source: molecuilder/src/boundary.cpp@ d3d15c

#include "molecules.hpp"
#include "boundary.hpp"

#define DEBUG 1
#define DoTecplotOutput 0
#define DoRaster3DOutput 1
#define TecplotSuffix ".dat"
#define Raster3DSuffix ".r3d"

// ======================================== Points on Boundary =================================

BoundaryPointSet::BoundaryPointSet()
{
  LinesCount = 0;
  Nr = -1;
}
;

BoundaryPointSet::BoundaryPointSet(atom *Walker)
{
  node = Walker;
  LinesCount = 0;
  Nr = Walker->nr;
}
;

BoundaryPointSet::~BoundaryPointSet()
{
  cout << Verbose(5) << "Erasing point nr. " << Nr << "." << endl;
  node = NULL;
}
;

void
BoundaryPointSet::AddLine(class BoundaryLineSet *line)
{
  cout << Verbose(6) << "Adding " << *this << " to line " << *line << "."
      << endl;
  if (line->endpoints[0] == this)
    {
      lines.insert(LinePair(line->endpoints[1]->Nr, line));
    }
  else
    {
      lines.insert(LinePair(line->endpoints[0]->Nr, line));
    }
  LinesCount++;
}
;

ostream &
operator <<(ostream &ost, BoundaryPointSet &a)
{
  ost << "[" << a.Nr << "|" << a.node->Name << "]";
  return ost;
}
;

// ======================================== Lines on Boundary =================================

BoundaryLineSet::BoundaryLineSet()
{
  for (int i = 0; i < 2; i++)
    endpoints[i] = NULL;
  TrianglesCount = 0;
  Nr = -1;
}
;

BoundaryLineSet::BoundaryLineSet(class BoundaryPointSet *Point[2], int number)
{
  // set number
  Nr = number;
  // set endpoints in ascending order
  SetEndpointsOrdered(endpoints, Point[0], Point[1]);
  // add this line to the hash maps of both endpoints
  Point[0]->AddLine(this); //Taken out, to check whether we can avoid unwanted double adding.
  Point[1]->AddLine(this); //
  // clear triangles list
  TrianglesCount = 0;
  cout << Verbose(5) << "New Line with endpoints " << *this << "." << endl;
}
;

BoundaryLineSet::~BoundaryLineSet()
{
  for (int i = 0; i < 2; i++)
    {
      cout << Verbose(5) << "Erasing Line Nr. " << Nr << " in boundary point "
          << *endpoints[i] << "." << endl;
      endpoints[i]->lines.erase(Nr);
      LineMap::iterator tester = endpoints[i]->lines.begin();
      tester++;
      if (tester == endpoints[i]->lines.end())
        {
          cout << Verbose(5) << *endpoints[i]
              << " has no more lines it's attached to, erasing." << endl;
          //delete(endpoints[i]);
        }
      else
        cout << Verbose(5) << *endpoints[i]
            << " has still lines it's attached to." << endl;
    }
}
;

void
BoundaryLineSet::AddTriangle(class BoundaryTriangleSet *triangle)
{
  cout << Verbose(6) << "Add " << triangle->Nr << " to line " << *this << "."
      << endl;
  triangles.insert(TrianglePair(TrianglesCount, triangle));
  TrianglesCount++;
}
;

ostream &
operator <<(ostream &ost, BoundaryLineSet &a)
{
  ost << "[" << a.Nr << "|" << a.endpoints[0]->node->Name << ","
      << a.endpoints[1]->node->Name << "]";
  return ost;
}
;

// ======================================== Triangles on Boundary =================================


BoundaryTriangleSet::BoundaryTriangleSet()
{
  for (int i = 0; i < 3; i++)
    {
      endpoints[i] = NULL;
      lines[i] = NULL;
    }
  Nr = -1;
}
;

BoundaryTriangleSet::BoundaryTriangleSet(class BoundaryLineSet *line[3],
    int number)
{
  // set number
  Nr = number;
  // set lines
  cout << Verbose(5) << "New triangle " << Nr << ":" << endl;
  for (int i = 0; i < 3; i++)
    {
      lines[i] = line[i];
      lines[i]->AddTriangle(this);
    }
  // get ascending order of endpoints
  map<int, class BoundaryPointSet *> OrderMap;
  for (int i = 0; i < 3; i++)
    // for all three lines
    for (int j = 0; j < 2; j++)
      { // for both endpoints
        OrderMap.insert(pair<int, class BoundaryPointSet *> (
            line[i]->endpoints[j]->Nr, line[i]->endpoints[j]));
        // and we don't care whether insertion fails
      }
  // set endpoints
  int Counter = 0;
  cout << Verbose(6) << " with end points ";
  for (map<int, class BoundaryPointSet *>::iterator runner = OrderMap.begin(); runner
      != OrderMap.end(); runner++)
    {
      endpoints[Counter] = runner->second;
      cout << " " << *endpoints[Counter];
      Counter++;
    }
  if (Counter < 3)
    {
      cerr << "ERROR! We have a triangle with only two distinct endpoints!"
          << endl;
      //exit(1);
    }
  cout << "." << endl;
}
;

BoundaryTriangleSet::~BoundaryTriangleSet()
{
  for (int i = 0; i < 3; i++)
    {
      cout << Verbose(5) << "Erasing triangle Nr." << Nr << endl;
      lines[i]->triangles.erase(Nr);
      TriangleMap::iterator tester = lines[i]->triangles.begin();
      tester++;
      if (tester == lines[i]->triangles.end())
        {
          cout << Verbose(5) << *lines[i]
              << " is no more attached to any triangle, erasing." << endl;
          delete (lines[i]);
        }
      else
        cout << Verbose(5) << *lines[i] << " is still attached to a triangle."
            << endl;
    }
}
;

void
BoundaryTriangleSet::GetNormalVector(Vector &OtherVector)
{
  // get normal vector
  NormalVector.MakeNormalVector(&endpoints[0]->node->x, &endpoints[1]->node->x,
      &endpoints[2]->node->x);

  // make it always point inward (any offset vector onto plane projected onto normal vector suffices)
  if (endpoints[0]->node->x.Projection(&OtherVector) > 0)
    NormalVector.Scale(-1.);
}
;

ostream &
operator <<(ostream &ost, BoundaryTriangleSet &a)
{
  ost << "[" << a.Nr << "|" << a.endpoints[0]->node->Name << ","
      << a.endpoints[1]->node->Name << "," << a.endpoints[2]->node->Name << "]";
  return ost;
}
;

// ========================================== F U N C T I O N S =================================

/** Finds the endpoint two lines are sharing.
 * \param *line1 first line
 * \param *line2 second line
 * \return point which is shared or NULL if none
 */
class BoundaryPointSet *
GetCommonEndpoint(class BoundaryLineSet * line1, class BoundaryLineSet * line2)
{
  class BoundaryLineSet * lines[2] =
    { line1, line2 };
  class BoundaryPointSet *node = NULL;
  map<int, class BoundaryPointSet *> OrderMap;
  pair<map<int, class BoundaryPointSet *>::iterator, bool> OrderTest;
  for (int i = 0; i < 2; i++)
    // for both lines
    for (int j = 0; j < 2; j++)
      { // for both endpoints
        OrderTest = OrderMap.insert(pair<int, class BoundaryPointSet *> (
            lines[i]->endpoints[j]->Nr, lines[i]->endpoints[j]));
        if (!OrderTest.second)
          { // if insertion fails, we have common endpoint
            node = OrderTest.first->second;
            cout << Verbose(5) << "Common endpoint of lines " << *line1
                << " and " << *line2 << " is: " << *node << "." << endl;
            j = 2;
            i = 2;
            break;
          }
      }
  return node;
}
;

/** Determines the boundary points of a cluster.
 * Does a projection per axis onto the orthogonal plane, transforms into spherical coordinates, sorts them by the angle
 * and looks at triples: if the middle has less a distance than the allowed maximum height of the triangle formed by the plane's
 * center and first and last point in the triple, it is thrown out.
 * \param *out output stream for debugging
 * \param *mol molecule structure representing the cluster
 */
Boundaries *
GetBoundaryPoints(ofstream *out, molecule *mol)
{
  atom *Walker = NULL;
  PointMap PointsOnBoundary;
  LineMap LinesOnBoundary;
  TriangleMap TrianglesOnBoundary;

  *out << Verbose(1) << "Finding all boundary points." << endl;
  Boundaries *BoundaryPoints = new Boundaries[NDIM]; // first is alpha, second is (r, nr)
  BoundariesTestPair BoundaryTestPair;
  Vector AxisVector, AngleReferenceVector, AngleReferenceNormalVector;
  double radius, angle;
  // 3a. Go through every axis
  for (int axis = 0; axis < NDIM; axis++)
    {
      AxisVector.Zero();
      AngleReferenceVector.Zero();
      AngleReferenceNormalVector.Zero();
      AxisVector.x[axis] = 1.;
      AngleReferenceVector.x[(axis + 1) % NDIM] = 1.;
      AngleReferenceNormalVector.x[(axis + 2) % NDIM] = 1.;
      //    *out << Verbose(1) << "Axisvector is ";
      //    AxisVector.Output(out);
      //    *out << " and AngleReferenceVector is ";
      //    AngleReferenceVector.Output(out);
      //    *out << "." << endl;
      //    *out << " and AngleReferenceNormalVector is ";
      //    AngleReferenceNormalVector.Output(out);
      //    *out << "." << endl;
      // 3b. construct set of all points, transformed into cylindrical system and with left and right neighbours
      Walker = mol->start;
      while (Walker->next != mol->end)
        {
          Walker = Walker->next;
          Vector ProjectedVector;
          ProjectedVector.CopyVector(&Walker->x);
          ProjectedVector.ProjectOntoPlane(&AxisVector);
          // correct for negative side
          //if (Projection(y) < 0)
          //angle = 2.*M_PI - angle;
          radius = ProjectedVector.Norm();
          if (fabs(radius) > MYEPSILON)
            angle = ProjectedVector.Angle(&AngleReferenceVector);
          else
            angle = 0.; // otherwise it's a vector in Axis Direction and unimportant for boundary issues

          //*out << "Checking sign in quadrant : " << ProjectedVector.Projection(&AngleReferenceNormalVector) << "." << endl;
          if (ProjectedVector.Projection(&AngleReferenceNormalVector) > 0)
            {
              angle = 2. * M_PI - angle;
            }
          //*out << Verbose(2) << "Inserting " << *Walker << ": (r, alpha) = (" << radius << "," << angle << "): ";
          //ProjectedVector.Output(out);
          //*out << endl;
          BoundaryTestPair = BoundaryPoints[axis].insert(BoundariesPair(angle,
              DistancePair (radius, Walker)));
          if (BoundaryTestPair.second)
            { // successfully inserted
            }
          else
            { // same point exists, check first r, then distance of original vectors to center of gravity
              *out << Verbose(2)
                  << "Encountered two vectors whose projection onto axis "
                  << axis << " is equal: " << endl;
              *out << Verbose(2) << "Present vector: ";
              BoundaryTestPair.first->second.second->x.Output(out);
              *out << endl;
              *out << Verbose(2) << "New vector: ";
              Walker->x.Output(out);
              *out << endl;
              double tmp = ProjectedVector.Norm();
              if (tmp > BoundaryTestPair.first->second.first)
                {
                  BoundaryTestPair.first->second.first = tmp;
                  BoundaryTestPair.first->second.second = Walker;
                  *out << Verbose(2) << "Keeping new vector." << endl;
                }
              else if (tmp == BoundaryTestPair.first->second.first)
                {
                  if (BoundaryTestPair.first->second.second->x.ScalarProduct(
                      &BoundaryTestPair.first->second.second->x)
                      < Walker->x.ScalarProduct(&Walker->x))
                    { // Norm() does a sqrt, which makes it a lot slower
                      BoundaryTestPair.first->second.second = Walker;
                      *out << Verbose(2) << "Keeping new vector." << endl;
                    }
                  else
                    {
                      *out << Verbose(2) << "Keeping present vector." << endl;
                    }
                }
              else
                {
                  *out << Verbose(2) << "Keeping present vector." << endl;
                }
            }
        }
      // printing all inserted for debugging
      //    {
      //      *out << Verbose(2) << "Printing list of candidates for axis " << axis << " which we have inserted so far." << endl;
      //      int i=0;
      //      for(Boundaries::iterator runner = BoundaryPoints[axis].begin(); runner != BoundaryPoints[axis].end(); runner++) {
      //        if (runner != BoundaryPoints[axis].begin())
      //          *out << ", " << i << ": " << *runner->second.second;
      //        else
      //          *out << i << ": " << *runner->second.second;
      //        i++;
      //      }
      //      *out << endl;
      //    }
      // 3c. throw out points whose distance is less than the mean of left and right neighbours
      bool flag = false;
      do
        { // do as long as we still throw one out per round
          *out << Verbose(1)
              << "Looking for candidates to kick out by convex condition ... "
              << endl;
          flag = false;
          Boundaries::iterator left = BoundaryPoints[axis].end();
          Boundaries::iterator right = BoundaryPoints[axis].end();
          for (Boundaries::iterator runner = BoundaryPoints[axis].begin(); runner
              != BoundaryPoints[axis].end(); runner++)
            {
              // set neighbours correctly
              if (runner == BoundaryPoints[axis].begin())
                {
                  left = BoundaryPoints[axis].end();
                }
              else
                {
                  left = runner;
                }
              left--;
              right = runner;
              right++;
              if (right == BoundaryPoints[axis].end())
                {
                  right = BoundaryPoints[axis].begin();
                }
              // check distance

