache[n];
  else
    return _vertexMapCache[n];
}

void GModel::getMeshVerticesForPhysicalGroup(int dim, int num, std::vector<MVertex*> &v)
{
  v.clear();
  std::map<int, std::vector<GEntity*> > groups[4];
  getPhysicalGroups(groups);
  std::map<int, std::vector<GEntity*> >::const_iterator it = groups[dim].find(num);
  if(it == groups[dim].end()) return;
  const std::vector<GEntity *> &entities = it->second;
  std::set<MVertex*> sv;
  for(unsigned int i = 0; i < entities.size(); i++){
    if(dim == 0){
      GVertex *g = (GVertex*)entities[i];
      sv.insert(g->mesh_vertices[0]);
    }
    else{
      for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
        MElement *e = entities[i]->getMeshElement(j);
        for(int k = 0; k < e->getNumVertices(); k++)
          sv.insert(e->getVertex(k));
      }
    }
  }
  v.insert(v.begin(), sv.begin(), sv.end());
}

MElement *GModel::getMeshElementByTag(int n)
{
  if(_elementVectorCache.empty() && _elementMapCache.empty()){
    Msg::Debug("Rebuilding mesh element cache");
    _elementVectorCache.clear();
    _elementMapCache.clear();
    bool dense = (getNumMeshElements() == _maxElementNum);
    std::vector<GEntity*> entities;
    getEntities(entities);
    if(dense){
      Msg::Debug("Good: we have a dense element numbering in the cache");
      // numbering starts at 1
      _elementVectorCache.resize(_maxElementNum + 1);
      for(unsigned int i = 0; i < entities.size(); i++)
        for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
          MElement *e = entities[i]->getMeshElement(j);
          _elementVectorCache[e->getNum()] = e;
        }
    }
    else{
      for(unsigned int i = 0; i < entities.size(); i++)
        for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
          MElement *e = entities[i]->getMeshElement(j);
          _elementMapCache[e->getNum()] = e;
        }
    }
  }

  if(n < (int)_elementVectorCache.size())
    return _elementVectorCache[n];
  else
    return _elementMapCache[n];
}

int GModel::getMeshElementIndex(MElement *e)
{
  if(!e) return 0;
  std::map<int, int>::iterator it = _elementIndexCache.find(e->getNum());
  if(it != _elementIndexCache.end()) return it->second;
  return e->getNum();
}

void GModel::setMeshElementIndex(MElement *e, int index)
{
  _elementIndexCache[e->getNum()] = index;
}

template <class T>
static void removeInvisible(std::vector<T*> &elements, bool all)
{
  std::vector<T*> tmp;
  for(unsigned int i = 0; i < elements.size(); i++){
    if(all || !elements[i]->getVisibility())
      delete elements[i];
    else
      tmp.push_back(elements[i]);
  }
  elements.clear();
  elements = tmp;
}

void GModel::removeInvisibleElements()
{
  for(riter it = firstRegion(); it != lastRegion(); ++it){
    bool all = !(*it)->getVisibility();
    removeInvisible((*it)->tetrahedra, all);
    removeInvisible((*it)->hexahedra, all);
    removeInvisible((*it)->prisms, all);
    removeInvisible((*it)->pyramids, all);
    removeInvisible((*it)->polyhedra, all);
    (*it)->deleteVertexArrays();
  }
  for(fiter it = firstFace(); it != lastFace(); ++it){
    bool all = !(*it)->getVisibility();
    removeInvisible((*it)->triangles, all);
    removeInvisible((*it)->quadrangles, all);
    removeInvisible((*it)->polygons, all);
    (*it)->deleteVertexArrays();
  }
  for(eiter it = firstEdge(); it != lastEdge(); ++it){
    bool all = !(*it)->getVisibility();
    removeInvisible((*it)->lines, all);
    (*it)->deleteVertexArrays();
  }
  destroyMeshCaches();
}

int GModel::indexMeshVertices(bool all, int singlePartition, bool renumber)
{
  std::vector<GEntity*> entities;
  getEntities(entities);

  // tag all mesh vertices with -1 (negative vertices will not be
  // saved)
  for(unsigned int i = 0; i < entities.size(); i++)
    for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++)
      entities[i]->mesh_vertices[j]->setIndex(-1);

  // tag all mesh vertices belonging to elements that need to be saved
  // with 0, or with -2 if they need to be taken into account in the
  // numbering but need not to be saved (because we save a single
  // partition and they are not used in that partition)
  for(unsigned int i = 0; i < entities.size(); i++){
    if(all || entities[i]->physicals.size()){
      for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
        MElement *e = entities[i]->getMeshElement(j);
        for(int k = 0; k < e->getNumVertices(); k++){
          if(singlePartition <= 0 || e->getPartition() == singlePartition)
            e->getVertex(k)->setIndex(0);
          else if(e->getVertex(k)->getIndex() == -1)
            e->getVertex(k)->setIndex(-2);
        }
      }
    }
  }

  // renumber all the mesh vertices tagged with 0
  int numVertices = 0, index = 0;
  for(unsigned int i = 0; i < entities.size(); i++){
    for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++){
      MVertex *v = entities[i]->mesh_vertices[j];
      if(!v->getIndex()){
        index++;
        numVertices++;
        if(renumber)
          v->setIndex(index);
        else
          v->setIndex(v->getNum());
      }
      else if(v->getIndex() == -2)
        index++;
    }
  }

  return numVertices;
}

void GModel::scaleMesh(double factor)
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  for(unsigned int i = 0; i < entities.size(); i++)
    for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++){
      MVertex *v = entities[i]->mesh_vertices[j];
      v->x() *= factor;
      v->y() *= factor;
      v->z() *= factor;
    }
}

void GModel::recomputeMeshPartitions()
{
  meshPartitions.clear();
  std::vector<GEntity*> entities;
  getEntities(entities);
  for(unsigned int i = 0; i < entities.size(); i++){
    for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
      int part = entities[i]->getMeshElement(j)->getPartition();
      if(part)  meshPartitions.insert(part);
    }
  }
}

void GModel::deleteMeshPartitions()
{
  std::vector<GEntity*> entities;
  getEntities(entities);
  for(unsigned int i = 0; i < entities.size(); i++)
    for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++)
      entities[i]->getMeshElement(j)->setPartition(0);
  meshPartitions.clear();
}

void GModel::store(std::vector<MVertex*> &vertices, int dim,
          std::map<int, std::vector<MElement*> > &entityMap,
          std::map<int, std::map<int, std::string> > &physicalMap)
{
  _storeVerticesInEntities(vertices);
  _storeElementsInEntities(entityMap);
  _storePhysicalTagsInEntities(dim, physicalMap);
  _associateEntityWithMeshVertices();
}

void GModel::storeChain(int dim,
                        std::map<int, std::vector<MElement*> > &entityMap,
                        std::map<int, std::map<int, std::string> > &physicalMap)
{
  _storeElementsInEntities(entityMap);
  _storePhysicalTagsInEntities(dim, physicalMap);
  std::map<int, std::vector<MElement*> >::iterator it;
  for(it = entityMap.begin(); it != entityMap.end(); it++) {
    if(dim == 0) _chainVertices.insert(getVertexByTag(it->first));
    else if(dim == 1) _chainEdges.insert(getEdgeByTag(it->first));
    else if(dim == 2) _chainFaces.insert(getFaceByTag(it->first));
    else if(dim == 3) _chainRegions.insert(getRegionByTag(it->first));
  }
}

template<class T>
static void _addElements(std::vector<T*> &dst, const std::vector<MElement*> &src)
{
  for(unsigned int i = 0; i < src.size(); i++) dst.push_back((T*)src[i]);
}

void GModel::_storeElementsInEntities(std::map< int, std::vector<MElement* > >& map)
{
  std::map<int, std::vector<MElement*> >::const_iterator it = map.begin();
  for(; it != map.end(); ++it){
    if(!it->second.size()) continue;
    int type = it->second[0]->getType();
    switch(type){
    case TYPE_PNT:
      {
        GVertex *v = getVertexByTag(it->first);
        if(!v){
          v = new discreteVertex(this, it->first);
          add(v);
        }
        if(!v->points.empty()) { // CAD points already have one by default
          v->points.clear();
          v->mesh_vertices.clear();
        }
        _addElements(v->points, it->second);
      }
      break;
    case TYPE_LIN:
      {
        GEdge *e = getEdgeByTag(it->first);
        if(!e){
          e = new discreteEdge(this, it->first, 0, 0);
          add(e);
        }
        _addElements(e->lines, it->second);
      }
      break;
    case TYPE_TRI: case TYPE_QUA: case TYPE_POLYG:
      {
        GFace *f = getFaceByTag(it->first);
        if(!f){
          f = new discreteFace(this, it->first);
          add(f);
        }
        if(type == TYPE_TRI) _addElements(f->triangles, it->second);
        else if(type == TYPE_QUA) _addElements(f->quadrangles, it->second);
        else _addElements(f->polygons, it->second);
      }
      break;
    case TYPE_TET: case TYPE_HEX: case TYPE_PYR: case TYPE_PRI: case TYPE_POLYH:
      {
        GRegion *r = getRegionByTag(it->first);
        if(!r){
          r = new discreteRegion(this, it->first);
          add(r);
        }
        if(type == TYPE_TET) _addElements(r->tetrahedra, it->second);
        else if(type == TYPE_HEX) _addElements(r->hexahedra, it->second);
        else if(type == TYPE_PRI) _addElements(r->prisms, it->second);
        else if(type == TYPE_PYR) _addElements(r->pyramids, it->second);
        else _addElements(r->polyhedra, it->second);
      }
      break;
    }
  }
}

template<class T>
static void _associateEntityWithElementVertices(GEntity *ge, std::vector<T*> &elements,
                                                bool force=false)
{
  for(unsigned int i = 0; i < elements.size(); i++){
    for(int j = 0; j < elements[i]->getNumVertices(); j++){
      if (force || !elements[i]->getVertex(j)->onWhat() ||
          elements[i]->getVertex(j)->onWhat()->dim() > ge->dim())
        elements[i]->getVertex(j)->setEntity(ge);
    }
  }
}

void GModel::_associateEntityWithMeshVertices()
{
  // loop on regions, then on faces, edges and vertices and store the
  // entity pointer in the the elements' vertices (this way we
  // associate the entity of lowest geometrical degree with each
  // vertex)
  for(riter it = firstRegion(); it != lastRegion(); ++it){
    _associateEntityWithElementVertices(*it, (*it)->tetrahedra);
    _associateEntityWithElementVertices(*it, (*it)->hexahedra);
    _associateEntityWithElementVertices(*it, (*it)->prisms);
    _associateEntityWithElementVertices(*it, (*it)->pyramids);
    _associateEntityWithElementVertices(*it, (*it)->polyhedra);
  }
  for(fiter it = firstFace(); it != lastFace(); ++it){
    _associateEntityWithElementVertices(*it, (*it)->triangles);
    _associateEntityWithElementVertices(*it, (*it)->quadrangles);
    _associateEntityWithElementVertices(*it, (*it)->polygons);
  }
  for(eiter it = firstEdge(); it != lastEdge(); ++it){
    _associateEntityWithElementVertices(*it, (*it)->lines);
  }
  for(viter it = firstVertex(); it != lastVertex(); ++it){
    _associateEntityWithElementVertices(*it, (*it)->points);
  }
}

void GModel::_storeVerticesInEntities(std::map<int, MVertex*> &vertices)
{
  std::map<int, MVertex*>::iterator it = vertices.begin();
  for(; it != vertices.end(); ++it){
    MVertex *v = it->second;
    GEntity *ge = v->onWhat();
    if(ge) ge->mesh_vertices.push_back(v);
    else{
      delete v; // we delete all unused vertices
      it->second = 0;
    }
  }
}

void GModel::_storeVerticesInEntities(std::vector<MVertex*> &vertices)
{
  for(unsigned int i = 0; i < vertices.size(); i++){
    MVertex *v = vertices[i];
    if(v){ // the vector is allowed to have null entries
      GEntity *ge = v->onWhat();
      if(ge) ge->mesh_vertices.push_back(v);
      else{
        delete v; // we delete all unused vertices
        vertices[i] = 0;
      }
    }
  }
}

