Changeset 73b510 for src

Timestamp:

Dec 17, 2009, 5:50:04 PM (16 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:

1cf5df

Parents:

2130dd (diff), 125b3c (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'FixDegeneratedTesselation' into CorrectDegeneratedPolygons

Location:

src

Files:

• Makefile.am (modified) (1 diff)
• bondgraph.cpp (modified) (1 diff)
• boundary.cpp (modified) (1 diff)
• boundary.hpp (modified) (1 diff)
• builder.cpp (modified) (3 diffs)
• config.cpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (1 diff)
• parser.cpp (modified) (1 diff)
• tesselation.cpp (modified) (21 diffs)
• tesselation.hpp (modified) (2 diffs)
• tesselationhelpers.cpp (modified) (2 diffs)
• vector.cpp (modified) (1 diff)
• vector.hpp (modified) (1 diff)

src/Makefile.am

@@ -25 +25 @@
 
 #EXTRA_DIST = ${molecuilder_DATA}
+
+FORCE:
+$(srcdir)/.git-version: FORCE
+        @if (test -d $(top_srcdir)/../.git && cd $(srcdir) && git describe HEAD) > .git-version-t 2>/dev/null \
+          && ! diff .git-version-t $(srcdir)/.git-version >/dev/null 2>&1; then \
+          mv -f .git-version-t $(srcdir)/.git-version; \
+        else \
+          rm -f .git-version-t; \
+        fi
+
+EXTRA_DIST = $(srcdir)/.git-version
+
+$(srcdir)/version.c: $(srcdir)/.git-version
+        echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@
+
+molecuilder_SOURCES += $(srcdir)/version.c

src/bondgraph.cpp

@@ -35 +35 @@
 /** Parses the bond lengths in a given file and puts them int a matrix form.
  * Allocates \a MatrixContainer for BondGraph::BondLengthMatrix, using MatrixContainer::ParseMatrix(),
- * but only if parsing is successfull. Otherwise variable is left as NULL.
+ * but only if parsing is successful. Otherwise variable is left as NULL.
  * \param *out output stream for debugging
  * \param filename file with bond lengths to parse

src/boundary.cpp

@@ -1041 +1041 @@
 //  TesselStruct->RemoveDegeneratedTriangles();
 
+  // check envelope for consistency
+  status = CheckListOfBaselines(TesselStruct);
+
+  // store before correction
+  StoreTrianglesinFile(mol, (const Tesselation *&)TesselStruct, filename, "");
+
   // correct degenerated polygons
   TesselStruct->CorrectAllDegeneratedPolygons();

src/boundary.hpp

@@ -36 +36 @@
 #define DEBUG 1
 #define DoSingleStepOutput 0
-#define SingleStepWidth 1
+#define SingleStepWidth 10
 
 #define DistancePair pair < double, atom* >

src/builder.cpp

@@ -65 +65 @@
 #include "molecule.hpp"
 #include "periodentafel.hpp"
+#include "version.h"
 
 /********************************************* Subsubmenu routine ************************************/
@@ -2106 +2107 @@
                 if (volume != -1)
                   ExitFlag = 255;
-                  eLog() << Verbose(0) << "Not enough arguments given for suspension: -u <density>" << endl;
+                  eLog() << Verbose(0) << "Not enough or invalid arguments given for suspension: -u <density>" << endl;
                   performCriticalExit();
               } else {
@@ -2222 +2223 @@
   int j;
 
+  cout << ESPACKVersion << endl;
+
   setVerbosity(0);
 

src/config.cpp

@@ -1074 +1074 @@
   // don't do this here ...
   //MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
-
-  delete(mol);
+  //delete(mol);
+
   delete(FileBuffer);
 };

src/molecule_graph.cpp

@@ -1117 +1117 @@
   bool status = true;
   if (ReferenceStack->IsEmpty()) {
-    eLog() << Verbose(0) << "ReferenceStack is empty!" << endl;
-    performCriticalExit();
+    Log() << Verbose(1) << "ReferenceStack is empty!" << endl;
     return false;
   }

src/moleculelist.cpp

@@ -402 +402 @@
   input.open(line.c_str());
   if (input == NULL) {
-    eLog() << Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
-    performCriticalExit();
+    Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
     return false;
   }

src/parser.cpp

@@ -158 +158 @@
   //Log() << Verbose(0) << "Opening " << name << " ... "  << input << endl;
   if (input == NULL) {
-    eLog() << Verbose(0) << endl << "Unable to open " << name << ", is the directory correct?" << endl;
-    performCriticalExit();
+    eLog() << Verbose(1) << endl << "Unable to open " << name << ", is the directory correct?" << endl;
+    //performCriticalExit();
     return false;
   }

src/tesselation.cpp

@@ -1587 +1587 @@
   bool insertNewLine = true;
 