              // construct the vector of each side of the triangle on the projected plane (defined by normal vector AxisVector)
                {
                  Vector SideA, SideB, SideC, SideH;
                  SideA.CopyVector(&left->second.second->x);
                  SideA.ProjectOntoPlane(&AxisVector);
                  //          *out << "SideA: ";
                  //          SideA.Output(out);
                  //          *out << endl;

                  SideB.CopyVector(&right->second.second->x);
                  SideB.ProjectOntoPlane(&AxisVector);
                  //          *out << "SideB: ";
                  //          SideB.Output(out);
                  //          *out << endl;

                  SideC.CopyVector(&left->second.second->x);
                  SideC.SubtractVector(&right->second.second->x);
                  SideC.ProjectOntoPlane(&AxisVector);
                  //          *out << "SideC: ";
                  //          SideC.Output(out);
                  //          *out << endl;

                  SideH.CopyVector(&runner->second.second->x);
                  SideH.ProjectOntoPlane(&AxisVector);
                  //          *out << "SideH: ";
                  //          SideH.Output(out);
                  //          *out << endl;

                  // calculate each length
                  double a = SideA.Norm();
                  //double b = SideB.Norm();
                  //double c = SideC.Norm();
                  double h = SideH.Norm();
                  // calculate the angles
                  double alpha = SideA.Angle(&SideH);
                  double beta = SideA.Angle(&SideC);
                  double gamma = SideB.Angle(&SideH);
                  double delta = SideC.Angle(&SideH);
                  double MinDistance = a * sin(beta) / (sin(delta)) * (((alpha
                      < M_PI / 2.) || (gamma < M_PI / 2.)) ? 1. : -1.);
                  //          *out << Verbose(2) << " I calculated: a = " << a << ", h = " << h << ", beta(" << left->second.second->Name << "," << left->second.second->Name << "-" << right->second.second->Name << ") = " << beta << ", delta(" << left->second.second->Name << "," << runner->second.second->Name << ") = " << delta << ", Min = " << MinDistance << "." << endl;
                  //*out << Verbose(1) << "Checking CoG distance of runner " << *runner->second.second << " " << h << " against triangle's side length spanned by (" << *left->second.second << "," << *right->second.second << ") of " << MinDistance << "." << endl;
                  if ((fabs(h / fabs(h) - MinDistance / fabs(MinDistance))
                      < MYEPSILON) && (h < MinDistance))
                    {
                      // throw out point
                      //*out << Verbose(1) << "Throwing out " << *runner->second.second << "." << endl;
                      BoundaryPoints[axis].erase(runner);
                      flag = true;
                    }
                }
            }
        }
      while (flag);
    }
  return BoundaryPoints;
}
;

/** Determines greatest diameters of a cluster defined by its convex envelope.
 * Looks at lines parallel to one axis and where they intersect on the projected planes
 * \param *out output stream for debugging
 * \param *BoundaryPoints NDIM set of boundary points defining the convex envelope on each projected plane
 * \param *mol molecule structure representing the cluster
 * \param IsAngstroem whether we have angstroem or atomic units
 * \return NDIM array of the diameters
 */
double *
GetDiametersOfCluster(ofstream *out, Boundaries *BoundaryPtr, molecule *mol,
    bool IsAngstroem)
{
  // get points on boundary of NULL was given as parameter
  bool BoundaryFreeFlag = false;
  Boundaries *BoundaryPoints = BoundaryPtr;
  if (BoundaryPoints == NULL)
    {
      BoundaryFreeFlag = true;
      BoundaryPoints = GetBoundaryPoints(out, mol);
    }
  else
    {
      *out << Verbose(1) << "Using given boundary points set." << endl;
    }
  // determine biggest "diameter" of cluster for each axis
  Boundaries::iterator Neighbour, OtherNeighbour;
  double *GreatestDiameter = new double[NDIM];
  for (int i = 0; i < NDIM; i++)
    GreatestDiameter[i] = 0.;
  double OldComponent, tmp, w1, w2;
  Vector DistanceVector, OtherVector;
  int component, Othercomponent;
  for (int axis = 0; axis < NDIM; axis++)
    { // regard each projected plane
      //*out << Verbose(1) << "Current axis is " << axis << "." << endl;
      for (int j = 0; j < 2; j++)
        { // and for both axis on the current plane
          component = (axis + j + 1) % NDIM;
          Othercomponent = (axis + 1 + ((j + 1) & 1)) % NDIM;
          //*out << Verbose(1) << "Current component is " << component << ", Othercomponent is " << Othercomponent << "." << endl;
          for (Boundaries::iterator runner = BoundaryPoints[axis].begin(); runner
              != BoundaryPoints[axis].end(); runner++)
            {
              //*out << Verbose(2) << "Current runner is " << *(runner->second.second) << "." << endl;
              // seek for the neighbours pair where the Othercomponent sign flips
              Neighbour = runner;
              Neighbour++;
              if (Neighbour == BoundaryPoints[axis].end()) // make it wrap around
                Neighbour = BoundaryPoints[axis].begin();
              DistanceVector.CopyVector(&runner->second.second->x);
              DistanceVector.SubtractVector(&Neighbour->second.second->x);
              do
                { // seek for neighbour pair where it flips
                  OldComponent = DistanceVector.x[Othercomponent];
                  Neighbour++;
                  if (Neighbour == BoundaryPoints[axis].end()) // make it wrap around
                    Neighbour = BoundaryPoints[axis].begin();
                  DistanceVector.CopyVector(&runner->second.second->x);
                  DistanceVector.SubtractVector(&Neighbour->second.second->x);
                  //*out << Verbose(3) << "OldComponent is " << OldComponent << ", new one is " << DistanceVector.x[Othercomponent] << "." << endl;
                }
              while ((runner != Neighbour) && (fabs(OldComponent / fabs(
                  OldComponent) - DistanceVector.x[Othercomponent] / fabs(
                  DistanceVector.x[Othercomponent])) < MYEPSILON)); // as long as sign does not flip
              if (runner != Neighbour)
                {
                  OtherNeighbour = Neighbour;
                  if (OtherNeighbour == BoundaryPoints[axis].begin()) // make it wrap around
                    OtherNeighbour = BoundaryPoints[axis].end();
                  OtherNeighbour--;
                  //*out << Verbose(2) << "The pair, where the sign of OtherComponent flips, is: " << *(Neighbour->second.second) << " and " << *(OtherNeighbour->second.second) << "." << endl;
                  // now we have found the pair: Neighbour and OtherNeighbour
                  OtherVector.CopyVector(&runner->second.second->x);
                  OtherVector.SubtractVector(&OtherNeighbour->second.second->x);
                  //*out << Verbose(2) << "Distances to Neighbour and OtherNeighbour are " << DistanceVector.x[component] << " and " << OtherVector.x[component] << "." << endl;
                  //*out << Verbose(2) << "OtherComponents to Neighbour and OtherNeighbour are " << DistanceVector.x[Othercomponent] << " and " << OtherVector.x[Othercomponent] << "." << endl;
                  // do linear interpolation between points (is exact) to extract exact intersection between Neighbour and OtherNeighbour
                  w1 = fabs(OtherVector.x[Othercomponent]);
                  w2 = fabs(DistanceVector.x[Othercomponent]);
                  tmp = fabs((w1 * DistanceVector.x[component] + w2
                      * OtherVector.x[component]) / (w1 + w2));
                  // mark if it has greater diameter
                  //*out << Verbose(2) << "Comparing current greatest " << GreatestDiameter[component] << " to new " << tmp << "." << endl;
                  GreatestDiameter[component] = (GreatestDiameter[component]
                      > tmp) ? GreatestDiameter[component] : tmp;
                } //else
              //*out << Verbose(2) << "Saw no sign flip, probably top or bottom node." << endl;
            }
        }
    }
  *out << Verbose(0) << "RESULT: The biggest diameters are "
      << GreatestDiameter[0] << " and " << GreatestDiameter[1] << " and "
      << GreatestDiameter[2] << " " << (IsAngstroem ? "angstrom"
      : "atomiclength") << "." << endl;

  // free reference lists
  if (BoundaryFreeFlag)
    delete[] (BoundaryPoints);

  return GreatestDiameter;
}
;

/** Creates the objects in a raster3d file (renderable with a header.r3d)
 * \param *out output stream for debugging
 * \param *tecplot output stream for tecplot data
 * \param *Tess Tesselation structure with constructed triangles
 * \param *mol molecule structure with atom positions
 */
void write_raster3d_file(ofstream *out, ofstream *rasterfile, class Tesselation *Tess, class molecule *mol)
{
  atom *Walker = mol->start;
  bond *Binder = mol->first;
  int i;
  Vector *center = mol->DetermineCenterOfAll(out);
  if (rasterfile != NULL) {
    //cout << Verbose(1) << "Writing Raster3D file ... ";
    *rasterfile << "# Raster3D object description, created by MoleCuilder" << endl;
    *rasterfile << "@header.r3d" << endl;
    *rasterfile << "# All atoms as spheres" << endl;
    while (Walker->next != mol->end) {
      Walker = Walker->next;
      *rasterfile << "2" << endl << "  "; // 2 is sphere type
      for (i=0;i<NDIM;i++)
        *rasterfile << Walker->x.x[i]+center->x[i] << " ";
      *rasterfile << "\t0.1\t1. 1. 1." << endl; // radius 0.05 and white as colour
    }

    *rasterfile << "# All bonds as vertices" << endl;
    while (Binder->next != mol->last) {
      Binder = Binder->next;
      *rasterfile << "3" << endl << "  "; // 2 is round-ended cylinder type
      for (i=0;i<NDIM;i++)
        *rasterfile << Binder->leftatom->x.x[i]+center->x[i] << " ";
      *rasterfile << "\t0.03\t";
      for (i=0;i<NDIM;i++)
        *rasterfile << Binder->rightatom->x.x[i]+center->x[i] << " ";
      *rasterfile << "\t0.03\t0. 0. 1." << endl; // radius 0.05 and blue as colour
    }

    *rasterfile << "# All tesselation triangles" << endl;
    for (TriangleMap::iterator TriangleRunner = Tess->TrianglesOnBoundary.begin(); TriangleRunner != Tess->TrianglesOnBoundary.end(); TriangleRunner++) {
      *rasterfile << "1" << endl << "  "; // 1 is triangle type
      for (i=0;i<3;i++) { // print each node
        for (int j=0;j<NDIM;j++)  // and for each node all NDIM coordinates
          *rasterfile << TriangleRunner->second->endpoints[i]->node->x.x[j]+center->x[j] << " ";
        *rasterfile << "\t";
      }
      *rasterfile << "1. 0. 0." << endl;  // red as colour
      *rasterfile << "18" << endl << "  0.5 0.5 0.5" << endl; // 18 is transparency type for previous object
    }
  } else {
    cerr << "ERROR: Given rasterfile is " << rasterfile << "." << endl;
  }
  delete(center);
};

