Changeset 244a84

Timestamp:

Jan 26, 2010, 12:52:31 PM (15 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

04b6f9, 481601

Parents:

315164

Message:

GetDistanceToSurface() separated, filling now with water instead of boron, DissectMoleculeIntoConnectedSubgraphs() now working on list of molecules instead of single one.

• MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() so far was working on a single molecule (given by parameter) instead of the list already contained in the list of its class.
• Tesselation::GetDistanceSquaredToSurface() is split up into function of same name, which calls finds the closest triangle and calls Tesselation::GetDistanceSquaredToTriangle() which contains the former code.
• PeriodicCorrelationToSurface() was adapted to the above split.
• in tesselation.cpp lots of list<> and set<>s were replaced by the already present and appropriate define's.

• small verbosity changes in: MatrixContainer::ParseMatrix(), TesselPoint::TesselPoint(), TesselPoint::~TesselPoint(), PointCloud::PointCloud(), PointCloud::~PointCloud(), Tesselation::GuessStartingTriangle(), BondGraph::LoadBondLengthTable() (status of parsing gives appropriate message).

Signed-off-by: Frederik Heber <heber@…>

Location:

src

Files:

• analysis_correlation.cpp (modified) (4 diffs)
• analysis_correlation.hpp (modified) (1 diff)
• bondgraph.cpp (modified) (3 diffs)
• builder.cpp (modified) (4 diffs)
• molecule.hpp (modified) (1 diff)
• moleculelist.cpp (modified) (3 diffs)
• parser.cpp (modified) (4 diffs)
• tesselation.cpp (modified) (12 diffs)
• tesselation.hpp (modified) (2 diffs)

src/analysis_correlation.cpp

@@ -308 +308 @@
   }
   outmap = new CorrelationToSurfaceMap;
+  double ShortestDistance = 0.;
+  BoundaryTriangleSet *ShortestTriangle = NULL;
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
@@ -321 +323 @@
           periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
           // go through every range in xyz and get distance
+          ShortestDistance = -1.;
           for (n[0]=-ranges[0]; n[0] <= ranges[0]; n[0]++)
             for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
@@ -327 +330 @@
                 checkX.AddVector(&periodicX);
                 checkX.MatrixMultiplication(FullMatrix);
-                triangle = Surface->FindClosestTriangleToVector(&checkX, LC );
-                if (triangle != NULL) {
-                  distance = DistanceToTrianglePlane(&checkX, triangle);
-                  outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
+                triangle = Surface->FindClosestTriangleToVector(&checkX, LC);
+                distance = Surface->GetDistanceSquaredToTriangle(checkX, triangle);
+                if ((ShortestDistance == -1.) || (distance < ShortestDistance)) {
+                  ShortestDistance = distance;
+                  ShortestTriangle = triangle;
                 }
-          }
+              }
+          // insert
+          ShortestDistance = sqrt(ShortestDistance);
+          outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(ShortestDistance, pair<atom *, BoundaryTriangleSet*> (Walker, ShortestTriangle) ) );
+          //Log() << Verbose(1) << "INFO: Inserting " << Walker << " with distance " << ShortestDistance << " to " << *ShortestTriangle << "." << endl;
         }
       }
@@ -406 +414 @@
   *file << "# BinStart\tTriangle" << endl;
   for (CorrelationToSurfaceMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
-    *file << runner->first << "\t" << *(runner->second.second) << endl;
-  }
-};
-
+    *file << runner->first << "\t" << *(runner->second.first) << "\t" << *(runner->second.second) << endl;
+  }
+};
+

src/analysis_correlation.hpp

@@ -53 +53 @@
 double GetBin ( const double value, const double BinWidth, const double BinStart );
 void OutputCorrelation( ofstream * const file, const BinPairMap * const map );
-void OutputPairCorrelation( ofstream * const file, const BinPairMap * const map );
-void OutputCorrelationToPoint( ofstream * const file, const BinPairMap * const map );
-void OutputCorrelationToSurface( ofstream * const file, const BinPairMap * const map );
+void OutputPairCorrelation( ofstream * const file, const PairCorrelationMap * const map );
+void OutputCorrelationToPoint( ofstream * const file, const CorrelationToPointMap * const map );
+void OutputCorrelationToSurface( ofstream * const file, const CorrelationToSurfaceMap * const map );
 