-  if (a->lines.find(b->node->nr) != a->lines.end()) {
-    LineMap::iterator FindLine = a->lines.find(b->node->nr);
+  LineMap::iterator FindLine = a->lines.find(b->node->nr);
+  if (FindLine != a->lines.end()) {
+    Log() << Verbose(1) << "INFO: There is at least one line between " << *a << " and " << *b << ": " << *(FindLine->second) << "." << endl;
+
     pair<LineMap::iterator,LineMap::iterator> FindPair;
     FindPair = a->lines.equal_range(b->node->nr);
-    Log() << Verbose(1) << "INFO: There is at least one line between " << *a << " and " << *b << ": " << *(FindLine->second) << "." << endl;
 
     for (FindLine = FindPair.first; FindLine != FindPair.second; FindLine++) {
@@ -1915 +1916 @@
   double maxCoordinate[NDIM];
   BoundaryLineSet BaseLine;
-  Vector Oben;
   Vector helper;
   Vector Chord;
   Vector SearchDirection;
-
-  Oben.Zero();
+  Vector CircleCenter;  // center of the circle, i.e. of the band of sphere's centers
+  Vector CirclePlaneNormal; // normal vector defining the plane this circle lives in
+  Vector SphereCenter;
+  Vector NormalVector;
+
+  NormalVector.Zero();
 
   for (i = 0; i < 3; i++) {
@@ -1955 +1959 @@
   BTS = NULL;
   for (int k=0;k<NDIM;k++) {
-    Oben.Zero();
-    Oben.x[k] = 1.;
+    NormalVector.Zero();
+    NormalVector.x[k] = 1.;
     BaseLine.endpoints[0] = new BoundaryPointSet(MaxPoint[k]);
     Log() << Verbose(0) << "Coordinates of start node at " << *BaseLine.endpoints[0]->node << "." << endl;
@@ -1963 +1967 @@
     ShortestAngle = 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.
 
-    FindSecondPointForTesselation(BaseLine.endpoints[0]->node, Oben, Temporary, &ShortestAngle, RADIUS, LC); // we give same point as next candidate as its bonds are looked into in find_second_...
+    FindSecondPointForTesselation(BaseLine.endpoints[0]->node, NormalVector, Temporary, &ShortestAngle, RADIUS, LC); // we give same point as next candidate as its bonds are looked into in find_second_...
     if (Temporary == NULL)  // have we found a second point?
       continue;
     BaseLine.endpoints[1] = new BoundaryPointSet(Temporary);
 
-    helper.CopyVector(BaseLine.endpoints[0]->node->node);
-    helper.SubtractVector(BaseLine.endpoints[1]->node->node);
-    helper.Normalize();
-    Oben.ProjectOntoPlane(&helper);
-    Oben.Normalize();
-    helper.VectorProduct(&Oben);
+    // construct center of circle
+    CircleCenter.CopyVector(BaseLine.endpoints[0]->node->node);
+    CircleCenter.AddVector(BaseLine.endpoints[1]->node->node);
+    CircleCenter.Scale(0.5);
+
+    // construct normal vector of circle
+    CirclePlaneNormal.CopyVector(BaseLine.endpoints[0]->node->node);
+    CirclePlaneNormal.SubtractVector(BaseLine.endpoints[1]->node->node);
+
+    double radius = CirclePlaneNormal.NormSquared();
+    double CircleRadius = sqrt(RADIUS*RADIUS - radius/4.);
+
+    NormalVector.ProjectOntoPlane(&CirclePlaneNormal);
+    NormalVector.Normalize();
     ShortestAngle = 2.*M_PI; // This will indicate the quadrant.
 