void GModel::_pruneMeshVertexAssociations()
{
  std::vector<GEntity*> entities;
  std::vector<MVertex*> vertices;
  getEntities(entities);
  for(unsigned int i = 0; i < entities.size(); i++) {
    for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++) {
      MVertex* v = entities[i]->mesh_vertices[j];
      v->setEntity(0);
      vertices.push_back(v);
    }
    entities[i]->mesh_vertices.clear();
  }
  _associateEntityWithMeshVertices();
  // associate mesh vertices primarily with chain entities
  for(riter it = _chainRegions.begin(); it != _chainRegions.end(); ++it){
    _associateEntityWithElementVertices(*it, (*it)->tetrahedra, true);
    _associateEntityWithElementVertices(*it, (*it)->hexahedra, true);
    _associateEntityWithElementVertices(*it, (*it)->prisms, true);
    _associateEntityWithElementVertices(*it, (*it)->pyramids, true);
    _associateEntityWithElementVertices(*it, (*it)->polyhedra, true);
  }
  for(fiter it = _chainFaces.begin(); it != _chainFaces.end(); ++it){
    _associateEntityWithElementVertices(*it, (*it)->triangles, true);
    _associateEntityWithElementVertices(*it, (*it)->quadrangles, true);
    _associateEntityWithElementVertices(*it, (*it)->polygons, true);
  }
  for(eiter it = _chainEdges.begin(); it != _chainEdges.end(); ++it){
    _associateEntityWithElementVertices(*it, (*it)->lines, true);
  }
  for(viter it = _chainVertices.begin(); it != _chainVertices.end(); ++it){
    _associateEntityWithElementVertices(*it, (*it)->points, true);
  }
  _storeVerticesInEntities(vertices);
}

void GModel::_storePhysicalTagsInEntities(int dim,
                                          std::map<int, std::map<int, std::string> > &map)
{
  std::map<int, std::map<int, std::string> >::const_iterator it = map.begin();
  for(; it != map.end(); ++it){
    GEntity *ge = 0;
    switch(dim){
    case 0: ge = getVertexByTag(it->first); break;
    case 1: ge = getEdgeByTag(it->first); break;
    case 2: ge = getFaceByTag(it->first); break;
    case 3: ge = getRegionByTag(it->first); break;
    }
    if(ge){
      std::map<int, std::string>::const_iterator it2 = it->second.begin();
      for(; it2 != it->second.end(); ++it2){
        if(std::find(ge->physicals.begin(), ge->physicals.end(), it2->first) ==
           ge->physicals.end()){
          ge->physicals.push_back(it2->first);
        }
      }
    }
  }
}

static bool getVertices(int num, int *indices, std::map<int, MVertex*> &map,
                        std::vector<MVertex*> &vertices)
{
  for(int i = 0; i < num; i++){
    if(!map.count(indices[i])){
      Msg::Error("Wrong vertex index %d", indices[i]);
      return false;
    }
    else
      vertices.push_back(map[indices[i]]);
  }
  return true;
}

static bool getVertices(int num, int *indices, std::vector<MVertex*> &vec,
                        std::vector<MVertex*> &vertices, int minVertex = 0)
{
  for(int i = 0; i < num; i++){
    if(indices[i] < minVertex || indices[i] > (int)(vec.size() - 1 + minVertex)){
      Msg::Error("Wrong vertex index %d", indices[i]);
      return false;
    }
    else
      vertices.push_back(vec[indices[i]]);
  }
  return true;
}

GModel *GModel::createGModel(std::map<int, MVertex*> &vertexMap,
                             std::vector<int> &elementNum,
                             std::vector<std::vector<int> > &vertexIndices,
                             std::vector<int> &elementType,
                             std::vector<int> &physical,
                             std::vector<int> &elementary,
                             std::vector<int> &partition)
{
  int numVertices = (int)vertexMap.size();
  int numElement = (int)elementNum.size();

  if(numElement != (int)vertexIndices.size()){
    Msg::Error("Dimension in vertices numbers");
    return 0;
  }
  if(numElement != (int)elementType.size()){
    Msg::Error("Dimension in elementType numbers");
    return 0;
  }
  if(numElement != (int)physical.size()){
    Msg::Error("Dimension in physical numbers");
    return 0;
  }
  if(numElement != (int)elementary.size()){
    Msg::Error("Dimension in elementary numbers");
    return 0;
  }
  if(numElement != (int)partition.size()){
    Msg::Error("Dimension in partition numbers");
    return 0;
  }

  GModel *gm = new GModel();
  std::map<int, std::vector<MElement*> > elements[10];
  std::map<int, std::map<int, std::string> > physicals[4];
  std::vector<MVertex*> vertexVector;

  std::map<int, MVertex*>::const_iterator it = vertexMap.begin();
  std::map<int, MVertex*>::const_iterator end = vertexMap.end();

  int maxVertex = std::numeric_limits<int>::min();
  int minVertex = std::numeric_limits<int>::max();
  int num;

  for(; it != end; ++it){
    num = it->first;
    minVertex = std::min(minVertex, num);
    maxVertex = std::max(maxVertex, num);
  }
  if(minVertex == std::numeric_limits<int>::max())
    Msg::Error("Could not determine the min index of vertices");

  // if the vertex numbering is dense, transfer the map into a vector to speed
  // up element creation
  if((minVertex == 1 && maxVertex == numVertices) ||
     (minVertex == 0 && maxVertex == numVertices - 1)){
    Msg::Info("Vertex numbering is dense");
    vertexVector.resize(vertexMap.size() + 1);
    if(minVertex == 1)
      vertexVector[0] = 0;
    else
      vertexVector[numVertices] = 0;
    std::map<int, MVertex*>::const_iterator it = vertexMap.begin();
    for(; it != vertexMap.end(); ++it)
      vertexVector[it->first] = it->second;
    vertexMap.clear();
  }

  int *indices;
  int nbVertices;
  for(int i = 0; i < numElement; ++i){
    num = elementNum[i];
    std::vector<MVertex*> vertices;
    nbVertices = (int)vertexIndices[i].size();
    indices = &vertexIndices[i][0];
    if(vertexVector.size()){
      if(!getVertices(nbVertices, indices, vertexVector, vertices)){
        Msg::Error("Vertex not found aborting");
        delete gm;
        return 0;
      }
    }
    else{
      if(!getVertices(nbVertices, indices, vertexMap, vertices)){
        Msg::Error("Vertex not found aborting");
        delete gm;
        return 0;
      }
    }

    MElementFactory f;
    MElement *e = f.create(elementType[i], vertices, num, partition[i]);
    if(!e){
      Msg::Error("Unknown type of element %d", elementType[i]);
      delete gm;
      return 0;
    }
    switch(e->getType()){
    case TYPE_PNT : elements[0][elementary[i]].push_back(e); break;
    case TYPE_LIN : elements[1][elementary[i]].push_back(e); break;
    case TYPE_TRI : elements[2][elementary[i]].push_back(e); break;
    case TYPE_QUA : elements[3][elementary[i]].push_back(e); break;
    case TYPE_TET : elements[4][elementary[i]].push_back(e); break;
    case TYPE_HEX : elements[5][elementary[i]].push_back(e); break;
    case TYPE_PRI : elements[6][elementary[i]].push_back(e); break;
    case TYPE_PYR : elements[7][elementary[i]].push_back(e); break;
    case TYPE_POLYG: elements[8][elementary[i]].push_back(e); break;
    case TYPE_POLYH: elements[9][elementary[i]].push_back(e); break;
    default : Msg::Error("Wrong type of element"); delete gm; return 0;
    }
    int dim = e->getDim();
    if(physical[i] && (!physicals[dim].count(elementary[i]) ||
                       !physicals[dim][elementary[i]].count(physical[i])))
      physicals[dim][elementary[i]][physical[i]] = "unnamed";
    if(partition[i]) gm->getMeshPartitions().insert(partition[i]);
  }

  // store the elements in their associated elementary entity. If the
  // entity does not exist, create a new (discrete) one.
  for(int i = 0; i < (int)(sizeof(elements) / sizeof(elements[0])); i++)
    gm->_storeElementsInEntities(elements[i]);

  // associate the correct geometrical entity with each mesh vertex
  gm->_associateEntityWithMeshVertices();

  // store the vertices in their associated geometrical entity
  if(vertexVector.size())
    gm->_storeVerticesInEntities(vertexVector);
  else
    gm->_storeVerticesInEntities(vertexMap);

  // store the physical tags
  for(int i = 0; i < 4; i++)
    gm->_storePhysicalTagsInEntities(i, physicals[i]);

  return gm;
}

GModel *GModel::createGModel
(std::map<int, std::vector<MElement*> > &entityToElementsMap,
 std::map<int, std::vector<int> > &entityToPhysicalsMap)
{
  GModel* gm = new GModel();

  std::map<int, MVertex*> vertexMap;
  std::map<int, std::map<int, std::string> > physicals[4];
  for(std::map<int, std::vector<MElement*> >::iterator it =
        entityToElementsMap.begin(); it != entityToElementsMap.end();
      it++) {
    int entity = it->first;
    for(unsigned int iE = 0; iE < it->second.size(); iE++) {
      MElement* me = it->second[iE];
      for(int iV = 0; iV < me->getNumVertices(); iV++) {
        vertexMap[me->getVertex(iV)->getNum()] = me->getVertex(iV);
      }
      if(me->getPartition()) {
        gm->getMeshPartitions().insert(me->getPartition());
      }
      std::vector<int> entityPhysicals = entityToPhysicalsMap[entity];
      for(unsigned int i = 0; i < entityPhysicals.size(); i++) {
        physicals[me->getDim()][entity][entityPhysicals[i]] = "unnamed";
      }
    }
  }

  gm->_storeElementsInEntities(entityToElementsMap);
  gm->_associateEntityWithMeshVertices();
  gm->_storeVerticesInEntities(vertexMap);
  for(int i = 0; i < 4; i++)
    gm->_storePhysicalTagsInEntities(i, physicals[i]);

  return gm;
}

void GModel::checkMeshCoherence(double tolerance)
{
  int numEle = getNumMeshElements();
  if(!numEle) return;

  Msg::StatusBar(true, "Checking mesh coherence (%d elements)...", numEle);

  SBoundingBox3d bbox = bounds();
  double lc = bbox.empty() ? 1. : norm(SVector3(bbox.max(), bbox.min()));
  double eps = lc * tolerance;

  std::vector<GEntity*> entities;
  getEntities(entities);

  // check for duplicate mesh vertices
  {
    Msg::Info("Checking for duplicate vertices...");
    std::vector<MVertex*> vertices;
    for(unsigned int i = 0; i < entities.size(); i++)
      vertices.insert(vertices.end(), entities[i]->mesh_vertices.begin(),
                      entities[i]->mesh_vertices.end());
    MVertexPositionSet pos(vertices);
    for(unsigned int i = 0; i < vertices.size(); i++)
      pos.find(vertices[i]->x(), vertices[i]->y(), vertices[i]->z(), eps);
    int num = 0;
    for(unsigned int i = 0; i < vertices.size(); i++)
      if(!vertices[i]->getIndex()){
        Msg::Info("Duplicate vertex at (%.16g,%.16g,%.16g)",
                  vertices[i]->x(), vertices[i]->y(), vertices[i]->z());
        num++;
      }
    if(num) Msg::Error("%d duplicate vert%s", num, num > 1 ? "ices" : "ex");
  }

  // check for duplicate elements
  {
    Msg::Info("Checking for duplicate elements...");
    std::vector<MVertex*> vertices;
    for(unsigned int i = 0; i < entities.size(); i++)
      for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
        MElement *e = entities[i]->getMeshElement(j);
        double vol = e->getVolume();
        if(vol < 0)
          Msg::Warning("Element %d has negative volume", e->getNum());
        else if(vol < 1e-12)
          Msg::Warning("Element %d has zero volume", e->getNum());
        SPoint3 p = e->barycenter();
        vertices.push_back(new MVertex(p.x(), p.y(), p.z()));
      }
    MVertexPositionSet pos(vertices);
    for(unsigned int i = 0; i < vertices.size(); i++)
      pos.find(vertices[i]->x(), vertices[i]->y(), vertices[i]->z(), eps);
    int num = 0;
    for(unsigned int i = 0; i < vertices.size(); i++){
      if(!vertices[i]->getIndex()){
        Msg::Info("Duplicate element with barycenter (%.16g,%.16g,%.16g)",
                  vertices[i]->x(), vertices[i]->y(), vertices[i]->z());
        num++;
      }
      delete vertices[i];
    }
    if(num) Msg::Error("%d duplicate element%s", num, num > 1 ? "s" : "");
  }

  Msg::StatusBar(true, "Done checking mesh coherence");
}

int GModel::removeDuplicateMeshVertices(double tolerance)
{
  Msg::StatusBar(true, "Removing duplicate mesh vertices...");

  SBoundingBox3d bbox = bounds();
  double lc = bbox.empty() ? 1. : norm(SVector3(bbox.max(), bbox.min()));
  double eps = lc * tolerance;

  std::vector<GEntity*> entities;
  getEntities(entities);

  std::vector<MVertex*> vertices;
  for(unsigned int i = 0; i < entities.size(); i++)
    for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++){
      MVertex *v = entities[i]->mesh_vertices[j];
      vertices.push_back(new MVertex(v->x(), v->y(), v->z()));
    }
  MVertexPositionSet pos(vertices);
  for(unsigned int i = 0; i < vertices.size(); i++)
    pos.find(vertices[i]->x(), vertices[i]->y(), vertices[i]->z(), eps);
  int num = 0;
  for(unsigned int i = 0; i < vertices.size(); i++)
    if(!vertices[i]->getIndex()) num++;