/*
 * This function creates the tecplot file, displaying the tesselation of the hull.
 * \param *out output stream for debugging
 * \param *tecplot output stream for tecplot data
 * \param N arbitrary number to differentiate various zones in the tecplot format
 */
void
write_tecplot_file(ofstream *out, ofstream *tecplot,
    class Tesselation *TesselStruct, class molecule *mol, int N)
{
  if (tecplot != NULL)
    {
      *tecplot << "TITLE = \"3D CONVEX SHELL\"" << endl;
      *tecplot << "VARIABLES = \"X\" \"Y\" \"Z\"" << endl;
      *tecplot << "ZONE T=\"TRIANGLES" << N << "\", N="
          << TesselStruct->PointsOnBoundaryCount << ", E="
          << TesselStruct->TrianglesOnBoundaryCount
          << ", DATAPACKING=POINT, ZONETYPE=FETRIANGLE" << endl;
      int *LookupList = new int[mol->AtomCount];
      for (int i = 0; i < mol->AtomCount; i++)
        LookupList[i] = -1;

      // print atom coordinates
      *out << Verbose(2) << "The following triangles were created:";
      int Counter = 1;
      atom *Walker = NULL;
      for (PointMap::iterator target = TesselStruct->PointsOnBoundary.begin(); target
          != TesselStruct->PointsOnBoundary.end(); target++)
        {
          Walker = target->second->node;
          LookupList[Walker->nr] = Counter++;
          *tecplot << Walker->x.x[0] << " " << Walker->x.x[1] << " "
              << Walker->x.x[2] << " " << endl;
        }
      *tecplot << endl;
      // print connectivity
      for (TriangleMap::iterator runner =
          TesselStruct->TrianglesOnBoundary.begin(); runner
          != TesselStruct->TrianglesOnBoundary.end(); runner++)
        {
          *out << " " << runner->second->endpoints[0]->node->Name << "<->"
              << runner->second->endpoints[1]->node->Name << "<->"
              << runner->second->endpoints[2]->node->Name;
          *tecplot << LookupList[runner->second->endpoints[0]->node->nr] << " "
              << LookupList[runner->second->endpoints[1]->node->nr] << " "
              << LookupList[runner->second->endpoints[2]->node->nr] << endl;
        }
      delete[] (LookupList);
      *out << endl;
    }
}

/** Determines the volume of a cluster.
 * Determines first the convex envelope, then tesselates it and calculates its volume.
 * \param *out output stream for debugging
 * \param *tecplot output stream for tecplot data
 * \param *configuration needed for path to store convex envelope file
 * \param *BoundaryPoints NDIM set of boundary points on the projected plane per axis, on return if desired
 * \param *mol molecule structure representing the cluster
 * \return determined volume of the cluster in cubed config:GetIsAngstroem()
 */
double
VolumeOfConvexEnvelope(ofstream *out, ofstream *tecplot, config *configuration,
    Boundaries *BoundaryPtr, molecule *mol)
{
  bool IsAngstroem = configuration->GetIsAngstroem();
  atom *Walker = NULL;
  struct Tesselation *TesselStruct = new Tesselation;
  bool BoundaryFreeFlag = false;
  Boundaries *BoundaryPoints = BoundaryPtr;
  double volume = 0.;
  double PyramidVolume = 0.;
  double G, h;
  Vector x, y;
  double a, b, c;

  //Find_non_convex_border(out, tecplot, *TesselStruct, mol); // Is now called from command line.

  // 1. calculate center of gravity
  *out << endl;
  Vector *CenterOfGravity = mol->DetermineCenterOfGravity(out);

  // 2. translate all points into CoG
  *out << Verbose(1) << "Translating system to Center of Gravity." << endl;
  Walker = mol->start;
  while (Walker->next != mol->end)
    {
      Walker = Walker->next;
      Walker->x.Translate(CenterOfGravity);
    }

  // 3. Find all points on the boundary
  if (BoundaryPoints == NULL)
    {
      BoundaryFreeFlag = true;
      BoundaryPoints = GetBoundaryPoints(out, mol);
    }
  else
    {
      *out << Verbose(1) << "Using given boundary points set." << endl;
    }

  // 4. fill the boundary point list
  for (int axis = 0; axis < NDIM; axis++)
    for (Boundaries::iterator runner = BoundaryPoints[axis].begin(); runner
        != BoundaryPoints[axis].end(); runner++)
      {
        TesselStruct->AddPoint(runner->second.second);
      }

  *out << Verbose(2) << "I found " << TesselStruct->PointsOnBoundaryCount
      << " points on the convex boundary." << endl;
  // now we have the whole set of edge points in the BoundaryList

  // listing for debugging
  //  *out << Verbose(1) << "Listing PointsOnBoundary:";
  //  for(PointMap::iterator runner = PointsOnBoundary.begin(); runner != PointsOnBoundary.end(); runner++) {
  //    *out << " " << *runner->second;
  //  }
  //  *out << endl;

  // 5a. guess starting triangle
  TesselStruct->GuessStartingTriangle(out);

  // 5b. go through all lines, that are not yet part of two triangles (only of one so far)
  TesselStruct->TesselateOnBoundary(out, configuration, mol);

  *out << Verbose(2) << "I created " << TesselStruct->TrianglesOnBoundaryCount
      << " triangles with " << TesselStruct->LinesOnBoundaryCount
      << " lines and " << TesselStruct->PointsOnBoundaryCount << " points."
      << endl;

  // 6a. Every triangle forms a pyramid with the center of gravity as its peak, sum up the volumes
  *out << Verbose(1)
      << "Calculating the volume of the pyramids formed out of triangles and center of gravity."
      << endl;
  for (TriangleMap::iterator runner = TesselStruct->TrianglesOnBoundary.begin(); runner
      != TesselStruct->TrianglesOnBoundary.end(); runner++)
    { // go through every triangle, calculate volume of its pyramid with CoG as peak
      x.CopyVector(&runner->second->endpoints[0]->node->x);
      x.SubtractVector(&runner->second->endpoints[1]->node->x);
      y.CopyVector(&runner->second->endpoints[0]->node->x);
      y.SubtractVector(&runner->second->endpoints[2]->node->x);
      a = sqrt(runner->second->endpoints[0]->node->x.Distance(
          &runner->second->endpoints[1]->node->x));
      b = sqrt(runner->second->endpoints[0]->node->x.Distance(
          &runner->second->endpoints[2]->node->x));
      c = sqrt(runner->second->endpoints[2]->node->x.Distance(
          &runner->second->endpoints[1]->node->x));
      G = sqrt(((a * a + b * b + c * c) * (a * a + b * b + c * c) - 2 * (a * a
          * a * a + b * b * b * b + c * c * c * c)) / 16.); // area of tesselated triangle
      x.MakeNormalVector(&runner->second->endpoints[0]->node->x,
          &runner->second->endpoints[1]->node->x,
          &runner->second->endpoints[2]->node->x);
      x.Scale(runner->second->endpoints[1]->node->x.Projection(&x));
      h = x.Norm(); // distance of CoG to triangle
      PyramidVolume = (1. / 3.) * G * h; // this formula holds for _all_ pyramids (independent of n-edge base or (not) centered peak)
      *out << Verbose(2) << "Area of triangle is " << G << " "
          << (IsAngstroem ? "angstrom" : "atomiclength") << "^2, height is "
          << h << " and the volume is " << PyramidVolume << " "
          << (IsAngstroem ? "angstrom" : "atomiclength") << "^3." << endl;
      volume += PyramidVolume;
    }
  *out << Verbose(0) << "RESULT: The summed volume is " << setprecision(10)
      << volume << " " << (IsAngstroem ? "angstrom" : "atomiclength") << "^3."
      << endl;

  // 7. translate all points back from CoG
  *out << Verbose(1) << "Translating system back from Center of Gravity."
      << endl;
  CenterOfGravity->Scale(-1);
  Walker = mol->start;
  while (Walker->next != mol->end)
    {
      Walker = Walker->next;
      Walker->x.Translate(CenterOfGravity);
    }

  // 8. Store triangles in tecplot file
  write_tecplot_file(out, tecplot, TesselStruct, mol, 0);

  // free reference lists
  if (BoundaryFreeFlag)
    delete[] (BoundaryPoints);

  return volume;
}
;

/** Creates multiples of the by \a *mol given cluster and suspends them in water with a given final density.
 * We get cluster volume by VolumeOfConvexEnvelope() and its diameters by GetDiametersOfCluster()
 * \param *out output stream for debugging
 * \param *configuration needed for path to store convex envelope file
 * \param *mol molecule structure representing the cluster
 * \param ClusterVolume guesstimated cluster volume, if equal 0 we used VolumeOfConvexEnvelope() instead.
 * \param celldensity desired average density in final cell
 */
void
PrepareClustersinWater(ofstream *out, config *configuration, molecule *mol,
    double ClusterVolume, double celldensity)
{
  // transform to PAS
  mol->PrincipalAxisSystem(out, true);

  // some preparations beforehand
  bool IsAngstroem = configuration->GetIsAngstroem();
  Boundaries *BoundaryPoints = GetBoundaryPoints(out, mol);
  double clustervolume;
  if (ClusterVolume == 0)
    clustervolume = VolumeOfConvexEnvelope(out, NULL, configuration,
        BoundaryPoints, mol);
  else
    clustervolume = ClusterVolume;
  double *GreatestDiameter = GetDiametersOfCluster(out, BoundaryPoints, mol,
      IsAngstroem);
  Vector BoxLengths;
  int repetition[NDIM] =
    { 1, 1, 1 };
  int TotalNoClusters = 1;
  for (int i = 0; i < NDIM; i++)
    TotalNoClusters *= repetition[i];

  // sum up the atomic masses
  double totalmass = 0.;
  atom *Walker = mol->start;
  while (Walker->next != mol->end)
    {
      Walker = Walker->next;
      totalmass += Walker->type->mass;
    }
  *out << Verbose(0) << "RESULT: The summed mass is " << setprecision(10)
      << totalmass << " atomicmassunit." << endl;

  *out << Verbose(0) << "RESULT: The average density is " << setprecision(10)
      << totalmass / clustervolume << " atomicmassunit/"
      << (IsAngstroem ? "angstrom" : "atomiclength") << "^3." << endl;

  // solve cubic polynomial
  *out << Verbose(1) << "Solving equidistant suspension in water problem ..."
      << endl;
  double cellvolume;
  if (IsAngstroem)
    cellvolume = (TotalNoClusters * totalmass / SOLVENTDENSITY_A - (totalmass
        / clustervolume)) / (celldensity - 1);
  else
    cellvolume = (TotalNoClusters * totalmass / SOLVENTDENSITY_a0 - (totalmass
        / clustervolume)) / (celldensity - 1);
  *out << Verbose(1) << "Cellvolume needed for a density of " << celldensity
      << " g/cm^3 is " << cellvolume << " " << (IsAngstroem ? "angstrom"
      : "atomiclength") << "^3." << endl;

  double minimumvolume = TotalNoClusters * (GreatestDiameter[0]
      * GreatestDiameter[1] * GreatestDiameter[2]);
  *out << Verbose(1)
      << "Minimum volume of the convex envelope contained in a rectangular box is "
      << minimumvolume << " atomicmassunit/" << (IsAngstroem ? "angstrom"
      : "atomiclength") << "^3." << endl;
  if (minimumvolume > cellvolume)
    {
      cerr << Verbose(0)
          << "ERROR: the containing box already has a greater volume than the envisaged cell volume!"
          << endl;
      cout << Verbose(0)
          << "Setting Box dimensions to minimum possible, the greatest diameters."
          << endl;
      for (int i = 0; i < NDIM; i++)
        BoxLengths.x[i] = GreatestDiameter[i];
      mol->CenterEdge(out, &BoxLengths);
    }
  else
    {
      BoxLengths.x[0] = (repetition[0] * GreatestDiameter[0] + repetition[1]
          * GreatestDiameter[1] + repetition[2] * GreatestDiameter[2]);
      BoxLengths.x[1] = (repetition[0] * repetition[1] * GreatestDiameter[0]
          * GreatestDiameter[1] + repetition[0] * repetition[2]
          * GreatestDiameter[0] * GreatestDiameter[2] + repetition[1]
          * repetition[2] * GreatestDiameter[1] * GreatestDiameter[2]);
      BoxLengths.x[2] = minimumvolume - cellvolume;
      double x0 = 0., x1 = 0., x2 = 0.;
      if (gsl_poly_solve_cubic(BoxLengths.x[0], BoxLengths.x[1],
          BoxLengths.x[2], &x0, &x1, &x2) == 1) // either 1 or 3 on return
        *out << Verbose(0) << "RESULT: The resulting spacing is: " << x0
            << " ." << endl;
      else
        {
          *out << Verbose(0) << "RESULT: The resulting spacings are: " << x0
              << " and " << x1 << " and " << x2 << " ." << endl;
          x0 = x2; // sorted in ascending order
        }

      cellvolume = 1;
      for (int i = 0; i < NDIM; i++)
        {
          BoxLengths.x[i] = repetition[i] * (x0 + GreatestDiameter[i]);
          cellvolume *= BoxLengths.x[i];
        }