-    Chord.CopyVector(BaseLine.endpoints[0]->node->node); // bring into calling function
-    Chord.SubtractVector(BaseLine.endpoints[1]->node->node);
-    double radius = Chord.ScalarProduct(&Chord);
-    double CircleRadius = sqrt(RADIUS*RADIUS - radius/4.);
-    helper.CopyVector(&Oben);
-    helper.Scale(CircleRadius);
-    // Now, oben and helper are two orthonormalized vectors in the plane defined by Chord (not normalized)
+    SphereCenter.CopyVector(&NormalVector);
+    SphereCenter.Scale(CircleRadius);
+    SphereCenter.AddVector(&CircleCenter);
+    // Now, NormalVector and SphereCenter are two orthonormalized vectors in the plane defined by CirclePlaneNormal (not normalized)
 
     // look in one direction of baseline for initial candidate
-    SearchDirection.MakeNormalVector(&Chord, &Oben);  // whether we look "left" first or "right" first is not important ...
+    SearchDirection.MakeNormalVector(&CirclePlaneNormal, &NormalVector);  // whether we look "left" first or "right" first is not important ...
 
     // adding point 1 and point 2 and add the line between them
@@ -1993 +2002 @@
     //Log() << Verbose(1) << "INFO: OldSphereCenter is at " << helper << ".\n";
     CandidateForTesselation OptCandidates(&BaseLine);
-    FindThirdPointForTesselation(Oben, SearchDirection, helper, OptCandidates, NULL, RADIUS, LC);
+    FindThirdPointForTesselation(NormalVector, SearchDirection, SphereCenter, OptCandidates, NULL, RADIUS, LC);
     Log() << Verbose(0) << "List of third Points is:" << endl;
     for (TesselPointList::iterator it = OptCandidates.pointlist.begin(); it != OptCandidates.pointlist.end(); it++) {
@@ -2167 +2176 @@
   Vector CircleCenter;
   Vector CirclePlaneNormal;
-  Vector OldSphereCenter;
+  Vector RelativeSphereCenter;
   Vector SearchDirection;
   Vector helper;
@@ -2174 +2183 @@
   double radius, CircleRadius;
 
-  Log() << Verbose(0) << "Current baseline is " << *CandidateLine.BaseLine << " of triangle " << T << "." << endl;
   for (int i=0;i<3;i++)
-    if ((T.endpoints[i]->node != CandidateLine.BaseLine->endpoints[0]->node) && (T.endpoints[i]->node != CandidateLine.BaseLine->endpoints[1]->node))
+    if ((T.endpoints[i]->node != CandidateLine.BaseLine->endpoints[0]->node) && (T.endpoints[i]->node != CandidateLine.BaseLine->endpoints[1]->node)) {
       ThirdNode = T.endpoints[i]->node;
+      break;
+    }
+  Log() << Verbose(0) << "Current baseline is " << *CandidateLine.BaseLine << " with ThirdNode " << *ThirdNode << " of triangle " << T << "." << endl;
 
   // construct center of circle
@@ -2191 +2202 @@
   radius = CirclePlaneNormal.ScalarProduct(&CirclePlaneNormal);
   if (radius/4. < RADIUS*RADIUS) {
+    // construct relative sphere center with now known CircleCenter
+    RelativeSphereCenter.CopyVector(&T.SphereCenter);
+    RelativeSphereCenter.SubtractVector(&CircleCenter);
+
     CircleRadius = RADIUS*RADIUS - radius/4.;
     CirclePlaneNormal.Normalize();
     Log() << Verbose(1) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
 