 

src/bondgraph.cpp

@@ -11 +11 @@
 #include "bondgraph.hpp"
 #include "element.hpp"
+#include "info.hpp"
 #include "log.hpp"
 #include "molecule.hpp"
@@ -42 +43 @@
 bool BondGraph::LoadBondLengthTable(const string &filename)
 {
+  Info FunctionInfo(__func__);
   bool status = true;
   MatrixContainer *TempContainer = NULL;
@@ -53 +55 @@
 
   // parse in matrix
-  status = TempContainer->ParseMatrix(filename.c_str(), 0, 1, 0);
+  if (status = TempContainer->ParseMatrix(filename.c_str(), 0, 1, 0)) {
+    Log() << Verbose(1) << "Parsing bond length matrix successful." << endl;
+  } else {
+    eLog() << Verbose(1) << "Parsing bond length matrix failed." << endl;
+  }
 
   // find greatest distance

src/builder.cpp

@@ -1551 +1551 @@
      if (configuration.BG == NULL) {
        configuration.BG = new BondGraph(configuration.GetIsAngstroem());
-       if ((BondGraphFileName.empty()) && (configuration.BG->LoadBondLengthTable(BondGraphFileName))) {
+       if ((!BondGraphFileName.empty()) && (configuration.BG->LoadBondLengthTable(BondGraphFileName))) {
          Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
        } else {
@@ -1660 +1660 @@
               Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl;
               // @TODO rather do the dissection afterwards
-              molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
+              molecules->DissectMoleculeIntoConnectedSubgraphs(periode, &configuration);
               mol = NULL;
               if (molecules->ListOfMolecules.size() != 0) {
@@ -1708 +1708 @@
                 int ranges[NDIM] = {1,1,1};
                 CorrelationToSurfaceMap *surfacemap = PeriodicCorrelationToSurface( molecules, elemental, TesselStruct, LCList, ranges );
+                //OutputCorrelationToSurface(&output, surfacemap);
                 BinPairMap *binmap = BinData( surfacemap, 0.5, 0., 0. );
                 OutputCorrelation ( &binoutput, binmap );
@@ -1744 +1745 @@
                 Log() << Verbose(1) << "Filling Box with water molecules." << endl;
                 // construct water molecule
-                molecule *filler = new molecule(periode);;
+                molecule *filler = new molecule(periode);
                 molecule *Filling = NULL;
-//                atom *second = NULL, *third = NULL;
+                atom *second = NULL, *third = NULL;
+//                first = new atom();
+//                first->type = periode->FindElement(5);
+//                first->x.Zero();
+//                filler->AddAtom(first);
                 first = new atom();
-                first->type = periode->FindElement(5);
-                first->x.Zero();
+                first->type = periode->FindElement(1);
+                first->x.Init(0.441, -0.143, 0.);
                 filler->AddAtom(first);
-//                first = new atom();
-//                first->type = periode->FindElement(1);
-//                first->x.Init(0.441, -0.143, 0.);
-//                filler->AddAtom(first);
-//                second = new atom();
-//                second->type = periode->FindElement(1);
-//                second->x.Init(-0.464, 1.137, 0.0);
-//                filler->AddAtom(second);
-//                third = new atom();
-//                third->type = periode->FindElement(8);
-//                third->x.Init(-0.464, 0.177, 0.);
-//                filler->AddAtom(third);
-//                filler->AddBond(first, third, 1);
-//                filler->AddBond(second, third, 1);
+                second = new atom();
+                second->type = periode->FindElement(1);
+                second->x.Init(-0.464, 1.137, 0.0);
+                filler->AddAtom(second);
+                third = new atom();
+                third->type = periode->FindElement(8);
+                third->x.Init(-0.464, 0.177, 0.);
+                filler->AddAtom(third);
+                filler->AddBond(first, third, 1);
+                filler->AddBond(second, third, 1);
                 // call routine
                 double distance[NDIM];