  Msg::Info("Found %d duplicate vertices ", num);

  if(!num){
    for(unsigned int i = 0; i < vertices.size(); i++)
      delete vertices[i];
    Msg::Info("No duplicate vertices found");
    return 0;
  }

  std::map<int, std::vector<MElement*> > elements[10];
  for(unsigned int i = 0; i < entities.size(); i++){
    for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
      MElement *e = entities[i]->getMeshElement(j);
      std::vector<MVertex*> verts;
      for(int k = 0; k < e->getNumVertices(); k++){
        MVertex *v = e->getVertex(k);
        MVertex *v2 = pos.find(v->x(), v->y(), v->z(), eps);
        if(v2) verts.push_back(v2);
      }
      if((int)verts.size() == e->getNumVertices()){
        MElementFactory factory;
        MElement *e2 = factory.create(e->getTypeForMSH(), verts, e->getNum(),
                                      e->getPartition());
        switch(e2->getType()){
        case TYPE_PNT: elements[0][entities[i]->tag()].push_back(e2); break;
        case TYPE_LIN: elements[1][entities[i]->tag()].push_back(e2); break;
        case TYPE_TRI: elements[2][entities[i]->tag()].push_back(e2); break;
        case TYPE_QUA: elements[3][entities[i]->tag()].push_back(e2); break;
        case TYPE_TET: elements[4][entities[i]->tag()].push_back(e2); break;
        case TYPE_HEX: elements[5][entities[i]->tag()].push_back(e2); break;
        case TYPE_PRI: elements[6][entities[i]->tag()].push_back(e2); break;
        case TYPE_PYR: elements[7][entities[i]->tag()].push_back(e2); break;
        case TYPE_POLYG: elements[8][entities[i]->tag()].push_back(e2); break;
        case TYPE_POLYH: elements[9][entities[i]->tag()].push_back(e2); break;
        }
      }
      else
        Msg::Error("Could not recreate element %d", e->getNum());
    }
  }

  for(unsigned int i = 0; i < entities.size(); i++)
    entities[i]->deleteMesh();

  for(int i = 0; i < (int)(sizeof(elements) / sizeof(elements[0])); i++)
    _storeElementsInEntities(elements[i]);
  _associateEntityWithMeshVertices();
  _storeVerticesInEntities(vertices);

  if(num)
    Msg::Info("Removed %d duplicate mesh %s", num, num > 1 ? "vertices" : "vertex");

  Msg::StatusBar(true, "Done removing duplicate mesh vertices");
  return num;
}


static void recurConnectMElementsByMFace(const MFace &f,
                                         std::multimap<MFace, MElement*, Less_Face> &e2f,
                                         std::set<MElement*> &group,
                                         std::set<MFace, Less_Face> &touched,
                                         int recur_level)
{
  // this is very slow...
  std::stack<MFace> _stack;
  _stack.push(f);

  while(!_stack.empty()){
    MFace ff = _stack.top();
    _stack.pop();
    if (touched.find(ff) == touched.end()){
      touched.insert(ff);
      for (std::multimap<MFace, MElement*, Less_Face>::iterator it = e2f.lower_bound(ff);
           it != e2f.upper_bound(ff); ++it){
        group.insert(it->second);
        for (int i = 0; i < it->second->getNumFaces(); ++i){
          _stack.push(it->second->getFace(i));
        }
      }
    }
  }
  //printf("group pf %d elements found\n",(int)group.size());
}

/*
static void recurConnectMElementsByMFaceOld(const MFace &f,
                                         std::multimap<MFace, MElement*, Less_Face> &e2f,
                                         std::set<MElement*> &group,
                                         std::set<MFace, Less_Face> &touched,
                                         int recur_level)
{
  if (touched.find(f) != touched.end()) return;
  touched.insert(f);
  for (std::multimap<MFace, MElement*, Less_Face>::iterator it = e2f.lower_bound(f);
       it != e2f.upper_bound(f); ++it){
    group.insert(it->second);
    for (int i = 0; i < it->second->getNumFaces(); ++i){
      recurConnectMElementsByMFace(it->second->getFace(i), e2f, group, touched, recur_level+1);
    }
  }
}
*/

static int connectedVolumes(std::vector<MElement*> &elements,
                            std::vector<std::vector<MElement*> > &regs)
{
  std::multimap<MFace, MElement*, Less_Face> e2f;
  for(unsigned int i = 0; i < elements.size(); ++i){
    for(int j = 0; j < elements[i]->getNumFaces(); j++){
      e2f.insert(std::make_pair(elements[i]->getFace(j), elements[i]));
    }
  }
  while(!e2f.empty()){
    std::set<MElement*> group;
    std::set<MFace, Less_Face> touched;
    recurConnectMElementsByMFace(e2f.begin()->first, e2f, group, touched, 0);
    std::vector<MElement*> temp;
    temp.insert(temp.begin(), group.begin(), group.end());
    regs.push_back(temp);
    for(std::set<MFace, Less_Face>::iterator it = touched.begin();
        it != touched.end(); ++it)
      e2f.erase(*it);
  }
  return regs.size();
}

static void recurConnectMElementsByMEdge(const MEdge &e,
                                         std::multimap<MEdge, MElement*, Less_Edge> &e2e,
                                         std::set<MElement*> &group,
                                         std::set<MEdge, Less_Edge> &touched)
{
  if (touched.find(e) != touched.end()) return;
  touched.insert(e);
  for (std::multimap <MEdge, MElement*, Less_Edge>::iterator it = e2e.lower_bound(e);
       it != e2e.upper_bound(e); ++it){
    group.insert(it->second);
    for (int i = 0; i < it->second->getNumEdges(); ++i){
      recurConnectMElementsByMEdge(it->second->getEdge(i), e2e, group, touched);
    }
  }
}

static int connectedSurfaces(std::vector<MElement*> &elements,
                             std::vector<std::vector<MElement*> > &faces)
{
  std::multimap<MEdge, MElement*, Less_Edge> e2e;
  for(unsigned int i = 0; i < elements.size(); ++i){
    for(int j = 0; j < elements[i]->getNumEdges(); j++){
      e2e.insert(std::make_pair(elements[i]->getEdge(j), elements[i]));
    }
  }
  while(!e2e.empty()){
    std::set<MElement*> group;
    std::set<MEdge, Less_Edge> touched;
    recurConnectMElementsByMEdge(e2e.begin()->first, e2e, group, touched);
    //printf("group pe %d elements found\n",(int)group.size());
    std::vector<MElement*> temp;
    temp.insert(temp.begin(), group.begin(), group.end());
    faces.push_back(temp);
    for(std::set<MEdge, Less_Edge>::iterator it = touched.begin();
        it != touched.end(); ++it)
      e2e.erase(*it);
  }
  return faces.size();
}

static void recurConnectMEdgesByMVertex(MVertex *v,
                                        std::multimap<MVertex*, MEdge> &v2e,
                                        std::set<MEdge, Less_Edge> &group,
                                        std::set<MVertex*> &touched)
{
  if (touched.find(v) != touched.end()) return;
  touched.insert(v);
  for (std::multimap <MVertex*, MEdge>::iterator it = v2e.lower_bound(v);
       it != v2e.upper_bound(v) ; ++it){
    group.insert(it->second);
    for (int i = 0; i < it->second.getNumVertices(); ++i){
      recurConnectMEdgesByMVertex(it->second.getVertex(i), v2e, group, touched);
    }
  }
}

static int connectedSurfaceBoundaries(std::set<MEdge, Less_Edge> &edges,
                                      std::vector<std::vector<MEdge> > &boundaries)
{
  std::multimap<MVertex*,MEdge> v2e;
  for(std::set<MEdge, Less_Edge>::iterator it = edges.begin(); it != edges.end(); it++){
    for (int j = 0; j < it->getNumVertices(); j++){
      v2e.insert(std::make_pair(it->getVertex(j), *it));
    }
  }

  while (!v2e.empty()){
    std::set<MEdge, Less_Edge> group;
    std::set<MVertex*> touched;
    recurConnectMEdgesByMVertex(v2e.begin()->first, v2e, group, touched);
    std::vector<MEdge> temp;
    temp.insert(temp.begin(), group.begin(), group.end());
    boundaries.push_back(temp);
    for (std::set<MVertex*>::iterator it = touched.begin() ; it != touched.end();++it)
      v2e.erase(*it);
  }

  return boundaries.size();
}

void GModel::makeDiscreteRegionsSimplyConnected()
{
  Msg::Debug("Making discrete regions simply connected...");

  std::vector<discreteRegion*> discRegions;
  for(riter it = firstRegion(); it != lastRegion(); it++)
    if((*it)->geomType() == GEntity::DiscreteVolume)
      discRegions.push_back((discreteRegion*) *it);

  std::set<MVertex*> touched;

  for(std::vector<discreteRegion*>::iterator itR = discRegions.begin();
      itR != discRegions.end(); itR++){

    std::vector<MElement*> allElements((*itR)->getNumMeshElements());
    for(unsigned int i = 0; i < (*itR)->getNumMeshElements(); i++)
      allElements[i] = (*itR)->getMeshElement(i);

    std::vector<std::vector<MElement*> > conRegions;
    int nbRegions = connectedVolumes(allElements, conRegions);
    if (nbRegions > 1) remove(*itR);

    for(int ire  = 0; ire < nbRegions; ire++){
      int numR = (nbRegions == 1) ? (*itR)->tag() : getMaxElementaryNumber(3) + 1;
      discreteRegion *r = new discreteRegion(this, numR);
      add(r);
      std::vector<MElement*> myElements = conRegions[ire];
      std::set<MVertex*> myVertices;
      for(unsigned int i = 0; i < myElements.size(); i++) {
        MElement *e = myElements[i];
        std::vector<MVertex*> verts;
        e->getVertices(verts);
        for(unsigned int k = 0; k < verts.size(); k++){
          if(verts[k]->onWhat() && verts[k]->onWhat()->dim() == 3){
            if(touched.find(verts[k]) == touched.end()){
              verts[k]->setEntity(r);
              myVertices.insert(verts[k]);
              touched.insert(verts[k]);
            }
          }
        }
        MElementFactory factory;
        MElement *e2 = factory.create(e->getTypeForMSH(), verts, e->getNum(),
                                      e->getPartition());
        switch(e2->getType()){
        case TYPE_TET: r->tetrahedra.push_back((MTetrahedron*)e2); break;
        case TYPE_HEX: r->hexahedra.push_back((MHexahedron*)e2); break;
        case TYPE_PRI: r->prisms.push_back((MPrism*)e2); break;
        case TYPE_PYR: r->pyramids.push_back((MPyramid*)e2); break;
        }
      }
      r->mesh_vertices.insert
        (r->mesh_vertices.begin(), myVertices.begin(), myVertices.end());
    }
  }

  Msg::Debug("Done making discrete regions simply connected");
}

void GModel::makeDiscreteFacesSimplyConnected()
{
  Msg::Debug("Making discrete faces simply connected...");

  std::vector<discreteFace*> discFaces;
  for(fiter it = firstFace(); it != lastFace(); it++)
    if((*it)->geomType() == GEntity::DiscreteSurface)
      discFaces.push_back((discreteFace*) *it);

  std::set<MVertex*> touched;

  for(std::vector<discreteFace*>::iterator itF = discFaces.begin();
      itF != discFaces.end(); itF++){

    std::vector<MElement*> allElements((*itF)->getNumMeshElements());
    for(unsigned int i = 0; i < (*itF)->getNumMeshElements(); i++)
      allElements[i] = (*itF)->getMeshElement(i);

    std::vector<std::vector<MElement*> > conFaces;
    int nbFaces = connectedSurfaces(allElements, conFaces);
    if (nbFaces > 1) remove(*itF);

    for(int ifa  = 0; ifa < nbFaces; ifa++){
      int numF = (nbFaces == 1) ? (*itF)->tag() : getMaxElementaryNumber(2) + 1;
      discreteFace *f = new discreteFace(this, numF);
      add(f);
      std::vector<MElement*> myElements = conFaces[ifa];
      std::set<MVertex*> myVertices;
      for(unsigned int i = 0; i < myElements.size(); i++) {
        MElement *e = myElements[i];
        std::vector<MVertex*> verts;
        e->getVertices(verts);
        for(unsigned int k = 0; k < verts.size(); k++){
          if(verts[k]->onWhat() && verts[k]->onWhat()->dim() == 2){
            if(touched.find(verts[k]) == touched.end()){
              verts[k]->setEntity(f);
              myVertices.insert(verts[k]);
              touched.insert(verts[k]);
            }
          }
        }
        MElementFactory factory;
        MElement *e2 = factory.create(e->getTypeForMSH(), verts, e->getNum(),
                                      e->getPartition());
        if(e2->getType() == TYPE_TRI)
          f->triangles.push_back((MTriangle*)e2);
        else
          f->quadrangles.push_back((MQuadrangle*)e2);
      }
      f->mesh_vertices.insert
        (f->mesh_vertices.begin(), myVertices.begin(), myVertices.end());
    }
  }

