#include <mystdlib.h>
#include <atomic>
#include "meshing.hpp"

namespace netgen
{

  static mutex buildsearchtree_mutex;

  Mesh :: Mesh ()
    : topology(*this), surfarea(*this)
  {
    // volelements.SetName ("vol elements");
    // surfelements.SetName ("surf elements");
    // points.SetName ("meshpoints");

    boundaryedges = NULL;
    surfelementht = NULL; 
    segmentht = NULL;

    lochfunc = NULL;
    mglevels = 1;
    elementsearchtree = NULL;
    elementsearchtreets = NextTimeStamp();
    majortimestamp = timestamp = NextTimeStamp();
    hglob = 1e10;
    hmin = 0;
    numvertices = -1;
    dimension = 3;

    // topology = new MeshTopology (*this);
    curvedelems = new CurvedElements (*this);
    clusters = new AnisotropicClusters (*this);
    ident = new Identifications (*this);

    hpelements = NULL;
    coarsemesh = NULL;

    ps_startelement = 0;

    geomtype = NO_GEOM;

    bcnames.SetSize(0);
    cd2names.SetSize(0);

#ifdef PARALLEL
    this->comm = MPI_COMM_WORLD;
    paralleltop = new ParallelMeshTopology (*this);
#endif
  }


  Mesh :: ~Mesh()
  {
    // cout << "******************** deleting Mesh **********" << endl;
    delete lochfunc;
    delete boundaryedges;
    delete surfelementht;
    delete segmentht;
    delete curvedelems;
    delete clusters;
    // delete topology;
    delete ident;
    delete elementsearchtree;
    delete coarsemesh;
    delete hpelements;

    for (int i = 0; i < materials.Size(); i++)
      delete materials[i];
    for(int i = 0; i < userdata_int.Size(); i++)
      delete userdata_int[i];
    for(int i = 0; i < userdata_double.Size(); i++)
      delete userdata_double[i];

    for (int i = 0; i < bcnames.Size(); i++ )
      delete bcnames[i];

    for (int i = 0; i < cd2names.Size(); i++)
      delete cd2names[i];

#ifdef PARALLEL
    delete paralleltop;
#endif
  }


  Mesh & Mesh :: operator= (const Mesh & mesh2)
  {
    points = mesh2.points;
    // eltyps = mesh2.eltyps;
    segments = mesh2.segments;
    surfelements = mesh2.surfelements;
    volelements = mesh2.volelements;
    lockedpoints = mesh2.lockedpoints;
    facedecoding = mesh2.facedecoding;
    dimension = mesh2.dimension;

    bcnames.SetSize( mesh2.bcnames.Size() );
    for ( int i = 0; i < mesh2.bcnames.Size(); i++ )
      if ( mesh2.bcnames[i] ) bcnames[i] = new string ( *mesh2.bcnames[i] );
      else bcnames[i] = 0;

    cd2names.SetSize(mesh2.cd2names.Size());
    for (int i=0; i < mesh2.cd2names.Size(); i++)
      if (mesh2.cd2names[i]) cd2names[i] = new string(*mesh2.cd2names[i]);
      else cd2names[i] = 0;

    return *this;
  }


  void Mesh :: DeleteMesh()
  {
    NgLock lock(mutex);
    lock.Lock();
    points.SetSize(0);
    segments.SetSize(0);
    surfelements.SetSize(0);
    volelements.SetSize(0);
    lockedpoints.SetSize(0);
    // surfacesonnode.SetSize(0);

    delete boundaryedges;
    boundaryedges = NULL;

    openelements.SetSize(0);
    facedecoding.SetSize(0);

    delete ident;
    ident = new Identifications (*this);
    // delete topology;
    // topology = new MeshTopology (*this);
    topology = MeshTopology (*this);
    delete curvedelems;
    curvedelems = new CurvedElements (*this);
    delete clusters;
    clusters = new AnisotropicClusters (*this);

    for ( int i = 0; i < bcnames.Size(); i++ )
      if ( bcnames[i] ) delete bcnames[i];
    for (int i= 0; i< cd2names.Size(); i++)
      if (cd2names[i]) delete cd2names[i];

#ifdef PARALLEL
    delete paralleltop;
    paralleltop = new ParallelMeshTopology (*this);
#endif

    lock.UnLock();

    timestamp = NextTimeStamp();
  }


  void Mesh :: ClearSurfaceElements()
  { 
    surfelements.SetSize(0); 
    for (int i = 0; i < facedecoding.Size(); i++)
      facedecoding[i].firstelement = -1;

    timestamp = NextTimeStamp();
  }



  PointIndex Mesh :: AddPoint (const Point3d & p, int layer)
  { 
    return AddPoint (p, layer, INNERPOINT);
    /*
    NgLock lock(mutex);
    lock.Lock();

    timestamp = NextTimeStamp();

    PointIndex pi = points.End();
    points.Append ( MeshPoint (p, layer, INNERPOINT) ); 

    lock.UnLock();

    return pi;
    */
  }

  PointIndex Mesh :: AddPoint (const Point3d & p, int layer, POINTTYPE type)
  { 
    NgLock lock(mutex);
    lock.Lock();

    timestamp = NextTimeStamp();

    PointIndex pi = points.End();
    points.Append ( MeshPoint (p, layer, type) ); 

    lock.UnLock();

    return pi;
  }

  /*
#ifdef PARALLEL
  PointIndex Mesh :: AddPoint (const Point3d & p, bool isghost,  int layer)
  { 
    NgLock lock(mutex);
    lock.Lock();

    timestamp = NextTimeStamp();

    PointIndex pi = points.Size() + PointIndex::BASE;
    points.Append ( MeshPoint (p, layer, INNERPOINT) ); 

    lock.UnLock();

    return pi;
  }

  PointIndex Mesh :: AddPoint (const Point3d & p, bool isghost, int layer, POINTTYPE type)
  { 
    NgLock lock(mutex);
    lock.Lock();

    timestamp = NextTimeStamp();

    PointIndex pi = points.Size() + PointIndex::BASE;
    points.Append ( MeshPoint (p, layer, type) ); 

    lock.UnLock();

    return pi;
  }

#endif
  */


  SegmentIndex Mesh :: AddSegment (const Segment & s)
  { 
    NgLock lock(mutex);	
    lock.Lock();
    timestamp = NextTimeStamp();

    int maxn = max2 (s[0], s[1]);
    maxn += 1-PointIndex::BASE;

    /*
      if (maxn > ptyps.Size())
      {
      int maxo = ptyps.Size();
      ptyps.SetSize (maxn);
      for (int i = maxo; i < maxn; i++)
      ptyps[i] = INNERPOINT;
      }

      if (ptyps[s[0]] > EDGEPOINT) ptyps[s[0]] = EDGEPOINT;
      if (ptyps[s[1]] > EDGEPOINT) ptyps[s[1]] = EDGEPOINT;
    */

    if (maxn <= points.Size())
      {
        if (points[s[0]].Type() > EDGEPOINT)
          points[s[0]].SetType (EDGEPOINT);
        if (points[s[1]].Type() > EDGEPOINT)
          points[s[1]].SetType (EDGEPOINT);
      }
    /*
      else
      {
      cerr << "edge points nrs > points.Size" << endl;
      }
    */

    SegmentIndex si = segments.Size();
    segments.Append (s); 

    lock.UnLock();
    return si;
  }

  SurfaceElementIndex Mesh :: AddSurfaceElement (const Element2d & el)
  {     
    NgLock lock(mutex);
    lock.Lock();
    timestamp = NextTimeStamp();

    int maxn = el[0];
    for (int i = 1; i < el.GetNP(); i++)
      if (el[i] > maxn) maxn = el[i];

    maxn += 1-PointIndex::BASE;

    /*
      if (maxn > ptyps.Size())
      {
      int maxo = ptyps.Size();
      ptyps.SetSize (maxn);
      for (i = maxo+PointIndex::BASE; 
      i < maxn+PointIndex::BASE; i++)
      ptyps[i] = INNERPOINT;

      }
    */
    if (maxn <= points.Size())
      {
        for (int i = 0; i < el.GetNP(); i++)
          if (points[el[i]].Type() > SURFACEPOINT)
            points[el[i]].SetType(SURFACEPOINT);
      }
    /*
      else
      {
      cerr << "surf points nrs > points.Size" << endl;      
      }
    */

    SurfaceElementIndex si = surfelements.Size();
    surfelements.Append (el); 

    if (el.index > facedecoding.Size())
      cerr << "has no facedecoding: fd.size = " << facedecoding.Size() << ", ind = " << el.index << endl;

    surfelements.Last().next = facedecoding[el.index-1].firstelement;
    facedecoding[el.index-1].firstelement = si;

    if (SurfaceArea().Valid())
      SurfaceArea().Add (el);

    lock.UnLock();
    return si;
  }

  void Mesh :: SetSurfaceElement (SurfaceElementIndex sei, const Element2d & el)
  {
    int maxn = el[0];
    for (int i = 1; i < el.GetNP(); i++)
      if (el[i] > maxn) maxn = el[i];

    maxn += 1-PointIndex::BASE;

    if (maxn <= points.Size())
      {
        for (int i = 0; i < el.GetNP(); i++)
          if (points[el[i]].Type() > SURFACEPOINT)
            points[el[i]].SetType(SURFACEPOINT);
      }

    surfelements[sei] = el;
    if (el.index > facedecoding.Size())
      cerr << "has no facedecoding: fd.size = " << facedecoding.Size() << ", ind = " << el.index << endl;

    // add lock-free to list ... slow, call RebuildSurfaceElementLists later
    /*
    surfelements[sei].next = facedecoding[el.index-1].firstelement;
    auto & head = reinterpret_cast<atomic<SurfaceElementIndex>&> (facedecoding[el.index-1].firstelement);
    while (!head.compare_exchange_weak (surfelements[sei].next, sei))
      ;
    */

    /*
    if (SurfaceArea().Valid())
      SurfaceArea().Add (el);
    */
  }


  ElementIndex Mesh :: AddVolumeElement (const Element & el)
  { 
    NgLock lock(mutex);
    lock.Lock();

    int maxn = el[0];
    for (int i = 1; i < el.GetNP(); i++)
      if (el[i] > maxn) maxn = el[i];

    maxn += 1-PointIndex::BASE;

    /*
      if (maxn > ptyps.Size())
      {
      int maxo = ptyps.Size();
      ptyps.SetSize (maxn);
      for (i = maxo+PointIndex::BASE; 
      i < maxn+PointIndex::BASE; i++)
      ptyps[i] = INNERPOINT;
      }
    */
    /*
      if (maxn > points.Size())
      {
      cerr << "add vol element before point" << endl;
      }
    */

    int ve = volelements.Size();

    volelements.Append (el); 
    volelements.Last().flags.illegal_valid = 0;

    // while (volelements.Size() > eltyps.Size())
    // eltyps.Append (FREEELEMENT);

    timestamp = NextTimeStamp();

    lock.UnLock();
    return ve;
  }

  void Mesh :: SetVolumeElement (ElementIndex ei, const Element & el)
  {
    /*
    int maxn = el[0];
    for (int i = 1; i < el.GetNP(); i++)
      if (el[i] > maxn) maxn = el[i];

    maxn += 1-PointIndex::BASE;
    */

    volelements[ei]  = el;
    volelements.Last().flags.illegal_valid = 0;
  }





  void Mesh :: Save (const string & filename) const
  {
    ostream * outfile;
    if (filename.find(".vol.gz")!=string::npos)
      outfile = new ogzstream(filename.c_str());
    else if (filename.find(".vol")!=string::npos)
      outfile = new ofstream(filename.c_str());
    else
      outfile = new ogzstream((filename+".vol.gz").c_str());

    Save(*outfile);
    delete outfile;
  }



  void Mesh :: Save (ostream & outfile) const
  {
    int i, j;

    double scale = 1;  // globflags.GetNumFlag ("scale", 1);
    int inverttets = 0;  // globflags.GetDefineFlag ("inverttets");
    int invertsurf = 0;  // globflags.GetDefineFlag ("invertsurfacemesh");



    outfile << "mesh3d" << "\n";

    outfile << "dimension\n" << GetDimension() << "\n";

    outfile << "geomtype\n" << int(geomtype) << "\n";


    outfile << "\n";
    outfile << "# surfnr    bcnr   domin  domout      np      p1      p2      p3"
            << "\n";


    switch (geomtype)
      {
      case GEOM_STL:
        outfile << "surfaceelementsgi" << "\n";
        break;
      case GEOM_OCC: case GEOM_ACIS:
        outfile << "surfaceelementsuv" << "\n";
        break;
      default:
        outfile << "surfaceelements" << "\n";
      }

    outfile << GetNSE() << "\n";

    SurfaceElementIndex sei;
    for (sei = 0; sei < GetNSE(); sei++)
      {
        if ((*this)[sei].GetIndex())
          {
            outfile << " " << GetFaceDescriptor((*this)[sei].GetIndex ()).SurfNr()+1;
            outfile << " " << GetFaceDescriptor((*this)[sei].GetIndex ()).BCProperty();
            outfile << " " << GetFaceDescriptor((*this)[sei].GetIndex ()).DomainIn();
            outfile << " " << GetFaceDescriptor((*this)[sei].GetIndex ()).DomainOut();
          }
        else
          outfile << " 0 0 0";

        Element2d sel = (*this)[sei];
        if (invertsurf)
          sel.Invert();

        outfile << " " << sel.GetNP();
        for (j = 0; j < sel.GetNP(); j++)
          outfile << " " << sel[j];

        switch (geomtype)
          {
          case GEOM_STL:
            for (j = 1; j <= sel.GetNP(); j++)
              outfile << " " << sel.GeomInfoPi(j).trignum;
            break;
          case GEOM_OCC: case GEOM_ACIS:
            for (j = 1; j <= sel.GetNP(); j++)
              {
                outfile << " " << sel.GeomInfoPi(j).u;
                outfile << " " << sel.GeomInfoPi(j).v;
              }
            break;
          default:
            ; 
          }
        outfile << "\n";
      }

    outfile << "\n" << "\n";
    outfile << "#  matnr      np      p1      p2      p3      p4" << "\n";
    outfile << "volumeelements" << "\n";
    outfile << GetNE() << "\n";

    for (ElementIndex ei = 0; ei < GetNE(); ei++)
      {
        outfile << (*this)[ei].GetIndex();
        outfile << " " << (*this)[ei].GetNP();

        Element el = (*this)[ei];
        if (inverttets) el.Invert();

        for (j = 0; j < el.GetNP(); j++)
	  outfile << " " << el[j];
        outfile << "\n";
      }


    outfile << "\n" << "\n";
    //     outfile << "   surf1   surf2      p1      p2" << "\n";
    outfile << "# surfid  0   p1   p2   trignum1    trignum2   domin/surfnr1    domout/surfnr2   ednr1   dist1   ednr2   dist2 \n";
    outfile << "edgesegmentsgi2" << "\n";
    outfile << GetNSeg() << "\n";

    for (i = 1; i <= GetNSeg(); i++)
      {
        const Segment & seg = LineSegment (i);
        outfile.width(8);
        outfile << seg.si; // 2D: bc number, 3D: wievielte Kante
        outfile.width(8);
        outfile << 0;
        outfile.width(8);
        outfile << seg[0];
        outfile.width(8);
        outfile << seg[1];
        outfile << " ";
        outfile.width(8);
        outfile << seg.geominfo[0].trignum;  // stl dreiecke
        outfile << " ";
        outfile.width(8);
        outfile << seg.geominfo[1].trignum; // << endl;  // stl dreieck

        if (dimension == 3)
          {
            outfile << " ";
            outfile.width(8);
            outfile << seg.surfnr1+1;
            outfile << " ";
            outfile.width(8);
            outfile << seg.surfnr2+1;
          }
        else
          {
            outfile << " ";
            outfile.width(8);
            outfile << seg.domin;
            outfile << " ";
            outfile.width(8);
            outfile << seg.domout;
          }

        outfile << " ";
        outfile.width(8);
        outfile << seg.edgenr;
        outfile << " ";
        outfile.width(12);
        outfile.precision(16);
        outfile << seg.epgeominfo[0].dist;  // splineparameter (2D)
        outfile << " ";
        outfile.width(8);
        outfile.precision(16);
        outfile << seg.epgeominfo[1].edgenr;  // geometry dependent
        outfile << " ";
        outfile.width(12);
        outfile << seg.epgeominfo[1].dist;

        outfile << "\n";
      }


    outfile << "\n" << "\n";
    outfile << "#          X             Y             Z" << "\n";
    outfile << "points" << "\n";
    outfile << GetNP() << "\n";
    outfile.precision(16);
    outfile.setf (ios::fixed, ios::floatfield);
    outfile.setf (ios::showpoint);

    PointIndex pi;
    for (pi = PointIndex::BASE; 
         pi < GetNP()+PointIndex::BASE; pi++)
      {
        outfile.width(22);
        outfile << (*this)[pi](0)/scale << "  ";
        outfile.width(22);
        outfile << (*this)[pi](1)/scale << "  ";
        outfile.width(22);
        outfile << (*this)[pi](2)/scale << "\n";
      }      

    if (ident -> GetMaxNr() > 0)
      {
        outfile << "identifications\n";
        Array<INDEX_2> identpairs;
        int cnt = 0;
        for (i = 1; i <= ident -> GetMaxNr(); i++)
          {
            ident -> GetPairs (i, identpairs);
            cnt += identpairs.Size();
          }
        outfile << cnt << "\n";
        for (i = 1; i <= ident -> GetMaxNr(); i++)
          {
            ident -> GetPairs (i, identpairs);
            for (j = 1; j <= identpairs.Size(); j++)
              {
                outfile.width (8);
                outfile << identpairs.Get(j).I1();
                outfile.width (8);
                outfile << identpairs.Get(j).I2();
                outfile.width (8);
                outfile << i << "\n";
              }
          }

        outfile << "identificationtypes\n";
        outfile << ident -> GetMaxNr() << "\n";
        for (i = 1; i <= ident -> GetMaxNr(); i++)
          {
            int type = ident -> GetType(i);
            outfile << " " << type;
          }
        outfile << "\n";
      }

    int cntmat = 0;
    for (i = 1; i <= materials.Size(); i++)
      if (materials.Get(i) && materials.Get(i)->length())
        cntmat++;

    if (cntmat)
      {
        outfile << "materials" << endl;
        outfile << cntmat << endl;
        for (i = 1; i <= materials.Size(); i++)
          if (materials.Get(i) && materials.Get(i)->length())
            outfile << i << " " << *materials.Get(i) << endl;
      }


    int cntbcnames = 0;
    for ( int ii = 0; ii < bcnames.Size(); ii++ )
      if ( bcnames[ii] ) cntbcnames++;

    if ( cntbcnames )
      {
        outfile << "\n\nbcnames" << endl << bcnames.Size() << endl;
        for ( i = 0; i < bcnames.Size(); i++ )
          outfile << i+1 << "\t" << GetBCName(i) << endl;
        outfile << endl << endl;
      }
    int cntcd2names = 0;
    for (int ii = 0; ii<cd2names.Size(); ii++)
      if(cd2names[ii]) cntcd2names++;

    if(cntcd2names)
      {
	outfile << "\n\ncd2names" << endl << cd2names.Size() << endl;
	for (i=0; i<cd2names.Size(); i++)
	  outfile << i+1 << "\t" << GetCD2Name(i) << endl;
	outfile << endl << endl;
      }