      // set new box dimensions
      *out << Verbose(0) << "Translating to box with these boundaries." << endl;
      mol->CenterInBox((ofstream *) &cout, &BoxLengths);
    }
  // update Box of atoms by boundary
  mol->SetBoxDimension(&BoxLengths);
  *out << Verbose(0) << "RESULT: The resulting cell dimensions are: "
      << BoxLengths.x[0] << " and " << BoxLengths.x[1] << " and "
      << BoxLengths.x[2] << " with total volume of " << cellvolume << " "
      << (IsAngstroem ? "angstrom" : "atomiclength") << "^3." << endl;
}
;

// =========================================================== class TESSELATION ===========================================

/** Constructor of class Tesselation.
 */
Tesselation::Tesselation()
{
  PointsOnBoundaryCount = 0;
  LinesOnBoundaryCount = 0;
  TrianglesOnBoundaryCount = 0;
  TriangleFilesWritten = 0;
}
;

/** Constructor of class Tesselation.
 * We have to free all points, lines and triangles.
 */
Tesselation::~Tesselation()
{
  cout << Verbose(1) << "Free'ing TesselStruct ... " << endl;
  for (TriangleMap::iterator runner = TrianglesOnBoundary.begin(); runner
      != TrianglesOnBoundary.end(); runner++)
    {
      delete (runner->second);
    }
}
;

/** Gueses first starting triangle of the convex envelope.
 * We guess the starting triangle by taking the smallest distance between two points and looking for a fitting third.
 * \param *out output stream for debugging
 * \param PointsOnBoundary set of boundary points defining the convex envelope of the cluster
 */
void
Tesselation::GuessStartingTriangle(ofstream *out)
{
  // 4b. create a starting triangle
  // 4b1. create all distances
  DistanceMultiMap DistanceMMap;
  double distance, tmp;
  Vector PlaneVector, TrialVector;
  PointMap::iterator A, B, C; // three nodes of the first triangle
  A = PointsOnBoundary.begin(); // the first may be chosen arbitrarily

  // with A chosen, take each pair B,C and sort
  if (A != PointsOnBoundary.end())
    {
      B = A;
      B++;
      for (; B != PointsOnBoundary.end(); B++)
        {
          C = B;
          C++;
          for (; C != PointsOnBoundary.end(); C++)
            {
              tmp = A->second->node->x.Distance(&B->second->node->x);
              distance = tmp * tmp;
              tmp = A->second->node->x.Distance(&C->second->node->x);
              distance += tmp * tmp;
              tmp = B->second->node->x.Distance(&C->second->node->x);
              distance += tmp * tmp;
              DistanceMMap.insert(DistanceMultiMapPair(distance, pair<
                  PointMap::iterator, PointMap::iterator> (B, C)));
            }
        }
    }
  //    // listing distances
  //    *out << Verbose(1) << "Listing DistanceMMap:";
  //    for(DistanceMultiMap::iterator runner = DistanceMMap.begin(); runner != DistanceMMap.end(); runner++) {
  //      *out << " " << runner->first << "(" << *runner->second.first->second << ", " << *runner->second.second->second << ")";
  //    }
  //    *out << endl;
  // 4b2. pick three baselines forming a triangle
  // 1. we take from the smallest sum of squared distance as the base line BC (with peak A) onward as the triangle candidate
  DistanceMultiMap::iterator baseline = DistanceMMap.begin();
  for (; baseline != DistanceMMap.end(); baseline++)
    {
      // we take from the smallest sum of squared distance as the base line BC (with peak A) onward as the triangle candidate
      // 2. next, we have to check whether all points reside on only one side of the triangle
      // 3. construct plane vector
      PlaneVector.MakeNormalVector(&A->second->node->x,
          &baseline->second.first->second->node->x,
          &baseline->second.second->second->node->x);
      *out << Verbose(2) << "Plane vector of candidate triangle is ";
      PlaneVector.Output(out);
      *out << endl;
      // 4. loop over all points
      double sign = 0.;
      PointMap::iterator checker = PointsOnBoundary.begin();
      for (; checker != PointsOnBoundary.end(); checker++)
        {
          // (neglecting A,B,C)
          if ((checker == A) || (checker == baseline->second.first) || (checker
              == baseline->second.second))
            continue;
          // 4a. project onto plane vector
          TrialVector.CopyVector(&checker->second->node->x);
          TrialVector.SubtractVector(&A->second->node->x);
          distance = TrialVector.Projection(&PlaneVector);
          if (fabs(distance) < 1e-4) // we need to have a small epsilon around 0 which is still ok
            continue;
          *out << Verbose(3) << "Projection of " << checker->second->node->Name
              << " yields distance of " << distance << "." << endl;
          tmp = distance / fabs(distance);
          // 4b. Any have different sign to than before? (i.e. would lie outside convex hull with this starting triangle)
          if ((sign != 0) && (tmp != sign))
            {
              // 4c. If so, break 4. loop and continue with next candidate in 1. loop
              *out << Verbose(2) << "Current candidates: "
                  << A->second->node->Name << ","
                  << baseline->second.first->second->node->Name << ","
                  << baseline->second.second->second->node->Name << " leave "
                  << checker->second->node->Name << " outside the convex hull."
                  << endl;
              break;
            }
          else
            { // note the sign for later
              *out << Verbose(2) << "Current candidates: "
                  << A->second->node->Name << ","
                  << baseline->second.first->second->node->Name << ","
                  << baseline->second.second->second->node->Name << " leave "
                  << checker->second->node->Name << " inside the convex hull."
                  << endl;
              sign = tmp;
            }
          // 4d. Check whether the point is inside the triangle (check distance to each node
          tmp = checker->second->node->x.Distance(&A->second->node->x);
          int innerpoint = 0;
          if ((tmp < A->second->node->x.Distance(
              &baseline->second.first->second->node->x)) && (tmp
              < A->second->node->x.Distance(
                  &baseline->second.second->second->node->x)))
            innerpoint++;
          tmp = checker->second->node->x.Distance(
              &baseline->second.first->second->node->x);
          if ((tmp < baseline->second.first->second->node->x.Distance(
              &A->second->node->x)) && (tmp
              < baseline->second.first->second->node->x.Distance(
                  &baseline->second.second->second->node->x)))
            innerpoint++;
          tmp = checker->second->node->x.Distance(
              &baseline->second.second->second->node->x);
          if ((tmp < baseline->second.second->second->node->x.Distance(
              &baseline->second.first->second->node->x)) && (tmp
              < baseline->second.second->second->node->x.Distance(
                  &A->second->node->x)))
            innerpoint++;
          // 4e. If so, break 4. loop and continue with next candidate in 1. loop
          if (innerpoint == 3)
            break;
        }
      // 5. come this far, all on same side? Then break 1. loop and construct triangle
      if (checker == PointsOnBoundary.end())
        {
          *out << "Looks like we have a candidate!" << endl;
          break;
        }
    }
  if (baseline != DistanceMMap.end())
    {
      BPS[0] = baseline->second.first->second;
      BPS[1] = baseline->second.second->second;
      BLS[0] = new class BoundaryLineSet(BPS, LinesOnBoundaryCount);
      BPS[0] = A->second;
      BPS[1] = baseline->second.second->second;
      BLS[1] = new class BoundaryLineSet(BPS, LinesOnBoundaryCount);
      BPS[0] = baseline->second.first->second;
      BPS[1] = A->second;
      BLS[2] = new class BoundaryLineSet(BPS, LinesOnBoundaryCount);

      // 4b3. insert created triangle
      BTS = new class BoundaryTriangleSet(BLS, TrianglesOnBoundaryCount);
      TrianglesOnBoundary.insert(TrianglePair(TrianglesOnBoundaryCount, BTS));
      TrianglesOnBoundaryCount++;
      for (int i = 0; i < NDIM; i++)
        {
          LinesOnBoundary.insert(LinePair(LinesOnBoundaryCount, BTS->lines[i]));
          LinesOnBoundaryCount++;
        }

      *out << Verbose(1) << "Starting triangle is " << *BTS << "." << endl;
    }
  else
    {
      *out << Verbose(1) << "No starting triangle found." << endl;
      exit(255);
    }
}
;

/** Tesselates the convex envelope of a cluster from a single starting triangle.
 * The starting triangle is made out of three baselines. Each line in the final tesselated cluster may belong to at most
 * 2 triangles. Hence, we go through all current lines:
 * -# if the lines contains to only one triangle
 * -# We search all points in the boundary
 *    -# if the triangle with the baseline and the current point has the smallest of angles (comparison between normal vectors
 *    -# if the triangle is in forward direction of the baseline (at most 90 degrees angle between vector orthogonal to
 *       baseline in triangle plane pointing out of the triangle and normal vector of new triangle)
 *    -# then we have a new triangle, whose baselines we again add (or increase their TriangleCount)
 * \param *out output stream for debugging
 * \param *configuration for IsAngstroem
 * \param *mol the cluster as a molecule structure
 */
void
Tesselation::TesselateOnBoundary(ofstream *out, config *configuration,
    molecule *mol)
{
  bool flag;
  PointMap::iterator winner;
  class BoundaryPointSet *peak = NULL;
  double SmallestAngle, TempAngle;
  Vector NormalVector, VirtualNormalVector, CenterVector, TempVector,
      PropagationVector;
  LineMap::iterator LineChecker[2];
  do
    {
      flag = false;
      for (LineMap::iterator baseline = LinesOnBoundary.begin(); baseline
          != LinesOnBoundary.end(); baseline++)
        if (baseline->second->TrianglesCount == 1)
          {
            *out << Verbose(2) << "Current baseline is between "
                << *(baseline->second) << "." << endl;
            // 5a. go through each boundary point if not _both_ edges between either endpoint of the current line and this point exist (and belong to 2 triangles)
            SmallestAngle = M_PI;
            BTS = baseline->second->triangles.begin()->second; // there is only one triangle so far
            // get peak point with respect to this base line's only triangle
            for (int i = 0; i < 3; i++)
              if ((BTS->endpoints[i] != baseline->second->endpoints[0])
                  && (BTS->endpoints[i] != baseline->second->endpoints[1]))
                peak = BTS->endpoints[i];
            *out << Verbose(3) << " and has peak " << *peak << "." << endl;
            // normal vector of triangle
            BTS->GetNormalVector(NormalVector);
            *out << Verbose(4) << "NormalVector of base triangle is ";
            NormalVector.Output(out);
            *out << endl;
            // offset to center of triangle
            CenterVector.Zero();
            for (int i = 0; i < 3; i++)
              CenterVector.AddVector(&BTS->endpoints[i]->node->x);
            CenterVector.Scale(1. / 3.);
            *out << Verbose(4) << "CenterVector of base triangle is ";
            CenterVector.Output(out);
            *out << endl;
            // vector in propagation direction (out of triangle)
            // project center vector onto triangle plane (points from intersection plane-NormalVector to plane-CenterVector intersection)
            TempVector.CopyVector(&baseline->second->endpoints[0]->node->x);
            TempVector.SubtractVector(&baseline->second->endpoints[1]->node->x);
            PropagationVector.MakeNormalVector(&TempVector, &NormalVector);
            TempVector.CopyVector(&CenterVector);
            TempVector.SubtractVector(&baseline->second->endpoints[0]->node->x); // TempVector is vector on triangle plane pointing from one baseline egde towards center!
            //*out << Verbose(2) << "Projection of propagation onto temp: " << PropagationVector.Projection(&TempVector) << "." << endl;
            if (PropagationVector.Projection(&TempVector) > 0) // make sure normal propagation vector points outward from baseline
              PropagationVector.Scale(-1.);
            *out << Verbose(4) << "PropagationVector of base triangle is ";
            PropagationVector.Output(out);
            *out << endl;
            winner = PointsOnBoundary.end();
            for (PointMap::iterator target = PointsOnBoundary.begin(); target
                != PointsOnBoundary.end(); target++)
              if ((target->second != baseline->second->endpoints[0])
                  && (target->second != baseline->second->endpoints[1]))
                { // don't take the same endpoints
                  *out << Verbose(3) << "Target point is " << *(target->second)
                      << ":";
                  bool continueflag = true;