  Msg::Debug("Done making discrete faces simply connected");
}

void GModel::createTopologyFromMesh(int ignoreHoles)
{
  Msg::StatusBar(true, "Creating topology from mesh...");
  double t1 = Cpu();

  removeDuplicateMeshVertices(CTX::instance()->geom.tolerance);
  makeDiscreteRegionsSimplyConnected();
  makeDiscreteFacesSimplyConnected();

  // create topology for all discrete regions
  std::vector<discreteRegion*> discRegions;
  for(riter it = firstRegion(); it != lastRegion(); it++)
    if((*it)->geomType() == GEntity::DiscreteVolume)
      discRegions.push_back((discreteRegion*) *it);
  createTopologyFromRegions(discRegions);

  // create topology for all discrete faces
  std::vector<discreteFace*> discFaces;
  for(fiter it = firstFace(); it != lastFace(); it++)
    if((*it)->geomType() == GEntity::DiscreteSurface)
      discFaces.push_back((discreteFace*) *it);
  createTopologyFromFaces(discFaces, ignoreHoles);

  //create old format (necessary e.g. for old-style extruded boundary layers)
  exportDiscreteGEOInternals();

  double t2 = Cpu();
  Msg::StatusBar(true, "Done creating topology from mesh (%g s)", t2 - t1);
}

void GModel::createTopologyFromRegions(std::vector<discreteRegion*> &discRegions)
{
  Msg::Debug("Creating topology from regions...");

  // find boundary mesh faces of each discrete region and put them in
  // map_faces, which associates each MFace with the tags of the
  // adjacent regions
  std::map<MFace, std::vector<int>, Less_Face > map_faces;
  for (std::vector<discreteRegion*>::iterator it = discRegions.begin();
       it != discRegions.end(); it++)
    (*it)->findFaces(map_faces);

  // get currently defined discrete faces
  std::vector<discreteFace*> discFaces;
  for(fiter it = firstFace(); it != lastFace(); it++)
    if((*it)->geomType() == GEntity::DiscreteSurface)
      discFaces.push_back((discreteFace*) *it);

  // create reverse map storing for each discrete region the list of
  // discrete faces on its boundary
  std::map<int, std::set<int> > region2Faces;
  std::set<MVertex*> touched;

  while (!map_faces.empty()){

    Msg::Debug("... %d mesh faces left to process", map_faces.size());

    // get mesh faces with identical region connections (i.e., a part
    // of region boundaries that can be later defined as a discrete
    // face)
    std::set<MFace, Less_Face> myFaces;
    std::vector<int> tagRegions = map_faces.begin()->second;
    myFaces.insert(map_faces.begin()->first);
    map_faces.erase(map_faces.begin());
    std::map<MFace, std::vector<int>, Less_Face>::iterator itmap = map_faces.begin();
    while (itmap != map_faces.end()){
      std::vector<int> tagRegions2 = itmap->second;
      if (tagRegions2 == tagRegions){
        myFaces.insert(itmap->first);
        map_faces.erase(itmap++);
      }
      else
        itmap++;
    }

    // if the mesh already contains discrete faces, check if the
    // candidate discrete face does contain any of those; if not,
    // create a new discreteFace. Then create populate the
    // region2Faces map that associates for each region the (old or
    // new) boundary discrete faces
    for (std::vector<discreteFace*>::iterator itF = discFaces.begin();
         itF != discFaces.end(); itF++){

      bool candidate = true;
      for (unsigned int i = 0; i < (*itF)->getNumMeshElements(); i++){
        MFace mf = (*itF)->getMeshElement(i)->getFace(0);
        std::set<MFace, Less_Face>::iterator itset = myFaces.find(mf);
        if (itset == myFaces.end()){
          candidate = false;
          break;
        }
      }

      if(candidate){
        std::set<int> tagFaces;
        tagFaces.insert((*itF)->tag());
        for (unsigned int i = 0; i < (*itF)->getNumMeshElements(); i++){
          MFace mf = (*itF)->getMeshElement(i)->getFace(0);
          std::set<MFace, Less_Face>::iterator itset = myFaces.find(mf);
          myFaces.erase(itset);
        }
        for(std::vector<int>::iterator itReg = tagRegions.begin();
            itReg != tagRegions.end(); itReg++) {
          std::map<int, std::set<int> >::iterator it = region2Faces.find(*itReg);
          if (it == region2Faces.end())
            region2Faces.insert(std::make_pair(*itReg, tagFaces));
          else{
            std::set<int> allFaces = it->second;
            allFaces.insert(tagFaces.begin(), tagFaces.end());
            it->second = allFaces;
          }
        }
      }
    }

    // create new discrete face
    if(myFaces.size()){
      int numF = getMaxElementaryNumber(2) + 1;
      discreteFace *f = new discreteFace(this, numF);
      add(f);
      discFaces.push_back(f);
      std::set<MVertex*> myVertices;
      for(std::set<MFace, Less_Face>::iterator it = myFaces.begin();
          it != myFaces.end(); it++){
        std::vector<MVertex*> verts(it->getNumVertices());
        for(int i = 0; i < it->getNumVertices(); i++){
          verts[i] = it->getVertex(i);
          if(verts[i]->onWhat() && verts[i]->onWhat()->dim() == 3){
            if(touched.find(verts[i]) != touched.end()){
              myVertices.insert(verts[i]);
              verts[i]->setEntity(f);
              touched.insert(verts[i]);
            }
          }
        }
        if(verts.size() == 4)
          f->quadrangles.push_back(new MQuadrangle(verts));
        else
          f->triangles.push_back(new MTriangle(verts));
      }
      f->mesh_vertices.insert(f->mesh_vertices.begin(),
                              myVertices.begin(), myVertices.end());

      for (std::vector<int>::iterator itReg = tagRegions.begin();
           itReg != tagRegions.end(); itReg++) {

        // delete mesh vertices of new edge from adjacent regions
        GRegion *dReg = getRegionByTag(*itReg);
        for (std::set<MVertex*>::iterator itv = myVertices.begin();
             itv != myVertices.end(); itv++) {
          std::vector<MVertex*>::iterator itve =
            std::find(dReg->mesh_vertices.begin(), dReg->mesh_vertices.end(), *itv);
          if (itve != dReg->mesh_vertices.end()) dReg->mesh_vertices.erase(itve);
        }

        // fill region2Faces with the new face
        std::map<int, std::set<int> >::iterator r2f = region2Faces.find(*itReg);
        if (r2f == region2Faces.end()){
          std::set<int> tagFaces;
          tagFaces.insert(numF);
          region2Faces.insert(std::make_pair(*itReg, tagFaces));
        }
        else{
          std::set<int> tagFaces = r2f->second;
          tagFaces.insert(numF);
          r2f->second = tagFaces;
        }
      }
    }
  }

  // set boundary faces for each region
  for (std::vector<discreteRegion*>::iterator it = discRegions.begin();
       it != discRegions.end(); it++){
    std::map<int, std::set<int> >::iterator itr = region2Faces.find((*it)->tag());
    if (itr != region2Faces.end()){
      std::set<int> bcFaces = itr->second;
      (*it)->setBoundFaces(bcFaces);
    }
  }

  Msg::Debug("Done creating topology from regions");
}

void GModel::createTopologyFromFaces(std::vector<discreteFace*> &discFaces, int ignoreHoles)
{
  Msg::Debug("Creating topology from faces...");

  // find boundary mesh edges of each discrete face and put them in
  // map_edges, which associates each MEdge with the tags of the
  // adjacent faces
  std::map<MEdge, std::vector<int>, Less_Edge > map_edges;
  for (std::vector<discreteFace*>::iterator it = discFaces.begin();
       it != discFaces.end(); it++)
    (*it)->findEdges(map_edges);

  // return if no boundary edges (torus, sphere, ...)
  if (map_edges.empty()) return;

  // get currently defined discrete edges
  std::vector<discreteEdge*> discEdges;
  for(eiter it = firstEdge(); it != lastEdge(); it++){
    if((*it)->geomType() == GEntity::DiscreteCurve)
      discEdges.push_back((discreteEdge*) *it);
  }

  // create reverse map storing for each discrete face the list of
  // discrete edges on its boundary
  std::map<int, std::vector<int> > face2Edges;

  while (!map_edges.empty()){

    Msg::Debug("... %d mesh edges left to process", map_edges.size());

    // get mesh edges with identical face connections (i.e., a part of
    // face boundaries that can be later defined as a discrete edge)
    std::set<MEdge, Less_Edge> myEdges;
    std::vector<int> tagFaces = map_edges.begin()->second;
    myEdges.insert(map_edges.begin()->first);
    map_edges.erase(map_edges.begin());
    std::map<MEdge, std::vector<int>, Less_Edge>::iterator itmap = map_edges.begin();
    while (itmap != map_edges.end()){
      std::vector<int> tagFaces2 = itmap->second;
      if (tagFaces2 == tagFaces){
        myEdges.insert(itmap->first);
        map_edges.erase(itmap++);
      }
      else
        itmap++;
    }

    // if the mesh already contains discrete edges, check if the
    // candidate discrete edge does contain any of those; if not,
    // create a discreteEdge. Then populate the face2Edges map that
    // associates for each face its boundary discrete edges
    for (std::vector<discreteEdge*>::iterator itE = discEdges.begin();
         itE != discEdges.end(); itE++){

      bool candidate = true;
      for (unsigned int i = 0; i < (*itE)->getNumMeshElements(); i++){
        MEdge me = (*itE)->getMeshElement(i)->getEdge(0);
        std::set<MEdge, Less_Edge >::iterator itset = myEdges.find(me);
        if (itset == myEdges.end()){
          candidate = false;
          break;
        }
      }

      if (candidate){
        std::vector<int> tagEdges;
        tagEdges.push_back((*itE)->tag());
        for (unsigned int i = 0; i < (*itE)->getNumMeshElements(); i++){
          MEdge me = (*itE)->getMeshElement(i)->getEdge(0);
          std::set<MEdge, Less_Edge >::iterator itset = myEdges.find(me);
          if (itset != myEdges.end()) myEdges.erase(itset);
        }
        for (std::vector<int>::iterator itFace = tagFaces.begin();
             itFace != tagFaces.end(); itFace++) {
          std::map<int, std::vector<int> >::iterator it = face2Edges.find(*itFace);
          if (it == face2Edges.end())
            face2Edges.insert(std::make_pair(*itFace, tagEdges));
          else{
            std::vector<int> allEdges = it->second;
            allEdges.insert(allEdges.begin(), tagEdges.begin(), tagEdges.end());
            it->second = allEdges;
          }
        }
      }
    }

    std::vector<std::vector<MEdge> > boundaries;
    int nbBounds = connectedSurfaceBoundaries(myEdges, boundaries);

    //EMI RBF fix
    if (ignoreHoles && nbBounds > 0){
      int index = 0;
      unsigned boundSize = 0;
      for (int ib = 0; ib < nbBounds; ib++){
        if (boundaries[ib].size() > boundSize){
          boundSize = boundaries[ib].size() ;
          index = ib;
        }
      }
      std::vector<std::vector<MEdge> > new_boundaries;
      new_boundaries.push_back(boundaries[index]);
      boundaries = new_boundaries;
    }

    // create new discrete edges
    for (unsigned ib = 0; ib < boundaries.size(); ib++){
      int numE = getMaxElementaryNumber(1) + 1;
      discreteEdge *e = new discreteEdge(this, numE, 0, 0);
      add(e);
      discEdges.push_back(e);
      std::set<MVertex*> allV;
      for(unsigned int i = 0; i < boundaries[ib].size(); i++) {
        MVertex *v0 = boundaries[ib][i].getVertex(0);
        MVertex *v1 = boundaries[ib][i].getVertex(1);
        e->lines.push_back(new MLine(v0, v1));
        allV.insert(v0);
        allV.insert(v1);
        v0->setEntity(e);
        v1->setEntity(e);
      }
      e->mesh_vertices.insert(e->mesh_vertices.begin(), allV.begin(), allV.end());
      for (std::vector<int>::iterator itFace = tagFaces.begin();
           itFace != tagFaces.end(); itFace++) {
        // delete mesh vertices of new edge from adjacent faces
        GFace *dFace = getFaceByTag(*itFace);
        for (std::set<MVertex*>::iterator itv = allV.begin(); itv != allV.end(); itv++) {
          std::vector<MVertex*>::iterator itve =
            std::find(dFace->mesh_vertices.begin(), dFace->mesh_vertices.end(), *itv);
          if (itve != dFace->mesh_vertices.end()) dFace->mesh_vertices.erase(itve);
        }
        // fill face2Edges with the new edge
        std::map<int, std::vector<int> >::iterator f2e = face2Edges.find(*itFace);
        if (f2e == face2Edges.end()){
          std::vector<int> tagEdges;
          tagEdges.push_back(numE);
          face2Edges.insert(std::make_pair(*itFace, tagEdges));
        }
        else{
          std::vector<int> tagEdges = f2e->second;
          tagEdges.push_back(numE);
          f2e->second = tagEdges;
        }
      }
    }