    /*
      if ( GetDimension() == 2 )
      {
      for (i = 1; i <= GetNSeg(); i++)
      {
      const Segment & seg = LineSegment (i);
      if ( ! bcprops.Contains(seg.si) && seg.GetBCName() != "" )
      {
      bcprops.Append(seg.si);
      cntbcnames++;
      }
      }
      }
      else
      {
      for (sei = 0; sei < GetNSE(); sei++)
      {
      if ((*this)[sei].GetIndex())
      {
      int bcp = GetFaceDescriptor((*this)[sei].GetIndex ()).BCProperty();
      string name = GetFaceDescriptor((*this)[sei].GetIndex ()).BCName();
      if ( !bcprops.Contains(bcp) &&
      name != "" )
      {
      bcprops.Append(bcp);
      cntbcnames++;
      }
      }
      }
      }

      bcprops.SetSize(0);
      if ( cntbcnames )
      {
      outfile << "\nbcnames" << endl << cntbcnames << endl;
      if ( GetDimension() == 2 )
      {
      for (i = 1; i <= GetNSeg(); i++)
      {
      const Segment & seg = LineSegment (i);
      if ( ! bcprops.Contains(seg.si) && seg.GetBCName() != "" )
      {
      bcprops.Append(seg.si);
      outfile << seg.si << "\t" << seg.GetBCName() << endl;
      }
      }
      }
      else
      {
      for (sei = 0; sei < GetNSE(); sei++)
      {
      if ((*this)[sei].GetIndex())
      {
      int bcp = GetFaceDescriptor((*this)[sei].GetIndex ()).BCProperty();
      string name = GetFaceDescriptor((*this)[sei].GetIndex ()).BCName();
      if ( !bcprops.Contains(bcp) &&
      name != "" )
      {
      bcprops.Append(bcp);
      outfile << bcp << "\t" << name << endl;
      }
      }
      }
      }
      outfile << endl << endl;
      }
    */

    int cnt_sing = 0;
    for (PointIndex pi = points.Begin(); pi < points.End(); pi++)
      if ((*this)[pi].Singularity()>=1.) cnt_sing++;

    if (cnt_sing)
      {
        outfile << "singular_points" << endl << cnt_sing << endl;
        for (PointIndex pi = points.Begin(); pi < points.End(); pi++)
          if ((*this)[pi].Singularity()>=1.) 
            outfile << int(pi) << "\t" << (*this)[pi].Singularity() << endl;
      }

    cnt_sing = 0;
    for (SegmentIndex si = 0; si < GetNSeg(); si++)
      if ( segments[si].singedge_left ) cnt_sing++;
    if (cnt_sing)
      {
        outfile << "singular_edge_left" << endl << cnt_sing << endl;
        for (SegmentIndex si = 0; si < GetNSeg(); si++)
          if ( segments[si].singedge_left )
            outfile << int(si) << "\t" << segments[si].singedge_left << endl;
      }

    cnt_sing = 0;
    for (SegmentIndex si = 0; si < GetNSeg(); si++)
      if ( segments[si].singedge_right ) cnt_sing++;
    if (cnt_sing)
      {
        outfile << "singular_edge_right" << endl << cnt_sing << endl;
        for (SegmentIndex si = 0; si < GetNSeg(); si++)
          if ( segments[si].singedge_right  )
            outfile << int(si) << "\t" << segments[si].singedge_right << endl;
      }


    cnt_sing = 0;
    for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
      if ( GetFaceDescriptor ((*this)[sei].GetIndex()).domin_singular) 
        cnt_sing++;

    if (cnt_sing)
      {
        outfile << "singular_face_inside" << endl << cnt_sing << endl;
        for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
          if ( GetFaceDescriptor ((*this)[sei].GetIndex()).domin_singular) 
            outfile << int(sei)  << "\t" << 
              GetFaceDescriptor ((*this)[sei].GetIndex()).domin_singular  << endl;
      }

    cnt_sing = 0;
    for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
      if ( GetFaceDescriptor ((*this)[sei].GetIndex()).domout_singular) cnt_sing++;
    if (cnt_sing)
      {
        outfile << "singular_face_outside" << endl << cnt_sing << endl;
        for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
          if ( GetFaceDescriptor ((*this)[sei].GetIndex()).domout_singular) 
            outfile << int(sei) << "\t" 
                    << GetFaceDescriptor ((*this)[sei].GetIndex()).domout_singular << endl;
      }


    // Philippose - 09/07/2009
    // Add mesh face colours to Netgen Vol file format
    // The colours are saved in RGB triplets
    int cnt_facedesc = GetNFD();
    if (cnt_facedesc)
    {
       outfile << endl << endl << "#   Surfnr     Red     Green     Blue" << endl;
       outfile << "face_colours" << endl << cnt_facedesc << endl;

       outfile.precision(8);
       outfile.setf(ios::fixed, ios::floatfield);
       outfile.setf(ios::showpoint);

       for(i = 1; i <= cnt_facedesc; i++)
       {
          outfile.width(8);
          outfile << GetFaceDescriptor(i).SurfNr()+1 << " ";
          outfile.width(12);
          outfile << GetFaceDescriptor(i).SurfColour().X() << " ";
          outfile.width(12);
          outfile << GetFaceDescriptor(i).SurfColour().Y() << " ";
          outfile.width(12);
          outfile << GetFaceDescriptor(i).SurfColour().Z();
          outfile << endl;
       }
    }

    outfile << endl << endl << "endmesh" << endl << endl;
    if (geometry)
      geometry -> SaveToMeshFile (outfile);
  }



  void Mesh :: Load (const string & filename)
  {
    cout << "filename = " << filename << endl;
    istream * infile = NULL;

    if (filename.find(".vol.gz") != string::npos)
      infile = new igzstream (filename.c_str());
    else
      infile = new ifstream (filename.c_str());

    // ifstream infile(filename.c_str());
    if (! (infile -> good()) )
      throw NgException ("mesh file not found");

    Load(*infile);
    delete infile;
  }




  void Mesh :: Load (istream & infile)
  {
    if (! (infile.good()) )
      {
        cout << "cannot load mesh" << endl;
        throw NgException ("mesh file not found");
      }

    char str[100];
    int i, n;

    double scale = 1;  // globflags.GetNumFlag ("scale", 1);
    int inverttets = 0;  // globflags.GetDefineFlag ("inverttets");
    int invertsurf = 0;  // globflags.GetDefineFlag ("invertsurfacemesh");


    facedecoding.SetSize(0);

    bool endmesh = false;
    

    while (infile.good() && !endmesh)
      {
        infile >> str;
        if (strcmp (str, "dimension") == 0)
          {
            infile >> dimension;
          }

        if (strcmp (str, "geomtype") == 0)
          {
            int hi;
            infile >> hi;
            geomtype = GEOM_TYPE(hi);
          }


        if (strcmp (str, "surfaceelements") == 0 || strcmp (str, "surfaceelementsgi")==0 || strcmp (str, "surfaceelementsuv") == 0)
          {
            infile >> n;
            PrintMessage (3, n, " surface elements");

	    bool geominfo = strcmp (str, "surfaceelementsgi") == 0;
	    bool uv = strcmp (str, "surfaceelementsuv") == 0;


            for (i = 1; i <= n; i++)
              {
                int surfnr, bcp, domin, domout, nep, faceind = 0;

                infile >> surfnr >> bcp >> domin >> domout;
                surfnr--;

		bool invert_el = false;
		/*
		if (domin == 0) 
		  {
		    invert_el = true;
		    Swap (domin, domout);
		  }
		*/
		
                for (int j = 1; j <= facedecoding.Size(); j++)
                  if (GetFaceDescriptor(j).SurfNr() == surfnr &&
                      GetFaceDescriptor(j).BCProperty() == bcp &&
                      GetFaceDescriptor(j).DomainIn() == domin &&
                      GetFaceDescriptor(j).DomainOut() == domout)
                    faceind = j;

		// if (facedecoding.Size()) faceind = 1;   // for timing 

                if (!faceind)
                  {
                    faceind = AddFaceDescriptor (FaceDescriptor(surfnr, domin, domout, 0));
                    GetFaceDescriptor(faceind).SetBCProperty (bcp);
                  }

                infile >> nep;
                if (!nep) nep = 3;

                Element2d tri(nep);
                tri.SetIndex(faceind);

                for (int j = 1; j <= nep; j++)
                  infile >> tri.PNum(j);

                if (geominfo)
                  for (int j = 1; j <= nep; j++)
                    infile >> tri.GeomInfoPi(j).trignum;

                if (uv)
                  for (int j = 1; j <= nep; j++)
                    infile >> tri.GeomInfoPi(j).u >> tri.GeomInfoPi(j).v;
		
                if (invertsurf) tri.Invert();
		if (invert_el) tri.Invert();

		AddSurfaceElement (tri);
              }
          }

        if (strcmp (str, "volumeelements") == 0)
          {
            infile >> n;
            PrintMessage (3, n, " volume elements");
            for (i = 1; i <= n; i++)
              {
                Element el(TET);
                int hi, nep;
                infile >> hi;
                if (hi == 0) hi = 1;
                el.SetIndex(hi);
                infile >> nep;
                el.SetNP(nep);
                el.SetCurved (nep != 4);
                for (int j = 0; j < nep; j++)
                  infile >> (int&)(el[j]);

                if (inverttets)
                  el.Invert();

		AddVolumeElement (el);
              }
          }


        if (strcmp (str, "edgesegments") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                Segment seg;
                int hi;
                infile >> seg.si >> hi >> seg[0] >> seg[1];
                AddSegment (seg);
              }
          }



        if (strcmp (str, "edgesegmentsgi") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                Segment seg;
                int hi;
                infile >> seg.si >> hi >> seg[0] >> seg[1]
                       >> seg.geominfo[0].trignum
                       >> seg.geominfo[1].trignum;
                AddSegment (seg);
              }
          }

        if (strcmp (str, "edgesegmentsgi2") == 0)
          {
            int a; 
            infile >> a;
            n=a; 

            PrintMessage (3, n, " curve elements");

            for (i = 1; i <= n; i++)
              {
                Segment seg;
                int hi;
                infile >> seg.si >> hi >> seg[0] >> seg[1]
                       >> seg.geominfo[0].trignum
                       >> seg.geominfo[1].trignum
                       >> seg.surfnr1 >> seg.surfnr2
                       >> seg.edgenr
                       >> seg.epgeominfo[0].dist
                       >> seg.epgeominfo[1].edgenr
                       >> seg.epgeominfo[1].dist;

                seg.epgeominfo[0].edgenr = seg.epgeominfo[1].edgenr;

                seg.domin = seg.surfnr1;
                seg.domout = seg.surfnr2;

                seg.surfnr1--;
                seg.surfnr2--;

                AddSegment (seg);
              }
          }

        if (strcmp (str, "points") == 0)
          {
            infile >> n;
            PrintMessage (3, n, " points");
            for (i = 1; i <= n; i++)
              {
                Point3d p;
                infile >> p.X() >> p.Y() >> p.Z();
                p.X() *= scale;
                p.Y() *= scale;
                p.Z() *= scale;
                AddPoint (p);
              }
	    PrintMessage (3, n, " points done");
          }

        if (strcmp (str, "identifications") == 0)
          {
            infile >> n;
            PrintMessage (3, n, " identifications");
            for (i = 1; i <= n; i++)
              {
                PointIndex pi1, pi2;
                int ind;
                infile >> pi1 >> pi2 >> ind;
                ident -> Add (pi1, pi2, ind);
              }
          }

        if (strcmp (str, "identificationtypes") == 0)
          {
            infile >> n;
            PrintMessage (3, n, " identificationtypes");
            for (i = 1; i <= n; i++)
              {
                int type;
                infile >> type;
                ident -> SetType(i,Identifications::ID_TYPE(type));
              }
          }

        if (strcmp (str, "materials") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                int nr;
                string mat;
                infile >> nr >> mat;
                SetMaterial (nr, mat.c_str());
              }
          }

        if ( strcmp (str, "bcnames" ) == 0 )
          {
            infile >> n;
            Array<int,0> bcnrs(n);
            SetNBCNames(n);
            for ( i = 1; i <= n; i++ )
              {
                string nextbcname;
                infile >> bcnrs[i-1] >> nextbcname;
                bcnames[bcnrs[i-1]-1] = new string(nextbcname);
              }

            if ( GetDimension() == 2 )
              {
                for (i = 1; i <= GetNSeg(); i++)
                  {
                    Segment & seg = LineSegment (i);
                    if ( seg.si <= n )
                      seg.SetBCName (bcnames[seg.si-1]);
                    else
                      seg.SetBCName(0);
                  }
              }
            else
              {
                for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
                  {
                    if ((*this)[sei].GetIndex())
                      {
                        int bcp = GetFaceDescriptor((*this)[sei].GetIndex ()).BCProperty();
                        if ( bcp <= n )
                          GetFaceDescriptor((*this)[sei].GetIndex ()).SetBCName(bcnames[bcp-1]);
                        else
                          GetFaceDescriptor((*this)[sei].GetIndex ()).SetBCName(0);

                      }
                  }

              }
          }

	if ( strcmp (str, "cd2names" ) == 0)
	  {
	    infile >> n;
	    Array<int,0> cd2nrs(n);
	    SetNCD2Names(n);
	    for( i=1; i<=n; i++)
	      {
		string nextcd2name;
		infile >> cd2nrs[i-1] >> nextcd2name;
		cd2names[cd2nrs[i-1]-1] = new string(nextcd2name);
	      }
	    if (GetDimension() == 2)
	      {
		throw NgException("co dim 2 elements not implemented for dimension 2");
	      }
	    else
	      {
		for (i = 1; i<= GetNSeg(); i++)
		  {
		    Segment & seg = LineSegment(i);
		    if ( seg.cd2i <= n )
		      seg.SetBCName (cd2names[seg.edgenr-1]);
		    else
		      seg.SetBCName(0);
		  }
	      }
	  }

        if (strcmp (str, "singular_points") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                PointIndex pi;
                double s; 
                infile >> pi;
                infile >> s; 
                (*this)[pi].Singularity (s);
              }
          }

        if (strcmp (str, "singular_edge_left") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                SegmentIndex si;
                double s; 
                infile >> si;
                infile >> s; 
                (*this)[si].singedge_left = s;
              }
          }
        if (strcmp (str, "singular_edge_right") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                SegmentIndex si;
                double s; 
                infile >> si;
                infile >> s; 
                (*this)[si].singedge_right = s;
              }
          }

        if (strcmp (str, "singular_face_inside") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                SurfaceElementIndex sei;
                double s; 
                infile >> sei;
                infile >> s; 
                GetFaceDescriptor((*this)[sei].GetIndex()).domin_singular = s;
              }
          }

        if (strcmp (str, "singular_face_outside") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                SurfaceElementIndex sei;
                double s; 
                infile >> sei;
                infile >> s; 
                GetFaceDescriptor((*this)[sei].GetIndex()).domout_singular = s;
              }
          }

        // Philippose - 09/07/2009
        // Add mesh face colours to Netgen Vol file format
        // The colours are read in as RGB triplets
        if (strcmp (str, "face_colours") == 0)
        {
           int cnt_facedesc = GetNFD();
           infile >> n;
           if(n == cnt_facedesc)
           {
              for(i = 1; i <= n; i++)
              {
                 int surfnr = 0;
                 Vec3d surfcolour(0.0,1.0,0.0);

                 infile >> surfnr 
                        >> surfcolour.X() 
                        >> surfcolour.Y() 
                        >> surfcolour.Z();

                 surfnr--;

                 if(surfnr > 0) 
                 {
                    for(int facedesc = 1; facedesc <= cnt_facedesc; facedesc++)
                    {
                       if(surfnr == GetFaceDescriptor(facedesc).SurfNr())
                       {
                          GetFaceDescriptor(facedesc).SetSurfColour(surfcolour);
                       }
                    }
                 }
              }
           }
        }

        if (strcmp (str, "endmesh") == 0)
          endmesh = true;



        strcpy (str, "");
      }




    CalcSurfacesOfNode ();
 
    if (ntasks == 1) // sequential run only
      {
	topology.Update();
	clusters -> Update();
      }

    SetNextMajorTimeStamp();
    //  PrintMemInfo (cout);
  }


  void Mesh :: DoArchive (ngstd::Archive & archive)
  {
    archive & dimension;
    archive & points;
    archive & surfelements;
    archive & volelements;
    archive & segments;
    archive & facedecoding;
    archive & materials & bcnames & cd2names;

    archive & *ident;


    // archive geometry
    if (archive.Output())
      {
        ostringstream ost;
        if (geometry)
          geometry -> SaveToMeshFile (ost);
        archive << ost.str();
      }
    else
      {
        string str;
        archive & str;
        istringstream ist(str);
        geometry = geometryregister.LoadFromMeshFile (ist);        
      }
    
    if (archive.Input())
      {
        RebuildSurfaceElementLists();
        
        CalcSurfacesOfNode ();
        if (ntasks == 1) // sequential run only
          {
            topology.Update();
            clusters -> Update();
          }
        SetNextMajorTimeStamp();
      }
  }


  void Mesh :: Merge (const string & filename, const int surfindex_offset)
  {
    ifstream infile(filename.c_str());
    if (!infile.good())
      throw NgException ("mesh file not found");

    Merge(infile,surfindex_offset);

  }



  void Mesh :: Merge (istream & infile, const int surfindex_offset)
  {
    char str[100];
    int i, n;


    int inverttets = 0;  // globflags.GetDefineFlag ("inverttets");

    int oldnp = GetNP();
    int oldne = GetNSeg();
    int oldnd = GetNDomains();

    for(SurfaceElementIndex si = 0; si < GetNSE(); si++)
      for(int j=1; j<=(*this)[si].GetNP(); j++) (*this)[si].GeomInfoPi(j).trignum = -1;

    int max_surfnr = 0;
    for (i = 1; i <= GetNFD(); i++)
      max_surfnr = max2 (max_surfnr, GetFaceDescriptor(i).SurfNr());
    max_surfnr++;

    if(max_surfnr < surfindex_offset) max_surfnr = surfindex_offset;


    bool endmesh = false;

    while (infile.good() && !endmesh)
      {
        infile >> str;

        if (strcmp (str, "surfaceelementsgi") == 0 || strcmp (str, "surfaceelements") == 0)
          {
            infile >> n;
            PrintMessage (3, n, " surface elements");
            for (i = 1; i <= n; i++)
              {
                int j;
                int surfnr, bcp, domin, domout, nep, faceind = 0;
                infile >> surfnr >> bcp >> domin >> domout;

                surfnr--;

                if(domin > 0) domin += oldnd;
                if(domout > 0) domout += oldnd;
                surfnr += max_surfnr;


                for (j = 1; j <= facedecoding.Size(); j++)
                  if (GetFaceDescriptor(j).SurfNr() == surfnr &&
                      GetFaceDescriptor(j).BCProperty() == bcp &&
                      GetFaceDescriptor(j).DomainIn() == domin &&
                      GetFaceDescriptor(j).DomainOut() == domout)
                    faceind = j;

                if (!faceind)
                  {
                    faceind = AddFaceDescriptor (FaceDescriptor(surfnr, domin, domout, 0));
                    if(GetDimension() == 2) bcp++;
                    GetFaceDescriptor(faceind).SetBCProperty (bcp);
                  }

                infile >> nep;
                if (!nep) nep = 3;

                Element2d tri(nep);
                tri.SetIndex(faceind);

                for (j = 1; j <= nep; j++)
                  {
                    infile >> tri.PNum(j);
                    tri.PNum(j) = tri.PNum(j) + oldnp;
                  }


                if (strcmp (str, "surfaceelementsgi") == 0)
                  for (j = 1; j <= nep; j++)
                    {
                      infile >> tri.GeomInfoPi(j).trignum;
                      tri.GeomInfoPi(j).trignum = -1;
                    }

                AddSurfaceElement (tri);
              }
          }


        if (strcmp (str, "edgesegments") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                Segment seg;
                int hi;
                infile >> seg.si >> hi >> seg[0] >> seg[1];
                seg[0] = seg[0] + oldnp;
                seg[1] = seg[1] + oldnp;
                AddSegment (seg);
              }
          }



        if (strcmp (str, "edgesegmentsgi") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                Segment seg;
                int hi;
                infile >> seg.si >> hi >> seg[0] >> seg[1]
                       >> seg.geominfo[0].trignum
                       >> seg.geominfo[1].trignum;
                seg[0] = seg[0] + oldnp;
                seg[1] = seg[1] + oldnp;
                AddSegment (seg);
              }
          }
        if (strcmp (str, "edgesegmentsgi2") == 0)
          {
            infile >> n;
            PrintMessage (3, n, " curve elements");

            for (i = 1; i <= n; i++)
              {
                Segment seg;
                int hi;
                infile >> seg.si >> hi >> seg[0] >> seg[1]
                       >> seg.geominfo[0].trignum
                       >> seg.geominfo[1].trignum
                       >> seg.surfnr1 >> seg.surfnr2
                       >> seg.edgenr
                       >> seg.epgeominfo[0].dist
                       >> seg.epgeominfo[1].edgenr
                       >> seg.epgeominfo[1].dist;
                seg.epgeominfo[0].edgenr = seg.epgeominfo[1].edgenr;

                seg.surfnr1--;
                seg.surfnr2--;

                if(seg.surfnr1 >= 0)  seg.surfnr1 = seg.surfnr1 + max_surfnr;
                if(seg.surfnr2 >= 0)  seg.surfnr2 = seg.surfnr2 + max_surfnr;
                seg[0] = seg[0] +oldnp;
                seg[1] = seg[1] +oldnp;
		*testout << "old edgenr: " << seg.edgenr << endl;
                seg.edgenr = seg.edgenr + oldne;
		*testout << "new edgenr: " << seg.edgenr << endl;
                seg.epgeominfo[1].edgenr = seg.epgeominfo[1].edgenr + oldne;

                AddSegment (seg);
              }
          }

        if (strcmp (str, "volumeelements") == 0)
          {
            infile >> n;
            PrintMessage (3, n, " volume elements");
            for (i = 1; i <= n; i++)
              {
                Element el(TET);
                int hi, nep;
                infile >> hi;
                if (hi == 0) hi = 1;
                el.SetIndex(hi+oldnd);
                infile >> nep;
                el.SetNP(nep);

                for (int j = 0; j < nep; j++)
                  {
                    infile >> (int&)(el[j]);
                    el[j] = el[j]+oldnp;
                  }

                if (inverttets)
                  el.Invert();

                AddVolumeElement (el);
              }
          }


        if (strcmp (str, "points") == 0)
          {
            infile >> n;
            PrintMessage (3, n, " points");
            for (i = 1; i <= n; i++)
              {
                Point3d p;
                infile >> p.X() >> p.Y() >> p.Z();
                AddPoint (p);
              }
          }


        if (strcmp (str, "endmesh") == 0)
          {
            endmesh = true;
          }


        if (strcmp (str, "materials") == 0)
          {
            infile >> n;
            for (i = 1; i <= n; i++)
              {
                int nr;
                string mat;
                infile >> nr >> mat;
                SetMaterial (nr+oldnd, mat.c_str());
              }
          }


        strcpy (str, "");
      }

    CalcSurfacesOfNode ();

    topology.Update();
    clusters -> Update();