src/molecule.hpp

@@ -323 +323 @@
   void Enumerate(ofstream *out);
   void Output(ofstream *out);
-  void DissectMoleculeIntoConnectedSubgraphs(molecule * const mol, config * const configuration);
+  void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
   int CountAllAtoms() const;
 

src/moleculelist.cpp

@@ -741 +741 @@
 /** Dissects given \a *mol into connected subgraphs and inserts them as new molecules but with old atoms into \a this.
  * \param *out output stream for debugging
- * \param *mol molecule with atoms to dissect
+ * \param *periode periodentafel
  * \param *configuration config with BondGraph
  */
-void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(molecule * const mol, config * const configuration)
-{
+void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration)
+{
+  molecule *mol = new molecule(periode);
+  atom *Walker = NULL;
+  atom *Advancer = NULL;
+  bond *Binder = NULL;
+  bond *Stepper = NULL;
+  // 0. gather all atoms into single molecule
+  for (MoleculeList::iterator MolRunner = ListOfMolecules.begin(); !ListOfMolecules.empty(); MolRunner = ListOfMolecules.begin()) {
+    // shift all atoms to new molecule
+    Advancer = (*MolRunner)->start->next;
+    while (Advancer != (*MolRunner)->end) {
+      Walker = Advancer;
+      Advancer = Advancer->next;
+      Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl;
+      unlink(Walker);
+      Walker->father = Walker;
+      mol->AddAtom(Walker);    // counting starts at 1
+    }
+    // remove all bonds
+    Stepper = (*MolRunner)->first->next;
+    while (Stepper != (*MolRunner)->last) {
+      Binder = Stepper;
+      Stepper = Stepper->next;
+      delete(Binder);
+    }
+    // remove the molecule
+    delete(*MolRunner);
+    ListOfMolecules.erase(MolRunner);
+  }
+
   // 1. dissect the molecule into connected subgraphs
   configuration->BG->ConstructBondGraph(mol);
@@ -779 +808 @@
   int *MolMap = Calloc<int>(mol->AtomCount, "config::Load() - *MolMap");
   MoleculeLeafClass *MolecularWalker = Subgraphs;
-  atom *Walker = NULL;
+  Walker = NULL;
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
@@ -809 +838 @@
   }
   // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
-  bond *Binder = mol->first;
+  Binder = mol->first;
   while (mol->first->next != mol->last) {
     Binder = mol->first->next;