  }

  // set boundary edges for each face
  for (std::vector<discreteFace*>::iterator it = discFaces.begin();
       it != discFaces.end(); it++){
    std::map<int, std::vector<int> >::iterator ite = face2Edges.find((*it)->tag());
    if (ite != face2Edges.end()){
      std::vector<int> bcEdges = ite->second;
      (*it)->setBoundEdges(this, bcEdges);
    }
  }

  Msg::Debug("Done creating topology from faces");

  Msg::Debug("Creating topology for %d edges...", discEdges.size());

  // for each discreteEdge, create topology
  std::map<GFace*, std::map<MVertex*, MVertex*, std::less<MVertex*> > > face2Vert;
  std::map<GRegion*, std::map<MVertex*, MVertex*, std::less<MVertex*> > > region2Vert;
  face2Vert.clear();
  region2Vert.clear();
  for (std::vector<discreteEdge*>::iterator it = discEdges.begin();
       it != discEdges.end(); it++){
    (*it)->createTopo();
    (*it)->parametrize(face2Vert, region2Vert);
  }

  // fill edgeLoops of Faces or correct sign of l_edges
  // for (std::vector<discreteFace*>::iterator itF = discFaces.begin();
  //       itF != discFaces.end(); itF++){
  //    //EMI, TODO
  //    std::list<GEdgeLoop> edgeLoops = (*itF)->edgeLoops;
  //    edgeLoops.clear();
  //    GEdgeLoop el((*itF)->edges());
  //    edgeLoops.push_back(el);
  //  }

  // we need to recreate all mesh elements because some mesh vertices
  // might have been changed during the parametrization process
  // (MVertices became MEdgeVertices)
  for (std::map<GFace*, std::map<MVertex*, MVertex*, std::less<MVertex*> > >::iterator
         iFace = face2Vert.begin(); iFace != face2Vert.end(); iFace++){
    std::map<MVertex*, MVertex*, std::less<MVertex*> > old2new = iFace->second;
    GFace *gf = iFace->first;
    std::vector<MTriangle*> newTriangles;
    std::vector<MQuadrangle*> newQuadrangles;
    for (unsigned int i = 0; i < gf->getNumMeshElements(); ++i){
      MElement *e = gf->getMeshElement(i);
      std::vector<MVertex *> v;
      e->getVertices(v);
      for (unsigned int j = 0; j < v.size(); j++){
        std::map<MVertex*, MVertex*, std::less<MVertex*> >::iterator
          itmap = old2new.find(v[j]);
        if (itmap != old2new.end())
          v[j] = itmap->second;
      }
      MElementFactory factory;
      MElement *e2 = factory.create(e->getTypeForMSH(), v, e->getNum(),
                                    e->getPartition());
      switch(e2->getType()){
      case TYPE_TRI: newTriangles.push_back((MTriangle*)e2); break;
      case TYPE_QUA: newQuadrangles.push_back((MQuadrangle*)e2); break;
      }
    }
    gf->deleteVertexArrays();
    for(unsigned int i = 0; i < gf->triangles.size(); i++) delete gf->triangles[i];
    for(unsigned int i = 0; i < gf->quadrangles.size(); i++) delete gf->quadrangles[i];
    gf->triangles = newTriangles;
    gf->quadrangles = newQuadrangles;
  }

  for (std::map<GRegion*, std::map<MVertex*, MVertex*, std::less<MVertex*> > >::iterator
         iRegion = region2Vert.begin(); iRegion != region2Vert.end(); iRegion++){
    std::map<MVertex*, MVertex*, std::less<MVertex*> > old2new = iRegion->second;
    GRegion *gr = iRegion->first;
    std::vector<MTetrahedron*> newTetrahedra;
    std::vector<MHexahedron*> newHexahedra;
    std::vector<MPrism*> newPrisms;
    std::vector<MPyramid*> newPyramids;
    for (unsigned int i = 0; i < gr->getNumMeshElements(); ++i){
      MElement *e = gr->getMeshElement(i);
      std::vector<MVertex *> v;
      e->getVertices(v);
      for (unsigned int j = 0; j < v.size(); j++){
        std::map<MVertex*, MVertex*, std::less<MVertex*> >::iterator
          itmap = old2new.find(v[j]);
        if (itmap != old2new.end())
          v[j] = itmap->second;
      }
      MElementFactory factory;
      MElement *e2 = factory.create(e->getTypeForMSH(), v, e->getNum(),
                                    e->getPartition());
      switch(e2->getType()){
      case TYPE_TET: newTetrahedra.push_back((MTetrahedron*)e2); break;
      case TYPE_HEX: newHexahedra.push_back((MHexahedron*)e2); break;
      case TYPE_PRI: newPrisms.push_back((MPrism*)e2); break;
      case TYPE_PYR: newPyramids.push_back((MPyramid*)e2); break;
      }
    }
    gr->deleteVertexArrays();
    for(unsigned int i = 0; i < gr->tetrahedra.size(); i++) delete gr->tetrahedra[i];
    for(unsigned int i = 0; i < gr->hexahedra.size(); i++) delete gr->hexahedra[i];
    for(unsigned int i = 0; i < gr->prisms.size(); i++) delete gr->prisms[i];
    for(unsigned int i = 0; i < gr->pyramids.size(); i++) delete gr->pyramids[i];
    gr->tetrahedra = newTetrahedra;
    gr->hexahedra = newHexahedra;
    gr->prisms = newPrisms;
    gr->pyramids = newPyramids;
  }

  Msg::Debug("Done creating topology for edges");
}

void makeSimplyConnected(std::map<int, std::vector<MElement*> > elements[10])
{
  //only for tetras and triangles
  Msg::Info("Make simply connected regions and surfaces.");
  std::vector<int> regs;
  for(std::map<int, std::vector<MElement*> >::iterator it = elements[4].begin();
      it != elements[4].end(); it++)
    regs.push_back(it->first);
  std::multimap<MFace, MElement*, Less_Face> f2e;
  if(regs.size() > 2){
    for(unsigned int i = 0; i < regs.size(); i++){
      for(unsigned int j = 0; j < elements[4][regs[i]].size(); j++){
        MElement *el = elements[4][regs[i]][j];
        for(int k = 0; k < el->getNumFaces(); k++)
          f2e.insert(std::make_pair(el->getFace(k), el));
      }
    }
  }
  for(unsigned int i = 0; i < regs.size(); i++){
    int ri = regs[i];
    std::vector<MElement*> allElements;
    for(unsigned int j = 0; j < elements[4][ri].size(); j++)
      allElements.push_back(elements[4][ri][j]);
    std::vector<std::vector<MElement*> > conRegions;
    int nbConRegions = connectedVolumes(allElements, conRegions);
    for(int j = 0; j < nbConRegions; j++){
      if(conRegions[j].size() < 3){ //remove conRegions containing 1 or 2 elements
        //find adjacent region
        int r2 = ri;
        if(regs.size() == 2)
          r2 = (ri + 1) % 2;
        else{
          for(unsigned int k = 0; k < conRegions[j].size(); k++){
            MElement *el = conRegions[j][k];
            for(int l = 0; l < el->getNumFaces(); l++){
              MFace mf = el->getFace(l);
              std::multimap<MFace, MElement*, Less_Face>::iterator itl = f2e.lower_bound(mf);
              for(; itl != f2e.upper_bound(mf); itl++){
                if(itl->second != el) break;
              }
              MElement *el2 = itl->second;
              bool sameRegion = false;
              for(unsigned int m = 0; m < conRegions[j].size(); m++)
                if(conRegions[j][m] == el2) {
                  sameRegion = true; break;
                }
              if(sameRegion) continue;
              for(unsigned int m = 0; m < regs.size(); m++){
                int rm = regs[m];
                if(rm == ri) continue;
                for(unsigned int n = 0; n < elements[4][rm].size(); n++)
                  if(elements[4][rm][n] == el2){
                    r2 = rm;
                    break;
                  }
                if(r2 != ri) break;
              }
              if(r2 != ri) break;
            }
            if(r2 != ri) break;
          }
          if(r2 == ri) Msg::Warning("Element not found for simply connected regions");
        }

        for(unsigned int k = 0; k < conRegions[j].size(); k++){
          MElement *el = conRegions[j][k];
          unsigned int l = 0;
          for(; l < elements[4][ri].size(); l++)
            if(elements[4][ri][l] == el) break;
          elements[4][ri].erase(elements[4][ri].begin() + l);
          elements[4][r2].push_back(el);
        }
      }
    }
  }

  std::vector<int> faces;
  for(std::map<int, std::vector<MElement*> >::iterator it = elements[2].begin();
      it != elements[2].end(); it++)
    faces.push_back(it->first);
  std::multimap<MEdge, MElement*, Less_Edge> e2e;
  if(faces.size() > 2){
    for(unsigned int i = 0; i < faces.size(); i++){
      for(unsigned int j = 0; j < elements[2][faces[i]].size(); j++){
        MElement *el = elements[2][faces[i]][j];
        for(int k = 0; k < el->getNumEdges(); k++)
          e2e.insert(std::make_pair(el->getEdge(k), el));
      }
    }
  }
  for(unsigned int i = 0; i < faces.size(); i++){
    int fi = faces[i];
    std::vector<MElement*> allElements;
    for(unsigned int j = 0; j < elements[2][fi].size(); j++)
      allElements.push_back(elements[2][fi][j]);
    std::vector<std::vector<MElement*> > conSurfaces;
    int nbSurfaces = connectedSurfaces(allElements, conSurfaces);
    for(int j = 0; j < nbSurfaces; j++){
      if(conSurfaces[j].size() < 3){ //remove conSurfaces containing 1 or 2 elements
        //find adjacent surface
        int f2 = fi;
        if(faces.size() == 2)
          f2 = (fi + 1) % 2;
        else{
          for(unsigned int k = 0; k < conSurfaces[j].size(); k++){
            MElement *el = conSurfaces[j][k];
            for(int l = 0; l < el->getNumEdges(); l++){
              MEdge me = el->getEdge(l);
              std::multimap<MEdge, MElement*, Less_Edge>::iterator itl = e2e.lower_bound(me);
              for(; itl != e2e.upper_bound(me); itl++){
                if(itl->second != el) break;
              }
              MElement *el2 = itl->second;
              bool sameSurface = false;
              for(unsigned int m = 0; m < conSurfaces[j].size(); m++)
                if(conSurfaces[j][m] == el2) {
                  sameSurface = true; break;
                }
              if(sameSurface) continue;
              for(unsigned int m = 0; m < faces.size(); m++){
                int fm = faces[m];
                if(fm == fi) continue;
                for(unsigned int n = 0; n < elements[2][fm].size(); n++)
                  if(elements[2][fm][n] == el2){
                    f2 = fm;
                    break;
                  }
                if(f2 != fi) break;
              }
              if(f2 != fi) break;
            }
            if(f2 != fi) break;
          }
          if(f2 == fi) Msg::Warning("Element not found for simply connected surfaces");
        }
        for(unsigned int k = 0; k < conSurfaces[j].size(); k++){
          MElement *el = conSurfaces[j][k];
          unsigned int l = 0;
          for(; l < elements[2][fi].size(); l++)
            if(elements[2][fi][l] == el) break;
          elements[2][fi].erase(elements[2][fi].begin() + l);
          elements[2][f2].push_back(el);
        }
      }
    }
  }
}

GModel *GModel::buildCutGModel(gLevelset *ls, bool cutElem, bool saveTri)
{

  if (saveTri)
    CTX::instance()->mesh.saveTri = 1;
  else
    CTX::instance()->mesh.saveTri = 0;

  std::map<int, std::vector<MElement*> > elements[10];
  std::map<int, std::map<int, std::string> > physicals[4];
  std::map<int, MVertex*> vertexMap;

  if(cutElem) Msg::Info("Cutting mesh...");
  else Msg::Info("Splitting mesh...");
  double t1 = Cpu();

  GModel *cutGM = buildCutMesh(this, ls, elements, vertexMap, physicals, cutElem);

  if(!cutElem)
    makeSimplyConnected(elements);

  for(int i = 0; i < (int)(sizeof(elements) / sizeof(elements[0])); i++)
    cutGM->_storeElementsInEntities(elements[i]);
  cutGM->_associateEntityWithMeshVertices();
  cutGM->_storeVerticesInEntities(vertexMap);

  for(int i = 0; i < 4; i++){
    cutGM->_storePhysicalTagsInEntities(i, physicals[i]);
    std::map<int, std::map<int, std::string> >::iterator it = physicals[i].begin();
    for(; it != physicals[i].end(); it++){
      std::map<int, std::string>::iterator it2 = it->second.begin();
      for(; it2 != it->second.end(); it2++)
        if(it2->second != "")
          cutGM->setPhysicalName(it2->second, i, it2->first);
    }
  }

  if(cutElem) Msg::Info("Mesh cutting completed (%g s)", Cpu() - t1);
  else Msg::Info("Mesh splitting completed (%g s)", Cpu() - t1);

  return cutGM;
}

void GModel::load(std::string fileName)
{
  GModel *temp = GModel::current();
  GModel::setCurrent(this);
  MergeFile(fileName, true);
  GModel::setCurrent(temp);
}

void GModel::save(std::string fileName)
{
  GModel *temp = GModel::current();
  GModel::setCurrent(this);
  int guess = GuessFileFormatFromFileName(fileName);
  CreateOutputFile(fileName, guess);
  GModel::setCurrent(temp);
}