    SetNextMajorTimeStamp();
  }










  bool Mesh :: TestOk () const
  {
    for (ElementIndex ei = 0; ei < volelements.Size(); ei++)
      {
        for (int j = 0; j < 4; j++)
          if ( (*this)[ei][j] <= PointIndex::BASE-1)
            {
              (*testout) << "El " << ei << " has 0 nodes: ";
              for (int k = 0; k < 4; k++)
                (*testout) << (*this)[ei][k];
              break;
            }
      }
    CheckMesh3D (*this);
    return 1;
  }

  void Mesh :: SetAllocSize(int nnodes, int nsegs, int nsel, int nel)
  {
    points.SetAllocSize(nnodes);
    segments.SetAllocSize(nsegs);
    surfelements.SetAllocSize(nsel);
    volelements.SetAllocSize(nel);
  }


  void Mesh :: BuildBoundaryEdges(void)
  {
    delete boundaryedges;

    boundaryedges = new INDEX_2_CLOSED_HASHTABLE<int>
      (3 * (GetNSE() + GetNOpenElements()) + GetNSeg() + 1);


    for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
      {
        const Element2d & sel = surfelements[sei];
        if (sel.IsDeleted()) continue;

        // int si = sel.GetIndex();

        if (sel.GetNP() <= 4)
          for (int j = 0; j < sel.GetNP(); j++)
            {
              INDEX_2 i2;
              i2.I1() = sel.PNumMod(j+1);
              i2.I2() = sel.PNumMod(j+2);
              i2.Sort();
              boundaryedges->Set (i2, 1);
            }
        else if (sel.GetType()==TRIG6)
          {
            for (int j = 0; j < 3; j++)
              {
                INDEX_2 i2;
                i2.I1() = sel[j];
                i2.I2() = sel[(j+1)%3];
                i2.Sort();
                boundaryedges->Set (i2, 1);
              }
          }
        else 
          cerr << "illegal element for buildboundaryedges" << endl;
      }


    for (int i = 0; i < openelements.Size(); i++)
      {
        const Element2d & sel = openelements[i];
        for (int j = 0; j < sel.GetNP(); j++)
          {
            INDEX_2 i2;
            i2.I1() = sel.PNumMod(j+1);
            i2.I2() = sel.PNumMod(j+2);
            i2.Sort();
            boundaryedges->Set (i2, 1);

            points[sel[j]].SetType(FIXEDPOINT);
          }
      }

    for (int i = 0; i < GetNSeg(); i++)
      {
        const Segment & seg = segments[i];
        INDEX_2 i2(seg[0], seg[1]);
        i2.Sort();

        boundaryedges -> Set (i2, 2);
        //segmentht -> Set (i2, i);
      }


  }

  void Mesh :: CalcSurfacesOfNode ()
  {
    // surfacesonnode.SetSize (GetNP());
    TABLE<int,PointIndex::BASE> surfacesonnode(GetNP());

    delete boundaryedges;
    boundaryedges = NULL;

    delete surfelementht;
    surfelementht = nullptr;
    delete segmentht;

    /*
      surfelementht = new INDEX_3_HASHTABLE<int> (GetNSE()/4 + 1);
      segmentht = new INDEX_2_HASHTABLE<int> (GetNSeg() + 1);
    */

    if (dimension == 3)
      surfelementht = new INDEX_3_CLOSED_HASHTABLE<int> (3*GetNSE() + 1);
    segmentht = new INDEX_2_CLOSED_HASHTABLE<int> (3*GetNSeg() + 1);

    if (dimension == 3)
    for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
      {
        const Element2d & sel = surfelements[sei];
        if (sel.IsDeleted()) continue;

        int si = sel.GetIndex();

        for (int j = 0; j < sel.GetNP(); j++)
          {
            PointIndex pi = sel[j];
            if (!surfacesonnode[pi].Contains(si))
              surfacesonnode.Add (pi, si);
            /*
            bool found = 0;
            for (int k = 0; k < surfacesonnode[pi].Size(); k++)
              if (surfacesonnode[pi][k] == si)
                {
                  found = 1;
                  break;
                }

            if (!found)
              surfacesonnode.Add (pi, si);
            */
          }
      }
    /*
      for (sei = 0; sei < GetNSE(); sei++)
      {
      const Element2d & sel = surfelements[sei];
      if (sel.IsDeleted()) continue;

      INDEX_3 i3;
      i3.I1() = sel.PNum(1);
      i3.I2() = sel.PNum(2);
      i3.I3() = sel.PNum(3);
      i3.Sort();
      surfelementht -> PrepareSet (i3);
      }

      surfelementht -> AllocateElements();
    */

    if (dimension==3)
    for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
      {
        const Element2d & sel = surfelements[sei];
        if (sel.IsDeleted()) continue;

        INDEX_3 i3;
        i3.I1() = sel.PNum(1);
        i3.I2() = sel.PNum(2);
        i3.I3() = sel.PNum(3);
        i3.Sort();
        surfelementht -> Set (i3, sei);   // war das wichtig ???    sel.GetIndex());
      }

    // int np = GetNP();

    if (dimension == 3)
      {
        for (PointIndex pi = points.Begin(); pi < points.End(); pi++)
          points[pi].SetType (INNERPOINT);

        if (GetNFD() == 0) 
          {
            for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
              {
                const Element2d & sel = surfelements[sei];
                if (sel.IsDeleted()) continue;
                for (int j = 0;  j < sel.GetNP(); j++)
                  {
                    PointIndex pi = SurfaceElement(sei)[j];
                    points[pi].SetType(FIXEDPOINT);
                  }
              }
          }
        else
          {
            for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
              {
                const Element2d & sel = surfelements[sei];
                if (sel.IsDeleted()) continue;
                for (int j = 0; j < sel.GetNP(); j++)
                  {
                    PointIndex pi = sel[j];
                    int ns = surfacesonnode[pi].Size();
                    if (ns == 1)
                      points[pi].SetType(SURFACEPOINT);
                    if (ns == 2)
                      points[pi].SetType(EDGEPOINT);
                    if (ns >= 3)
                      points[pi].SetType(FIXEDPOINT);
                  }      
              }
          }
      }

    for (int i = 0; i < segments.Size(); i++)
      {
        const Segment & seg = segments[i];
        for (int j = 1; j <= 2; j++)
          {
            PointIndex hi = (j == 1) ? seg[0] : seg[1];
            if (points[hi].Type() == INNERPOINT ||
                points[hi].Type() == SURFACEPOINT)
              points[hi].SetType(EDGEPOINT);
          }
      }
    
    for (int i = 0; i < lockedpoints.Size(); i++)
      points[lockedpoints[i]].SetType(FIXEDPOINT);


    /*
      for (i = 0; i < openelements.Size(); i++)
      {
      const Element2d & sel = openelements[i];
      for (j = 0; j < sel.GetNP(); j++)
      {
      INDEX_2 i2;
      i2.I1() = sel.PNumMod(j+1);
      i2.I2() = sel.PNumMod(j+2);
      i2.Sort();
      boundaryedges->Set (i2, 1);

      points[sel[j]].SetType(FIXEDPOINT);
      }
      }
    */

    // eltyps.SetSize (GetNE());
    // eltyps = FREEELEMENT;

    for (int i = 0; i < GetNSeg(); i++)
      {
        const Segment & seg = segments[i];
        INDEX_2 i2(seg[0], seg[1]);
        i2.Sort();

        //boundaryedges -> Set (i2, 2);
        segmentht -> Set (i2, i);
      }
  }


  void Mesh :: FixPoints (const BitArray & fixpoints)
  {
    if (fixpoints.Size() != GetNP())
      {
        cerr << "Mesh::FixPoints: sizes don't fit" << endl;
        return;
      }
    int np = GetNP();
    for (int i = 1; i <= np; i++)
      if (fixpoints.Test(i))
        {
          points.Elem(i).SetType (FIXEDPOINT);
        }
  }


  void Mesh :: FindOpenElements (int dom)
  {
    static int timer = NgProfiler::CreateTimer ("Mesh::FindOpenElements");
    NgProfiler::RegionTimer reg (timer);

    int np = GetNP();
    int ne = GetNE();
    int nse = GetNSE();

    Array<int,PointIndex::BASE> numonpoint(np);

    numonpoint = 0;

    for (ElementIndex ei = 0; ei < ne; ei++)
      {
        const Element & el = (*this)[ei];
        if (dom == 0 || dom == el.GetIndex())
          {
            if (el.GetNP() == 4)
              {
                INDEX_4 i4(el[0], el[1], el[2], el[3]);
                i4.Sort();
                numonpoint[i4.I1()]++;
                numonpoint[i4.I2()]++;
              }
            else
              for (int j = 0; j < el.GetNP(); j++)
                numonpoint[el[j]]++;
          }
      }

    TABLE<ElementIndex,PointIndex::BASE> elsonpoint(numonpoint);
    for (ElementIndex ei = 0; ei < ne; ei++)
      {
        const Element & el = (*this)[ei];
        if (dom == 0 || dom == el.GetIndex())
          {
            if (el.GetNP() == 4)
              {
                INDEX_4 i4(el[0], el[1], el[2], el[3]);
                i4.Sort();
                elsonpoint.Add (i4.I1(), ei);
                elsonpoint.Add (i4.I2(), ei);
              }
            else
              for (int j = 0; j < el.GetNP(); j++)
                elsonpoint.Add (el[j], ei);
          }
      }


    Array<char, 1> hasface(GetNFD());

    int i;
    for (i = 1; i <= GetNFD(); i++)
      {
        int domin = GetFaceDescriptor(i).DomainIn();
        int domout = GetFaceDescriptor(i).DomainOut();
        hasface[i] = 
          ( dom == 0 && (domin != 0 || domout != 0) ) ||
          ( dom != 0 && (domin == dom || domout == dom) );
      }

    numonpoint = 0;
    for (SurfaceElementIndex sii = 0; sii < nse; sii++)
      {
        int ind = surfelements[sii].GetIndex();
        /*
          if (
          GetFaceDescriptor(ind).DomainIn() && 
          (dom == 0 || dom == GetFaceDescriptor(ind).DomainIn())
          ||
          GetFaceDescriptor(ind).DomainOut() && 
          (dom == 0 || dom == GetFaceDescriptor(ind).DomainOut())
          )
        */
        if (hasface[ind])
          {
            /*
              Element2d hel = surfelements[i];
              hel.NormalizeNumbering();	  
              numonpoint[hel[0]]++;
            */
            const Element2d & hel = surfelements[sii];
            int mini = 0;
            for (int j = 1; j < hel.GetNP(); j++)
              if (hel[j] < hel[mini])
                mini = j;
            numonpoint[hel[mini]]++;
          }
      }

    TABLE<SurfaceElementIndex,PointIndex::BASE> selsonpoint(numonpoint);
    for (SurfaceElementIndex sii = 0; sii < nse; sii++)
      {
        int ind = surfelements[sii].GetIndex();

        /*
          if (
          GetFaceDescriptor(ind).DomainIn() && 
          (dom == 0 || dom == GetFaceDescriptor(ind).DomainIn())
          ||
          GetFaceDescriptor(ind).DomainOut() && 
          (dom == 0 || dom == GetFaceDescriptor(ind).DomainOut())
          )
        */
        if (hasface[ind])
          {
            /*
              Element2d hel = surfelements[i];
              hel.NormalizeNumbering();	  
              selsonpoint.Add (hel[0], i);
            */
            const Element2d & hel = surfelements[sii];
            int mini = 0;
            for (int j = 1; j < hel.GetNP(); j++)
              if (hel[j] < hel[mini])
                mini = j;
            selsonpoint.Add (hel[mini], sii);
          }
      }


    int ii;
    PointIndex pi;
    SurfaceElementIndex sei;
    // Element2d hel;


    INDEX_3_CLOSED_HASHTABLE<INDEX_2> faceht(100);   
    openelements.SetSize(0);

    for (PointIndex pi = points.Begin(); pi < points.End(); pi++)
      if (selsonpoint[pi].Size()+elsonpoint[pi].Size())
        {
          faceht.SetSize (2 * selsonpoint[pi].Size() + 4 * elsonpoint[pi].Size());

          FlatArray<SurfaceElementIndex> row = selsonpoint[pi];
          for (ii = 0; ii < row.Size(); ii++)
            {
              Element2d hel = SurfaceElement(row[ii]);
              if (hel.GetType() == TRIG6) hel.SetType(TRIG);
              int ind = hel.GetIndex();	  

              if (GetFaceDescriptor(ind).DomainIn() && 
                  (dom == 0 || dom == GetFaceDescriptor(ind).DomainIn()) )
                {
                  hel.NormalizeNumbering();
                  if (hel.PNum(1) == pi)
                    {
                      INDEX_3 i3(hel[0], hel[1], hel[2]);
                      INDEX_2 i2 (GetFaceDescriptor(ind).DomainIn(), 
                                  (hel.GetNP() == 3) 
                                  ? PointIndex (PointIndex::BASE-1)
                                  : hel.PNum(4));
                      faceht.Set (i3, i2);
                    }
                }
              if (GetFaceDescriptor(ind).DomainOut() &&
                  (dom == 0 || dom == GetFaceDescriptor(ind).DomainOut()) )
                {
                  hel.Invert();
                  hel.NormalizeNumbering();
                  if (hel.PNum(1) == pi)
                    {
                      INDEX_3 i3(hel[0], hel[1], hel[2]);
                      INDEX_2 i2 (GetFaceDescriptor(ind).DomainOut(), 
                                  (hel.GetNP() == 3) 
                                  ? PointIndex (PointIndex::BASE-1)
                                  : hel.PNum(4));
                      faceht.Set (i3, i2);
                    }
                }
            }


          FlatArray<ElementIndex> rowel = elsonpoint[pi];
          for (ii = 0; ii < rowel.Size(); ii++)
            {
              const Element & el = VolumeElement(rowel[ii]);

              if (dom == 0 || el.GetIndex() == dom)
                {
                  for (int j = 1; j <= el.GetNFaces(); j++)
                    {
                      Element2d hel(TRIG);
                      el.GetFace (j, hel);
                      hel.Invert();
                      hel.NormalizeNumbering();

                      if (hel[0] == pi)
                        {
                          INDEX_3 i3(hel[0], hel[1], hel[2]);

                          if (faceht.Used (i3))
                            {
                              INDEX_2 i2 = faceht.Get(i3);
                              if (i2.I1() == el.GetIndex())
                                {
                                  i2.I1() = PointIndex::BASE-1;
                                  faceht.Set (i3, i2);
                                }
                              else
                                {
                                  if (i2.I1() == 0)
                                    {
                                      PrintSysError ("more elements on face");
                                      (*testout)  << "more elements on face!!!" << endl;
                                      (*testout) << "el = " << el << endl;
                                      (*testout) << "hel = " << hel << endl;
                                      (*testout) << "face = " << i3 << endl;
                                      (*testout) << "points = " << endl;
                                      for (int jj = 1; jj <= 3; jj++)
                                        (*testout) << "p = " << Point(i3.I(jj)) << endl;
                                    }
                                }
                            }
                          else
                            {
                              hel.Invert();
                              hel.NormalizeNumbering();
                              INDEX_3 i3(hel[0], hel[1], hel[2]);
                              INDEX_2 i2(el.GetIndex(), 
                                         (hel.GetNP() == 3) 
                                         ? PointIndex (PointIndex::BASE-1)
                                         : hel[3]);
                              faceht.Set (i3, i2);
                            }
                        }
                    }
                }
            }
          for (int i = 0; i < faceht.Size(); i++)
            if (faceht.UsedPos (i))
              {
                INDEX_3 i3;
                INDEX_2 i2;
                faceht.GetData (i, i3, i2);
                if (i2.I1() != PointIndex::BASE-1)
                  {
                    // Element2d tri;
                    // tri.SetType ( (i2.I2() == PointIndex::BASE-1) ? TRIG : QUAD);
                    Element2d tri ( (i2.I2() == PointIndex::BASE-1) ? TRIG : QUAD);
                    for (int l = 0; l < 3; l++)
                      tri[l] = i3.I(l+1);
                    tri.PNum(4) = i2.I2();
                    tri.SetIndex (i2.I1());

                    //	tri.Invert();

                    openelements.Append (tri);
                  }
              }
        }

    int cnt3 = 0;
    for (i = 0; i < openelements.Size(); i++)
      if (openelements[i].GetNP() == 3)
        cnt3++;

    int cnt4 = openelements.Size() - cnt3;


    MyStr treequad;
    if (cnt4)
      treequad = MyStr(" (") + MyStr(cnt3) + MyStr (" + ") + 
        MyStr(cnt4) + MyStr(")");

    PrintMessage (5, openelements.Size(), treequad, " open elements");

    BuildBoundaryEdges();


    for (int i = 1; i <= openelements.Size(); i++)
      {
        const Element2d & sel = openelements.Get(i);

        if (boundaryedges)
          for (int j = 1; j <= sel.GetNP(); j++)
            {
              INDEX_2 i2;
              i2.I1() = sel.PNumMod(j);
              i2.I2() = sel.PNumMod(j+1);
              i2.Sort();
              boundaryedges->Set (i2, 1);
            }

        for (int j = 1; j <= 3; j++)
          {
            PointIndex pi = sel.PNum(j);
            if (pi < points.End())
              points[pi].SetType (FIXEDPOINT);
          }
      }



    /*
      for (i = 1; i <= GetNSeg(); i++)
      {
      const Segment & seg = LineSegment(i);
      INDEX_2 i2(seg[0], seg[1]);
      i2.Sort();

      if (!boundaryedges->Used (i2))
      cerr << "WARNING: no boundedge, but seg edge: " << i2 << endl;

      boundaryedges -> Set (i2, 2);
      segmentht -> Set (i2, i-1);
      }
    */
  }

  bool Mesh :: HasOpenQuads () const
  {
    int no = GetNOpenElements();
    for (int i = 0; i < no; i++)
      if (openelements[i].GetNP() == 4)
        return true;
    return false;
  }





  void Mesh :: FindOpenSegments (int surfnr)
  {
    // int i, j, k;

    // new version, general elements
    // hash index: pnum1-2
    // hash data : surfnr,  surfel-nr (pos) or segment nr(neg)
    INDEX_2_HASHTABLE<INDEX_2> faceht(4 * GetNSE()+GetNSeg()+1);   

    PrintMessage (5, "Test Opensegments");
    for (int i = 1; i <= GetNSeg(); i++)
      {
        const Segment & seg = LineSegment (i);

        if (surfnr == 0 || seg.si == surfnr)
          {
            INDEX_2 key(seg[0], seg[1]);
            INDEX_2 data(seg.si, -i);

            if (faceht.Used (key))
              {
                cerr << "ERROR: Segment " << seg << " already used" << endl;
                (*testout) << "ERROR: Segment " << seg << " already used" << endl;
              }

            faceht.Set (key, data);
          }
      }


    for (int i = 1; i <= GetNSeg(); i++)
      {
        const Segment & seg = LineSegment (i);

        if (surfnr == 0 || seg.si == surfnr)
          {
            INDEX_2 key(seg[1], seg[0]);
            if (!faceht.Used(key))
              {
                cerr << "ERROR: Segment " << seg << " brother not used" << endl;
                (*testout) << "ERROR: Segment " << seg << " brother not used" << endl;
              }
          }
      }

    // bool buggy = false;
    // ofstream bout("buggy.out");

    for (int i = 1; i <= GetNSE(); i++)
      {
        const Element2d & el = SurfaceElement(i);
        if (el.IsDeleted()) continue;

        if (surfnr == 0 || el.GetIndex() == surfnr)
          {
            for (int j = 1; j <= el.GetNP(); j++)
              {
                INDEX_2 seg (el.PNumMod(j), el.PNumMod(j+1));
                INDEX_2 data;

                if (seg.I1() < PointIndex::BASE || seg.I2() < PointIndex::BASE)
                  cerr << "seg = " << seg << endl;

                if (faceht.Used(seg))
                  {
                    data = faceht.Get(seg);
                    if (data.I1() == el.GetIndex())
                      {
                        data.I1() = 0;
                        faceht.Set (seg, data);
                      }
                    else
                      {
			// buggy = true;
                        PrintWarning ("hash table si not fitting for segment: ",
                                       seg.I1(), "-", seg.I2(), " other = ",
                                       data.I2());
			// cout << "me: index = " << el.GetIndex() << ", el = " << el << endl;

			/*
			bout << "has index = " << seg << endl;
			bout << "hash value = " << faceht.HashValue (seg) << endl;

			if (data.I2() > 0)
			  {
			    int io = data.I2();
			    cout << "other trig: index = " << SurfaceElement(io).GetIndex()
				 << ", el = " << SurfaceElement(io) << endl;
			  }
			else
			  {
			    cout << "other seg " << -data.I2() << ", si = " << data.I1() << endl;
			  }

			
			bout << "me: index = " << el.GetIndex() << ", el = " << el << endl;
			if (data.I2() > 0)
			  {
			    int io = data.I2();
			    bout << "other trig: index = " << SurfaceElement(io).GetIndex()
				 << ", el = " << SurfaceElement(io) << endl;
			  } 
			else
			  {
			    bout << "other seg " << -data.I2() << ", si = " << data.I1() << endl;
			  }
			*/
                      }
                  }
                else
                  {
                    Swap (seg.I1(), seg.I2());
                    data.I1() = el.GetIndex();
                    data.I2() = i;

                    faceht.Set (seg, data);
                  }
              }
          }
      }  

    /*
    if (buggy)
      {
	for (int i = 1; i <= GetNSeg(); i++)
	  bout << "seg" << i << " " << LineSegment(i) << endl;

	for (int i = 1; i <= GetNSE(); i++)
	  bout << "sel" << i << " " << SurfaceElement(i) << " ind = " 
	       << SurfaceElement(i).GetIndex() << endl;

	bout << "hashtable: " << endl;
	for (int j = 1; j <= faceht.GetNBags(); j++)
	  {
	    bout << "bag " << j << ":" << endl;
	    for (int k = 1; k <= faceht.GetBagSize(j); k++)
	      {
		INDEX_2 i2, data;
		faceht.GetData (j, k, i2, data);
		bout << "key = " << i2 << ", data = " << data << endl;
	      }
	  }
	exit(1);
      }
    */