src/parser.cpp

@@ -158 +158 @@
 
   input.open(name, ios::in);
-  //Log() << Verbose(0) << "Opening " << name << " ... "  << input << endl;
+  //Log() << Verbose(1) << "Opening " << name << " ... "  << input << endl;
   if (input == NULL) {
     eLog() << Verbose(1) << endl << "Unable to open " << name << ", is the directory correct?" << endl;
@@ -181 +181 @@
   }
   //Log() << Verbose(0) << line.str() << endl;
-  //Log() << Verbose(0) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << "." << endl;
+  //Log() << Verbose(1) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << "." << endl;
   if (ColumnCounter[MatrixNr] == 0) {
     eLog() << Verbose(0) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl;
@@ -197 +197 @@
     }
   }
-  //Log() << Verbose(0) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << "." << endl;
+  //Log() << Verbose(1) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << "." << endl;
   if (RowCounter[MatrixNr] == 0) {
     eLog() << Verbose(0) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl;
@@ -220 +220 @@
       input.getline(filename, 1023);
       stringstream lines(filename);
-      //Log() << Verbose(0) << "Matrix at level " << j << ":";// << filename << endl;
+      //Log() << Verbose(2) << "Matrix at level " << j << ":";// << filename << endl;
       for(int k=skipcolumns;k--;)
         lines >> filename;
       for(int k=0;(k<ColumnCounter[MatrixNr]) && (!lines.eof());k++) {
         lines >> Matrix[MatrixNr][j][k];
-        //Log() << Verbose(0) << " " << setprecision(2) << Matrix[MatrixNr][j][k];;
+        //Log() << Verbose(1) << " " << setprecision(2) << Matrix[MatrixNr][j][k] << endl;
       }
-      //Log() << Verbose(0) << endl;
       Matrix[MatrixNr][ RowCounter[MatrixNr] ] = Malloc<double>(ColumnCounter[MatrixNr], "MatrixContainer::ParseMatrix: *Matrix[RowCounter[MatrixNr]][]");
       for(int j=ColumnCounter[MatrixNr];j--;)

src/tesselation.cpp

@@ -939 +939 @@
 TesselPoint::TesselPoint()
 {
-  Info FunctionInfo(__func__);
+  //Info FunctionInfo(__func__);
   node = NULL;
   nr = -1;
@@ -949 +949 @@
 TesselPoint::~TesselPoint()
 {
-  Info FunctionInfo(__func__);
+  //Info FunctionInfo(__func__);
 };
 
@@ -976 +976 @@
 PointCloud::PointCloud()
 {
-        Info FunctionInfo(__func__);
+        //Info FunctionInfo(__func__);
 };
 
@@ -983 +983 @@
 PointCloud::~PointCloud()
 {
-        Info FunctionInfo(__func__);
+        //Info FunctionInfo(__func__);
 };
 
@@ -1174 +1174 @@
  * \param PointsOnBoundary set of boundary points defining the convex envelope of the cluster
  */
-void
-Tesselation::GuessStartingTriangle()
+void Tesselation::GuessStartingTriangle()
 {
         Info FunctionInfo(__func__);
@@ -3378 +3377 @@
  * @param *LC LinkedCell structure
  *
- * @return >0 if outside, ==0 if on surface, <0 if inside (Note that distance can be at most LinkedCell::RADIUS.)
- */
-double Tesselation::GetDistanceSquaredToSurface(const Vector &Point, const LinkedCell* const LC) const
+ * @return >0 if outside, ==0 if on surface, <0 if inside
+ */
+double Tesselation::GetDistanceSquaredToTriangle(const Vector &Point, const BoundaryTriangleSet* const triangle) const
 {
   Info FunctionInfo(__func__);
-  class BoundaryTriangleSet *result = FindClosestTriangleToVector(&Point, LC);
   Vector Center;
   Vector helper;
@@ -3390 +3388 @@
   double distance = 0.;
 
-  if (result == NULL) {// is boundary point or only point in point cloud?
-    Log() << Verbose(1) << Point << " is the only point in vicinity." << endl;
-    return LC->RADIUS;
+  if (triangle == NULL) {// is boundary point or only point in point cloud?
+    Log() << Verbose(1) << "No triangle given!" << endl;
+    return -1.;
   } else {
-    Log() << Verbose(1) << "INFO: Closest triangle found is " << *result << " with normal vector " << result->NormalVector << "." << endl;
-  }
-
-  result->GetCenter(&Center);
+    Log() << Verbose(1) << "INFO: Closest triangle found is " << *triangle << " with normal vector " << triangle->NormalVector << "." << endl;
+  }
+
+  triangle->GetCenter(&Center);
   Log() << Verbose(2) << "INFO: Central point of the triangle is " << Center << "." << endl;
   DistanceToCenter.CopyVector(&Center);
@@ -3404 +3402 @@
 