GEdge* GModel::addCompoundEdge(std::vector<GEdge*> edges, int num){

  if (num ==-1) num =  getMaxElementaryNumber(1) + 1;
  GEdgeCompound *gec = new GEdgeCompound(this, num, edges);
  add(gec);

  //create old geo format for the compound edge
  //necessary for boundary layers
  if(FindCurve(num)){
    Msg::Error("Curve %d already exists", num);
  }
  else{
    Curve *c = Create_Curve(num, MSH_SEGM_COMPOUND, 1, NULL, NULL, -1, -1, 0., 1.);
    for(unsigned int i= 0; i < edges.size(); i++)
      c->compound.push_back(edges[i]->tag());
    List_T *points = Tree2List(getGEOInternals()->Points);
    GVertex *gvb = gec->getBeginVertex();
    GVertex *gve = gec->getEndVertex();
    int nb = 2 ;
    c->Control_Points = List_Create(nb, 1, sizeof(Vertex *));
    for(int i = 0; i < List_Nbr(points); i++) {
      Vertex *v;
      List_Read(points, i, &v);
      if (v->Num == gvb->tag()) {
        List_Add(c->Control_Points, &v);
        c->beg = v;
      }
      if (v->Num == gve->tag()) {
        List_Add(c->Control_Points, &v);
        c->end = v;
      }
    }

    End_Curve(c);
    Tree_Add(getGEOInternals()->Curves, &c);
    CreateReversedCurve(c);

    // c->Method  =  gec->meshAttributes.method;
    // c->nbPointsTransfinite = gec->meshAttributes.nbPointsTransfinite;
    // c->typeTransfinite =  gec->meshAttributes.typeTransfinite ;
    // c->coeffTransfinite =  gec->meshAttributes.coeffTransfinite ;
    // c->Extrude =   gec->meshAttributes.extrude ;
    // c->ReverseMesh =  gec->meshAttributes.reverseMesh ;

  }

  return gec;
}

GFace* GModel::addCompoundFace(std::vector<GFace*> faces, int param, int split, int num)
{
#if defined(HAVE_SOLVER)
  if (num ==-1) num = getMaxElementaryNumber(2) + 1;

  std::list<GFace*> faces_comp(faces.begin(), faces.end());
  std::list<GEdge*> U0;

  GFaceCompound::typeOfCompound typ = GFaceCompound::HARMONIC_CIRCLE;
  if (param == 1) typ =  GFaceCompound::CONFORMAL_SPECTRAL;
  if (param == 2) typ =  GFaceCompound::RADIAL_BASIS;
  if (param == 3) typ =  GFaceCompound::HARMONIC_PLANE;
  if (param == 4) typ =  GFaceCompound::CONVEX_CIRCLE;
  if (param == 5) typ =  GFaceCompound::CONVEX_PLANE;
  if (param == 6) typ =  GFaceCompound::HARMONIC_SQUARE;
  if (param == 7) typ =  GFaceCompound::CONFORMAL_FE;

  GFaceCompound *gfc = new GFaceCompound(this, num, faces_comp, U0, typ, split);

  //create old geo format for the compound face
  //necessary for boundary layers
  if(FindSurface(num)){
    Msg::Error("Surface %d already exists", num);
  }
  else{
    Surface *s = Create_Surface(num, MSH_SURF_COMPOUND);
    for(unsigned int i= 0; i < faces.size(); i++)
      s->compound.push_back(faces[i]->tag());

     std::list<GEdge*> edges = gfc->edges();

     //Replace edges by their compounds
     std::set<GEdge*> mySet;
     std::list<GEdge*>::iterator it = edges.begin();
     while(it != edges.end()){
       if((*it)->getCompound()){
         mySet.insert((*it)->getCompound());
       }
       else{
         mySet.insert(*it);
       }
       ++it;
     }
     edges.clear();
     edges.insert(edges.begin(), mySet.begin(), mySet.end());

     s->Generatrices = List_Create(edges.size(), 1, sizeof(Curve *));
     List_T *curves = Tree2List(_geo_internals->Curves);
     Curve *c;
     for(std::list<GEdge*>::iterator ite = edges.begin(); ite != edges.end(); ite++){
       for(int i = 0; i < List_Nbr(curves); i++) {
         List_Read(curves, i, &c);
         if (c->Num == (*ite)->tag()) {
           List_Add(s->Generatrices, &c);
         }
       }
     }

    Tree_Add(_geo_internals->Surfaces, &s);
  }

  add(gfc);
  return gfc;
#else
  return 0;
#endif
}

GVertex *GModel::addVertex(double x, double y, double z, double lc)
{
  if(_factory) return _factory->addVertex(this, x, y, z, lc);
  return 0;
}

GEdge *GModel::addLine(GVertex *v1, GVertex *v2)
{
  if(_factory) return _factory->addLine(this, v1, v2);
  return 0;
}

GEdge *GModel::addCircleArcCenter(double x, double y, double z, GVertex *start,
                                  GVertex *end)
{
  if(_factory)
    return _factory->addCircleArc(this, GModelFactory::CENTER_START_END,
                                  start, end, SPoint3(x, y, z));
  return 0;
}

GEdge *GModel::addCircleArcCenter(GVertex *start, GVertex *center, GVertex *end)
{
  if(_factory)
    return _factory->addCircleArc(this, start, center, end);
  return 0;
}

GEdge *GModel::addCircleArc3Points(double x, double y, double z, GVertex *start,
                                   GVertex *end)
{
  if(_factory)
    return _factory->addCircleArc(this, GModelFactory::THREE_POINTS,
                                  start, end, SPoint3(x, y, z));
  return 0;
}

GEdge *GModel::addBezier(GVertex *start, GVertex *end,
                         std::vector<std::vector<double> > points)
{
  if(_factory)
    return _factory->addSpline(this, GModelFactory::BEZIER, start, end,
                               points);
  return 0;
}

GEdge *GModel::addNURBS(GVertex *start, GVertex *end,
                        std::vector<std::vector<double> > points,
                        std::vector<double> knots,
                        std::vector<double> weights,
                        std::vector<int> mult)
{
  if(_factory)
    return _factory->addNURBS(this, start,end,points,knots,weights, mult);
  return 0;
}

void GModel::addRuledFaces (std::vector<std::vector<GEdge *> > edges)
{
  if(_factory)
    _factory->addRuledFaces(this, edges);
}

GFace* GModel::addFace (std::vector<GEdge *> edges,
                        std::vector< std::vector<double > > points)
{
  if(_factory)
    return _factory->addFace(this, edges, points);
  return 0;
}

GFace* GModel::addPlanarFace (std::vector<std::vector<GEdge *> > edges){
  if(_factory)
    return _factory->addPlanarFace(this, edges);
  return 0;
}

GRegion* GModel::addVolume (std::vector<std::vector<GFace *> > faces){
  if(_factory)
    return _factory->addVolume(this, faces);
  return 0;
}

GFace *GModel::add2Drect(double x0, double y0, double dx, double dy)
{
  if(_factory)
    return _factory->add2Drect(this, x0, y0, dx, dy);
  return 0;
}

GFace *GModel::add2Dellips(double xc, double yc, double rx, double ry)
{
  if(_factory)
    return _factory->add2Dellips(this, xc, yc, rx, ry);
  return 0;
}

GEntity *GModel::revolve(GEntity *e, std::vector<double> p1, std::vector<double> p2,
                         double angle)
{
  if(_factory)
    return _factory->revolve(this, e, p1, p2, angle);
  return 0;
}

GEntity *GModel::extrude(GEntity *e, std::vector<double> p1, std::vector<double> p2)
{
  if(_factory)
    return _factory->extrude(this, e, p1, p2);
  return 0;
}

std::vector<GEntity*> GModel::extrudeBoundaryLayer(GEntity *e, int nbLayers, double hLayers, int dir, int view)
{
  if(_factory)
    return _factory->extrudeBoundaryLayer(this, e, nbLayers,hLayers, dir, view);
  std::vector<GEntity*> empty;
  return empty;
}

GEntity *GModel::addPipe(GEntity *e, std::vector<GEdge *>  edges)
{
  if(_factory)
    return _factory->addPipe(this,e,edges);
  return 0;
}

GEntity *GModel::addSphere(double cx, double cy, double cz, double radius)
{
  if(_factory) return _factory->addSphere(this, cx, cy, cz, radius);
  return 0;
}

GEntity *GModel::addCylinder(std::vector<double> p1, std::vector<double> p2,
                             double radius)
{
  if(_factory) return _factory->addCylinder(this, p1, p2, radius);
  return 0;
}

GEntity *GModel::addTorus(std::vector<double> p1, std::vector<double> p2,
                          double radius1, double radius2)
{
  if(_factory) return _factory->addTorus(this, p1, p2, radius1, radius2);
  return 0;
}

GEntity *GModel::addBlock(std::vector<double> p1, std::vector<double> p2)
{
  if(_factory) return _factory->addBlock(this, p1, p2);
  return 0;
}

GEntity *GModel::add3DBlock(std::vector<double> p1, double dx, double dy, double dz )
{
  if(_factory) return _factory->add3DBlock(this, p1, dx, dy, dz);
  return 0;
}

GEntity *GModel::addCone(std::vector<double> p1, std::vector<double> p2,
                         double radius1, double radius2)
{
  if(_factory) return _factory->addCone(this, p1, p2,radius1, radius2);
  return 0;
}

GModel *GModel::computeBooleanUnion(GModel *tool, int createNewModel)
{
  if(_factory)
    return _factory->computeBooleanUnion(this, tool, createNewModel);
  return 0;
}

GModel *GModel::computeBooleanIntersection(GModel *tool, int createNewModel)
{
  if(_factory)
    return _factory->computeBooleanIntersection(this, tool, createNewModel);
  return 0;
}

GModel *GModel::computeBooleanDifference(GModel *tool, int createNewModel)
{
  if(_factory)
    return _factory->computeBooleanDifference(this, tool, createNewModel);
  return 0;
}

void GModel::salomeconnect()
{
  if(_factory) _factory->salomeconnect(this);
}

void GModel::occconnect()
{
  if(_factory) _factory->occconnect(this);
}

void GModel::setPeriodicAllFaces(std::vector<double> FaceTranslationVector)
{
  if(_factory) _factory->setPeriodicAllFaces(this, FaceTranslationVector);
}

void GModel::setPeriodicPairOfFaces(int numFaceMaster, std::vector<int> EdgeListMaster,
                                    int numFaceSlave, std::vector<int> EdgeListSlave)
{
  if(_factory)
    _factory->setPeriodicPairOfFaces(this, numFaceMaster, EdgeListMaster,
                                     numFaceSlave, EdgeListSlave);
}

void GModel::setPhysicalNumToEntitiesInBox(int EntityType, int PhysicalGroupNumber,
                                           std::vector<double> p1, std::vector<double> p2)
{
  if(_factory)
    _factory->setPhysicalNumToEntitiesInBox(this, EntityType, PhysicalGroupNumber, p1, p2);
}

static void computeDuplicates(GModel *model,
                              std::multimap<GVertex*, GVertex*> &Unique2Duplicates,
                              std::map<GVertex*, GVertex*> &Duplicates2Unique,
                              const double &eps)
{
  // FIXME: currently we use a greedy algorithm in n^2 (using a kd-tree:
  // cf. MVertexPositionSet)