    (*testout) << "open segments: " << endl;
    opensegments.SetSize(0);
    for (int i = 1; i <= faceht.GetNBags(); i++)
      for (int j = 1; j <= faceht.GetBagSize(i); j++)
        {
          INDEX_2 i2;
          INDEX_2 data;
          faceht.GetData (i, j, i2, data);
          if (data.I1())  // surfnr
            {
              Segment seg;
              seg[0] = i2.I1();
              seg[1] = i2.I2();
              seg.si = data.I1();

              // find geomdata:
              if (data.I2() > 0)
                {
                  // segment due to triangle
                  const Element2d & el = SurfaceElement (data.I2());
                  for (int k = 1; k <= el.GetNP(); k++)
                    {
                      if (seg[0] == el.PNum(k))
                        seg.geominfo[0] = el.GeomInfoPi(k);
                      if (seg[1] == el.PNum(k))
                        seg.geominfo[1] = el.GeomInfoPi(k);
                    }

                  (*testout) << "trig seg: ";
                }
              else
                {
                  // segment due to line
                  const Segment & lseg = LineSegment (-data.I2());
                  seg.geominfo[0] = lseg.geominfo[0];
                  seg.geominfo[1] = lseg.geominfo[1];

                  (*testout) << "line seg: ";
                }

              (*testout) << seg[0] << " - " << seg[1] 
                         << " len = " << Dist (Point(seg[0]), Point(seg[1]))
                         << endl;

              opensegments.Append (seg);
              if (seg.geominfo[0].trignum <= 0 || seg.geominfo[1].trignum <= 0)
                {
                  (*testout) << "Problem with open segment: " << seg << endl;
                }

            }
        }

    PrintMessage (3, opensegments.Size(), " open segments found");
    (*testout) << opensegments.Size() << " open segments found" << endl;

    /*
      ptyps.SetSize (GetNP());
      for (i = 1; i <= ptyps.Size(); i++)
      ptyps.Elem(i) = SURFACEPOINT;

      for (i = 1; i <= GetNSeg(); i++)
      {
      const Segment & seg = LineSegment (i);
      ptyps.Elem(seg[0]) = EDGEPOINT;
      ptyps.Elem(seg[1]) = EDGEPOINT;
      }
      for (i = 1; i <= GetNOpenSegments(); i++)
      {
      const Segment & seg = GetOpenSegment (i);
      ptyps.Elem(seg[0]) = EDGEPOINT;
      ptyps.Elem(seg[1]) = EDGEPOINT;
      }
    */
    for (int i = 1; i <= points.Size(); i++)
      points.Elem(i).SetType(SURFACEPOINT);

    for (int i = 1; i <= GetNSeg(); i++)
      {
        const Segment & seg = LineSegment (i);
        points[seg[0]].SetType(EDGEPOINT);
        points[seg[1]].SetType(EDGEPOINT);
      }
    for (int i = 1; i <= GetNOpenSegments(); i++)
      {
        const Segment & seg = GetOpenSegment (i);
        points[seg[0]].SetType (EDGEPOINT);
        points[seg[1]].SetType (EDGEPOINT);
      }



    /*

    for (i = 1; i <= openelements.Size(); i++)
    {
    const Element2d & sel = openelements.Get(i);

    if (boundaryedges)
    for (j = 1; j <= sel.GetNP(); j++)
    {
    INDEX_2 i2;
    i2.I1() = sel.PNumMod(j);
    i2.I2() = sel.PNumMod(j+1);
    i2.Sort();
    boundaryedges->Set (i2, 1);
    }

    for (j = 1; j <= 3; j++)
    {
    int pi = sel.PNum(j);
    if (pi <= ptyps.Size())
    ptyps.Elem(pi) = FIXEDPOINT;
    }
    }
    */
  }


  void Mesh :: RemoveOneLayerSurfaceElements ()
  {
    int np = GetNP();

    FindOpenSegments();
    BitArray frontpoints(np+1);  // for 0- and 1-based
    frontpoints.Clear();
    
    for (int i = 1; i <= GetNOpenSegments(); i++)
      {
        const Segment & seg = GetOpenSegment(i);
        frontpoints.Set (seg[0]);
        frontpoints.Set (seg[1]);
      }

    for (int i = 1; i <= GetNSE(); i++)
      {
        Element2d & sel = surfelements.Elem(i);
        bool remove = false;
        for (int j = 1; j <= sel.GetNP(); j++)
          if (frontpoints.Test(sel.PNum(j)))
            remove = true;
        if (remove)
          sel.PNum(1).Invalidate();
      }

    for (int i = surfelements.Size(); i >= 1; i--)
      {
        if (!surfelements.Elem(i).PNum(1).IsValid())
          {
            surfelements.Elem(i) = surfelements.Last();
            surfelements.DeleteLast();
          }
      }

    RebuildSurfaceElementLists ();
    /*
    for (int i = 0; i < facedecoding.Size(); i++)
      facedecoding[i].firstelement = -1;
    for (int i = surfelements.Size()-1; i >= 0; i--)
      {
        int ind = surfelements[i].GetIndex();
        surfelements[i].next = facedecoding[ind-1].firstelement;
        facedecoding[ind-1].firstelement = i;
      }
    */

    timestamp = NextTimeStamp();
    //  Compress();
  }





  void Mesh :: FreeOpenElementsEnvironment (int layers)
  {
    int i, j, k;
    PointIndex pi;
    const int large = 9999;
    Array<int,PointIndex::BASE> dist(GetNP());

    dist = large;

    for (int i = 1; i <= GetNOpenElements(); i++)
      {
        const Element2d & face = OpenElement(i);
        for (j = 0; j < face.GetNP(); j++)
          dist[face[j]] = 1;
      }

    for (k = 1; k <= layers; k++)
      for (i = 1; i <= GetNE(); i++)
        {
          const Element & el = VolumeElement(i);
          if (el[0] == -1 || el.IsDeleted()) continue;

          int elmin = large;
          for (j = 0; j < el.GetNP(); j++)
            if (dist[el[j]] < elmin)
              elmin = dist[el[j]];

          if (elmin < large)
            {
              for (j = 0; j < el.GetNP(); j++)
                if (dist[el[j]] > elmin+1)
                  dist[el[j]] = elmin+1;
            }
        }

    int cntfree = 0;
    for (i = 1; i <= GetNE(); i++)
      {
        Element & el = VolumeElement(i);
        if (el[0] == -1 || el.IsDeleted()) continue;

        int elmin = large;
        for (j = 0; j < el.GetNP(); j++)
          if (dist[el[j]] < elmin)
            elmin = dist[el[j]];

        el.flags.fixed = elmin > layers;
        // eltyps.Elem(i) = (elmin <= layers) ? 
        // FREEELEMENT : FIXEDELEMENT;
        if (elmin <= layers)
          cntfree++;
      }

    PrintMessage (5, "free: ", cntfree, ", fixed: ", GetNE()-cntfree);
    (*testout) << "free: " << cntfree << ", fixed: " << GetNE()-cntfree << endl;

    for (pi = PointIndex::BASE; 
         pi < GetNP()+PointIndex::BASE; pi++)
      {
        if (dist[pi] > layers+1)
          points[pi].SetType(FIXEDPOINT);
      }
  }



  void Mesh :: SetLocalH (netgen::Point<3> pmin, netgen::Point<3> pmax, double grading)
  {
    using netgen::Point;
    Point<3> c = Center (pmin, pmax);
    double d = max3 (pmax(0)-pmin(0),
                     pmax(1)-pmin(1),
                     pmax(2)-pmin(2));
    d /= 2;
    Point<3> pmin2 = c - Vec<3> (d, d, d);
    Point<3> pmax2 = c + Vec<3> (d, d, d);

    delete lochfunc;
    lochfunc = new LocalH (pmin2, pmax2, grading, dimension);
  }

  void Mesh :: RestrictLocalH (const Point3d & p, double hloc)
  {
    if(hloc < hmin)
      hloc = hmin;

    //cout << "restrict h in " << p << " to " << hloc << endl;
    if (!lochfunc)
      {
        PrintWarning("RestrictLocalH called, creating mesh-size tree");

        Point3d boxmin, boxmax;
        GetBox (boxmin, boxmax);
        SetLocalH (boxmin, boxmax, 0.8);
      }

    lochfunc -> SetH (p, hloc);
  }

  void Mesh :: RestrictLocalHLine (const Point3d & p1, 
                                   const Point3d & p2,
                                   double hloc)
  {
    if(hloc < hmin)
      hloc = hmin;

    // cout << "restrict h along " << p1 << " - " << p2 << " to " << hloc << endl;
    int i;
    int steps = int (Dist (p1, p2) / hloc) + 2;
    Vec3d v(p1, p2);

    for (i = 0; i <= steps; i++)
      {
        Point3d p = p1 + (double(i)/double(steps) * v);
        RestrictLocalH (p, hloc);
      }
  }


  void Mesh :: SetMinimalH (double h)
  {
    hmin = h;
  }


  void Mesh :: SetGlobalH (double h)
  {
    hglob = h;
  }

  double Mesh :: MaxHDomain (int dom) const
  {
    if (maxhdomain.Size())
      return maxhdomain.Get(dom);
    else
      return 1e10;
  }

  void Mesh :: SetMaxHDomain (const Array<double> & mhd)
  {
    maxhdomain.SetSize(mhd.Size());
    for (int i = 1; i <= mhd.Size(); i++)
      maxhdomain.Elem(i) = mhd.Get(i);
  }


  double Mesh :: GetH (const Point3d & p) const
  {
    double hmin = hglob;
    if (lochfunc)
      {
        double hl = lochfunc->GetH (p);
        if (hl < hglob)
          hmin = hl;
      }
    return hmin;
  }

  double Mesh :: GetMinH (const Point3d & pmin, const Point3d & pmax)
  {
    double hmin = hglob;
    if (lochfunc)
      {
        double hl = lochfunc->GetMinH (pmin, pmax);
        if (hl < hmin)
          hmin = hl;
      }
    return hmin;
  }





  double Mesh :: AverageH (int surfnr) const
  {
    int i, j, n;
    double hi, hsum;
    double maxh = 0, minh = 1e10;

    hsum = 0;
    n = 0;
    for (i = 1; i <= GetNSE(); i++)
      {
        const Element2d & el = SurfaceElement(i);
        if (surfnr == 0 || el.GetIndex() == surfnr)
          {
            for (j = 1; j <= 3; j++)
              {
                hi = Dist (Point (el.PNumMod(j)), 
                           Point (el.PNumMod(j+1)));

                hsum += hi;

                if (hi > maxh) maxh = hi;
                if (hi < minh) minh = hi;
                n++;
              }
          }
      }

    PrintMessage (5, "minh = ", minh, " avh = ", (hsum/n), " maxh = ", maxh);
    return (hsum / n);
  }



  void Mesh :: CalcLocalH (double grading) 
  {
    if (!lochfunc)
      {
        Point3d pmin, pmax;
        GetBox (pmin, pmax);
        // SetLocalH (pmin, pmax, mparam.grading);
	SetLocalH (pmin, pmax, grading);
      }

    PrintMessage (3,
                  "CalcLocalH: ", 
                  GetNP(), " Points ", 
                  GetNE(), " Elements ", 
                  GetNSE(), " Surface Elements");


    for (int i = 0; i < GetNSE(); i++)
      {
        const Element2d & el = surfelements[i];
        int j;

        if (el.GetNP() == 3)
          {
            double hel = -1;
            for (j = 1; j <= 3; j++)
              {
                const Point3d & p1 = points[el.PNumMod(j)];
                const Point3d & p2 = points[el.PNumMod(j+1)];

                /*
                  INDEX_2 i21(el.PNumMod(j), el.PNumMod(j+1));
                  INDEX_2 i22(el.PNumMod(j+1), el.PNumMod(j));
                  if (! identifiedpoints->Used (i21) &&
                  ! identifiedpoints->Used (i22) )
                */
                if (!ident -> UsedSymmetric (el.PNumMod(j),
                                             el.PNumMod(j+1)))
                  {
                    double hedge = Dist (p1, p2);
                    if (hedge > hel)
                      hel = hedge;
                    //		  lochfunc->SetH (Center (p1, p2), 2 * Dist (p1, p2));
                    //		  (*testout) << "trigseth, p1,2 = " << el.PNumMod(j) << ", " << el.PNumMod(j+1) 
                    //			     << " h = " << (2 * Dist(p1, p2)) << endl;
                  }
              }

            if (hel > 0)
              {
                const Point3d & p1 = points[el.PNum(1)];
                const Point3d & p2 = points[el.PNum(2)];
                const Point3d & p3 = points[el.PNum(3)];
                lochfunc->SetH (Center (p1, p2, p3), hel);
              }
          }
        else
          {
            {
              const Point3d & p1 = points[el.PNum(1)];
              const Point3d & p2 = points[el.PNum(2)];
              lochfunc->SetH (Center (p1, p2), 2 * Dist (p1, p2));
            }
            {
              const Point3d & p1 = points[el.PNum(3)];
              const Point3d & p2 = points[el.PNum(4)];
              lochfunc->SetH (Center (p1, p2), 2 * Dist (p1, p2));
            }
          }
      }

    for (int i = 0; i < GetNSeg(); i++)
      {
        const Segment & seg = segments[i];
        const Point3d & p1 = points[seg[0]];
        const Point3d & p2 = points[seg[1]];
        /*
          INDEX_2 i21(seg[0], seg[1]);
          INDEX_2 i22(seg[1], seg[0]);
          if (identifiedpoints)
          if (!identifiedpoints->Used (i21) && !identifiedpoints->Used (i22))
        */
        if (!ident -> UsedSymmetric (seg[0], seg[1]))
          {
            lochfunc->SetH (Center (p1, p2), Dist (p1, p2));
          }
      }
    /*
      cerr << "do vol" << endl;
      for (i = 1; i <= GetNE(); i++)
      {
      const Element & el = VolumeElement(i);
      if (el.GetType() == TET)
      {
      int j, k;
      for (j = 2; j <= 4; j++)
      for (k = 1; k < j; k++)  
      {
      const Point3d & p1 = Point (el.PNum(j));
      const Point3d & p2 = Point (el.PNum(k));
      lochfunc->SetH (Center (p1, p2), 2 * Dist (p1, p2));
      (*testout) << "set vol h to " << (2 * Dist (p1, p2)) << endl;

      }
      }
      }
    */

    /*
      const char * meshsizefilename = 
      globflags.GetStringFlag ("meshsize", NULL);
      if (meshsizefilename)
      {
      ifstream msf(meshsizefilename);
      if (msf)
      {
      int nmsp;
      msf >> nmsp;
      for (i = 1; i <= nmsp; i++)
      {
      Point3d pi;
      double hi;
      msf >> pi.X() >> pi.Y() >> pi.Z();
      msf >> hi;
      lochfunc->SetH (pi, hi);
      }
      }
      }
    */
    //  lochfunc -> Convexify();
    //  lochfunc -> PrintMemInfo (cout);
  }


  void Mesh :: CalcLocalHFromPointDistances(double grading)
  {
    PrintMessage (3, "Calculating local h from point distances");

    if (!lochfunc)
      {
        Point3d pmin, pmax;
        GetBox (pmin, pmax);

        // SetLocalH (pmin, pmax, mparam.grading);
	SetLocalH (pmin, pmax, grading);
      }

    PointIndex i,j;
    double hl;


    for (i = PointIndex::BASE; 
         i < GetNP()+PointIndex::BASE; i++)
      {
        for(j=i+1; j<GetNP()+PointIndex::BASE; j++)
          {
            const Point3d & p1 = points[i];
            const Point3d & p2 = points[j];
            hl = Dist(p1,p2);
            RestrictLocalH(p1,hl);
            RestrictLocalH(p2,hl);
            //cout << "restricted h at " << p1 << " and " << p2 << " to " << hl << endl;
          }
      }


  }


  void Mesh :: CalcLocalHFromSurfaceCurvature (double grading, double elperr) 
  {
    PrintMessage (3, "Calculating local h from surface curvature");

    if (!lochfunc)
      {
        Point3d pmin, pmax;
        GetBox (pmin, pmax);

        // SetLocalH (pmin, pmax, mparam.grading);
	SetLocalH (pmin, pmax, grading);
      }


    INDEX_2_HASHTABLE<int> edges(3 * GetNP() + 2);
    INDEX_2_HASHTABLE<int> bedges(GetNSeg() + 2);
    int i, j;

    for (i = 1; i <= GetNSeg(); i++)
      {
        const Segment & seg = LineSegment(i);
        INDEX_2 i2(seg[0], seg[1]);
        i2.Sort();
        bedges.Set (i2, 1);
      }
    for (i = 1; i <= GetNSE(); i++)
      {
        const Element2d & sel = SurfaceElement(i);
        if (!sel.PNum(1))
          continue;
        for (j = 1; j <= 3; j++)
          {
            INDEX_2 i2(sel.PNumMod(j), sel.PNumMod(j+1));
            i2.Sort();
            if (bedges.Used(i2)) continue;

            if (edges.Used(i2))
              {
                int other = edges.Get(i2);

                const Element2d & elother = SurfaceElement(other);

                int pi3 = 1;
                while ( (sel.PNum(pi3) == i2.I1()) || 
                        (sel.PNum(pi3) == i2.I2()))
                  pi3++;
                pi3 = sel.PNum(pi3);

                int pi4 = 1;
                while ( (elother.PNum(pi4) == i2.I1()) || 
                        (elother.PNum(pi4) == i2.I2()))
                  pi4++;
                pi4 = elother.PNum(pi4);

                double rad = ComputeCylinderRadius (Point (i2.I1()),
                                                    Point (i2.I2()),
                                                    Point (pi3), 
                                                    Point (pi4));

                RestrictLocalHLine (Point(i2.I1()), Point(i2.I2()), rad/elperr);


                /*	      
                  (*testout) << "pi1,2, 3, 4 = " << i2.I1() << ", " << i2.I2() << ", " << pi3 << ", " << pi4
                  << " p1 = " << Point(i2.I1()) 
                  << ", p2 = " << Point(i2.I2()) 
                  //			 << ", p3 = " << Point(pi3) 
                  //			 << ", p4 = " << Point(pi4) 
                  << ", rad = " << rad << endl;
                */
              }
            else
              edges.Set (i2, i);
          }
      }


    // Restrict h due to line segments

    for (i = 1; i <= GetNSeg(); i++)
      {
        const Segment & seg = LineSegment(i);
        const Point3d & p1 = Point(seg[0]);
        const Point3d & p2 = Point(seg[1]);
        RestrictLocalH (Center (p1, p2),  Dist (p1, p2));
      }



    /*


    int i, j;
    int np = GetNP();
    int nseg = GetNSeg();
    int nse = GetNSE();

    Array<Vec3d> normals(np);
    BitArray linepoint(np);

    linepoint.Clear();
    for (i = 1; i <= nseg; i++)
    {
    linepoint.Set (LineSegment(i)[0]);
    linepoint.Set (LineSegment(i)[1]);
    }

    for (i = 1; i <= np; i++)
    normals.Elem(i) = Vec3d(0,0,0);

    for (i = 1; i <= nse; i++)
    {
    Element2d & el = SurfaceElement(i);
    Vec3d nf = Cross (Vec3d (Point (el.PNum(1)), Point(el.PNum(2))),
    Vec3d (Point (el.PNum(1)), Point(el.PNum(3))));
    for (j = 1; j <= 3; j++)
    normals.Elem(el.PNum(j)) += nf;
    }

    for (i = 1; i <= np; i++)
    normals.Elem(i) /= (1e-12 + normals.Elem(i).Length());

    for (i = 1; i <= nse; i++)
    {
    Element2d & el = SurfaceElement(i);
    Vec3d nf = Cross (Vec3d (Point (el.PNum(1)), Point(el.PNum(2))),
    Vec3d (Point (el.PNum(1)), Point(el.PNum(3))));
    nf /= nf.Length();
    Point3d c = Center (Point(el.PNum(1)),
    Point(el.PNum(2)),
    Point(el.PNum(3)));

    for (j = 1; j <= 3; j++)
    {
    if (!linepoint.Test (el.PNum(j)))
    {
    double dist = Dist (c, Point(el.PNum(j)));
    double dn = (nf - normals.Get(el.PNum(j))).Length();