   // check whether we are on boundary
-  if (fabs(DistanceToCenter.ScalarProduct(&result->NormalVector)) < MYEPSILON) {
+  if (fabs(DistanceToCenter.ScalarProduct(&triangle->NormalVector)) < MYEPSILON) {
     // calculate whether inside of triangle
     DistanceToCenter.CopyVector(&Point);
     Center.CopyVector(&Point);
-    Center.SubtractVector(&result->NormalVector); // points towards MolCenter
-    DistanceToCenter.AddVector(&result->NormalVector); // points outside
+    Center.SubtractVector(&triangle->NormalVector); // points towards MolCenter
+    DistanceToCenter.AddVector(&triangle->NormalVector); // points outside
     Log() << Verbose(1) << "INFO: Calling Intersection with " << Center << " and " << DistanceToCenter << "." << endl;
-    if (result->GetIntersectionInsideTriangle(&Center, &DistanceToCenter, &Intersection)) {
+    if (triangle->GetIntersectionInsideTriangle(&Center, &DistanceToCenter, &Intersection)) {
       Log() << Verbose(1) << Point << " is inner point: sufficiently close to boundary, " << Intersection << "." << endl;
       return 0.;
@@ -3420 +3418 @@
   } else {
     // calculate smallest distance
-    distance = result->GetClosestPointInsideTriangle(&Point, &Intersection);
+    distance = triangle->GetClosestPointInsideTriangle(&Point, &Intersection);
     Log() << Verbose(1) << "Closest point on triangle is " << Intersection << "." << endl;
-    distance = Min(distance, (LC->RADIUS*LC->RADIUS));
 
     // then check direction to boundary
-    if (DistanceToCenter.ScalarProduct(&result->NormalVector) > MYEPSILON) {
+    if (DistanceToCenter.ScalarProduct(&triangle->NormalVector) > MYEPSILON) {
       Log() << Verbose(1) << Point << " is an inner point, " << distance << " below surface." << endl;
       return -distance;
@@ -3433 +3430 @@
     }
   }
+};
+
+/** Calculates distance to a tesselated surface.
+ * Combines \sa FindClosestTrianglesToVector() and \sa GetDistanceSquaredToTriangle().
+ * \param &Point point to calculate distance from
+ * \param *LC needed for finding closest points fast
+ * \return distance squared to closest point on surface
+ */
+double Tesselation::GetDistanceSquaredToSurface(const Vector &Point, const LinkedCell* const LC) const
+{
+  BoundaryTriangleSet *triangle = FindClosestTriangleToVector(&Point, LC);
+  const double distance = GetDistanceSquaredToTriangle(Point, triangle);
+  return Min(distance, LC->RADIUS);
 };
 
@@ -3695 +3705 @@
  * @return list of the all points linked to the provided one
  */
-list< TesselPointList *> * Tesselation::GetPathsOfConnectedPoints(const TesselPoint* const Point) const
+ListOfTesselPointList * Tesselation::GetPathsOfConnectedPoints(const TesselPoint* const Point) const
 {
         Info FunctionInfo(__func__);
@@ -3811 +3821 @@
  * @return list of the closed paths
  */
-list<TesselPointList *> * Tesselation::GetClosedPathsOfConnectedPoints(const TesselPoint* const Point) const
+ListOfTesselPointList * Tesselation::GetClosedPathsOfConnectedPoints(const TesselPoint* const Point) const
 {
         Info FunctionInfo(__func__);

src/tesselation.hpp

@@ -87 +87 @@
 #define TesselPointList list <TesselPoint *>
 #define TesselPointSet set <TesselPoint *>
+
+#define ListOfTesselPointList list<list <TesselPoint *> *>
 