  // FIXME: add option to remove orphaned entities after duplicate check
  std::list<GVertex*> v;
  v.insert(v.begin(), model->firstVertex(), model->lastVertex());

  while(!v.empty()){
    GVertex *pv = *v.begin();
    v.erase(v.begin());
    bool found = false;
    for (std::multimap<GVertex*,GVertex*>::iterator it = Unique2Duplicates.begin();
         it != Unique2Duplicates.end(); ++it){
      GVertex *unique = it->first;
      const double d = sqrt((unique->x() - pv->x()) * (unique->x() - pv->x()) +
                            (unique->y() - pv->y()) * (unique->y() - pv->y()) +
                            (unique->z() - pv->z()) * (unique->z() - pv->z()));
      if (d <= eps && pv->geomType() == unique->geomType()) {
        found = true;
        Unique2Duplicates.insert(std::make_pair(unique, pv));
        Duplicates2Unique[pv] = unique;
        break;
      }
    }
    if (!found) {
      Unique2Duplicates.insert(std::make_pair(pv, pv));
      Duplicates2Unique[pv] = pv;
    }
  }
}

static void glueVerticesInEdges(GModel *model,
                                std::multimap<GVertex*, GVertex*> &Unique2Duplicates,
                                std::map<GVertex*, GVertex*> &Duplicates2Unique)
{
  Msg::Debug("Gluing Edges");
  for (GModel::eiter it = model->firstEdge(); it != model->lastEdge(); ++it){
    GEdge *e = *it;
    GVertex *v1 = e->getBeginVertex();
    GVertex *v2 = e->getEndVertex();
    GVertex *replacementOfv1 = Duplicates2Unique[v1];
    GVertex *replacementOfv2 = Duplicates2Unique[v2];
    if ((v1 != replacementOfv1) || (v2 != replacementOfv2)){
      Msg::Debug("Model Edge %d is re-build", e->tag());
      e->replaceEndingPoints (replacementOfv1, replacementOfv2);
    }
  }
}

static void computeDuplicates(GModel *model,
                              std::multimap<GEdge*, GEdge*> &Unique2Duplicates,
                              std::map<GEdge*,GEdge*> &Duplicates2Unique,
                              const double &eps)
{
  std::list<GEdge*> e;
  e.insert(e.begin(), model->firstEdge(), model->lastEdge());

  while(!e.empty()){
    GEdge *pe = *e.begin();
    e.erase(e.begin());
    bool found = false;
    for (std::multimap<GEdge*,GEdge*>::iterator it = Unique2Duplicates.begin();
         it != Unique2Duplicates.end(); ++it ){
      GEdge *unique = it->first;
      // first check edges that have same endpoints
      if (((unique->getBeginVertex() == pe->getBeginVertex() &&
            unique->getEndVertex() == pe->getEndVertex()) ||
           (unique->getEndVertex() == pe->getBeginVertex() &&
            unique->getBeginVertex() == pe->getEndVertex())) &&
          unique->geomType() == pe->geomType()){
        if ((unique->geomType() == GEntity::Line && pe->geomType() == GEntity::Line) ||
            unique->geomType() == GEntity::DiscreteCurve ||
            pe->geomType() == GEntity::DiscreteCurve ||
            unique->geomType() == GEntity::BoundaryLayerCurve ||
            pe->geomType() == GEntity::BoundaryLayerCurve){
          found = true;
          Unique2Duplicates.insert(std::make_pair(unique,pe));
          Duplicates2Unique[pe] = unique;
          break;
        }
        // compute a point
        Range<double> r = pe->parBounds(0);
        GPoint gp = pe->point(0.5 * (r.low() + r.high()));
        double t;
        GPoint gp2 = pe->closestPoint(SPoint3(gp.x(),gp.y(),gp.z()),t);
        const double d = sqrt((gp.x() - gp2.x()) * (gp.x() - gp2.x()) +
                              (gp.y() - gp2.y()) * (gp.y() - gp2.y()) +
                              (gp.z() - gp2.z()) * (gp.z() - gp2.z()));
        if (t >= r.low() && t <= r.high() && d <= eps) {
          found = true;
          Unique2Duplicates.insert(std::make_pair(unique,pe));
          Duplicates2Unique[pe] = unique;
          break;
        }
      }
    }
    if (!found) {
      Unique2Duplicates.insert(std::make_pair(pe,pe));
      Duplicates2Unique[pe] = pe;
    }
  }
}

static void glueEdgesInFaces(GModel *model,
                             std::multimap<GEdge*, GEdge*> &Unique2Duplicates,
                             std::map<GEdge*, GEdge*> &Duplicates2Unique)
{
  Msg::Debug("Gluing Model Faces");
  for (GModel::fiter it = model->firstFace(); it != model->lastFace(); ++it){
    GFace *f = *it;
    bool aDifferenceExists = false;
    std::list<GEdge*> old = f->edges(), enew;
    for (std::list<GEdge*>::iterator eit = old.begin(); eit !=old.end(); eit++){
      GEdge *temp = Duplicates2Unique[*eit];
      enew.push_back(temp);
      if (temp != *eit){
        aDifferenceExists = true;
      }
    }
    if (aDifferenceExists){
      Msg::Debug("Model Face %d is re-build", f->tag());
      f->replaceEdges(enew);
    }
  }
}

static void computeDuplicates(GModel *model,
                              std::multimap<GFace*, GFace*> &Unique2Duplicates,
                              std::map<GFace*,GFace*> &Duplicates2Unique,
                              const double &eps)
{
  std::list<GFace*> f;
  f.insert(f.begin(),model->firstFace(),model->lastFace());

  while(!f.empty()){
    GFace *pf = *f.begin();
    Range<double> r = pf->parBounds(0);
    Range<double> s = pf->parBounds(1);
    f.erase(f.begin());
    std::list<GEdge*> pf_edges = pf->edges();
    pf_edges.sort();
    bool found = false;
    for (std::multimap<GFace*,GFace*>::iterator it = Unique2Duplicates.begin();
         it != Unique2Duplicates.end(); ++it){
      GFace *unique = it->first;
      std::list<GEdge*> unique_edges = unique->edges();
      if (pf->geomType() == unique->geomType() &&
          unique_edges.size() == pf_edges.size()){
        unique_edges.sort();
        std::list<GEdge*>::iterator it_pf = pf_edges.begin();
        std::list<GEdge*>::iterator it_unique = unique_edges.begin();
        bool all_similar = true;
        // first check faces that have same edges
        for (; it_pf !=  pf_edges.end() ;  ++it_pf,it_unique++){
          if (*it_pf != *it_unique) all_similar = false;
        }
        if (all_similar){
          if (unique->geomType() == GEntity::Plane && pf->geomType() == GEntity::Plane){
            found = true;
            Unique2Duplicates.insert(std::make_pair(unique,pf));
            Duplicates2Unique[pf] = unique;
            break;
          }
          double t[2]={0,0};
          // FIXME: evaluate a point on the surface (use e.g. buildRepresentationCross)
          const double d = 1.0;
          if (t[0] >= r.low() && t[0] <= r.high() &&
              t[1] >= s.low() && t[1] <= s.high() && d <= eps) {
            found = true;
            Unique2Duplicates.insert(std::make_pair(unique,pf));
            Duplicates2Unique[pf] = unique;
            break;
          }
        }
      }
    }
    if (!found) {
      Unique2Duplicates.insert(std::make_pair(pf,pf));
      Duplicates2Unique[pf] = pf;
    }
  }
}

static void glueFacesInRegions(GModel *model,
                               std::multimap<GFace*, GFace*> &Unique2Duplicates,
                               std::map<GFace*, GFace*> &Duplicates2Unique)
{
  Msg::Debug("Gluing Regions");
  for (GModel::riter it = model->firstRegion(); it != model->lastRegion();++it){
    GRegion *r = *it;
    bool aDifferenceExists = false;
    std::list<GFace*> old = r->faces(), fnew;
    for (std::list<GFace*>::iterator fit = old.begin(); fit != old.end(); fit++){
      std::map<GFace*, GFace*>::iterator itR = Duplicates2Unique.find(*fit);
      if (itR == Duplicates2Unique.end()){
        Msg::Error("Error in the gluing process");
        return;
      }
      GFace *temp = itR->second;;
      fnew.push_back(temp);
      if (temp != *fit){
        aDifferenceExists = true;
      }
    }
    if (aDifferenceExists){
      Msg::Debug("Model Region %d is re-build", r->tag());
      r->replaceFaces (fnew);
    }
  }
}

void GModel::glue(double eps)
{
  {
    std::multimap<GVertex*,GVertex*> Unique2Duplicates;
    std::map<GVertex*,GVertex*> Duplicates2Unique;
    computeDuplicates(this, Unique2Duplicates, Duplicates2Unique, eps);
    glueVerticesInEdges(this, Unique2Duplicates, Duplicates2Unique);
  }
  {
    std::multimap<GEdge*,GEdge*> Unique2Duplicates;
    std::map<GEdge*,GEdge*> Duplicates2Unique;
    computeDuplicates(this, Unique2Duplicates, Duplicates2Unique, eps);
    glueEdgesInFaces(this, Unique2Duplicates, Duplicates2Unique);
  }
  {
    std::multimap<GFace*,GFace*> Unique2Duplicates;
    std::map<GFace*,GFace*> Duplicates2Unique;
    computeDuplicates(this, Unique2Duplicates, Duplicates2Unique, eps);
    glueFacesInRegions(this, Unique2Duplicates, Duplicates2Unique);
  }
}

GEdge *getNewModelEdge(GFace *gf1, GFace *gf2,
                       std::map<std::pair<int, int>, GEdge*> &newEdges)
{
  int t1 = gf1 ? gf1->tag() : -1;
  int t2 = gf2 ? gf2->tag() : -1;
  int i1 = std::min(t1, t2);
  int i2 = std::max(t1, t2);

  if(i1 == i2) return 0;

  std::map<std::pair<int, int>, GEdge*>::iterator it =
    newEdges.find(std::make_pair(i1, i2));
  if(it == newEdges.end()){
    discreteEdge *ge = new discreteEdge
      (GModel::current(), GModel::current()->getMaxElementaryNumber(1) + 1, 0, 0);
    GModel::current()->add(ge);
    newEdges[std::make_pair(i1, i2)] = ge;
    return ge;
  }
  else
    return it->second;
}

#if defined(HAVE_MESH)

void recurClassifyEdges(MTri3 *t, std::map<MTriangle*, GFace*> &reverse,
                        std::map<MLine*, GEdge*, compareMLinePtr> &lines,
                        std::set<MLine*> &touched, std::set<MTri3*> &trisTouched,
                        std::map<std::pair<int, int>, GEdge*> &newEdges)
{
  if(!t->isDeleted()){
    trisTouched.erase(t);
    t->setDeleted(true);
    GFace *gf1 = reverse[t->tri()];
    for(int i = 0; i < 3; i++){
      GFace *gf2 = 0;
      MTri3 *tn = t->getNeigh(i);
      if(tn)
        gf2 = reverse[tn->tri()];
      edgeXface exf(t, i);
      MLine ml(exf.v[0], exf.v[1]);
      std::map<MLine*, GEdge*, compareMLinePtr>::iterator it = lines.find(&ml);
      if(it != lines.end()){
        if(touched.find(it->first) == touched.end()){
          GEdge *ge =  getNewModelEdge(gf1, gf2, newEdges);
          if(ge) ge->lines.push_back(it->first);
          touched.insert(it->first);
        }
      }
      if(tn)
        recurClassifyEdges(tn, reverse, lines, touched, trisTouched,newEdges);
    }
  }
}

void recurClassify(MTri3 *t, GFace *gf,
                   std::map<MLine*, GEdge*, compareMLinePtr> &lines,
                   std::map<MTriangle*, GFace*> &reverse)
{
  if(!t->isDeleted()){
    gf->triangles.push_back(t->tri());
    reverse[t->tri()] = gf;
    t->setDeleted(true);
    for(int i = 0; i < 3; i++){
      MTri3 *tn = t->getNeigh(i);
      if(tn){
        edgeXface exf(t, i);
        MLine ml(exf.v[0], exf.v[1]);
        std::map<MLine*, GEdge*, compareMLinePtr>::iterator it = lines.find(&ml);
        if(it == lines.end())
          recurClassify(tn, gf, lines, reverse);
      }
    }
  }
}

#endif

void GModel::detectEdges(double _tresholdAngle)
{
#if defined(HAVE_MESH)
  e2t_cont adj;
  std::vector<MTriangle*> elements;
  std::vector<edge_angle> edges_detected, edges_lonly;
  for(GModel::fiter it = GModel::current()->firstFace();
      it != GModel::current()->lastFace(); ++it)
    elements.insert(elements.end(), (*it)->triangles.begin(),
                    (*it)->triangles.end());
  buildEdgeToTriangle(elements, adj);
  buildListOfEdgeAngle(adj, edges_detected, edges_lonly);
  GEdge *selected = new discreteEdge
    (this, getMaxElementaryNumber(1) + 1, 0, 0);
  add(selected);

  for(unsigned int i = 0; i < edges_detected.size(); i++){
    edge_angle ea = edges_detected[i];
    if(ea.angle <= _tresholdAngle) break;
    selected->lines.push_back(new MLine(ea.v1, ea.v2));
  }

  for(unsigned int i = 0 ; i < edges_lonly.size(); i++){
    edge_angle ea = edges_lonly[i];
    selected->lines.push_back(new MLine(ea.v1, ea.v2));
  }
  std::set<GFace*> _temp;
  _temp.insert(faces.begin(),faces.end());
  classifyFaces(_temp);
  remove(selected);
  //  delete selected;
#endif
}

void GModel::classifyFaces(std::set<GFace*> &_faces)
{
#if defined(HAVE_MESH)
  std::map<MLine*, GEdge*, compareMLinePtr> lines;

  for(GModel::eiter it = GModel::current()->firstEdge();
      it != GModel::current()->lastEdge(); ++it){
    for(unsigned int i = 0; i < (*it)->lines.size();i++)
      lines[(*it)->lines[i]] = *it;
  }

  std::map<MTriangle*, GFace*> reverse_old;
  std::list<MTri3*> tris;
  {
    std::set<GFace*>::iterator it = _faces.begin();
    while(it != _faces.end()){
      GFace *gf = *it;
      for(unsigned int i = 0; i < gf->triangles.size(); i++){
        tris.push_back(new MTri3(gf->triangles[i], 0));
        reverse_old[gf->triangles[i]] = gf;
      }
      gf->triangles.clear();
      gf->mesh_vertices.clear();
      ++it;
    }
  }
  if(tris.empty()) return;

  connectTriangles(tris);

  std::map<MTriangle*, GFace*> reverse;
  std::multimap<GFace*, GFace*> replacedBy;
  // color all triangles
  std::list<MTri3*> ::iterator it = tris.begin();
  std::list<GFace*> newf;
  while(it != tris.end()){
    if(!(*it)->isDeleted()){
      discreteFace *gf = new discreteFace
        (GModel::current(), GModel::current()->getMaxElementaryNumber(2) + 1);
      recurClassify(*it, gf, lines, reverse);
      GModel::current()->add(gf);
      newf.push_back(gf);

      for (unsigned int i = 0; i < gf->triangles.size(); i++){
        replacedBy.insert(std::make_pair(reverse_old[gf->triangles[i]],gf));
      }
    }
    ++it;
  }