    RestrictLocalH (Point(el.PNum(j)), dist / (dn+1e-12) /elperr);
    }
    }
    }
    */
  }


  void Mesh :: RestrictLocalH (resthtype rht, int nr, double loch)
  {
    int i;
    switch (rht)
      {
      case RESTRICTH_FACE:
        {
          for (i = 1; i <= GetNSE(); i++)
            {
              const Element2d & sel = SurfaceElement(i);
              if (sel.GetIndex() == nr)
                RestrictLocalH (RESTRICTH_SURFACEELEMENT, i, loch);
            }
          break;
        }
      case RESTRICTH_EDGE:
        {
          for (i = 1; i <= GetNSeg(); i++)
            {
              const Segment & seg = LineSegment(i);
              if (seg.edgenr == nr)
                RestrictLocalH (RESTRICTH_SEGMENT, i, loch);
            }
          break;
        }
      case RESTRICTH_POINT:
        {
          RestrictLocalH (Point (nr), loch);
          break;
        }

      case RESTRICTH_SURFACEELEMENT:
        {
          const Element2d & sel = SurfaceElement(nr);
          Point3d p = Center (Point(sel.PNum(1)),
                              Point(sel.PNum(2)),
                              Point(sel.PNum(3)));
          RestrictLocalH (p, loch);
          break;
        }
      case RESTRICTH_SEGMENT:
        {
          const Segment & seg = LineSegment(nr);
          RestrictLocalHLine (Point (seg[0]), Point(seg[1]), loch);
          break;
        }
      }
  }


  void Mesh :: LoadLocalMeshSize (const string &  meshsizefilename)
  {
    // Philippose - 10/03/2009
    // Improve error checking when loading and reading
    // the local mesh size file

    if (meshsizefilename.empty()) return;

    ifstream msf(meshsizefilename.c_str());

    // Philippose - 09/03/2009
    // Adding print message information in case the specified 
    // does not exist, or does not load successfully due to 
    // other reasons such as access rights, etc...
    if (!msf) 
      {
        PrintMessage(3, "Error loading mesh size file: ", meshsizefilename, "....","Skipping!");
        return;
      }

    PrintMessage (3, "Load local mesh-size file: ", meshsizefilename);

    int nmsp = 0;
    int nmsl = 0;

    msf >> nmsp;
    if(!msf.good())
      throw NgException ("Mesh-size file error: No points found\n");

    if(nmsp > 0)
      PrintMessage (4, "Number of mesh-size restriction points: ", nmsp);

    for (int i = 0; i < nmsp; i++)
      {
        Point3d pi;
        double hi;
        msf >> pi.X() >> pi.Y() >> pi.Z();
        msf >> hi;
        if (!msf.good())
          throw NgException ("Mesh-size file error: Number of points don't match specified list size\n");
        RestrictLocalH (pi, hi);
      }

    msf >> nmsl;
    if(!msf.good())
      throw NgException ("Mesh-size file error: No line definitions found\n");

    if(nmsl > 0)
      PrintMessage (4, "Number of mesh-size restriction lines: ", nmsl);

    for (int i = 0; i < nmsl; i++)
      {
        Point3d p1, p2;
        double hi;
        msf >> p1.X() >> p1.Y() >> p1.Z();
        msf >> p2.X() >> p2.Y() >> p2.Z();
        msf >> hi;
        if (!msf.good())
          throw NgException ("Mesh-size file error: Number of line definitions don't match specified list size\n");
        RestrictLocalHLine (p1, p2, hi);
      }

    msf.close();
  }



  void Mesh :: GetBox (Point3d & pmin, Point3d & pmax, int dom) const
  {
    if (points.Size() == 0)
      {
        pmin = pmax = Point3d(0,0,0);
        return;
      }

    if (dom <= 0)
      {
        pmin = Point3d (1e10, 1e10, 1e10);
        pmax = Point3d (-1e10, -1e10, -1e10); 

        for (PointIndex pi = points.Begin(); pi < points.End(); pi++)
          {
            pmin.SetToMin ( (*this) [pi] );
            pmax.SetToMax ( (*this) [pi] );
          }
      }
    else
      {
        int j, nse = GetNSE();
        SurfaceElementIndex sei;

        pmin = Point3d (1e10, 1e10, 1e10);
        pmax = Point3d (-1e10, -1e10, -1e10); 
        for (sei = 0; sei < nse; sei++)
          {
            const Element2d & el = (*this)[sei];
            if (el.IsDeleted() ) continue;

            if (dom == -1 || el.GetIndex() == dom)
              {
                for (j = 0; j < 3; j++)
                  {
                    pmin.SetToMin ( (*this) [el[j]] );
                    pmax.SetToMax ( (*this) [el[j]] );
                  }
              }
          }
      }

    if (pmin.X() > 0.5e10)
      {
        pmin = pmax = Point3d(0,0,0);
      }
  }




  void Mesh :: GetBox (Point3d & pmin, Point3d & pmax, POINTTYPE ptyp) const
  {
    if (points.Size() == 0)
      {
        pmin = pmax = Point3d(0,0,0);
        return;
      }

    pmin = Point3d (1e10, 1e10, 1e10);
    pmax = Point3d (-1e10, -1e10, -1e10); 

    for (PointIndex pi = points.Begin(); pi < points.End(); pi++)
      if (points[pi].Type() <= ptyp)
        {
          pmin.SetToMin ( (*this) [pi] );
          pmax.SetToMax ( (*this) [pi] );
        }
  }




  double Mesh :: ElementError (int eli, const MeshingParameters & mp) const
  {
    const Element & el = volelements.Get(eli);
    return CalcTetBadness (points.Get(el[0]), points.Get(el[1]),
                           points.Get(el[2]), points.Get(el[3]), -1, mp);
  }

  void Mesh :: AddLockedPoint (PointIndex pi)
  { 
    lockedpoints.Append (pi); 
  }

  void Mesh :: ClearLockedPoints ()
  { 
    lockedpoints.SetSize (0); 
  }



  void Mesh :: Compress ()
  {
    Array<PointIndex,PointIndex::BASE,PointIndex> op2np(GetNP());
    Array<MeshPoint> hpoints;
    BitArrayChar<PointIndex::BASE> pused(GetNP());

    /*
      (*testout) << "volels: " << endl;
      for (i = 1; i <= volelements.Size(); i++)
      {
      for (j = 1; j <= volelements.Get(i).GetNP(); j++)
      (*testout) << volelements.Get(i).PNum(j) << " ";
      (*testout) << endl;
      }
      (*testout) << "np: " << GetNP() << endl;
    */

    for (int i = 0; i < volelements.Size(); i++)
      if (volelements[i][0] <= PointIndex::BASE-1 ||
          volelements[i].IsDeleted())
        {
          volelements.Delete(i);
          i--;
        }


    for (int i = 0; i < surfelements.Size(); i++)
      if (surfelements[i].IsDeleted())
        {
          surfelements.Delete(i);
          i--;
        }

    for (int i = 0; i < segments.Size(); i++)
      if (segments[i][0] <= PointIndex::BASE-1)
        {
          segments.Delete(i);
          i--;
        }

    for(int i=0; i < segments.Size(); i++)
      if(segments[i].edgenr < 0)
          segments.Delete(i--);

    pused.Clear();
    for (int i = 0; i < volelements.Size(); i++)
      {
        const Element & el = volelements[i];
        for (int j = 0; j < el.GetNP(); j++)
          pused.Set (el[j]);
      }

    for (int i = 0; i < surfelements.Size(); i++)
      {
        const Element2d & el = surfelements[i];
        for (int j = 0; j < el.GetNP(); j++)
          pused.Set (el[j]);
      }

    for (int i = 0; i < segments.Size(); i++)
      {
        const Segment & seg = segments[i];
        pused.Set (seg[0]);
        pused.Set (seg[1]);
      }

    for (int i = 0; i < openelements.Size(); i++)
      {
        const Element2d & el = openelements[i];
        for (int j = 0; j < el.GetNP(); j++)
          pused.Set(el[j]);
      }

    for (int i = 0; i < lockedpoints.Size(); i++)
      pused.Set (lockedpoints[i]);


    /*
    // compress points doesn't work for identified points !
    if (identifiedpoints)
    {
    for (i = 1; i <= identifiedpoints->GetNBags(); i++)
    if (identifiedpoints->GetBagSize(i))
    {
    pused.Set ();
    break;
    }
    }
    */
    //  pused.Set();


    int npi = PointIndex::BASE-1;

    for (PointIndex pi = points.Begin(); pi < points.End(); pi++)
      if (pused.Test(pi))
        {
          npi++;
          op2np[pi] = npi;
          hpoints.Append (points[pi]);
        }
      else
        op2np[pi] = -1;



    points.SetSize(0);
    for (int i = 0; i < hpoints.Size(); i++)
      points.Append (hpoints[i]);

    for (int i = 1; i <= volelements.Size(); i++)
      {
        Element & el = VolumeElement(i);
        for (int j = 0; j < el.GetNP(); j++)
          el[j] = op2np[el[j]];
      }

    for (int i = 1; i <= surfelements.Size(); i++)
      {
        Element2d & el = SurfaceElement(i);
        for (int j = 0; j < el.GetNP(); j++)
          el[j] = op2np[el[j]];
      }

    for (int i = 0; i < segments.Size(); i++)
      {
        Segment & seg = segments[i];
        seg[0] = op2np[seg[0]];
        seg[1] = op2np[seg[1]];
      }

    for (int i = 1; i <= openelements.Size(); i++)
      {
        Element2d & el = openelements.Elem(i);
        for (int j = 0; j < el.GetNP(); j++)
          el[j] = op2np[el[j]];
      }  


    for (int i = 0; i < lockedpoints.Size(); i++)
      lockedpoints[i] = op2np[lockedpoints[i]];

    for (int i = 0; i < facedecoding.Size(); i++)
      facedecoding[i].firstelement = -1;
    for (int i = surfelements.Size()-1; i >= 0; i--)
      {
        int ind = surfelements[i].GetIndex();
        surfelements[i].next = facedecoding[ind-1].firstelement;
        facedecoding[ind-1].firstelement = i;
      }

    CalcSurfacesOfNode();


    //  FindOpenElements();
    timestamp = NextTimeStamp();
  }

  void Mesh :: OrderElements()
  {
    for (auto & el : surfelements)
      {
        if (el.GetType() == TRIG)
          while (el[0] > el[1] || el[0] > el[2])
            { // rotate element
              auto hp = el[0];
              el[0] = el[1];
              el[1] = el[2];
              el[2] = hp;
              auto hgi = el.GeomInfoPi(1);
              el.GeomInfoPi(1) = el.GeomInfoPi(2);
              el.GeomInfoPi(2) = el.GeomInfoPi(3);
              el.GeomInfoPi(3) = hgi;
            }
      }

    for (auto & el : volelements)
      if (el.GetType() == TET)
        {
          // lowest index first ...
          int mini = 0;
          for (int i = 1; i < 4; i++)
            if (el[i] < el[mini]) mini = i;
          if (mini != 0)
            { // swap 0 with mini, and the other two ...
              int i3 = -1, i4 = -1;
              for (int i = 1; i < 4; i++)
                if (i != mini)
                  {
                    i4 = i3;
                    i3 = i;
                  }
              swap (el[0], el[mini]);
              swap (el[i3], el[i4]);
            }
          
          while (el[1] > el[2] || el[1] > el[3])
            { // rotate element to move second index to second position
              auto hp = el[1];
              el[1] = el[2];
              el[2] = el[3];
              el[3] = hp;
            }
        }
  }

  int Mesh :: CheckConsistentBoundary () const
  {
    int nf = GetNOpenElements();
    INDEX_2_HASHTABLE<int> edges(nf+2);
    INDEX_2 i2, i2s, edge;
    int err = 0;

    for (int i = 1; i <= nf; i++)
      {
        const Element2d & sel = OpenElement(i);

        for (int j = 1; j <= sel.GetNP(); j++)
          {
            i2.I1() = sel.PNumMod(j);
            i2.I2() = sel.PNumMod(j+1);

            int sign = (i2.I2() > i2.I1()) ? 1 : -1;
            i2.Sort();
            if (!edges.Used (i2))
              edges.Set (i2, 0);
            edges.Set (i2, edges.Get(i2) + sign);
          }
      }

    for (int i = 1; i <= edges.GetNBags(); i++)
      for (int j = 1; j <= edges.GetBagSize(i); j++)
        {
          int cnt = 0;
          edges.GetData (i, j, i2, cnt);
          if (cnt)
            {
              PrintError ("Edge ", i2.I1() , " - ", i2.I2(), " multiple times in surface mesh");

              (*testout) << "Edge " << i2 << " multiple times in surface mesh" << endl;
              i2s = i2;
              i2s.Sort();
              for (int k = 1; k <= nf; k++)
                {
                  const Element2d & sel = OpenElement(k);
                  for (int l = 1; l <= sel.GetNP(); l++)
                    {
                      edge.I1() = sel.PNumMod(l);
                      edge.I2() = sel.PNumMod(l+1);
                      edge.Sort();

                      if (edge == i2s) 
                        (*testout) << "edge of element " << sel << endl;
                    }
                }


              err = 2;
            }
        }

    return err;
  }



  int Mesh :: CheckOverlappingBoundary () 
  {
    int i, j, k;

    Point3d pmin, pmax;
    GetBox (pmin, pmax);
    BoxTree<3> setree(pmin, pmax);
    Array<int> inters;

    bool overlap = 0;
    bool incons_layers = 0;


    for (i = 1; i <= GetNSE(); i++)
      SurfaceElement(i).badel = 0;


    for (i = 1; i <= GetNSE(); i++)
      {
        const Element2d & tri = SurfaceElement(i);

        Point3d tpmin (Point(tri[0]));
        Point3d tpmax (tpmin);

        for (k = 1; k < tri.GetNP(); k++)
          {
            tpmin.SetToMin (Point (tri[k]));
            tpmax.SetToMax (Point (tri[k]));
          }
        Vec3d diag(tpmin, tpmax);

        tpmax = tpmax + 0.1 * diag;
        tpmin = tpmin - 0.1 * diag;

        setree.Insert (tpmin, tpmax, i);
      }

    for (i = 1; i <= GetNSE(); i++)
      {
        const Element2d & tri = SurfaceElement(i);

        Point3d tpmin (Point(tri[0]));
        Point3d tpmax (tpmin);

        for (k = 1; k < tri.GetNP(); k++)
          {
            tpmin.SetToMin (Point (tri[k]));
            tpmax.SetToMax (Point (tri[k]));
          }

        setree.GetIntersecting (tpmin, tpmax, inters);

        for (j = 1; j <= inters.Size(); j++)
          {
            const Element2d & tri2 = SurfaceElement(inters.Get(j));	  

            if ( (*this)[tri[0]].GetLayer() != (*this)[tri2[0]].GetLayer())
              continue;

            if ( (*this)[tri[0]].GetLayer() != (*this)[tri[1]].GetLayer() ||
                 (*this)[tri[0]].GetLayer() != (*this)[tri[2]].GetLayer())
              {
                incons_layers = 1;
                cout << "inconsistent layers in triangle" << endl;
              }


            const netgen::Point<3> *trip1[3], *trip2[3];	  
            for (k = 1; k <= 3; k++)
              {
                trip1[k-1] = &Point (tri.PNum(k));
                trip2[k-1] = &Point (tri2.PNum(k));
              }

            if (IntersectTriangleTriangle (&trip1[0], &trip2[0]))
              {
                overlap = 1;
                PrintWarning ("Intersecting elements " 
                              ,i, " and ", inters.Get(j));

                (*testout) << "Intersecting: " << endl;
                (*testout) << "openelement " << i << " with open element " << inters.Get(j) << endl;

                cout << "el1 = " << tri << endl;
                cout << "el2 = " << tri2 << endl;
                cout << "layer1 = " <<  (*this)[tri[0]].GetLayer() << endl;
                cout << "layer2 = " <<  (*this)[tri2[0]].GetLayer() << endl;


                for (k = 1; k <= 3; k++)
                  (*testout) << tri.PNum(k) << "  ";
                (*testout) << endl;
                for (k = 1; k <= 3; k++)
                  (*testout) << tri2.PNum(k) << "  ";
                (*testout) << endl;

                for (k = 0; k <= 2; k++)
                  (*testout) << *trip1[k] << "   ";
                (*testout) << endl;
                for (k = 0; k <= 2; k++)
                  (*testout) << *trip2[k] << "   ";
                (*testout) << endl;

                (*testout) << "Face1 = " << GetFaceDescriptor(tri.GetIndex()) << endl;
                (*testout) << "Face1 = " << GetFaceDescriptor(tri2.GetIndex()) << endl;

                /*
                  INDEX_3 i3(tri.PNum(1), tri.PNum(2), tri.PNum(3));
                  i3.Sort();
                  for (k = 1; k <= GetNSE(); k++)
                  {
                  const Element2d & el2 = SurfaceElement(k);
                  INDEX_3 i3b(el2.PNum(1), el2.PNum(2), el2.PNum(3));
                  i3b.Sort();
                  if (i3 == i3b)
                  {
                  SurfaceElement(k).badel = 1;
                  }
                  }
                */
                SurfaceElement(i).badel = 1;
                SurfaceElement(inters.Get(j)).badel = 1;
              }
          }
      }

    // bug 'fix'
    if (incons_layers) overlap = 0;

    return overlap;
  }


  int Mesh :: CheckVolumeMesh () const
  {
    PrintMessage (3, "Checking volume mesh");

    int ne = GetNE();
    DenseMatrix dtrans(3,3);
    int i, j;

    PrintMessage (5, "elements: ", ne);
    for (i = 1; i <= ne; i++)
      {
        Element & el = (Element&) VolumeElement(i);
        el.flags.badel = 0;
        int nip = el.GetNIP();
        for (j = 1; j <= nip; j++)
          {
            el.GetTransformation (j, Points(), dtrans);
            double det = dtrans.Det();
            if (det > 0)
              {
                PrintError ("Element ", i , " has wrong orientation");
                el.flags.badel = 1;
              }
          }
      }

    return 0;
  }


  bool Mesh :: LegalTrig (const Element2d & el) const
  {
    return 1;
    if ( /* hp */ 1)  // needed for old, simple hp-refinement
      { 
        // trigs with 2 or more segments are illegal
        int i;
        int nseg = 0;

        if (!segmentht)
          {
            cerr << "no segmentht allocated" << endl;
            return 0;
          }

        //      Point3d cp(0.5, 0.5, 0.5);
        for (i = 1; i <= 3; i++)
          {
            INDEX_2 i2(el.PNumMod (i), el.PNumMod (i+1));
            i2.Sort();
            if (segmentht -> Used (i2))
              nseg++;
          }
        if (nseg >= 2) 
          return 0;
      }
    return 1;
  }




  ///
  bool Mesh :: LegalTet2 (Element & el) const
  {
    // static int timer1 = NgProfiler::CreateTimer ("Legaltet2");

    // Test, whether 4 points have a common surface plus
    // at least 4 edges at the boundary

    if(!boundaryedges)
      const_cast<Mesh *>(this)->BuildBoundaryEdges();


    // non-tets are always legal
    if (el.GetType() != TET)
      {
        el.SetLegal (1);
        return 1;
      }

    POINTTYPE pointtype[4];
    for(int i = 0; i < 4; i++)
      pointtype[i] = (*this)[el[i]].Type();



    // element has at least 2 inner points ---> legal
    int cnti = 0;
    for (int j = 0; j < 4; j++)
      if ( pointtype[j] == INNERPOINT)
        {
          cnti++;
          if (cnti >= 2)
            {
              el.SetLegal (1);
              return 1;
            }
        }



    // which faces are boundary faces ?
    int bface[4];
    for (int i = 0; i < 4; i++)
      {
        bface[i] = surfelementht->Used (INDEX_3::Sort(el[gftetfacesa[i][0]],
                                                      el[gftetfacesa[i][1]],
                                                      el[gftetfacesa[i][2]]));
      }

    int bedge[4][4];
    int segedge[4][4];
    static const int pi3map[4][4] = { { -1,  2,  1,  1 },
                                      {  2, -1,  0,  0 },
                                      {  1,  0, -1,  0 },
                                      {  1,  0,  0, -1 } };

    static const int pi4map[4][4] = { { -1,  3,  3,  2 },
                                      {  3, -1,  3,  2 },
                                      {  3,  3, -1,  1 },
                                      {  2,  2,  1, -1 } };


    for (int i = 0; i < 4; i++)
      for (int j = 0; j < i; j++)
        {
          bool sege = false, be = false;

          int pos = boundaryedges -> Position0(INDEX_2::Sort(el[i], el[j]));
          if (pos != -1)
            {
              be = true;
              if (boundaryedges -> GetData0(pos) == 2)
                sege = true;
            }

          segedge[j][i] = segedge[i][j] = sege;
          bedge[j][i] = bedge[i][j] = be;
        }

    // two boundary faces and no edge is illegal
    for (int i = 0; i < 3; i++)
      for (int j = i+1; j < 4; j++)
        {
          if (bface[i] && bface[j])
            if (!segedge[pi3map[i][j]][pi4map[i][j]])
              {
                // 2 boundary faces withoud edge in between
                el.SetLegal (0);
                return 0;
              }
        }

    // three boundary edges meeting in a Surface point
    for (int i = 0; i < 4; i++)
      {
        if ( pointtype[i] == SURFACEPOINT)
          {
            bool alledges = 1;
            for (int j = 0; j < 4; j++)
              if (j != i && !bedge[i][j])
                {
                  alledges = 0;
                  break;
                }
            if (alledges)
              {
                // cout << "tet illegal due to unmarked node" << endl;
                el.SetLegal (0);
                return 0;
              }
          }
      }



    for (int fnr = 0; fnr < 4; fnr++)
      if (!bface[fnr])
        for (int i = 0; i < 4; i++)
          if (i != fnr)
            {
              int pi1 = pi3map[i][fnr];
              int pi2 = pi4map[i][fnr];

              if ( pointtype[i] == SURFACEPOINT)
                {
                  // two connected edges on surface, but no face
                  if (bedge[i][pi1] && bedge[i][pi2])
                    {
                      el.SetLegal (0);
                      return 0;
                    }
                }

              if ( pointtype[i] == EDGEPOINT)
                {
                  // connected surface edge and edge edge, but no face
                  if ( (bedge[i][pi1] && segedge[i][pi2]) ||
                       (bedge[i][pi2] && segedge[i][pi1]) )
                    {
                      el.SetLegal (0);
                      return 0;
                    }
                }