 /********************************************** declarations *******************************/
@@ -298 +300 @@
     double PickFarthestofTwoBaselines(class BoundaryLineSet *Base);
     class BoundaryPointSet *IsConvexRectangle(class BoundaryLineSet *Base);
-    map<int, int> * FindAllDegeneratedTriangles();
-    map<int, int> * FindAllDegeneratedLines();
+    IndexToIndex * FindAllDegeneratedTriangles();
+    IndexToIndex * FindAllDegeneratedLines();
     void RemoveDegeneratedTriangles();
     void AddBoundaryPointByDegeneratedTriangle(class TesselPoint *point, LinkedCell *LC);
     int CorrectAllDegeneratedPolygons();
 
-    set<TesselPoint*> * GetAllConnectedPoints(const TesselPoint* const Point) const;
-    set<BoundaryTriangleSet*> *GetAllTriangles(const BoundaryPointSet * const Point) const;
-    list<list<TesselPoint*> *> * GetPathsOfConnectedPoints(const TesselPoint* const Point) const;
-    list<list<TesselPoint*> *> * GetClosedPathsOfConnectedPoints(const TesselPoint* const Point) const;
-    list<TesselPoint*> * GetCircleOfSetOfPoints(set<TesselPoint*> *SetOfNeighbours, const TesselPoint* const Point, const Vector * const Reference = NULL) const;
-    list<TesselPoint*> * GetCircleOfConnectedTriangles(set<TesselPoint*> *SetOfNeighbours, const TesselPoint* const Point, const Vector * const Reference) const;
-    class BoundaryPointSet *GetCommonEndpoint(const BoundaryLineSet * line1, const BoundaryLineSet * line2) const;
-    list<BoundaryTriangleSet*> *FindTriangles(const TesselPoint* const Points[3]) const;
-    list<BoundaryTriangleSet*> * FindClosestTrianglesToPoint(const Vector *x, const LinkedCell* LC) const;
-    class BoundaryTriangleSet * FindClosestTriangleToPoint(const Vector *x, const LinkedCell* LC) const;
+    TesselPointSet * GetAllConnectedPoints(const TesselPoint* const Point) const;
+    TriangleSet * GetAllTriangles(const BoundaryPointSet * const Point) const;
+    ListOfTesselPointList * GetPathsOfConnectedPoints(const TesselPoint* const Point) const;
+    ListOfTesselPointList * GetClosedPathsOfConnectedPoints(const TesselPoint* const Point) const;
+    TesselPointList * GetCircleOfSetOfPoints(TesselPointSet *SetOfNeighbours, const TesselPoint* const Point, const Vector * const Reference = NULL) const;
+    TesselPointList * GetCircleOfConnectedTriangles(TesselPointSet *SetOfNeighbours, const TesselPoint* const Point, const Vector * const Reference) const;
+    class BoundaryPointSet * GetCommonEndpoint(const BoundaryLineSet * line1, const BoundaryLineSet * line2) const;
+    TriangleList * FindTriangles(const TesselPoint* const Points[3]) const;
+    TriangleList * FindClosestTrianglesToVector(const Vector *x, const LinkedCell* LC) const;
+    BoundaryTriangleSet * FindClosestTriangleToVector(const Vector *x, const LinkedCell* LC) const;
     bool IsInnerPoint(const Vector &Point, const LinkedCell* const LC) const;
+    double GetDistanceSquaredToTriangle(const Vector &Point, const BoundaryTriangleSet* const triangle) const;
     double GetDistanceSquaredToSurface(const Vector &Point, const LinkedCell* const LC) const;
     bool AddBoundaryPoint(TesselPoint * Walker, const int n);
     DistanceToPointMap * FindClosestBoundaryPointsToVector(const Vector *x, const LinkedCell* LC) const;
     BoundaryLineSet * FindClosestBoundaryLineToVector(const Vector *x, const LinkedCell* LC) const;
-    TriangleList * FindClosestTrianglesToVector(const Vector *x, const LinkedCell* LC) const;
-    BoundaryTriangleSet* FindClosestTriangleToVector(const Vector *x, const LinkedCell* LC) const;
 
     // print for debugging