  // now we have all faces coloured. If some regions were existing, replace
  // their faces by the new ones

  for (riter rit = firstRegion(); rit != lastRegion(); ++rit){
    std::list<GFace *> _xfaces = (*rit)->faces();
    std::set<GFace *> _newFaces;
    for (std::list<GFace *>::iterator itf = _xfaces.begin(); itf != _xfaces.end(); ++itf){
      std::multimap<GFace*, GFace*>::iterator itLow = replacedBy.lower_bound(*itf);
      std::multimap<GFace*, GFace*>::iterator itUp = replacedBy.upper_bound(*itf);
      for (; itLow != itUp; ++itLow)
        _newFaces.insert(itLow->second);
    }
    std::list<GFace *> _temp;
    _temp.insert(_temp.begin(),_newFaces.begin(),_newFaces.end());
    (*rit)->set(_temp);
  }

  // color some lines
  it = tris.begin();
  while(it != tris.end()){
    (*it)->setDeleted(false);
    ++it;
  }

  // classify edges that are bound by different GFaces
  std::map<std::pair<int, int>, GEdge*> newEdges;
  std::set<MLine*> touched;
  std::set<MTri3*> trisTouched;
  // bug fix : multiply connected domains

  trisTouched.insert(tris.begin(),tris.end());
  while(!trisTouched.empty())
    recurClassifyEdges(*trisTouched.begin(), reverse, lines, touched, trisTouched,newEdges);

  std::map<discreteFace*,std::vector<int> > newFaceTopology;

  // check if new edges should not be splitted
  // splitted if composed of several open or closed edges

  std::map<MVertex*,GVertex*> modelVertices;

  for (std::map<std::pair<int, int>, GEdge*>::iterator ite = newEdges.begin();
       ite != newEdges.end() ; ++ite){
    std::list<MLine*> allSegments;
    for(unsigned int i = 0; i < ite->second->lines.size(); i++)
      allSegments.push_back(ite->second->lines[i]);

    while (!allSegments.empty()) {
      std::list<MLine*> segmentsForThisDiscreteEdge;
      MVertex *vB = (*allSegments.begin())->getVertex(0);
      MVertex *vE = (*allSegments.begin())->getVertex(1);
      segmentsForThisDiscreteEdge.push_back(*allSegments.begin());
      allSegments.erase(allSegments.begin());
      while(1){
        bool found = false;
        for (std::list<MLine*>::iterator it = allSegments.begin();
             it != allSegments.end(); ++it){
          MVertex *v1 = (*it)->getVertex(0);
          MVertex *v2 = (*it)->getVertex(1);
          if (v1 == vE || v2 == vE){
            segmentsForThisDiscreteEdge.push_back(*it);
            if (v2 == vE) (*it)->reverse();
            vE = (v1 == vE) ? v2 : v1;
            found = true;
            allSegments.erase(it);
            break;
          }
          if (v1 == vB || v2 == vB){
            segmentsForThisDiscreteEdge.push_front(*it);
            if (v1 == vB) (*it)->reverse();
            vB = (v1 == vB) ? v2 : v1;
            found = true;
            allSegments.erase(it);
            break;
          }
        }
        if (vE == vB)break;
        if (!found)break;
      }

      std::map<MVertex*,GVertex*>::iterator itMV = modelVertices.find(vB);
      if (itMV == modelVertices.end()){
        GVertex *newGv = new discreteVertex
          (GModel::current(), GModel::current()->getMaxElementaryNumber(0) + 1);
        newGv->mesh_vertices.push_back(vB);
        vB->setEntity(newGv);
        newGv->points.push_back(new MPoint(vB));
        GModel::current()->add(newGv);
        modelVertices[vB] = newGv;
      }
      itMV = modelVertices.find(vE);
      if (itMV == modelVertices.end()){
        GVertex *newGv = new discreteVertex
          (GModel::current(), GModel::current()->getMaxElementaryNumber(0) + 1);
        newGv->mesh_vertices.push_back(vE);
        newGv->points.push_back(new MPoint(vE));
        vE->setEntity(newGv);
        GModel::current()->add(newGv);
        modelVertices[vE] = newGv;
      }

      GEdge *newGe = new discreteEdge
        (GModel::current(), GModel::current()->getMaxElementaryNumber(1) + 1,
         modelVertices[vB], modelVertices[vE]);
      newGe->lines.insert(newGe->lines.end(), segmentsForThisDiscreteEdge.begin(),
                          segmentsForThisDiscreteEdge.end());

      for (std::list<MLine*>::iterator itL =  segmentsForThisDiscreteEdge.begin();
           itL !=  segmentsForThisDiscreteEdge.end(); ++itL){
        if((*itL)->getVertex(0)->onWhat()->dim() != 0){
          newGe->mesh_vertices.push_back((*itL)->getVertex(0));
          (*itL)->getVertex(0)->setEntity(newGe);
        }
      }

      GModel::current()->add(newGe);
      discreteFace *gf1 = dynamic_cast<discreteFace*>
        (GModel::current()->getFaceByTag(ite->first.first));
      discreteFace *gf2 = dynamic_cast<discreteFace*>
        (GModel::current()->getFaceByTag(ite->first.second));
      if (gf1)newFaceTopology[gf1].push_back(newGe->tag());
      if (gf2)newFaceTopology[gf2].push_back(newGe->tag());
    }
  }

  std::map<discreteFace*,std::vector<int> >::iterator itFT =  newFaceTopology.begin();
  for (;itFT != newFaceTopology.end();++itFT){
    itFT->first->setBoundEdges(this, itFT->second);
  }

  for (std::map<std::pair<int, int>, GEdge*>::iterator it = newEdges.begin();
       it != newEdges.end(); ++it){
    GEdge *ge = it->second;
    GModel::current()->remove(ge);
    //    delete ge;
  }

  it = tris.begin();
  while(it != tris.end()){
    delete *it;
    ++it;
  }

  // delete empty mesh faces and reclasssify
  std::set<GFace*, GEntityLessThan> fac = faces;
  for (fiter fit = fac.begin() ; fit !=fac.end() ; ++fit){
    std::set<MVertex *> _verts;
    (*fit)->mesh_vertices.clear();
    for (unsigned int i = 0; i < (*fit)->triangles.size(); i++){
      for (int j = 0; j < 3; j++){
        if ((*fit)->triangles[i]->getVertex(j)->onWhat()->dim() > 1){
          (*fit)->triangles[i]->getVertex(j)->setEntity(*fit);
          _verts.insert((*fit)->triangles[i]->getVertex(j));
        }
      }
    }
    if ((*fit)->triangles.size())
      (*fit)->mesh_vertices.insert((*fit)->mesh_vertices.begin(),
                                   _verts.begin(), _verts.end());
    else
      remove(*fit);
  }
#endif
}

void GModel::createPartitionBoundaries(int createGhostCells, int createAllDims)
{
#if (defined(HAVE_CHACO) || defined(HAVE_METIS)) && defined(HAVE_MESH)
  CreatePartitionBoundaries(this, createGhostCells, createAllDims);
#endif
}

void GModel::addHomologyRequest(const std::string &type,
                                std::vector<int> &domain,
                                std::vector<int> &subdomain,
                                std::vector<int> &dim)
{
  typedef std::pair<std::vector<int>, std::vector<int> > dpair;
  typedef std::pair<std::string, std::vector<int> > tpair;
  dpair p(domain, subdomain);
  tpair p2(type, dim);
  _homologyRequests.insert(std::pair<dpair, tpair>(p, p2));
}

void GModel::computeHomology()
{
  if(_homologyRequests.empty()) return;

#if defined(HAVE_KBIPACK)
  double t1 = Cpu();

  // find unique domain/subdomain requests
  typedef std::pair<std::vector<int>, std::vector<int> > dpair;
  typedef std::pair<std::string, std::vector<int> > tpair;
  std::set<dpair> domains;
  for(std::multimap<dpair, tpair>::iterator it = _homologyRequests.begin();
      it != _homologyRequests.end(); it++)
    domains.insert(it->first);
  Msg::Info("Number of cell complexes to construct: %d", domains.size());

  for(std::set<dpair>::iterator it = domains.begin(); it != domains.end(); it++){
    std::pair<std::multimap<dpair, tpair>::iterator,
              std::multimap<dpair, tpair>::iterator> itp =
      _homologyRequests.equal_range(*it);
    bool prepareToRestore = (itp.first != --itp.second);
    itp.second++;
    std::vector<int> imdomain;
    Homology* homology = new Homology(this, itp.first->first.first,
                                      itp.first->first.second, imdomain,
                                      prepareToRestore);

    for(std::multimap<dpair, tpair>::iterator itt = itp.first;
        itt != itp.second; itt++){
      std::string type = itt->second.first;
      std::vector<int> dim0 = itt->second.second;
      std::vector<int> dim;

      std::stringstream ss;
      for(unsigned int i = 0; i < dim0.size(); i++) {
        int d = dim0.at(i);
        if(d >= 0 && d <= getDim()) {
          dim.push_back(d);
          ss << "H";
          if(type == "Homology") ss << "_";
          if(type == "Cohomology") ss << "^";
          ss << d;
          if(i < dim0.size()-1 && dim0.at(i+1) >=0 && dim0.at(i+1) <= getDim())
            ss << ", ";
        }
      }
      std::string dims = ss.str();

      if(type != "Homology" && type != "Cohomology" && type != "Betti") {
        Msg::Error("Unknown type of homology computation: %s", type.c_str());
      }
      else if(dim.empty() || type == "Betti") {
        homology->findBettiNumbers();
      }
      else if(type == "Homology" && !homology->isHomologyComputed(dim)) {

        homology->findHomologyBasis(dim);

        Msg::Info("Homology space basis chains to save: %s.", dims.c_str());
        for(unsigned int i = 0; i < dim.size(); i++) {
          homology->addChainsToModel(dim.at(i));
        }
      }
      else if(type == "Cohomology" && !homology->isCohomologyComputed(dim)) {

        homology->findCohomologyBasis(dim);

        Msg::Info("Cohomology space basis cochains to save: %s.", dims.c_str());
        for(unsigned int i = 0; i < dim.size(); i++) {
          homology->addCochainsToModel(dim.at(i));
        }
      }
    }
    _pruneMeshVertexAssociations();
    delete homology;
  }
  Msg::Info("");

  double t2 = Cpu();
  Msg::StatusBar(true, "Done homology and cohomology computation (%g s)",
                 t2 - t1);

#else
  Msg::Error("Homology computation requires KBIPACK");
#endif
}

void GModel::setCompoundVisibility()
{
  // force visibility status of compound entities

  for(eiter eit = firstEdge(); eit != lastEdge(); eit++){
    GEdge *ge = *eit;
    if (ge->getCompound()){
      if(CTX::instance()->geom.hideCompounds) {
        // use visibility info of compound edge if this edge belongs to it
        ge->setVisibility(0, true);
        bool val2 = ge->getCompound()->getVisibility();
        if(ge->getCompound()->getBeginVertex())
          ge->getCompound()->getBeginVertex()->setVisibility(val2);
        if(ge->getCompound()->getEndVertex())
          ge->getCompound()->getEndVertex()->setVisibility(val2);
      }
      else {
        ge->setVisibility(1, true);
      }
    }
  }

  for(fiter fit = firstFace(); fit != lastFace(); fit++){
    GFace *gf = *fit;
    if (gf->getCompound()){
      if(CTX::instance()->geom.hideCompounds) {
        gf->setVisibility(0, true);
        std::list<GEdge*> edgesComp = gf->getCompound()->edges();
        bool val2 = gf->getCompound()->getVisibility();
        // show edges of the compound surface
        for (std::list<GEdge*>::iterator it = edgesComp.begin(); it != edgesComp.end(); ++it) {
          if((*it)->getCompound())
            (*it)->getCompound()->setVisibility(val2, true);
          else
            (*it)->setVisibility(val2, true);
        }
      }
      else {
        gf->setVisibility(1, true);
      }
    }
  }

}