            }


    el.SetLegal (1);
    return 1;

  }



  int Mesh :: GetNDomains() const
  {
    int ndom = 0;

    for (int k = 0; k < facedecoding.Size(); k++)
      {
        if (facedecoding[k].DomainIn() > ndom)
          ndom = facedecoding[k].DomainIn();
        if (facedecoding[k].DomainOut() > ndom)
          ndom = facedecoding[k].DomainOut();
      }

    return ndom;
  }



  void Mesh :: SurfaceMeshOrientation ()
  {
    int i, j;
    int nse = GetNSE();

    BitArray used(nse);
    used.Clear();
    INDEX_2_HASHTABLE<int> edges(nse+1);

    bool haschanged = 0;


    const Element2d & tri = SurfaceElement(1);
    for (j = 1; j <= 3; j++)
      {
        INDEX_2 i2(tri.PNumMod(j), tri.PNumMod(j+1));
        edges.Set (i2, 1);
      }
    used.Set(1);

    bool unused;
    do
      {
        bool changed;
        do
          {
            changed = 0;
            for (i = 1; i <= nse; i++)
              if (!used.Test(i))
                {
                  Element2d & el = surfelements.Elem(i);
                  int found = 0, foundrev = 0;
                  for (j = 1; j <= 3; j++)
                    {
                      INDEX_2 i2(el.PNumMod(j), el.PNumMod(j+1));
                      if (edges.Used(i2))
                        foundrev = 1;
                      swap (i2.I1(), i2.I2());
                      if (edges.Used(i2))
                        found = 1;
                    }

                  if (found || foundrev)
                    {
                      if (foundrev)
                        swap (el.PNum(2), el.PNum(3));

                      changed = 1;
                      for (j = 1; j <= 3; j++)
                        {
                          INDEX_2 i2(el.PNumMod(j), el.PNumMod(j+1));
                          edges.Set (i2, 1);
                        }
                      used.Set (i);
                    }
                }
            if (changed)
              haschanged = 1;
          }
        while (changed);


        unused = 0;
        for (i = 1; i <= nse; i++)
          if (!used.Test(i))
            {
              unused = 1;
              const Element2d & tri = SurfaceElement(i);
              for (j = 1; j <= 3; j++)
                {
                  INDEX_2 i2(tri.PNumMod(j), tri.PNumMod(j+1));
                  edges.Set (i2, 1);
                }
              used.Set(i);
              break;
            }
      }
    while (unused);

    if (haschanged)
      timestamp = NextTimeStamp();
  }


  void Mesh :: Split2Tets()
  {
    PrintMessage (1, "Split To Tets");
    bool has_prisms = 0;

    int oldne = GetNE(); 
    for (int i = 1; i <= oldne; i++)
      {
        Element el = VolumeElement(i);

        if (el.GetType() == PRISM)
          {
            // prism, to 3 tets

            // make minimal node to node 1
            int minpi=0;
            PointIndex minpnum;
            minpnum = GetNP() + 1;

            for (int j = 1; j <= 6; j++)
              {
                if (el.PNum(j) < minpnum)
                  {
                    minpnum = el.PNum(j);
                    minpi = j;
                  }
              }

            if (minpi >= 4)
              {
                for (int j = 1; j <= 3; j++)
                  swap (el.PNum(j), el.PNum(j+3));
                minpi -= 3;
              }

            while (minpi > 1)
              {
                int hi = 0;
                for (int j = 0; j <= 3; j+= 3)
                  {
                    hi = el.PNum(1+j);
                    el.PNum(1+j) = el.PNum(2+j);
                    el.PNum(2+j) = el.PNum(3+j);
                    el.PNum(3+j) = hi;
                  }
                minpi--;
              }

            /*
              version 1: edge from pi2 to pi6,
              version 2: edge from pi3 to pi5,
            */

            static const int ntets[2][12] =
              { { 1, 4, 5, 6, 1, 2, 3, 6, 1, 2, 5, 6 },
                { 1, 4, 5, 6, 1, 2, 3, 5, 3, 1, 5, 6 } };

            const int * min2pi;

            if (min2 (el.PNum(2), el.PNum(6)) <
                min2 (el.PNum(3), el.PNum(5)))
              {
                min2pi = &ntets[0][0];
                // (*testout) << "version 1 ";
              }
            else
              {
                min2pi = &ntets[1][0];
                // (*testout) << "version 2 ";
              }


            int firsttet = 1;
            for (int j = 1; j <= 3; j++)
              {
                Element nel(TET);
                for (int k = 1; k <= 4; k++)
                  nel.PNum(k) = el.PNum(min2pi[4 * j + k - 5]);
                nel.SetIndex (el.GetIndex());

                int legal = 1;
                for (int k = 1; k <= 3; k++)
                  for (int l = k+1; l <= 4; l++)
                    if (nel.PNum(k) == nel.PNum(l))
                      legal = 0;

                // (*testout) << nel << " ";
                if (legal)
                  {
                    if (firsttet)
                      {
                        VolumeElement(i) = nel;
                        firsttet = 0;
                      }
                    else
                      {
                        AddVolumeElement(nel);
                      }
                  }
              }
            if (firsttet) cout << "no legal";
            (*testout) << endl;
          }



        else if (el.GetType() == HEX)
          {
            // hex to A) 2 prisms or B) to 5 tets

            // make minimal node to node 1
            int minpi=0;
            PointIndex minpnum;
            minpnum = GetNP() + 1;

            for (int j = 1; j <= 8; j++)
              {
                if (el.PNum(j) < minpnum)
                  {
                    minpnum = el.PNum(j);
                    minpi = j;
                  }
              }

            if (minpi >= 5)
              {
                for (int j = 1; j <= 4; j++)
                  swap (el.PNum(j), el.PNum(j+4));
                minpi -= 4;
              }

            while (minpi > 1)
              {
                int hi = 0;
                for (int j = 0; j <= 4; j+= 4)
                  {
                    hi = el.PNum(1+j);
                    el.PNum(1+j) = el.PNum(2+j);
                    el.PNum(2+j) = el.PNum(3+j);
                    el.PNum(3+j) = el.PNum(4+j);
                    el.PNum(4+j) = hi;
                  }
                minpi--;
              }



            static const int to_prisms[3][12] =
              { { 0, 1, 2, 4, 5, 6, 0, 2, 3, 4, 6, 7 },
                { 0, 1, 5, 3, 2, 6, 0, 5, 4, 3, 6, 7 },
                { 0, 7, 4, 1, 6, 5, 0, 3, 7, 1, 2, 6 },
              };

            const int * min2pi = 0;
            if (min2 (el[4], el[6]) < min2 (el[5], el[7]))
              min2pi = &to_prisms[0][0];
            else if (min2 (el[3], el[6]) < min2 (el[2], el[7]))
              min2pi = &to_prisms[1][0];
            else if (min2 (el[1], el[6]) < min2 (el[2], el[5]))
              min2pi = &to_prisms[2][0];

            if (min2pi)
              {
                has_prisms = 1;
                for (int j = 0; j < 2; j++)
                  {
                    Element nel(PRISM);
                    for (int k = 0; k < 6; k++)
                      nel[k] = el[min2pi[6*j + k]];
                    nel.SetIndex (el.GetIndex());

                    if (j == 0)
                      VolumeElement(i) = nel;
                    else
                      AddVolumeElement(nel);
                  }
              }
            else
              {
                // split to 5 tets

                static const int to_tets[20] =
                  {
                    1, 2, 0, 5,
                    3, 0, 2, 7,
                    4, 5, 7, 0,
                    6, 7, 5, 2,
                    0, 2, 7, 5
                  };

                for (int j = 0; j < 5; j++)
                  {
                    Element nel(TET);
                    for (int k = 0; k < 4; k++)
                      nel[k] = el[to_tets[4*j + k]];
                    nel.SetIndex (el.GetIndex());

                    if (j == 0)
                      VolumeElement(i) = nel;
                    else
                      AddVolumeElement(nel);
                  }

              }
          }





        else if (el.GetType() == PYRAMID)
          {
            // pyramid, to 2 tets

            // cout << "pyramid: " << el << endl;

            static const int ntets[2][8] =
              { { 1, 2, 3, 5, 1, 3, 4, 5 },
                { 1, 2, 4, 5, 4, 2, 3, 5 }};

            const int * min2pi;

            if (min2 (el[0], el[2]) < min2 (el[1], el[3]))
              min2pi = &ntets[0][0];
            else
              min2pi = &ntets[1][0];

            bool firsttet = 1;
            for (int j = 0; j < 2; j++)
              {
                Element nel(TET);
                for (int k = 0; k < 4; k++)
                  nel[k] = el[min2pi[4*j + k]-1];
                nel.SetIndex (el.GetIndex());

                // cout << "pyramid-tet: " << nel << endl;

                bool legal = 1;
                for (int k = 0; k < 3; k++)
                  for (int l = k+1; l < 4; l++)
                    if (nel[k] == nel[l])
                      legal = 0;

                if (legal)
                  {
                    (*testout) << nel << " ";
                    if (firsttet)
                      VolumeElement(i) = nel;
                    else
                      AddVolumeElement(nel);

                    firsttet = 0;
                  }
              }
            if (firsttet) cout << "no legal";
            (*testout) << endl;
          }
      }


    int oldnse = GetNSE(); 
    for (int i = 1; i <= oldnse; i++)
      {
        Element2d el = SurfaceElement(i);
        if (el.GetNP() == 4)
          {
            (*testout) << "split el: " << el << " to ";

            static const int ntris[2][6] =
              { { 1, 2, 3, 1, 3, 4 },
                { 1, 2, 4, 4, 2, 3 }};

            const int * min2pi;

            if (min2 (el.PNum(1), el.PNum(3)) <
                min2 (el.PNum(2), el.PNum(4)))
              min2pi = &ntris[0][0];
            else
              min2pi = &ntris[1][0];

            for (int j = 0; j <6; j++)
              (*testout) << min2pi[j] << " ";


            int firsttri = 1;
            for (int j = 1; j <= 2; j++)
              {
                Element2d nel(3);
                for (int k = 1; k <= 3; k++)
                  nel.PNum(k) = el.PNum(min2pi[3 * j + k - 4]);
                nel.SetIndex (el.GetIndex());

                int legal = 1;
                for (int k = 1; k <= 2; k++)
                  for (int l = k+1; l <= 3; l++)
                    if (nel.PNum(k) == nel.PNum(l))
                      legal = 0;

                if (legal)
                  {
                    (*testout) << nel << " ";
                    if (firsttri)
                      {
                        SurfaceElement(i) = nel;
                        firsttri = 0;
                      }
                    else
                      {
                        AddSurfaceElement(nel);
                      }
                  }
              }
            (*testout) << endl;

          }
      }


    if (has_prisms)

      Split2Tets();

    else
      {
        for (int i = 1; i <= GetNE(); i++)
          {
            Element & el = VolumeElement(i);
            const Point3d & p1 = Point (el.PNum(1));
            const Point3d & p2 = Point (el.PNum(2));
            const Point3d & p3 = Point (el.PNum(3));
            const Point3d & p4 = Point (el.PNum(4));

            double vol = (Vec3d (p1, p2) * 
                          Cross (Vec3d (p1, p3), Vec3d(p1, p4)));
            if (vol > 0)
              swap (el.PNum(3), el.PNum(4));
          }



        UpdateTopology();
        timestamp = NextTimeStamp();
      }

    RebuildSurfaceElementLists();
  }

  void Mesh :: BuildElementSearchTree ()
  {
    if (elementsearchtreets == GetTimeStamp()) return;

    {
      std::lock_guard<std::mutex> guard(buildsearchtree_mutex);
      if (elementsearchtreets != GetTimeStamp())
        {
          NgLock lock(mutex);
          lock.Lock();
          
          PrintMessage (4, "Rebuild element searchtree");
          
          delete elementsearchtree;
          elementsearchtree = NULL;
          
          int ne = (dimension == 2) ? GetNSE() : GetNE();
          
          if (ne) 
            {
              if (dimension == 2)
                {
                  Box<3> box (Box<3>::EMPTY_BOX);
                  for (SurfaceElementIndex sei = 0; sei < ne; sei++)
                    box.Add (points[surfelements[sei].PNums()]);
                  
                  box.Increase (1.01 * box.Diam());
                  elementsearchtree = new BoxTree<3> (box);
                  
                  for (SurfaceElementIndex sei = 0; sei < ne; sei++)
                    {
                      box.Set (points[surfelements[sei].PNums()]);
                      elementsearchtree -> Insert (box, sei+1);
                    }
                }
              else
                {
                  Box<3> box (Box<3>::EMPTY_BOX);
                  for (ElementIndex ei = 0; ei < ne; ei++)
                    box.Add (points[volelements[ei].PNums()]);
                  
                  box.Increase (1.01 * box.Diam());
                  elementsearchtree = new BoxTree<3> (box);
                  
                  for (ElementIndex ei = 0; ei < ne; ei++)
                    {
                      box.Set (points[volelements[ei].PNums()]);
                      elementsearchtree -> Insert (box, ei+1);
                    }
                }
              
              elementsearchtreets = GetTimeStamp();
            }
        }
    }
  }

  
  int SolveLinearSystemLS (const Vec3d & col1,
                           const Vec3d & col2,
                           const Vec3d & rhs,
                           Vec2d & sol)
  {
    double a11 = col1 * col1;
    double a12 = col1 * col2;
    double a22 = col2 * col2;
    
    double det = a11 * a22 - a12 * a12;
    
    if (det*det <= 1e-24 * a11 * a22)
      {
        sol = Vec2d (0, 0);
        return 1;
      }
    
    Vec2d aTrhs;
    aTrhs.X() = col1*rhs;
    aTrhs.Y() = col2*rhs;

    sol.X() = ( a22 * aTrhs.X() - a12 * aTrhs.Y()) / det;
    sol.Y() = (-a12 * aTrhs.X() + a11 * aTrhs.Y()) / det;
    return 0;
  }
  

  bool Mesh :: PointContainedIn2DElement(const Point3d & p,
                                         double lami[3],
                                         const int element,
                                         bool consider3D) const
  {
    Vec3d col1, col2, col3;
    Vec3d rhs, sol;
    const double eps = 1e-6;

    Array<Element2d> loctrigs;

    
    //SZ 
    if(SurfaceElement(element).GetType()==QUAD)
      {
        const Element2d & el = SurfaceElement(element); 

        const Point3d & p1 = Point(el.PNum(1)); 
        const Point3d & p2 = Point(el.PNum(2));
        const Point3d & p3 = Point(el.PNum(3));
        const Point3d & p4 = Point(el.PNum(4));

        // Coefficients of Bilinear Mapping from Ref-Elem to global Elem
        // X = a + b x + c y + d x y 
        Vec3d a = p1; 
        Vec3d b = p2 - a; 
        Vec3d c = p4 - a; 
        Vec3d d = p3 - a - b - c;

     
        double dxb = d.X()*b.Y()-d.Y()*b.X();
        double dxc = d.X()*c.Y()-d.Y()*c.X(); 
        double dxa = d.X()*a.Y()-d.Y()*a.X(); 
        double dxp = d.X()*p.Y()-d.Y()*p.X();
	
	
        double c0,c1,c2; // ,rt; 
        lami[2]=0.; 
        double eps = 1.E-12;

	Vec3d dp13 = p3-p1;
	Vec3d dp24 = p4-p2;
	double d1 = dp13.Length2();
	double d2 = dp24.Length2();

	// if(fabs(d.X()) <= eps && fabs(d.Y())<= eps)
	//if (d.Length2() < sqr(eps))
        if (d.Length2() < sqr(eps)*d1 && d.Length2() < sqr(eps)*d2)
          {
	    //Solve Linear System
	    Vec2d sol;
            SolveLinearSystemLS (b, c, p-a, sol);
            lami[0] = sol.X();
            lami[1] = sol.Y();

	    if(lami[1]<=1.+eps && lami[1]>=0.-eps && lami[0]<=1.+eps && lami[0]>=0.-eps)
	      return true;
	    
            /*
            lami[0]=(c.Y()*(p.X()-a.X())-c.X()*(p.Y()-a.Y()))/
              (b.X()*c.Y() -b.Y()*c.X()); 
            lami[1]=(-b.Y()*(p.X()-a.X())+b.X()*(p.Y()-a.Y()))/
              (b.X()*c.Y() -b.Y()*c.X()); 
            */
          } 
        else
          if(fabs(dxb) <= eps*fabs(dxc))
            {
	      lami[1] = (dxp-dxa)/dxc;
              if(fabs(b.X()+d.X()*lami[1])>=fabs(b.Y()+d.Y()*lami[1]))
                lami[0] = (p.X()-a.X() - c.X()*lami[1])/(b.X()+d.X()*lami[1]); 
              else
                lami[0] = (p.Y()-a.Y() - c.Y()*lami[1])/(b.Y()+d.Y()*lami[1]);

	      if(lami[1]<=1.+eps && lami[1]>=0.-eps && lami[0]<=1.+eps && lami[0]>=0.-eps)
		return true;
            }
          else
            if(fabs(dxc) <= eps*fabs(dxb))
              {
		lami[0] = (dxp-dxa)/dxb;
                if(fabs(c.X()+d.X()*lami[0])>=fabs(c.Y()+d.Y()*lami[0]))
                  lami[1] = (p.X()-a.X() - b.X()*lami[0])/(c.X()+d.X()*lami[0]); 
                else
                  lami[1] = (p.Y()-a.Y() - b.Y()*lami[0])/(c.Y()+d.Y()*lami[0]);

		if(lami[1]<=1.+eps && lami[1]>=0.-eps && lami[0]<=1.+eps && lami[0]>=0.-eps)
		  return true;
              }
            else //Solve quadratic equation
              {
		c2 = -d.X()*dxb;
		c1 = b.X()*dxc - c.X()*dxb + d.X()*(dxp-dxa);
		c0 = c.X()*(dxp-dxa) + (a.X()-p.X())*dxc;
		double rt =  c1*c1 - 4*c2*c0;
		
		if (rt < 0.) return false; 
		lami[1] = (-c1 + sqrt(rt))/2/c2;


		if(lami[1]<=1.+eps && lami[1]>=0.-eps)
		  {
		    lami[0] = (dxp - dxa -dxb*lami[1])/dxc;
		    
		    if(lami[0]<=1.+eps && lami[0]>=0.-eps)
		      return true;
		  }
		lami[1] = (-c1 - sqrt(rt))/2/c2;

		lami[0] = (dxp - dxa -dxb*lami[1])/dxc;

		if(lami[1]<=1.+eps && lami[1]>=0.-eps && lami[0]<=1.+eps && lami[0]>=0.-eps)
		  return true;

		c2 = d.Y()*dxb;
		c1 = b.Y()*dxc - c.Y()*dxb + d.Y()*(dxp-dxa);
		c0 = c.Y()*(dxp -dxa) + (a.Y()-p.Y())*dxc;
		rt =  c1*c1 - 4*c2*c0;
		
		if (rt < 0.) return false; 
		lami[1] = (-c1 + sqrt(rt))/2/c2;

		if(lami[1]<=1.+eps && lami[1]>=0.-eps)
		  {
		    lami[0] = (dxp - dxa -dxb*lami[1])/dxc;

		    if(lami[0]<=1.+eps && lami[0]>=0.-eps)
		      return true;
		  }
		lami[1] = (-c1 - sqrt(rt))/2/c2;

		lami[0] = (dxp - dxa -dxb*lami[1])/dxc;

		if(lami[1]<=1.+eps && lami[1]>=0.-eps && lami[0]<=1.+eps && lami[0]>=0.-eps)
		  return true;

		c2 = -d.X()*dxc;
		c1 = -b.X()*dxc + c.X()*dxb + d.X()*(dxp-dxa);
		c0 = b.X()*(dxp -dxa) + (a.X()-p.X())*dxb;
		rt =  c1*c1 - 4*c2*c0;
		
		if (rt < 0.) return false; 
		lami[1] = (-c1 + sqrt(rt))/2/c2;

		if(lami[1]<=1.+eps && lami[1]>=0.-eps)
		  {
		    lami[0] = (dxp - dxa -dxc*lami[1])/dxb;

		    if(lami[0]<=1.+eps && lami[0]>=0.-eps)
		      return true;
		  }
		lami[1] = (-c1 - sqrt(rt))/2/c2;

		lami[0] = (dxp - dxa -dxc*lami[1])/dxb;

		if(lami[1]<=1.+eps && lami[1]>=0.-eps && lami[0]<=1.+eps && lami[0]>=0.-eps)
		  return true;
	      }

      
        //cout << "lam0,1 = " << lami[0] << ", " << lami[1] << endl;
        