                  VirtualNormalVector.CopyVector(
                      &baseline->second->endpoints[0]->node->x);
                  VirtualNormalVector.AddVector(
                      &baseline->second->endpoints[0]->node->x);
                  VirtualNormalVector.Scale(-1. / 2.); // points now to center of base line
                  VirtualNormalVector.AddVector(&target->second->node->x); // points from center of base line to target
                  TempAngle = VirtualNormalVector.Angle(&PropagationVector);
                  continueflag = continueflag && (TempAngle < (M_PI/2.)); // no bends bigger than Pi/2 (90 degrees)
                  if (!continueflag)
                    {
                      *out << Verbose(4)
                          << "Angle between propagation direction and base line to "
                          << *(target->second) << " is " << TempAngle
                          << ", bad direction!" << endl;
                      continue;
                    }
                  else
                    *out << Verbose(4)
                        << "Angle between propagation direction and base line to "
                        << *(target->second) << " is " << TempAngle
                        << ", good direction!" << endl;
                  LineChecker[0] = baseline->second->endpoints[0]->lines.find(
                      target->first);
                  LineChecker[1] = baseline->second->endpoints[1]->lines.find(
                      target->first);
                  //            if (LineChecker[0] != baseline->second->endpoints[0]->lines.end())
                  //              *out << Verbose(4) << *(baseline->second->endpoints[0]) << " has line " << *(LineChecker[0]->second) << " to " << *(target->second) << " as endpoint with " << LineChecker[0]->second->TrianglesCount << " triangles." << endl;
                  //            else
                  //              *out << Verbose(4) << *(baseline->second->endpoints[0]) << " has no line to " << *(target->second) << " as endpoint." << endl;
                  //            if (LineChecker[1] != baseline->second->endpoints[1]->lines.end())
                  //              *out << Verbose(4) << *(baseline->second->endpoints[1]) << " has line " << *(LineChecker[1]->second) << " to " << *(target->second) << " as endpoint with " << LineChecker[1]->second->TrianglesCount << " triangles." << endl;
                  //            else
                  //              *out << Verbose(4) << *(baseline->second->endpoints[1]) << " has no line to " << *(target->second) << " as endpoint." << endl;
                  // check first endpoint (if any connecting line goes to target or at least not more than 1)
                  continueflag = continueflag && (((LineChecker[0]
                      == baseline->second->endpoints[0]->lines.end())
                      || (LineChecker[0]->second->TrianglesCount == 1)));
                  if (!continueflag)
                    {
                      *out << Verbose(4) << *(baseline->second->endpoints[0])
                          << " has line " << *(LineChecker[0]->second)
                          << " to " << *(target->second)
                          << " as endpoint with "
                          << LineChecker[0]->second->TrianglesCount
                          << " triangles." << endl;
                      continue;
                    }
                  // check second endpoint (if any connecting line goes to target or at least not more than 1)
                  continueflag = continueflag && (((LineChecker[1]
                      == baseline->second->endpoints[1]->lines.end())
                      || (LineChecker[1]->second->TrianglesCount == 1)));
                  if (!continueflag)
                    {
                      *out << Verbose(4) << *(baseline->second->endpoints[1])
                          << " has line " << *(LineChecker[1]->second)
                          << " to " << *(target->second)
                          << " as endpoint with "
                          << LineChecker[1]->second->TrianglesCount
                          << " triangles." << endl;
                      continue;
                    }
                  // check whether the envisaged triangle does not already exist (if both lines exist and have same endpoint)
                  continueflag = continueflag && (!(((LineChecker[0]
                      != baseline->second->endpoints[0]->lines.end())
                      && (LineChecker[1]
                          != baseline->second->endpoints[1]->lines.end())
                      && (GetCommonEndpoint(LineChecker[0]->second,
                          LineChecker[1]->second) == peak))));
                  if (!continueflag)
                    {
                      *out << Verbose(4) << "Current target is peak!" << endl;
                      continue;
                    }
                  // in case NOT both were found
                  if (continueflag)
                    { // create virtually this triangle, get its normal vector, calculate angle
                      flag = true;
                      VirtualNormalVector.MakeNormalVector(
                          &baseline->second->endpoints[0]->node->x,
                          &baseline->second->endpoints[1]->node->x,
                          &target->second->node->x);
                      // make it always point inward
                      if (baseline->second->endpoints[0]->node->x.Projection(
                          &VirtualNormalVector) > 0)
                        VirtualNormalVector.Scale(-1.);
                      // calculate angle
                      TempAngle = NormalVector.Angle(&VirtualNormalVector);
                      *out << Verbose(4) << "NormalVector is ";
                      VirtualNormalVector.Output(out);
                      *out << " and the angle is " << TempAngle << "." << endl;
                      if (SmallestAngle > TempAngle)
                        { // set to new possible winner
                          SmallestAngle = TempAngle;
                          winner = target;
                        }
                    }
                }
            // 5b. The point of the above whose triangle has the greatest angle with the triangle the current line belongs to (it only belongs to one, remember!): New triangle
            if (winner != PointsOnBoundary.end())
              {
                *out << Verbose(2) << "Winning target point is "
                    << *(winner->second) << " with angle " << SmallestAngle
                    << "." << endl;
                // create the lins of not yet present
                BLS[0] = baseline->second;
                // 5c. add lines to the line set if those were new (not yet part of a triangle), delete lines that belong to two triangles)
                LineChecker[0] = baseline->second->endpoints[0]->lines.find(
                    winner->first);
                LineChecker[1] = baseline->second->endpoints[1]->lines.find(
                    winner->first);
                if (LineChecker[0]
                    == baseline->second->endpoints[0]->lines.end())
                  { // create
                    BPS[0] = baseline->second->endpoints[0];
                    BPS[1] = winner->second;
                    BLS[1] = new class BoundaryLineSet(BPS,
                        LinesOnBoundaryCount);
                    LinesOnBoundary.insert(LinePair(LinesOnBoundaryCount,
                        BLS[1]));
                    LinesOnBoundaryCount++;
                  }
                else
                  BLS[1] = LineChecker[0]->second;
                if (LineChecker[1]
                    == baseline->second->endpoints[1]->lines.end())
                  { // create
                    BPS[0] = baseline->second->endpoints[1];
                    BPS[1] = winner->second;
                    BLS[2] = new class BoundaryLineSet(BPS,
                        LinesOnBoundaryCount);
                    LinesOnBoundary.insert(LinePair(LinesOnBoundaryCount,
                        BLS[2]));
                    LinesOnBoundaryCount++;
                  }
                else
                  BLS[2] = LineChecker[1]->second;
                BTS = new class BoundaryTriangleSet(BLS,
                    TrianglesOnBoundaryCount);
                TrianglesOnBoundary.insert(TrianglePair(
                    TrianglesOnBoundaryCount, BTS));
                TrianglesOnBoundaryCount++;
              }
            else
              {
                *out << Verbose(1)
                    << "I could not determine a winner for this baseline "
                    << *(baseline->second) << "." << endl;
              }

            // 5d. If the set of lines is not yet empty, go to 5. and continue
          }
        else
          *out << Verbose(2) << "Baseline candidate " << *(baseline->second)
              << " has a triangle count of "
              << baseline->second->TrianglesCount << "." << endl;
    }
  while (flag);

}
;

/** Adds an atom to the tesselation::PointsOnBoundary list.
 * \param *Walker atom to add
 */
void
Tesselation::AddPoint(atom *Walker)
{
  PointTestPair InsertUnique;
  BPS[0] = new class BoundaryPointSet(Walker);
  InsertUnique = PointsOnBoundary.insert(PointPair(Walker->nr, BPS[0]));
  if (InsertUnique.second) // if new point was not present before, increase counter
    PointsOnBoundaryCount++;
}
;

/** Adds point to Tesselation::PointsOnBoundary if not yet present.
 * Tesselation::TPS is set to either this new BoundaryPointSet or to the existing one of not unique.
 * @param Candidate point to add
 * @param n index for this point in Tesselation::TPS array
 */
void
Tesselation::AddTrianglePoint(atom* Candidate, int n)
{
  PointTestPair InsertUnique;
  TPS[n] = new class BoundaryPointSet(Candidate);
  InsertUnique = PointsOnBoundary.insert(PointPair(Candidate->nr, TPS[n]));
  if (InsertUnique.second) // if new point was not present before, increase counter
    {
      PointsOnBoundaryCount++;
    }
  else
    {
      delete TPS[n];
      cout << Verbose(2) << "Atom " << *((InsertUnique.first)->second->node)
          << " gibt's schon in der PointMap." << endl;
      TPS[n] = (InsertUnique.first)->second;
    }
}
;

/** Function tries to add line from current Points in BPS to BoundaryLineSet.
 * If succesful it raises the line count and inserts the new line into the BLS,
 * if unsuccesful, it writes the line which had been present into the BLS, deleting the new constructed one.
 * @param *a first endpoint
 * @param *b second endpoint
 * @param n index of Tesselation::BLS giving the line with both endpoints
 */
void
Tesselation::AddTriangleLine(class BoundaryPointSet *a,
    class BoundaryPointSet *b, int n)
{
  LineMap::iterator LineWalker;
  //cout << "Manually checking endpoints for line." << endl;
  if ((a->lines.find(b->node->nr))->first == b->node->nr)
  //If a line is there, how do I recognize that beyond a shadow of a doubt?
    {
      //cout << Verbose(2) << "Line exists already, retrieving it from LinesOnBoundarySet" << endl;

      LineWalker = LinesOnBoundary.end();
      LineWalker--;

      while (LineWalker->second->endpoints[0]->node->nr != min(a->node->nr,
          b->node->nr) or LineWalker->second->endpoints[1]->node->nr != max(
          a->node->nr, b->node->nr))
        {
          //cout << Verbose(1) << "Looking for line which already exists"<< endl;
          LineWalker--;
        }
      BPS[0] = LineWalker->second->endpoints[0];
      BPS[1] = LineWalker->second->endpoints[1];
      BLS[n] = LineWalker->second;

    }
  else
    {
      cout << Verbose(2)
          << "Adding line which has not been used before between "
          << *(a->node) << " and " << *(b->node) << "." << endl;
      BPS[0] = a;
      BPS[1] = b;
      BLS[n] = new class BoundaryLineSet(BPS, LinesOnBoundaryCount);

      LinesOnBoundary.insert(LinePair(LinesOnBoundaryCount, BLS[n]));
      LinesOnBoundaryCount++;

    }
}
;

/** Function tries to add Triangle just created to Triangle and remarks if already existent (Failure of algorithm).
 * Furthermore it adds the triangle to all of its lines, in order to recognize those which are saturated later.
 */
void
Tesselation::AddTriangleToLines()
{

  cout << Verbose(1) << "Adding triangle to its lines" << endl;
  int i = 0;
  TrianglesOnBoundary.insert(TrianglePair(TrianglesOnBoundaryCount, BTS));
  TrianglesOnBoundaryCount++;

  /*
   * this is apparently done when constructing triangle

   for (i=0; i<3; i++)
   {
   BLS[i]->AddTriangle(BTS);
   }
   */
}
;

/**
 * Function returns center of sphere with RADIUS, which rests on points a, b, c
 * @param Center this vector will be used for return
 * @param a vector first point of triangle
 * @param b vector second point of triangle
 * @param c vector third point of triangle
 * @param Direction vector indicates up/down
 * @param AlternativeDirection vecotr, needed in case the triangles have 90 deg angle
 * @param Halfplaneindicator double indicates whether Direction is up or down
 * @param AlternativeIndicator doube indicates in case of orthogonal triangles which direction of AlternativeDirection is suitable
 * @param alpha double angle at a
 * @param beta double, angle at b
 * @param gamma, double, angle at c
 * @param Radius, double
 * @param Umkreisradius double radius of circumscribing circle
 */

  void Get_center_of_sphere(Vector* Center, Vector a, Vector b, Vector c, Vector* Direction, Vector* AlternativeDirection,
      double HalfplaneIndicator, double AlternativeIndicator, double alpha, double beta, double gamma, double RADIUS, double Umkreisradius)
  {
    Vector TempNormal, helper;
    double Restradius;