        /*if( lami[0] <= 1.+eps  && lami[0] >= -eps && lami[1]<=1.+eps && lami[1]>=-eps)
          {
            if(consider3D)
              {
                Vec3d n = Cross(b,c);
                lami[2] = 0;
                for(int i=1; i<=3; i++)
                  lami[2] +=(p.X(i)-a.X(i)-lami[0]*b.X(i)-lami[1]*c.X(i)) * n.X(i);
                if(lami[2] >= -eps && lami[2] <= eps)
                  return true;
              }
            else
              return true;
	      }*/

        return false;

      }
    else
      {
        //	  SurfaceElement(element).GetTets (loctets);
        loctrigs.SetSize(1);
        loctrigs.Elem(1) = SurfaceElement(element);



        for (int j = 1; j <= loctrigs.Size(); j++)
          {
            const Element2d & el = loctrigs.Get(j);


            const Point3d & p1 = Point(el.PNum(1));
            const Point3d & p2 = Point(el.PNum(2));
            const Point3d & p3 = Point(el.PNum(3));
            /*
              Box3d box;
              box.SetPoint (p1);
              box.AddPoint (p2);
              box.AddPoint (p3);
              box.AddPoint (p4);
              if (!box.IsIn (p))
              continue;
            */
            col1 = p2-p1;
            col2 = p3-p1;
            col3 = Cross(col1,col2);
            //col3 = Vec3d(0, 0, 1);
            rhs = p - p1;

            // int retval = 
            SolveLinearSystem (col1, col2, col3, rhs, sol);

            //(*testout) << "retval " << retval << endl;

            //(*testout) << "col1 " << col1 << " col2 " << col2 << " col3 " << col3 << " rhs " << rhs << endl;
            //(*testout) << "sol " << sol << endl;

            if (sol.X() >= -eps && sol.Y() >= -eps && 
                sol.X() + sol.Y() <= 1+eps)
              {
                if(!consider3D || (sol.Z() >= -eps && sol.Z() <= eps))
                  {
                    lami[0] = sol.X();
                    lami[1] = sol.Y();
                    lami[2] = sol.Z();

                    return true;
                  }
              }
          }
      }

    return false;

  }




  bool Mesh :: PointContainedIn3DElement(const Point3d & p,
                                         double lami[3],
                                         const int element) const
  {
    //bool oldresult = PointContainedIn3DElementOld(p,lami,element);
    //(*testout) << "old result: " << oldresult
    //       << " lam " << lami[0] << " " << lami[1] << " " << lami[2] << endl;

    //if(!curvedelems->IsElementCurved(element-1))
    //  return PointContainedIn3DElementOld(p,lami,element);


    const double eps = 1.e-4;
    const Element & el = VolumeElement(element);

    netgen::Point<3> lam = 0.0;

    if (el.GetType() == TET || el.GetType() == TET10)
      {
        lam = 0.25;
      }
    else if (el.GetType() == PRISM)
      {
        lam(0) = 0.33; lam(1) = 0.33; lam(2) = 0.5;
      }
    else if (el.GetType() == PYRAMID)
      {
        lam(0) = 0.4; lam(1) = 0.4; lam(2) = 0.2;
      }
    else if (el.GetType() == HEX)
      {
        lam = 0.5;
      }


    Vec<3> deltalam,rhs;
    netgen::Point<3> x;
    Mat<3,3> Jac,Jact;

    double delta=1;

    bool retval;

    int i = 0;

    const int maxits = 30;
    while(delta > 1e-16 && i<maxits)
      {
        curvedelems->CalcElementTransformation(lam,element-1,x,Jac);
        rhs = p-x;
        Jac.Solve(rhs,deltalam);

        lam += deltalam;

        delta = deltalam.Length2();

        i++;
        //(*testout) << "pcie i " << i << " delta " << delta << " p " << p << " x " << x << " lam " << lam << endl;
        //<< "Jac " << Jac << endl;
      }

    if(i==maxits)
      return false;

    for(i=0; i<3; i++)
      lami[i] = lam(i);



    if (el.GetType() == TET || el.GetType() == TET10)
      {
        retval = (lam(0) > -eps && 
                  lam(1) > -eps && 
                  lam(2) > -eps && 
                  lam(0) + lam(1) + lam(2) < 1+eps);
      }
    else if (el.GetType() == PRISM)
      {
        retval = (lam(0) > -eps &&
                  lam(1) > -eps &&
                  lam(2) > -eps &&
                  lam(2) < 1+eps &&
                  lam(0) + lam(1) < 1+eps);
      }
    else if (el.GetType() == PYRAMID)
      {
        retval = (lam(0) > -eps &&
                  lam(1) > -eps &&
                  lam(2) > -eps &&
                  lam(0) + lam(2) < 1+eps &&
                  lam(1) + lam(2) < 1+eps);
      }
    else if (el.GetType() == HEX)
      {
        retval = (lam(0) > -eps && lam(0) < 1+eps &&
                  lam(1) > -eps && lam(1) < 1+eps &&
                  lam(2) > -eps && lam(2) < 1+eps);
      }
    else
      throw NgException("Da haun i wos vagessn");

    return retval;
  }



  bool Mesh :: PointContainedIn3DElementOld(const Point3d & p,
                                            double lami[3],
                                            const int element) const
  {
    Vec3d col1, col2, col3;
    Vec3d rhs, sol;
    const double eps = 1.e-4;

    Array<Element> loctets;

    VolumeElement(element).GetTets (loctets);

    for (int j = 1; j <= loctets.Size(); j++)
      {
        const Element & el = loctets.Get(j);

        const Point3d & p1 = Point(el.PNum(1));
        const Point3d & p2 = Point(el.PNum(2));
        const Point3d & p3 = Point(el.PNum(3));
        const Point3d & p4 = Point(el.PNum(4));

        Box3d box;
        box.SetPoint (p1);
        box.AddPoint (p2);
        box.AddPoint (p3);
        box.AddPoint (p4);
        if (!box.IsIn (p))
          continue;

        col1 = p2-p1;
        col2 = p3-p1;
        col3 = p4-p1;
        rhs = p - p1;

        SolveLinearSystem (col1, col2, col3, rhs, sol);

        if (sol.X() >= -eps && sol.Y() >= -eps && sol.Z() >= -eps &&
            sol.X() + sol.Y() + sol.Z() <= 1+eps)
          {
            Array<Element> loctetsloc;
            Array<netgen::Point<3> > pointsloc;

            VolumeElement(element).GetTetsLocal (loctetsloc);
            VolumeElement(element).GetNodesLocalNew (pointsloc);

            const Element & le = loctetsloc.Get(j);


            Point3d pp = 
              pointsloc.Get(le.PNum(1)) 
              + sol.X() * Vec3d (pointsloc.Get(le.PNum(1)), pointsloc.Get(le.PNum(2))) 
              + sol.Y() * Vec3d (pointsloc.Get(le.PNum(1)), pointsloc.Get(le.PNum(3))) 
              + sol.Z() * Vec3d (pointsloc.Get(le.PNum(1)), pointsloc.Get(le.PNum(4))) ;

            lami[0] = pp.X();
            lami[1] = pp.Y();
            lami[2] = pp.Z();
            return true;
          }
      }
    return false;
  }


  int Mesh :: GetElementOfPoint (const netgen::Point<3> & p,
                                 double lami[3],
                                 bool build_searchtree,
                                 const int index,
                                 const bool allowindex) const
  {
    if(index != -1) 
      {
        Array<int> dummy(1);
        dummy[0] = index;
        return GetElementOfPoint(p,lami,&dummy,build_searchtree,allowindex);
      }
    else
      return GetElementOfPoint(p,lami,NULL,build_searchtree,allowindex);
  }




  int Mesh :: GetElementOfPoint (const netgen::Point<3> & p,
                                 double lami[3],
                                 const Array<int> * const indices,
                                 bool build_searchtree,
                                 const bool allowindex) const
  {
    const double pointtol = 1e-12;
    netgen::Point<3> pmin = p - Vec<3> (pointtol, pointtol, pointtol);
    netgen::Point<3> pmax = p + Vec<3> (pointtol, pointtol, pointtol);
    if (dimension == 2)
      {
        int ne;
        int ps_startelement = 0;  // disable global buffering

        if(ps_startelement != 0 && ps_startelement <= GetNSE() && PointContainedIn2DElement(p,lami,ps_startelement))
          return ps_startelement;

        Array<int> locels;
        if (elementsearchtree || build_searchtree)
          {
            // update if necessary:
            const_cast<Mesh&>(*this).BuildElementSearchTree (); 
            elementsearchtree->GetIntersecting (pmin, pmax, locels);
            ne = locels.Size();
          }
        else
          ne = GetNSE();

        for (int i = 1; i <= ne; i++)
          {
            int ii;

            if (elementsearchtree)
              ii = locels.Get(i);
            else
              ii = i;

            if(ii == ps_startelement) continue;

            if(indices != NULL && indices->Size() > 0)
              {
                bool contained = indices->Contains(SurfaceElement(ii).GetIndex());
                if((allowindex && !contained) || (!allowindex && contained)) continue;
              }

            if(PointContainedIn2DElement(p,lami,ii)) return ii;

          }
        return 0;
      }
    else

      {
        int ps_startelement = 0;  // disable global buffering
        // int i, j;
        int ne;

        if(ps_startelement != 0 && PointContainedIn3DElement(p,lami,ps_startelement))
          return ps_startelement;

        Array<int> locels;
        if (elementsearchtree || build_searchtree)
          {
            // update if necessary:
            const_cast<Mesh&>(*this).BuildElementSearchTree (); 
            elementsearchtree->GetIntersecting (pmin, pmax, locels);
            ne = locels.Size();
          }
        else
          ne = GetNE();

        for (int i = 1; i <= ne; i++)
          {
            int ii;

            if (elementsearchtree)
              ii = locels.Get(i);
            else
              ii = i;
            if(ii == ps_startelement) continue;

            if(indices != NULL && indices->Size() > 0)
              {
                bool contained = indices->Contains(VolumeElement(ii).GetIndex());
                if((allowindex && !contained) || (!allowindex && contained)) continue;
              }

            if(PointContainedIn3DElement(p,lami,ii)) 
              {
                ps_startelement = ii;
                return ii;
              }
          }

        // Not found, try uncurved variant:
        for (int i = 1; i <= ne; i++)
          {
            int ii;

            if (elementsearchtree)
              ii = locels.Get(i);
            else
              ii = i;

            if(indices != NULL && indices->Size() > 0)
              {
                bool contained = indices->Contains(VolumeElement(ii).GetIndex());
                if((allowindex && !contained) || (!allowindex && contained)) continue;
              }


            if(PointContainedIn3DElementOld(p,lami,ii)) 
              {
                ps_startelement = ii;
                (*testout) << "WARNING: found element of point " << p <<" only for uncurved mesh" << endl;
                return ii;
              }
          }


        return 0;
      }
  }



  int Mesh :: GetSurfaceElementOfPoint (const netgen::Point<3> & p,
                                        double lami[3],
                                        bool build_searchtree,
                                        const int index,
                                        const bool allowindex) const
  {
    if(index != -1) 
      {
        Array<int> dummy(1);
        dummy[0] = index;
        return GetSurfaceElementOfPoint(p,lami,&dummy,build_searchtree,allowindex);
      }
    else
      return GetSurfaceElementOfPoint(p,lami,NULL,build_searchtree,allowindex);
  }




  int Mesh :: GetSurfaceElementOfPoint (const netgen::Point<3> & p,
                                        double lami[3],
                                        const Array<int> * const indices,
                                        bool build_searchtree,
                                        const bool allowindex) const
  {
    if (dimension == 2)
      {
        throw NgException("GetSurfaceElementOfPoint not yet implemented for 2D meshes");
      }
    else
      {
        double vlam[3];
        int velement = GetElementOfPoint(p,vlam,NULL,build_searchtree,allowindex);

        //(*testout) << "p " << p << endl;
        //(*testout) << "velement " << velement << endl;

        Array<int> faces;
        topology.GetElementFaces(velement,faces);

        //(*testout) << "faces " << faces << endl;

        for(int i=0; i<faces.Size(); i++)
          faces[i] = topology.GetFace2SurfaceElement(faces[i]);

        //(*testout) << "surfel " << faces << endl;

        for(int i=0; i<faces.Size(); i++)
          {
            if(faces[i] == 0)
              continue;

            if(indices && indices->Size() != 0)
              {
                if(indices->Contains(SurfaceElement(faces[i]).GetIndex()) &&
                   PointContainedIn2DElement(p,lami,faces[i],true))
                  return faces[i];
              }
            else
              {
                if(PointContainedIn2DElement(p,lami,faces[i],true))
                  {
                    //(*testout) << "found point " << p << " in sel " << faces[i]
                    //	       << ", lam " << lami[0] << ", " << lami[1] << ", " << lami[2] << endl;
                    return faces[i];
                  }
              }
          }

        Array<int> faces2;
        topology.GetElementFaces(velement,faces2);
        /*
        cout << "no matching surf element" << endl
             << "p = " << p << endl
             << "faces-orig = " << faces2 << endl
             << "faces = " << faces << endl
             << ", vol el = " << velement
             << ", vlam = " << vlam[0] << "," << vlam[1] << "," << vlam[2] << endl;
        */
      }

    return 0;
  }


  void Mesh::GetIntersectingVolEls(const Point3d& p1, const Point3d& p2, 
                                   Array<int> & locels) const
  {
    elementsearchtree->GetIntersecting (p1, p2, locels);
  }

  void Mesh :: SplitIntoParts()
  {
    int i, j, dom;
    int ne = GetNE();
    int np = GetNP();
    int nse = GetNSE();

    BitArray surfused(nse);
    BitArray pused (np);

    surfused.Clear();

    dom = 0;

    while (1)
      {
        int cntd = 1;

        dom++;

        pused.Clear();

        int found = 0;
        for (i = 1; i <= nse; i++)
          if (!surfused.Test(i))
            {
              SurfaceElement(i).SetIndex (dom);
              for (j = 1; j <= 3; j++)
                pused.Set (SurfaceElement(i).PNum(j));
              found = 1;
              cntd = 1;
              surfused.Set(i);
              break;
            }

        if (!found)
          break;

        int change;
        do
          {
            change = 0;
            for (i = 1; i <= nse; i++)
              {
                int is = 0, isnot = 0;
                for (j = 1; j <= 3; j++)
                  if (pused.Test(SurfaceElement(i).PNum(j)))
                    is = 1;
                  else
                    isnot = 1;

                if (is && isnot)
                  {
                    change = 1;
                    for (j = 1; j <= 3; j++)
                      pused.Set (SurfaceElement(i).PNum(j));
                  }

                if (is) 
                  {
                    if (!surfused.Test(i))
                      {
                        surfused.Set(i);
                        SurfaceElement(i).SetIndex (dom);
                        cntd++;
                      }
                  }
              }


            for (i = 1; i <= ne; i++)
              {
                int is = 0, isnot = 0;
                for (j = 1; j <= 4; j++)
                  if (pused.Test(VolumeElement(i).PNum(j)))
                    is = 1;
                  else
                    isnot = 1;

                if (is && isnot)
                  {
                    change = 1;
                    for (j = 1; j <= 4; j++)
                      pused.Set (VolumeElement(i).PNum(j));
                  }

                if (is)
                  {
                    VolumeElement(i).SetIndex (dom);
                  }
              }
          }
        while (change);

        PrintMessage (3, "domain ", dom, " has ", cntd, " surfaceelements");
      }

    /*
      facedecoding.SetSize (dom);
      for (i = 1; i <= dom; i++)
      {
      facedecoding.Elem(i).surfnr = 0;
      facedecoding.Elem(i).domin = i;
      facedecoding.Elem(i).domout = 0;
      }
    */
    ClearFaceDescriptors();
    for (i = 1; i <= dom; i++)
      AddFaceDescriptor (FaceDescriptor (0, i, 0, 0));
    CalcSurfacesOfNode();
    timestamp = NextTimeStamp();
  }

  void Mesh :: SplitSeparatedFaces ()
  {
    PrintMessage (3, "SplitSeparateFaces");
    int fdi;
    int np = GetNP();

    BitArray usedp(np);
    Array<SurfaceElementIndex> els_of_face;

    fdi = 1;
    while (fdi <= GetNFD())
      {
        GetSurfaceElementsOfFace (fdi, els_of_face);

        if (els_of_face.Size() == 0) continue;

        SurfaceElementIndex firstel = els_of_face[0];

        usedp.Clear();
        for (int j = 1; j <= SurfaceElement(firstel).GetNP(); j++)
          usedp.Set (SurfaceElement(firstel).PNum(j));

        bool changed;
        do
          {
            changed = false;

            for (int i = 0; i < els_of_face.Size(); i++)
              {
                const Element2d & el = SurfaceElement(els_of_face[i]);

                bool has = 0;
                bool hasno = 0;
                for (int j = 0; j < el.GetNP(); j++)
                  {
                    if (usedp.Test(el[j]))
                      has = true;
                    else
                      hasno = true;
                  }

                if (has && hasno)
                  changed = true;

                if (has)
                  for (int j = 0; j < el.GetNP(); j++)
                    usedp.Set (el[j]);
              }
          }
        while (changed);

        int nface = 0;
        for (int i = 0; i < els_of_face.Size(); i++)
          {
            Element2d & el = SurfaceElement(els_of_face[i]);

            int hasno = 0;
            for (int j = 1; j <= el.GetNP(); j++)
              if (!usedp.Test(el.PNum(j)))
                hasno = 1;

            if (hasno)
              {
                if (!nface)
                  {
                    FaceDescriptor nfd = GetFaceDescriptor(fdi);
                    nface = AddFaceDescriptor (nfd);
                  }

                el.SetIndex (nface);
              }
          }

        // reconnect list
        if (nface)
          {
            facedecoding[nface-1].firstelement = -1;
            facedecoding[fdi-1].firstelement = -1;

            for (int i = 0; i < els_of_face.Size(); i++)
              {
                int ind = SurfaceElement(els_of_face[i]).GetIndex();
                SurfaceElement(els_of_face[i]).next = facedecoding[ind-1].firstelement;
                facedecoding[ind-1].firstelement = els_of_face[i];
              }
          }

        fdi++;
      }


    /*
      fdi = 1;
      while (fdi <= GetNFD())
      {
      int firstel = 0;
      for (int i = 1; i <= GetNSE(); i++)
      if (SurfaceElement(i).GetIndex() == fdi)
      {
      firstel = i;
      break;
      }
      if (!firstel) continue;

      usedp.Clear();
      for (int j = 1; j <= SurfaceElement(firstel).GetNP(); j++)
      usedp.Set (SurfaceElement(firstel).PNum(j));

      int changed;
      do
      {
      changed = 0;
      for (int i = 1; i <= GetNSE(); i++)
      {
      const Element2d & el = SurfaceElement(i);
      if (el.GetIndex() != fdi)
      continue;

      int has = 0;
      int hasno = 0;
      for (int j = 1; j <= el.GetNP(); j++)
      {
      if (usedp.Test(el.PNum(j)))
      has = 1;
      else
      hasno = 1;
      }
      if (has && hasno)
      changed = 1;

      if (has)
      for (int j = 1; j <= el.GetNP(); j++)
      usedp.Set (el.PNum(j));
      }
      }
      while (changed);

      int nface = 0;
      for (int i = 1; i <= GetNSE(); i++)
      {
      Element2d & el = SurfaceElement(i);
      if (el.GetIndex() != fdi)
      continue;	  

      int hasno = 0;
      for (int j = 1; j <= el.GetNP(); j++)
      {
      if (!usedp.Test(el.PNum(j)))
      hasno = 1;
      }

      if (hasno)
      {
      if (!nface)
      {
      FaceDescriptor nfd = GetFaceDescriptor(fdi);
      nface = AddFaceDescriptor (nfd);
      }

      el.SetIndex (nface);
      }
      }
      fdi++;
      }
    */
  }



  void Mesh :: RebuildSurfaceElementLists ()
  {
    for (int i = 0; i < facedecoding.Size(); i++)
      facedecoding[i].firstelement = -1;
    for (int i = surfelements.Size()-1; i >= 0; i--)
      {
        int ind = surfelements[i].GetIndex();
        surfelements[i].next = facedecoding[ind-1].firstelement;
        facedecoding[ind-1].firstelement = i;
      }
  }

  void Mesh :: GetSurfaceElementsOfFace (int facenr, Array<SurfaceElementIndex> & sei) const
  {
    static int timer = NgProfiler::CreateTimer ("GetSurfaceElementsOfFace");
    NgProfiler::RegionTimer reg (timer);

     /*
     sei.SetSize (0);
     for (SurfaceElementIndex i = 0; i < GetNSE(); i++)
     {
        if ( (*this)[i].GetIndex () == facenr && (*this)[i][0] >= PointIndex::BASE &&
           !(*this)[i].IsDeleted() )
        {
           sei.Append (i);
        }
     }
     */

     /* Philippose - 01/10/2009
     Commented out the following lines, and activated the originally 
     commented out lines above because of a bug which causes corruption 
     of the variable "facedecoding" when a mesh is converted to second order
     */

     //      int size1 = sei.Size();
     sei.SetSize(0);

     SurfaceElementIndex si = facedecoding[facenr-1].firstelement;
     while (si != -1)
     {
        if ( (*this)[si].GetIndex () == facenr && (*this)[si][0] >= PointIndex::BASE &&
             !(*this)[si].IsDeleted() )
        {
           sei.Append (si);
        }

        si = (*this)[si].next;
     }
     
     /*
     // *testout << "with list = " << endl << sei << endl;

     if (size1 != sei.Size()) 
     {
        cout << "size mismatch" << endl;
        exit(1);
     }
     */
  }




  void Mesh :: CalcMinMaxAngle (double badellimit, double * retvalues) 
  {
    int i, j;
    int lpi1, lpi2, lpi3, lpi4;
    double phimax = 0, phimin = 10;
    double facephimax = 0, facephimin = 10;
    int illegaltets = 0, negativetets = 0, badtets = 0;

    for (i = 1; i <= GetNE(); i++)
      {
        int badel = 0;

        Element & el = VolumeElement(i);

        if (el.GetType() != TET)
          {
            VolumeElement(i).flags.badel = 0;
            continue;
          }

        if (el.Volume(Points()) < 0)
          {
            badel = 1;
            negativetets++;
          }


        if (!LegalTet (el)) 
          {
            badel = 1;
            illegaltets++;
            (*testout) << "illegal tet: " << i << " ";
            for (j = 1; j <= el.GetNP(); j++)
              (*testout) << el.PNum(j) << " ";
            (*testout) << endl;
          }


        // angles between faces
        for (lpi1 = 1; lpi1 <= 3; lpi1++)
          for (lpi2 = lpi1+1; lpi2 <= 4; lpi2++)
            {
              lpi3 = 1;
              while (lpi3 == lpi1 || lpi3 == lpi2)
                lpi3++;
              lpi4 = 10 - lpi1 - lpi2 - lpi3;

              const Point3d & p1 = Point (el.PNum(lpi1));
              const Point3d & p2 = Point (el.PNum(lpi2));
              const Point3d & p3 = Point (el.PNum(lpi3));
              const Point3d & p4 = Point (el.PNum(lpi4));

              Vec3d n(p1, p2);
              n /= n.Length();
              Vec3d v1(p1, p3);
              Vec3d v2(p1, p4);

              v1 -= (n * v1) * n;
              v2 -= (n * v2) * n;

              double cosphi = (v1 * v2) / (v1.Length() * v2.Length());
              double phi = acos (cosphi);
              if (phi > phimax) phimax = phi;
              if (phi < phimin) phimin = phi;

              if ((180/M_PI) * phi > badellimit)
                badel = 1;
            }


        // angles in faces
        for (j = 1; j <= 4; j++)
          {
            Element2d face(TRIG);
            el.GetFace (j, face);
            for (lpi1 = 1; lpi1 <= 3; lpi1++)
              {
                lpi2 = lpi1 % 3 + 1;
                lpi3 = lpi2 % 3 + 1;

                const Point3d & p1 = Point (el.PNum(lpi1));
                const Point3d & p2 = Point (el.PNum(lpi2));
                const Point3d & p3 = Point (el.PNum(lpi3));

                Vec3d v1(p1, p2);
                Vec3d v2(p1, p3);
                double cosphi = (v1 * v2) / (v1.Length() * v2.Length());
                double phi = acos (cosphi);
                if (phi > facephimax) facephimax = phi;
                if (phi < facephimin) facephimin = phi;

                if ((180/M_PI) * phi > badellimit)
                  badel = 1;

              }
          }


        VolumeElement(i).flags.badel = badel;
        if (badel) badtets++;
      }

    if (!GetNE())
      {
        phimin = phimax = facephimin = facephimax = 0;
      }

    if (!retvalues)
      {
        PrintMessage (1, "");
        PrintMessage (1, "between planes:  phimin = ", (180/M_PI) * phimin,
                      " phimax = ", (180/M_PI) *phimax);
        PrintMessage (1, "inside planes:   phimin = ", (180/M_PI) * facephimin,
                      " phimax = ", (180/M_PI) * facephimax);
        PrintMessage (1, "");      
      }
    else
      {
        retvalues[0] = (180/M_PI) * facephimin;
        retvalues[1] = (180/M_PI) * facephimax;
        retvalues[2] = (180/M_PI) * phimin;
        retvalues[3] = (180/M_PI) * phimax;
      }
    PrintMessage (3, "negative tets: ", negativetets);
    PrintMessage (3, "illegal tets:  ", illegaltets);
    PrintMessage (3, "bad tets:      ", badtets);
  }


  int Mesh :: MarkIllegalElements ()
  {
    int cnt = 0;
    for (auto & el : VolumeElements())
      if (!LegalTet (el))
        cnt++;
    return cnt;
  }

  // #ifdef NONE
  //   void Mesh :: AddIdentification (int pi1, int pi2, int identnr)
  //   {
  //     INDEX_2 pair(pi1, pi2);
  //     //  pair.Sort();
  //     identifiedpoints->Set (pair, identnr);
  //     if (identnr > maxidentnr)
  //       maxidentnr = identnr;
  //     timestamp = NextTimeStamp();
  //   }

  //   int Mesh :: GetIdentification (int pi1, int pi2) const
  //   {
  //     INDEX_2 pair(pi1, pi2);
  //     if (identifiedpoints->Used (pair))
  //       return identifiedpoints->Get(pair);
  //     else
  //       return 0;
  //   }

  //   int Mesh :: GetIdentificationSym (int pi1, int pi2) const
  //   {
  //     INDEX_2 pair(pi1, pi2);
  //     if (identifiedpoints->Used (pair))
  //       return identifiedpoints->Get(pair);

  //     pair = INDEX_2 (pi2, pi1);
  //     if (identifiedpoints->Used (pair))
  //       return identifiedpoints->Get(pair);

  //     return 0;
  //   }


  //   void Mesh :: GetIdentificationMap (int identnr, Array<int> & identmap) const
  //   {
  //     int i, j;

  //     identmap.SetSize (GetNP());
  //     for (i = 1; i <= identmap.Size(); i++)
  //       identmap.Elem(i) = 0;

  //     for (i = 1; i <= identifiedpoints->GetNBags(); i++)
  //       for (j = 1; j <= identifiedpoints->GetBagSize(i); j++)
  // 	{
  // 	  INDEX_2 i2;
  // 	  int nr;
  // 	  identifiedpoints->GetData (i, j, i2, nr);

  // 	  if (nr == identnr)
  // 	    {
  // 	      identmap.Elem(i2.I1()) = i2.I2();
  // 	    }
  // 	}
  //   }


  //   void Mesh :: GetIdentificationPairs (int identnr, Array<INDEX_2> & identpairs) const
  //   {
  //     int i, j;

  //     identpairs.SetSize(0);

  //     for (i = 1; i <= identifiedpoints->GetNBags(); i++)
  //       for (j = 1; j <= identifiedpoints->GetBagSize(i); j++)
  // 	{
  // 	  INDEX_2 i2;
  // 	  int nr;
  // 	  identifiedpoints->GetData (i, j, i2, nr);

  // 	  if (identnr == 0 || nr == identnr)
  // 	    identpairs.Append (i2);
  // 	}
  //   }
  // #endif



  void Mesh :: InitPointCurve(double red, double green, double blue) const
  {
    pointcurves_startpoint.Append(pointcurves.Size());
    pointcurves_red.Append(red);
    pointcurves_green.Append(green);
    pointcurves_blue.Append(blue);
  }
  void Mesh :: AddPointCurvePoint(const Point3d & pt) const
  {
    pointcurves.Append(pt);
  }
  int Mesh :: GetNumPointCurves(void) const
  {
    return pointcurves_startpoint.Size();
  }
  int Mesh :: GetNumPointsOfPointCurve(int curve) const
  {
    if(curve == pointcurves_startpoint.Size()-1)
      return (pointcurves.Size() - pointcurves_startpoint.Last());
    else
      return (pointcurves_startpoint[curve+1]-pointcurves_startpoint[curve]);
  }

  Point3d & Mesh :: GetPointCurvePoint(int curve, int n) const
  {
    return pointcurves[pointcurves_startpoint[curve]+n];
  }

  void Mesh :: GetPointCurveColor(int curve, double & red, double & green, double & blue) const
  {
    red = pointcurves_red[curve];
    green = pointcurves_green[curve];
    blue = pointcurves_blue[curve];
  }


  void Mesh :: ComputeNVertices ()
  {
    int i, j, nv;
    int ne = GetNE();
    // int nse = GetNSE();

    numvertices = 0;
    for (i = 1; i <= ne; i++)
      {
        const Element & el = VolumeElement(i);
        nv = el.GetNV();
        for (j = 0; j < nv; j++)
          if (el[j] > numvertices)
            numvertices = el[j];
      }
    /*
    for (i = 1; i <= nse; i++)
      {
        const Element2d & el = SurfaceElement(i);
        nv = el.GetNV();
        for (j = 1; j <= nv; j++)
          if (el.PNum(j) > numvertices)
            numvertices = el.PNum(j);
      } 
    */
    for (auto & el : SurfaceElements())
      for (PointIndex v : el.Vertices())
        if (v > numvertices) numvertices = v;

    numvertices += 1- PointIndex::BASE;
  }

  int Mesh :: GetNV () const
  {
    if (numvertices < 0)
      return GetNP();
    else
      return numvertices;
  }

  void Mesh :: SetNP (int np)
  {
    points.SetSize(np);
    //  ptyps.SetSize(np);

    int mlold = mlbetweennodes.Size();
    mlbetweennodes.SetSize(np);
    if (np > mlold)
      for (int i = mlold+PointIndex::BASE; 
           i < np+PointIndex::BASE; i++)
        {
          mlbetweennodes[i].I1() = PointIndex::BASE-1;
          mlbetweennodes[i].I2() = PointIndex::BASE-1;
        }

    GetIdentifications().SetMaxPointNr (np + PointIndex::BASE-1);
  }


  /*
    void Mesh :: BuildConnectedNodes ()
    {
    if (PureTetMesh())
    {
    connectedtonode.SetSize(0);
    return;
    }


    int i, j, k;
    int np = GetNP();
    int ne = GetNE();
    TABLE<int> conto(np);
    for (i = 1; i <= ne; i++)
    {
    const Element & el = VolumeElement(i);

    if (el.GetType() == PRISM)
    {
    for (j = 1; j <= 6; j++)
    {
    int n1 = el.PNum (j);
    int n2 = el.PNum ((j+2)%6+1);
    //	    if (n1 != n2)
    {
    int found = 0;
    for (k = 1; k <= conto.EntrySize(n1); k++)
    if (conto.Get(n1, k) == n2)
    {
    found = 1;
    break;
    }
    if (!found)
    conto.Add (n1, n2);
    }
    }
    }
    else if (el.GetType() == PYRAMID)
    {
    for (j = 1; j <= 4; j++)
    {
    int n1, n2;
    switch (j)
    {
    case 1: n1 = 1; n2 = 4; break;
    case 2: n1 = 4; n2 = 1; break;
    case 3: n1 = 2; n2 = 3; break;
    case 4: n1 = 3; n2 = 2; break;
    }

    int found = 0;
    for (k = 1; k <= conto.EntrySize(n1); k++)
    if (conto.Get(n1, k) == n2)
    {
    found = 1;
    break;
    }
    if (!found)
    conto.Add (n1, n2);
    }
    }
    }

    connectedtonode.SetSize(np);
    for (i = 1; i <= np; i++)
    connectedtonode.Elem(i) = 0;

    for (i = 1; i <= np; i++)
    if (connectedtonode.Elem(i) == 0)
    {
    connectedtonode.Elem(i) = i;
    ConnectToNodeRec (i, i, conto);
    }



    }

    void Mesh :: ConnectToNodeRec (int node, int tonode, 
    const TABLE<int> & conto)
    {
    int i, n2;
    //  (*testout) << "connect " << node << " to " << tonode << endl;
    for (i = 1; i <= conto.EntrySize(node); i++)
    {
    n2 = conto.Get(node, i);
    if (!connectedtonode.Get(n2))
    {
    connectedtonode.Elem(n2) = tonode;
    ConnectToNodeRec (n2, tonode, conto);
    }
    }
    }
  */


  bool Mesh :: PureTrigMesh (int faceindex) const
  {
    // if (!faceindex) return !mparam.quad;
    
    if (!faceindex)
      {
	for (int i = 1; i <= GetNSE(); i++)
	  if (SurfaceElement(i).GetNP() != 3)
	    return false;
	return true;
      }

    for (int i = 1; i <= GetNSE(); i++)
      if (SurfaceElement(i).GetIndex() == faceindex &&
          SurfaceElement(i).GetNP() != 3)
        return false;
    return true;
  }

  bool Mesh :: PureTetMesh () const
  {
    for (ElementIndex ei = 0; ei < GetNE(); ei++)
      if (VolumeElement(ei).GetNP() != 4)
        return 0;
    return 1;
  }

  void Mesh :: UpdateTopology (TaskManager tm,
                               Tracer tracer)
  {
    topology.Update(tm, tracer);
    (*tracer)("call update clusters", false);
    clusters->Update(tm, tracer);
    (*tracer)("call update clusters", true);
#ifdef PARALLEL
    if (paralleltop)
      {
        paralleltop->Reset();
        paralleltop->UpdateCoarseGrid();
      }
#endif
  }

  void Mesh :: BuildCurvedElements  (const Refinement * ref, int aorder, bool arational)
  {
    GetCurvedElements().BuildCurvedElements (ref, aorder, arational);

    for (SegmentIndex seg = 0; seg < GetNSeg(); seg++)
      (*this)[seg].SetCurved (GetCurvedElements().IsSegmentCurved (seg));
    for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
      (*this)[sei].SetCurved (GetCurvedElements().IsSurfaceElementCurved (sei));
    for (ElementIndex ei = 0; ei < GetNE(); ei++)
      (*this)[ei].SetCurved (GetCurvedElements().IsElementCurved (ei));
    
    SetNextMajorTimeStamp();
  }

  void Mesh :: BuildCurvedElements (int aorder)
  {
    if (!GetGeometry())
      throw NgException ("don't have a geometry for mesh curving");
    
    GetCurvedElements().BuildCurvedElements (&GetGeometry()->GetRefinement(), aorder, false);

    for (SegmentIndex seg = 0; seg < GetNSeg(); seg++)
      (*this)[seg].SetCurved (GetCurvedElements().IsSegmentCurved (seg));
    for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
      (*this)[sei].SetCurved (GetCurvedElements().IsSurfaceElementCurved (sei));
    for (ElementIndex ei = 0; ei < GetNE(); ei++)
      (*this)[ei].SetCurved (GetCurvedElements().IsElementCurved (ei));
    
    SetNextMajorTimeStamp();
  }

  void Mesh :: SetMaterial (int domnr, const string & mat)
  {
    if (domnr > materials.Size())
      {
        int olds = materials.Size();
        materials.SetSize (domnr);
        for (int i = olds; i < domnr-1; i++)
          materials[i] = new string("default");
      }
    /*
    materials.Elem(domnr) = new char[strlen(mat)+1];
    strcpy (materials.Elem(domnr), mat);
    */
    materials.Elem(domnr) = new string(mat);
  }

  string Mesh :: defaultmat = "default";
  const string & Mesh :: GetMaterial (int domnr) const
  {
    if (domnr <= materials.Size())
      return *materials.Get(domnr);
    static string emptystring("default");
    return emptystring;
  }

  void Mesh ::SetNBCNames ( int nbcn )
  {
    if ( bcnames.Size() )
      for ( int i = 0; i < bcnames.Size(); i++)
        if ( bcnames[i] ) delete bcnames[i];
    bcnames.SetSize(nbcn);
    bcnames = 0;
  }

  void Mesh ::SetBCName ( int bcnr, const string & abcname )
  {
    if (bcnr >= bcnames.Size())
      {
        int oldsize = bcnames.Size();
        bcnames.SetSize (bcnr+1);  // keeps contents
        for (int i = oldsize; i <= bcnr; i++)
          bcnames[i] = nullptr;
      }

    if ( bcnames[bcnr] ) delete bcnames[bcnr];
    if ( abcname != "default" )
      bcnames[bcnr] = new string ( abcname );
    else
      bcnames[bcnr] = nullptr;

    for (auto & fd : facedecoding)
      if (fd.BCProperty() <= bcnames.Size())
        fd.SetBCName (bcnames[fd.BCProperty()-1]);
  }

  const string & Mesh ::GetBCName ( int bcnr ) const
  {
    static string defaultstring = "default";

    if ( !bcnames.Size() )
      return defaultstring;

    if (bcnr < 0 || bcnr >= bcnames.Size())
      throw NgException ("illegal bc-number");

    if ( bcnames[bcnr] )
      return *bcnames[bcnr];
    else
      return defaultstring;
  }

  void Mesh :: SetNCD2Names( int ncd2n )
  {
    if (cd2names.Size())
      for(int i=0; i<cd2names.Size(); i++)
	if(cd2names[i]) delete cd2names[i];
    cd2names.SetSize(ncd2n);
    cd2names = 0;
  }

  void Mesh :: SetCD2Name ( int cd2nr, const string & abcname )
  {
    cd2nr--;
    (*testout) << "setCD2Name on edge " << cd2nr << " to " << abcname << endl;
    if (cd2nr >= cd2names.Size())
      {
	int oldsize = cd2names.Size();
	cd2names.SetSize(cd2nr+1);
	for(int i= oldsize; i<= cd2nr; i++)
	  cd2names[i] = nullptr;
      }
    //if (cd2names[cd2nr]) delete cd2names[cd2nr];
    if (abcname != "default")
      cd2names[cd2nr] = new string(abcname);
    else
      cd2names[cd2nr] = nullptr;
  }

  string Mesh :: cd2_default_name = "default";
  string Mesh :: default_bc = "default";
  const string & Mesh :: GetCD2Name (int cd2nr) const
  {
    static string defaultstring  = "default";
    if (!cd2names.Size())
      return defaultstring;

    if (cd2nr < 0 || cd2nr >= cd2names.Size())
      return defaultstring;

    if (cd2names[cd2nr])
      return *cd2names[cd2nr];
    else
      return defaultstring;
  }

  void Mesh :: SetNCD3Names( int ncd3n )
  {
    if (cd3names.Size())
      for(int i=0; i<cd3names.Size(); i++)
	if(cd3names[i]) delete cd3names[i];
    cd3names.SetSize(ncd3n);
    cd3names = 0;
  }

  void Mesh :: SetCD3Name ( int cd3nr, const string & abcname )
  {
    cd3nr--;
    (*testout) << "setCD3Name on vertex " << cd3nr << " to " << abcname << endl;
    if (cd3nr >= cd3names.Size())
      {
	int oldsize = cd3names.Size();
	cd3names.SetSize(cd3nr+1);
	for(int i= oldsize; i<= cd3nr; i++)
	  cd3names[i] = nullptr;
      }
    if (abcname != "default")
      cd3names[cd3nr] = new string(abcname);
    else
      cd3names[cd3nr] = nullptr;
  }

  string Mesh :: cd3_default_name = "default";
  const string & Mesh :: GetCD3Name (int cd3nr) const
  {
    static string defaultstring  = "default";
    if (!cd3names.Size())
      return defaultstring;

    if (cd3nr < 0 || cd3nr >= cd3names.Size())
      return defaultstring;

    if (cd3names[cd3nr])
      return *cd3names[cd3nr];
    else
      return defaultstring;
  }

  void Mesh :: SetUserData(const char * id, Array<int> & data)
  {
    if(userdata_int.Used(id))
      delete userdata_int.Get(id);

    Array<int> * newdata = new Array<int>(data);

    userdata_int.Set(id,newdata);      
  }
  bool Mesh :: GetUserData(const char * id, Array<int> & data, int shift) const
  {
    if(userdata_int.Used(id))
      {
        if(data.Size() < (*userdata_int.Get(id)).Size()+shift)
          data.SetSize((*userdata_int.Get(id)).Size()+shift);
        for(int i=0; i<(*userdata_int.Get(id)).Size(); i++)
          data[i+shift] = (*userdata_int.Get(id))[i];
        return true;
      }
    else
      {
        data.SetSize(0);
        return false;
      }
  }
  void Mesh :: SetUserData(const char * id, Array<double> & data)
  {
    if(userdata_double.Used(id))
      delete userdata_double.Get(id);

    Array<double> * newdata = new Array<double>(data);

    userdata_double.Set(id,newdata);      
  }
  bool Mesh :: GetUserData(const char * id, Array<double> & data, int shift) const
  {
    if(userdata_double.Used(id))
      {
        if(data.Size() < (*userdata_double.Get(id)).Size()+shift)
          data.SetSize((*userdata_double.Get(id)).Size()+shift);
        for(int i=0; i<(*userdata_double.Get(id)).Size(); i++)
          data[i+shift] = (*userdata_double.Get(id))[i];
        return true;
      }
    else
      {
        data.SetSize(0);
        return false;
      }
  }



  void Mesh :: PrintMemInfo (ostream & ost) const
  {
    ost << "Mesh Mem:" << endl;

    ost << GetNP() << " Points, of size " 
        << sizeof (Point3d) << " + " << sizeof(POINTTYPE) << " = "
        << GetNP() * (sizeof (Point3d) + sizeof(POINTTYPE)) << endl;

    ost << GetNSE() << " Surface elements, of size " 
        << sizeof (Element2d) << " = " 
        << GetNSE() * sizeof(Element2d) << endl;

    ost << GetNE() << " Volume elements, of size " 
        << sizeof (Element) << " = " 
        << GetNE() * sizeof(Element) << endl;

    // ost << "surfs on node:";
    // surfacesonnode.PrintMemInfo (cout);

    ost << "boundaryedges: ";
    if (boundaryedges)
      boundaryedges->PrintMemInfo (cout);

    ost << "surfelementht: ";
    if (surfelementht)
      surfelementht->PrintMemInfo (cout);
  }
}