    *Center = a * sin(2.*alpha) + b * sin(2.*beta) + c * sin(2.*gamma) ;
    Center->Scale(1./(sin(2.*alpha) + sin(2.*beta) + sin(2.*gamma)));
    // Here we calculated center of circumscribing circle, using barycentric coordinates

    TempNormal.CopyVector(&a);
    TempNormal.SubtractVector(&b);
    helper.CopyVector(&a);
    helper.SubtractVector(&c);
    TempNormal.VectorProduct(&helper);
    if (fabs(HalfplaneIndicator) < MYEPSILON)
      {
        if ((TempNormal.ScalarProduct(AlternativeDirection) <0 and AlternativeIndicator >0) or (TempNormal.ScalarProduct(AlternativeDirection) >0 and AlternativeIndicator <0))
          {
            TempNormal.Scale(-1);
          }
      }
    else
      {
        if (TempNormal.ScalarProduct(Direction)<0 && HalfplaneIndicator >0 || TempNormal.ScalarProduct(Direction)>0 && HalfplaneIndicator<0)
          {
            TempNormal.Scale(-1);
          }
      }

    TempNormal.Normalize();
    Restradius = sqrt(RADIUS*RADIUS - Umkreisradius*Umkreisradius);
    TempNormal.Scale(Restradius);

    Center->AddVector(&TempNormal);
  }
  ;


/** This recursive function finds a third point, to form a triangle with two given ones.
 * Two atoms are fixed, a candidate is supplied, additionally two vectors for direction distinction, a Storage area to \
 *  supply results to the calling function, the radius of the sphere which the triangle shall support and the molecule \
 *  upon which we operate.
 *  If the candidate is more fitting to support the sphere than the already stored atom is, then we write its general \
 *  direction and angle into Storage.
 *  We the determine the recursive level we have reached and if this is not on the threshold yet, call this function again, \
 *  with all neighbours of the candidate.
 * @param a first point
 * @param b second point
 * *param c atom old third point of old triangle
 * @param Candidate base point along whose bonds to start looking from
 * @param Parent point to avoid during search as its wrong direction
 * @param RecursionLevel contains current recursion depth
 * @param Chord baseline vector of first and second point
 * @param direction1 second in plane vector (along with \a Chord) of the triangle the baseline belongs to
 * @param OldNormal normal of the triangle which the baseline belongs to
 * @param ReferencePoint Vector of center of circumscribing circle from which we look towards center of sphere
 * @param Opt_Candidate candidate reference to return
 * @param Storage array containing two angles of current Opt_Candidate
 * @param RADIUS radius of ball
 * @param mol molecule structure with atoms and bonds
 */

void Find_next_suitable_point_via_Angle_of_Sphere(atom* a, atom* b, atom* c, atom* Candidate, atom* Parent,
    int RecursionLevel, Vector *Chord, Vector *direction1, Vector *OldNormal, Vector ReferencePoint,
    atom*& Opt_Candidate, double *Storage, const double RADIUS, molecule* mol)
{
  //cout << "ReferencePoint is " << ReferencePoint.x[0] << " "<< ReferencePoint.x[1] << " "<< ReferencePoint.x[2] << " "<< endl;
  /* OldNormal is normal vector on the old triangle
   * direction1 is normal on the triangle line, from which we come, as well as on OldNormal.
   * Chord points from b to a!!!
   */
  Vector dif_a; //Vector from a to candidate
  Vector dif_b; //Vector from b to candidate
  Vector AngleCheck;
  Vector TempNormal, Umkreismittelpunkt;
  Vector Mittelpunkt;

  double CurrentEpsilon = 0.1;
  double alpha, beta, gamma, SideA, SideB, SideC, sign, Umkreisradius, Restradius, Distance;
  double BallAngle, AlternativeSign;
  atom *Walker; // variable atom point


  dif_a.CopyVector(&(a->x));
  dif_a.SubtractVector(&(Candidate->x));
  dif_b.CopyVector(&(b->x));
  dif_b.SubtractVector(&(Candidate->x));
  AngleCheck.CopyVector(&(Candidate->x));
  AngleCheck.SubtractVector(&(a->x));
  AngleCheck.ProjectOntoPlane(Chord);

  SideA = dif_b.Norm();
  SideB = dif_a.Norm();
  SideC = Chord->Norm();
  //Chord->Scale(-1);

  alpha = Chord->Angle(&dif_a);
  beta = M_PI - Chord->Angle(&dif_b);
  gamma = dif_a.Angle(&dif_b);


  if (a != Candidate and b != Candidate and c != Candidate)
    {

      Umkreisradius = SideA / 2.0 / sin(alpha);
      //cout << Umkreisradius << endl;
      //cout << SideB / 2.0 / sin(beta) << endl;
      //cout << SideC / 2.0 / sin(gamma) << endl;

      if (Umkreisradius < RADIUS) //Checking whether ball will at least rest on points.
        {
          cout << Verbose(1) << "Candidate is "<< *Candidate << endl;
          sign = AngleCheck.ScalarProduct(direction1);
          if (fabs(sign)<MYEPSILON)
            {
              if (AngleCheck.ScalarProduct(OldNormal)<0)
                {
                  sign =0;
                  AlternativeSign=1;
                }
              else
                {
                  sign =0;
                  AlternativeSign=-1;
                }
            }
          else
            {
              sign /= fabs(sign);
            }



          Get_center_of_sphere(&Mittelpunkt, (a->x), (b->x), (Candidate->x), OldNormal, direction1, sign, AlternativeSign, alpha, beta, gamma, RADIUS, Umkreisradius);

          AngleCheck.CopyVector(&ReferencePoint);
          AngleCheck.Scale(-1);
          //cout << "AngleCheck is " << AngleCheck.x[0] << " "<< AngleCheck.x[1] << " "<< AngleCheck.x[2] << " "<< endl;
          AngleCheck.AddVector(&Mittelpunkt);
          //cout << "AngleCheck is " << AngleCheck.x[0] << " "<< AngleCheck.x[1] << " "<< AngleCheck.x[2] << " "<< endl;

          BallAngle = AngleCheck.Angle(OldNormal);

          //cout << "direction1 is " << direction1->x[0] <<" "<< direction1->x[1] <<" "<< direction1->x[2] <<" " << endl;
          //cout << "AngleCheck is " << AngleCheck.x[0] << " "<< AngleCheck.x[1] << " "<< AngleCheck.x[2] << " "<< endl;

          cout << Verbose(1) << "BallAngle is " << BallAngle << " Sign is " << sign << endl;

          if (AngleCheck.ScalarProduct(direction1) >=0)
            {
              if (Storage[0]< -1.5) // first Candidate at all
                {

                  cout << "Next better candidate is " << *Candidate << " with ";
                  Opt_Candidate = Candidate;
                  Storage[0] = sign;
                  Storage[1] = AlternativeSign;
                  Storage[2] = BallAngle;
                  cout << "Angle is " << Storage[2] << ", Halbraum ist "
                    << Storage[0] << endl;


                }
              else
                {
                  if ( Storage[2] > BallAngle)
                    {
                      cout << "Next better candidate is " << *Candidate << " with ";
                      Opt_Candidate = Candidate;
                      Storage[0] = sign;
                      Storage[1] = AlternativeSign;
                      Storage[2] = BallAngle;
                      cout << "Angle is " << Storage[2] << ", Halbraum ist "
                        << Storage[0] << endl;
                    }
                  else
                    {
                      //if (DEBUG)
                        cout << "Looses to better candidate" << endl;

                    }
                }
              }
            else
              {
                //if (DEBUG)
                  cout << "Refused due to bad direction of ball centre." << endl;
              }
          }
        else
          {
            //if (DEBUG)
              cout << "Doesn't satisfy requirements for circumscribing circle" << endl;
          }
      }
    else
      {
        //if (DEBUG)
          cout << "identisch mit Ursprungslinie" << endl;

      }



  if (RecursionLevel < 9) // Seven is the recursion level threshold.
    {
      for (int i = 0; i < mol->NumberOfBondsPerAtom[Candidate->nr]; i++) // go through all bond
        {
          Walker = mol->ListOfBondsPerAtom[Candidate->nr][i]->GetOtherAtom(
              Candidate);
          if (Walker == Parent)
            { // don't go back the same bond
              continue;
            }
          else
            {
              Find_next_suitable_point_via_Angle_of_Sphere(a, b, c, Walker, Candidate, RecursionLevel
                  + 1, Chord, direction1, OldNormal, ReferencePoint, Opt_Candidate, Storage, RADIUS,
                  mol); //call function again
            }
        }
    }
}
;


  /** This recursive function finds a third point, to form a triangle with two given ones.
   * Two atoms are fixed, a candidate is supplied, additionally two vectors for direction distinction, a Storage area to \
   *  supply results to the calling function, the radius of the sphere which the triangle shall support and the molecule \
   *  upon which we operate.
   *  If the candidate is more fitting to support the sphere than the already stored atom is, then we write its general \
   *  direction and angle into Storage.
   *  We the determine the recursive level we have reached and if this is not on the threshold yet, call this function again, \
   *  with all neighbours of the candidate.
   * @param a first point
   * @param b second point
   * @param Candidate base point along whose bonds to start looking from
   * @param Parent point to avoid during search as its wrong direction
   * @param RecursionLevel contains current recursion depth
   * @param Chord baseline vector of first and second point
   * @param d1 second in plane vector (along with \a Chord) of the triangle the baseline belongs to
   * @param OldNormal normal of the triangle which the baseline belongs to
   * @param Opt_Candidate candidate reference to return
   * @param Opt_Mittelpunkt Centerpoint of ball, when resting on Opt_Candidate
   * @param Storage array containing two angles of current Opt_Candidate
   * @param RADIUS radius of ball
   * @param mol molecule structure with atoms and bonds
   */

void Find_next_suitable_point(atom* a, atom* b, atom* Candidate, atom* Parent,
    int RecursionLevel, Vector *Chord, Vector *d1, Vector *OldNormal,
    atom*& Opt_Candidate, Vector *Opt_Mittelpunkt, double *Storage, const double RADIUS, molecule* mol)
{
  /* OldNormal is normal vector on the old triangle
   * d1 is normal on the triangle line, from which we come, as well as on OldNormal.
   * Chord points from b to a!!!
   */
  Vector dif_a; //Vector from a to candidate
  Vector dif_b; //Vector from b to candidate
  Vector AngleCheck, AngleCheckReference, DirectionCheckPoint;
  Vector TempNormal, Umkreismittelpunkt, Mittelpunkt;

  double CurrentEpsilon = 0.1;
  double alpha, beta, gamma, SideA, SideB, SideC, sign, Umkreisradius, Restradius, Distance;
  double BallAngle;
  atom *Walker; // variable atom point


  dif_a.CopyVector(&(a->x));
  dif_a.SubtractVector(&(Candidate->x));
  dif_b.CopyVector(&(b->x));
  dif_b.SubtractVector(&(Candidate->x));
  DirectionCheckPoint.CopyVector(&dif_a);
  DirectionCheckPoint.Scale(-1);
  DirectionCheckPoint.ProjectOntoPlane(Chord);

  SideA = dif_b.Norm();
  SideB = dif_a.Norm();
  SideC = Chord->Norm();
  //Chord->Scale(-1);

  alpha = Chord->Angle(&dif_a);
  beta = M_PI - Chord->Angle(&dif_b);
  gamma = dif_a.Angle(&dif_b);


  if (DEBUG)
    {
      cout << "Atom number" << Candidate->nr << endl;
      Candidate->x.Output((ofstream *) &cout);
      cout << "number of bonds " << mol->NumberOfBondsPerAtom[Candidate->nr]
          << endl;
    }

  if (a != Candidate and b != Candidate)
    {
      //      alpha = dif_a.Angle(&dif_b) / 2.;
      //      SideA = Chord->Norm() / 2.;// (Chord->Norm()/2.) / sin(0.5*alpha);
      //      SideB = dif_a.Norm();
      //      centerline = SideA * SideA + SideB * SideB - 2. * SideA * SideB * cos(
      //          alpha); // note this is squared of center line length
      //      centerline = (Chord->Norm()/2.) / sin(0.5*alpha);
      // Those are remains from Freddie. Needed?



      Umkreisradius = SideA / 2.0 / sin(alpha);
      //cout << Umkreisradius << endl;
      //cout << SideB / 2.0 / sin(beta) << endl;
      //cout << SideC / 2.0 / sin(gamma) << endl;

      if (Umkreisradius < RADIUS && DirectionCheckPoint.ScalarProduct(&(Candidate->x))>0) //Checking whether ball will at least rest o points.
        {

          // intermediate calculations to aquire centre of sphere, called Mittelpunkt:

          Umkreismittelpunkt = (a->x) * sin(2.*alpha) + b->x * sin(2.*beta) + (Candidate->x) * sin(2.*gamma) ;
          Umkreismittelpunkt.Scale(1/(sin(2*alpha) + sin(2*beta) + sin(2*gamma)));

          TempNormal.CopyVector(&dif_a);
          TempNormal.VectorProduct(&dif_b);
          if (TempNormal.ScalarProduct(OldNormal)<0 && sign>0 || TempNormal.ScalarProduct(OldNormal)>0 && sign<0)
            {
              TempNormal.Scale(-1);
            }
          TempNormal.Normalize();
          Restradius = sqrt(RADIUS*RADIUS - Umkreisradius*Umkreisradius);
          TempNormal.Scale(Restradius);

          Mittelpunkt.CopyVector(&Umkreismittelpunkt);
          Mittelpunkt.AddVector(&TempNormal);  //this is center of sphere supported by a, b and Candidate

          AngleCheck.CopyVector(Chord);
          AngleCheck.Scale(-0.5);
          AngleCheck.SubtractVector(&(b->x));
          AngleCheckReference.CopyVector(&AngleCheck);
          AngleCheckReference.AddVector(Opt_Mittelpunkt);
          AngleCheck.AddVector(&Mittelpunkt);

          BallAngle = AngleCheck.Angle(&AngleCheckReference);

          d1->ProjectOntoPlane(&AngleCheckReference);
          sign = AngleCheck.ScalarProduct(d1);
          sign /= fabs(sign); // +1 if in direction of triangle plane, -1 if in other direction...


          if (Storage[0]< -1.5) // first Candidate at all
            {

              cout << "Next better candidate is " << *Candidate << " with ";
              Opt_Candidate = Candidate;
              Storage[0] = sign;
              Storage[1] = BallAngle;
              Opt_Mittelpunkt->CopyVector(&Mittelpunkt);
              cout << "Angle is " << Storage[1] << ", Halbraum ist "
                  << Storage[0] << endl;


            }
          else
            {
              /*
               * removed due to change in criterium, now checking angle of ball to old normal.
              //We will now check for non interference, that is if the new candidate would have the Opt_Candidate
              //within the ball.

              Distance = Opt_Candidate->x.Distance(&Mittelpunkt);
              //cout << "Opt_Candidate " << Opt_Candidate << " has distance " << Distance << " to Center of Candidate " << endl;


              if (Distance >RADIUS) // We have no interference and may now check whether the new point is better.
                */
                {
                  //cout << "Atom " << Candidate << " has distance " << Candidate->x.Distance(Opt_Mittelpunkt) << " to Center of Candidate " << endl;

                  if (((Storage[0] < 0 && fabs(sign - Storage[0]) > CurrentEpsilon)))  //This will give absolute preference to those in "right-hand" quadrants
                      //(Candidate->x.Distance(Opt_Mittelpunkt) < RADIUS))    //and those where Candidate would be within old Sphere.
                    {
                      cout << "Next better candidate is " << *Candidate << " with ";
                      Opt_Candidate = Candidate;
                      Storage[0] = sign;
                      Storage[1] = BallAngle;
                      Opt_Mittelpunkt->CopyVector(&Mittelpunkt);
                      cout << "Angle is " << Storage[1] << ", Halbraum ist "
                          << Storage[0] << endl;


                    }
                  else
                    {
                      if ((fabs(sign - Storage[0]) < CurrentEpsilon && sign > 0
                          && Storage[1] > BallAngle) ||
                          (fabs(sign - Storage[0]) < CurrentEpsilon && sign < 0
                          && Storage[1] < BallAngle))
                      //Depending on quadrant we prefer higher or lower atom with respect to Triangle normal first.
                        {
                          cout << "Next better candidate is " << *Candidate << " with ";
                          Opt_Candidate = Candidate;
                          Storage[0] = sign;
                          Storage[1] = BallAngle;
                          Opt_Mittelpunkt->CopyVector(&Mittelpunkt);
                          cout << "Angle is " << Storage[1] << ", Halbraum ist "
                              << Storage[0] << endl;
                        }

                    }
                }
              /*
               * This is for checking point-angle and presence of Candidates in Ball, currently we are checking the ball Angle.
               *
                else
                {
                  if (sign>0 && BallAngle>0 && Storage[0]<0)
                    {
                      cout << "Next better candidate is " << *Candidate << " with ";
                      Opt_Candidate = Candidate;
                      Storage[0] = sign;
                      Storage[1] = BallAngle;
                      Opt_Mittelpunkt->CopyVector(&Mittelpunkt);
                      cout << "Angle is " << Storage[1] << ", Halbraum ist "
                      << Storage[0] << endl;

//Debugging purposes only
                      cout << "Umkreismittelpunkt has coordinates" << Umkreismittelpunkt.x[0] << " "<< Umkreismittelpunkt.x[1] <<" "<<Umkreismittelpunkt.x[2] << endl;
                      cout << "Candidate has coordinates" << Candidate->x.x[0]<< " " << Candidate->x.x[1] << " " << Candidate->x.x[2] << endl;
                      cout << "a has coordinates" << a->x.x[0]<< " " << a->x.x[1] << " " << a->x.x[2] << endl;
                      cout << "b has coordinates" << b->x.x[0]<< " " << b->x.x[1] << " " << b->x.x[2] << endl;
                      cout << "Mittelpunkt has coordinates" << Mittelpunkt.x[0] << " " << Mittelpunkt.x[1]<< " "  <<Mittelpunkt.x[2] << endl;
                      cout << "Umkreisradius ist " << Umkreisradius << endl;
                      cout << "Restradius ist " << Restradius << endl;
                      cout << "TempNormal has coordinates " << TempNormal.x[0] << " " << TempNormal.x[1] << " " << TempNormal.x[2] << " " << endl;
                      cout << "OldNormal has coordinates " << OldNormal->x[0] << " " << OldNormal->x[1] << " " << OldNormal->x[2] << " " << endl;
                      cout << "Dist a to UmkreisMittelpunkt " << a->x.Distance(&Umkreismittelpunkt) << endl;
                      cout << "Dist b to UmkreisMittelpunkt " << b->x.Distance(&Umkreismittelpunkt) << endl;
                      cout << "Dist Candidate to UmkreisMittelpunkt " << Candidate->x.Distance(&Umkreismittelpunkt) << endl;
                      cout << "Dist a to Mittelpunkt " << a->x.Distance(&Mittelpunkt) << endl;
                      cout << "Dist b to Mittelpunkt " << b->x.Distance(&Mittelpunkt) << endl;
                      cout << "Dist Candidate to Mittelpunkt " << Candidate->x.Distance(&Mittelpunkt) << endl;



                    }
                  else
                    {
                      if (DEBUG)
                        cout << "Looses to better candidate" << endl;
                    }
                }
                */
            }
        }
      else
        {
          if (DEBUG)
            {
              cout << "Doesn't satisfy requirements for circumscribing circle" << endl;
            }
        }
    }

  else
    {
      if (DEBUG)
        cout << "identisch mit Ursprungslinie" << endl;
    }

  if (RecursionLevel < 9) // Five is the recursion level threshold.
    {
      for (int i = 0; i < mol->NumberOfBondsPerAtom[Candidate->nr]; i++) // go through all bond
        {
          Walker = mol->ListOfBondsPerAtom[Candidate->nr][i]->GetOtherAtom(
              Candidate);
          if (Walker == Parent)
            { // don't go back the same bond
              continue;
            }
          else
            {
              Find_next_suitable_point(a, b, Walker, Candidate, RecursionLevel
                  + 1, Chord, d1, OldNormal, Opt_Candidate, Opt_Mittelpunkt, Storage, RADIUS,
                  mol); //call function again

            }
        }
    }
}
;

/** This function finds a triangle to a line, adjacent to an existing one.
 * @param out   output stream for debugging
 * @param mol molecule structure with all atoms and bonds
 * @param Line current baseline to search from
 * @param T current triangle which \a Line is edge of
 * @param RADIUS radius of the rolling ball
 * @param N number of found triangles
 */
void Tesselation::Find_next_suitable_triangle(ofstream *out,
    molecule* mol, BoundaryLineSet &Line, BoundaryTriangleSet &T,
    const double& RADIUS, int N, const char *tempbasename)
{
  cout << Verbose(1) << "Looking for next suitable triangle \n";
  Vector direction1;
  Vector helper;
  Vector Chord;
  ofstream *tempstream = NULL;
  char NumberName[255];
  double tmp;
  //atom* Walker;
  atom* OldThirdPoint;

  double Storage[3];
  Storage[0] = -2.; // This direction is either +1 or -1 one, so any result will take precedence over initial values
  Storage[1] = -2.; // This is also lower then any value produced by an eligible atom, which are all positive
  Storage[2] = 9999999.;
  atom* Opt_Candidate = NULL;
  Vector Opt_Mittelpunkt;

  cout << Verbose(1) << "Constructing helpful vectors ... " << endl;
  helper.CopyVector(&(Line.endpoints[0]->node->x));
  for (int i = 0; i < 3; i++)
    {
      if (T.endpoints[i]->node->nr != Line.endpoints[0]->node->nr
          && T.endpoints[i]->node->nr != Line.endpoints[1]->node->nr)
        {
          OldThirdPoint = T.endpoints[i]->node;
          helper.SubtractVector(&T.endpoints[i]->node->x);
          break;
        }
    }

  direction1.CopyVector(&Line.endpoints[0]->node->x);
  direction1.SubtractVector(&Line.endpoints[1]->node->x);
  direction1.VectorProduct(&(T.NormalVector));

  if (direction1.ScalarProduct(&helper) < 0)
    {
      direction1.Scale(-1);
    }

  Chord.CopyVector(&(Line.endpoints[0]->node->x)); // bring into calling function
  Chord.SubtractVector(&(Line.endpoints[1]->node->x));


    Vector Umkreismittelpunkt, a, b, c;
    double alpha, beta, gamma;
    a.CopyVector(&(T.endpoints[0]->node->x));
    b.CopyVector(&(T.endpoints[1]->node->x));
    c.CopyVector(&(T.endpoints[2]->node->x));
    a.SubtractVector(&(T.endpoints[1]->node->x));
    b.SubtractVector(&(T.endpoints[2]->node->x));
    c.SubtractVector(&(T.endpoints[0]->node->x));

    alpha = M_PI - a.Angle(&c);
    beta = M_PI - b.Angle(&a);
    gamma = M_PI - c.Angle(&b);

    Umkreismittelpunkt = (T.endpoints[0]->node->x) * sin(2.*alpha) + T.endpoints[1]->node->x * sin(2.*beta) + (T.endpoints[2]->node->x) * sin(2.*gamma) ;
    //cout << "UmkreisMittelpunkt is " << Umkreismittelpunkt.x[0] << " "<< Umkreismittelpunkt.x[1] << " "<< Umkreismittelpunkt.x[2] << " "<< endl;
    Umkreismittelpunkt.Scale(1/(sin(2*alpha) + sin(2*beta) + sin(2*gamma)));
    cout << "UmkreisMittelpunkt is " << Umkreismittelpunkt.x[0] << " "<< Umkreismittelpunkt.x[1] << " "<< Umkreismittelpunkt.x[2] << " "<< endl;
    cout << " We look over line " << Line << " in direction " << direction1.x[0] << " " << direction1.x[1] << " " << direction1.x[2] << " " << endl;
    cout << " Old Normal is " <<  (T.NormalVector.x)[0] << " " << T.NormalVector.x[1] << " " << (T.NormalVector.x)[2] << " " << endl;


  cout << Verbose(1) << "Looking for third point candidates for triangle ... " << endl;

  Find_next_suitable_point_via_Angle_of_Sphere(Line.endpoints[0]->node, Line.endpoints[1]->node, OldThirdPoint,
      Line.endpoints[0]->node, Line.endpoints[1]->node, 0, &Chord, &direction1,
      &(T.NormalVector), Umkreismittelpunkt, Opt_Candidate, Storage, RADIUS, mol);
  Find_next_suitable_point_via_Angle_of_Sphere(Line.endpoints[0]->node, Line.endpoints[1]->node, OldThirdPoint,
      Line.endpoints[1]->node, Line.endpoints[0]->node, 0, &Chord, &direction1,
      &(T.NormalVector), Umkreismittelpunkt, Opt_Candidate, Storage, RADIUS, mol);


      cout << "Letzter Winkel bei " << TrianglesOnBoundaryCount << " Winkel ist " << Storage[2] << endl;

  if ((TrianglesOnBoundaryCount % 10) == 0) {
    sprintf(NumberName, "-%d", TriangleFilesWritten);
    if (DoTecplotOutput) {
      string NameofTempFile(tempbasename);
      NameofTempFile.append(NumberName);
      NameofTempFile.append(TecplotSuffix);
      cout << Verbose(1) << "Writing temporary non convex hull to file " << NameofTempFile << ".\n";
      tempstream = new ofstream(NameofTempFile.c_str(), ios::trunc);
      write_tecplot_file(out, tempstream, this, mol, TriangleFilesWritten);
      tempstream->close();
      tempstream->flush();
      delete(tempstream);
    }
    if (DoRaster3DOutput) {
      string NameofTempFile(tempbasename);
      NameofTempFile.append(NumberName);
      NameofTempFile.append(Raster3DSuffix);
      cout << Verbose(1) << "Writing temporary non convex hull to file " << NameofTempFile << ".\n";
      tempstream = new ofstream(NameofTempFile.c_str(), ios::trunc);
      write_raster3d_file(out, tempstream, this, mol);
      tempstream->close();
      tempstream->flush();
      delete(tempstream);
    }
    if (DoTecplotOutput || DoRaster3DOutput)
      TriangleFilesWritten++;
  }

      // Konstruiere nun neues Dreieck am Ende der Liste der Dreiecke

  cout << " Optimal candidate is " << *Opt_Candidate << endl;

  AddTrianglePoint(Opt_Candidate, 0);
  AddTrianglePoint(Line.endpoints[0]->node, 1);
  AddTrianglePoint(Line.endpoints[1]->node, 2);

  AddTriangleLine(TPS[0], TPS[1], 0);
  AddTriangleLine(TPS[0], TPS[2], 1);
  AddTriangleLine(TPS[1], TPS[2], 2);

  BTS = new class BoundaryTriangleSet(BLS, TrianglesOnBoundaryCount);
  AddTriangleToLines();
  cout << "New triangle with " << *BTS << endl;
  cout << "We have "<< TrianglesOnBoundaryCount << endl;
  cout << Verbose(1) << "Constructing normal vector for this triangle ... " << endl;

  BTS->GetNormalVector(BTS->NormalVector);

  if ((BTS->NormalVector.ScalarProduct(&(T.NormalVector)) < 0 && Storage[0] > 0)  ||
      (BTS->NormalVector.ScalarProduct(&(T.NormalVector)) > 0 && Storage[0] < 0) ||
      (fabs(Storage[0]) < MYEPSILON && Storage[1]*BTS->NormalVector.ScalarProduct(&direction1) < 0) )

    {
      BTS->NormalVector.Scale(-1);
    };

}
;

void Find_second_point_for_Tesselation(atom* a, atom* Candidate, atom* Parent,
    int RecursionLevel, Vector Oben, atom*& Opt_Candidate, double Storage[3],
    molecule* mol, double RADIUS)
{
  cout << Verbose(1)
      << "Looking for second point of starting triangle, recursive level "
      << RecursionLevel << endl;;
  int i;
  Vector AngleCheck;
  atom* Walker;
  double norm = -1.;

  // check if we only have one unique point yet ...
  if (a != Candidate)
    {
      AngleCheck.CopyVector(&(Candidate->x));
      AngleCheck.SubtractVector(&(a->x));
      norm = AngleCheck.Norm();
      // second point shall have smallest angle with respect to Oben vector
      if (norm < RADIUS)
        {
          if (AngleCheck.Angle(&Oben) < Storage[0])
            {
              //cout << Verbose(1) << "Old values of Storage: %lf %lf \n", Storage[0], Storage[2]);
              cout << "Next better candidate is " << *Candidate
                  << " with distance " << norm << ".\n";
              Opt_Candidate = Candidate;
              Storage[0] = AngleCheck.Angle(&Oben);
              //cout << Verbose(1) << "Changing something in Storage: %lf %lf. \n", Storage[0], Storage[2]);
            }
          else
            {
              cout << Verbose(1) << "Supposedly looses to a better candidate "
                  << *Opt_Candidate << endl;
            }
        }
      else
        {
          cout << Verbose(1) << *Candidate << " refused due to Radius " << norm
              << endl;
        }
    }

  // if not recursed to deeply, look at all its bonds
  if (RecursionLevel < 7)
    {
      for (i = 0; i < mol->NumberOfBondsPerAtom[Candidate->nr]; i++)
        {
          Walker = mol->ListOfBondsPerAtom[Candidate->nr][i]->GetOtherAtom(
              Candidate);
          if (Walker == Parent) // don't go back along the bond we came from
            continue;
          else
            Find_second_point_for_Tesselation(a, Walker, Candidate,
                RecursionLevel + 1, Oben, Opt_Candidate, Storage, mol, RADIUS);
        };
    };
}
;

void Tesselation::Find_starting_triangle(molecule* mol, const double RADIUS)
{
  cout << Verbose(1) << "Looking for starting triangle \n";
  int i = 0;
  atom* Walker;
  atom* FirstPoint;
  atom* SecondPoint;
  atom* max_index[3];
  double max_coordinate[3];
  Vector Oben;
  Vector helper;
  Vector Chord;
  Vector CenterOfFirstLine;

  Oben.Zero();

  for (i = 0; i < 3; i++)
    {
      max_index[i] = NULL;
      max_coordinate[i] = -1;
    }
  cout << Verbose(1) << "Molecule mol is there and has " << mol->AtomCount
      << " Atoms \n";

  // 1. searching topmost atom with respect to each axis
  Walker = mol->start;
  while (Walker->next != mol->end)
    {
      Walker = Walker->next;
      for (i = 0; i < 3; i++)
        {
          if (Walker->x.x[i] > max_coordinate[i])
            {
              max_coordinate[i] = Walker->x.x[i];
              max_index[i] = Walker;
            }
        }
    }

  cout << Verbose(1) << "Found maximum coordinates. " << endl;
  //Koennen dies fuer alle Richtungen, legen hier erstmal Richtung auf k=0
  const int k = 1;
  Oben.x[k] = 1.;
  FirstPoint = max_index[k];

  cout << Verbose(1) << "Coordinates of start atom " << *FirstPoint << ": "
      << FirstPoint->x.x[0] << endl;
  double Storage[3];
  atom* Opt_Candidate = NULL;
  Storage[0] = 999999.; // This will contain the angle, which will be always positive (when looking for second point), when looking for third point this will be the quadrant.
  Storage[1] = 999999.; // This will be an angle looking for the third point.
  Storage[2] = 999999.;
  cout << Verbose(1) << "Number of Bonds: "
      << mol->NumberOfBondsPerAtom[FirstPoint->nr] << endl;

  Find_second_point_for_Tesselation(FirstPoint, FirstPoint, FirstPoint, 0,
      Oben, Opt_Candidate, Storage, mol, RADIUS); // we give same point as next candidate as its bonds are looked into in find_second_...
  SecondPoint = Opt_Candidate;
  cout << Verbose(1) << "Found second point is " << *SecondPoint << ".\n";

  helper.CopyVector(&(FirstPoint->x));
  helper.SubtractVector(&(SecondPoint->x));
  helper.Normalize();
  Oben.ProjectOntoPlane(&helper);
  Oben.Normalize();
  helper.VectorProduct(&Oben);
  Storage[0] = -2.; // This will indicate the quadrant.
  Storage[1] = 9999999.; // This will be an angle looking for the third point.
  Storage[2] = 9999999.;

  Chord.CopyVector(&(FirstPoint->x)); // bring into calling function
  Chord.SubtractVector(&(SecondPoint->x));
  // Now, oben and helper are two orthonormalized vectors in the plane defined by Chord (not normalized)

  cout << Verbose(1) << "Looking for third point candidates \n";
  cout << Verbose(1) << " In direction " << helper.x[0] << " " << helper.x[1] << " " << helper.x[2] << " " << endl;
  // look in one direction of baseline for initial candidate
  Opt_Candidate = NULL;
  CenterOfFirstLine.CopyVector(&Chord);
  CenterOfFirstLine.Scale(0.5);
  CenterOfFirstLine.AddVector(&(SecondPoint->x));

  Find_next_suitable_point_via_Angle_of_Sphere(FirstPoint, SecondPoint, SecondPoint, SecondPoint, FirstPoint, 0,
      &Chord, &helper, &Oben, CenterOfFirstLine,  Opt_Candidate, Storage, RADIUS, mol);
  // look in other direction of baseline for possible better candidate
  Find_next_suitable_point_via_Angle_of_Sphere(FirstPoint, SecondPoint, SecondPoint, FirstPoint, SecondPoint, 0,
      &Chord, &helper, &Oben, CenterOfFirstLine, Opt_Candidate, Storage, RADIUS, mol);
  cout << Verbose(1) << "Third Point is " << *Opt_Candidate << endl;

  // FOUND Starting Triangle: FirstPoint, SecondPoint, Opt_Candidate

  cout << Verbose(1) << "The found starting triangle consists of "
      << *FirstPoint << ", " << *SecondPoint << " and " << *Opt_Candidate
      << "." << endl;

  // Finally, we only have to add the found points
  AddTrianglePoint(FirstPoint, 0);
  AddTrianglePoint(SecondPoint, 1);
  AddTrianglePoint(Opt_Candidate, 2);
  // ... and respective lines
  AddTriangleLine(TPS[0], TPS[1], 0);
  AddTriangleLine(TPS[1], TPS[2], 1);
  AddTriangleLine(TPS[0], TPS[2], 2);
  // ... and triangles to the Maps of the Tesselation class
  BTS = new class BoundaryTriangleSet(BLS, TrianglesOnBoundaryCount);
  AddTriangleToLines();
  // ... and calculate its normal vector (with correct orientation)
  Oben.Scale(-1.);
  BTS->GetNormalVector(Oben);
}
;

void Find_non_convex_border(ofstream *out, const char *filename, molecule* mol)
{
  int N = 0;
  struct Tesselation *Tess = new Tesselation;
  cout << Verbose(1) << "Entering search for non convex hull. " << endl;
  cout << flush;
  const double RADIUS = 6.;
  LineMap::iterator baseline;
  cout << Verbose(0) << "Begin of Find_non_convex_border\n";
  bool flag = false;  // marks whether we went once through all baselines without finding any without two triangles

  if ((mol->first->next == mol->last) || (mol->last->previous == mol->first))
    mol->CreateAdjacencyList((ofstream *)&cout, 1.6, true);

  Tess->Find_starting_triangle(mol, RADIUS);

  baseline = Tess->LinesOnBoundary.begin();
  while (baseline != Tess->LinesOnBoundary.end())
    {
      if (baseline->second->TrianglesCount == 1)
        {
          cout << Verbose(1) << "Begin of Tesselation ... " << endl;
          Tess->Find_next_suitable_triangle(out, mol,
              *(baseline->second),
              *(((baseline->second->triangles.begin()))->second), RADIUS, N, filename); //the line is there, so there is a triangle, but only one.
          flag = true;
          cout << Verbose(1) << "End of Tesselation ... " << endl;
        }
      else
        {
          cout << Verbose(1) << "There is a line with "
              << baseline->second->TrianglesCount << " triangles adjacent"
              << endl;
        }
      N++;
      baseline++;
    }
  cout << Verbose(1) << "Writing final tecplot file\n";
  if (DoTecplotOutput) {
    string Name(filename);
    Name.append(TecplotSuffix);
    ofstream tecplot(Name.c_str(), ios::trunc);
    write_tecplot_file(out, &tecplot, Tess, mol, -1);
    tecplot.close();
  }
  if (DoRaster3DOutput) {
    string Name(filename);
    Name.append(Raster3DSuffix);
    ofstream raster(Name.c_str(), ios::trunc);
    write_raster3d_file(out, &raster, Tess, mol);
    raster.close();
  }
}
;