-    // construct old center
-    GetCenterofCircumcircle(&OldSphereCenter, *T.endpoints[0]->node->node, *T.endpoints[1]->node->node, *T.endpoints[2]->node->node);
-    helper.CopyVector(&T.NormalVector);  // normal vector ensures that this is correct center of the two possible ones
-    radius = CandidateLine.BaseLine->endpoints[0]->node->node->DistanceSquared(&OldSphereCenter);
-    helper.Scale(sqrt(RADIUS*RADIUS - radius));
-    OldSphereCenter.AddVector(&helper);
-    OldSphereCenter.SubtractVector(&CircleCenter);
-    Log() << Verbose(1) << "INFO: OldSphereCenter is at " << OldSphereCenter << "." << endl;
-
-    // construct SearchDirection
-    SearchDirection.MakeNormalVector(&T.NormalVector, &CirclePlaneNormal);
-    helper.CopyVector(CandidateLine.BaseLine->endpoints[0]->node->node);
+    Log() << Verbose(1) << "INFO: OldSphereCenter is at " << T.SphereCenter << "." << endl;
+
+    // construct SearchDirection and an "outward pointer"
+    SearchDirection.MakeNormalVector(&RelativeSphereCenter, &CirclePlaneNormal);
+    helper.CopyVector(&CircleCenter);
     helper.SubtractVector(ThirdNode->node);
     if (helper.ScalarProduct(&SearchDirection) < -HULLEPSILON)// ohoh, SearchDirection points inwards!
       SearchDirection.Scale(-1.);
-    SearchDirection.ProjectOntoPlane(&OldSphereCenter);
-    SearchDirection.Normalize();
     Log() << Verbose(1) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
-    if (fabs(OldSphereCenter.ScalarProduct(&SearchDirection)) > HULLEPSILON) {
+    if (fabs(RelativeSphereCenter.ScalarProduct(&SearchDirection)) > HULLEPSILON) {
       // rotated the wrong way!
       eLog() << Verbose(1) << "SearchDirection and RelativeOldSphereCenter are still not orthogonal!" << endl;
@@ -2219 +2225 @@
 
     // add third point
-    FindThirdPointForTesselation(T.NormalVector, SearchDirection, OldSphereCenter, CandidateLine, ThirdNode, RADIUS, LC);
+    FindThirdPointForTesselation(T.NormalVector, SearchDirection, T.SphereCenter, CandidateLine, ThirdNode, RADIUS, LC);
 
   } else {
@@ -2350 +2356 @@
     AddTesselationPoint((*Sprinter), 2);
 
-    Center.CopyVector(&CandidateLine.OptCenter);
+
     // add the lines
     AddTesselationLine(TPS[0], TPS[1], 0);
@@ -2359 +2365 @@
     BTS = new class BoundaryTriangleSet(BLS, TrianglesOnBoundaryCount);
     AddTesselationTriangle();
-    Center.Scale(-1.);
+    BTS->GetCenter(&Center);
+    Center.SubtractVector(&CandidateLine.OptCenter);
+    BTS->SphereCenter.CopyVector(&CandidateLine.OptCenter);
     BTS->GetNormalVector(Center);
 
@@ -2766 +2774 @@
   Vector NewNormalVector;   // normal vector of the Candidate's triangle
   Vector helper, OptCandidateCenter, OtherOptCandidateCenter;
+  Vector RelativeOldSphereCenter;
+  Vector NewPlaneCenter;
   double CircleRadius; // radius of this circle
   double radius;
+  double otherradius;
   double alpha, Otheralpha; // angles (i.e. parameter for the circle).
   int N[NDIM], Nlower[NDIM], Nupper[NDIM];
@@ -2783 +2794 @@
   CirclePlaneNormal.SubtractVector(CandidateLine.BaseLine->endpoints[1]->node->node);
 
+  RelativeOldSphereCenter.CopyVector(&OldSphereCenter);
+  RelativeOldSphereCenter.SubtractVector(&CircleCenter);
+
   // calculate squared radius TesselPoint *ThirdNode,f circle
-  radius = CirclePlaneNormal.ScalarProduct(&CirclePlaneNormal);
-  if (radius/4. < RADIUS*RADIUS) {
-    CircleRadius = RADIUS*RADIUS - radius/4.;
+  radius = CirclePlaneNormal.NormSquared()/4.;
+  if (radius < RADIUS*RADIUS) {
+    CircleRadius = RADIUS*RADIUS - radius;
     CirclePlaneNormal.Normalize();
-    //Log() << Verbose(1) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
+    Log() << Verbose(1) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
 
     // test whether old center is on the band's plane
-    if (fabs(OldSphereCenter.ScalarProduct(&CirclePlaneNormal)) > HULLEPSILON) {
-      eLog() << Verbose(1) << "Something's very wrong here: OldSphereCenter is not on the band's plane as desired by " << fabs(OldSphereCenter.ScalarProduct(&CirclePlaneNormal)) << "!" << endl;
-      OldSphereCenter.ProjectOntoPlane(&CirclePlaneNormal);
-    }
-    radius = OldSphereCenter.ScalarProduct(&OldSphereCenter);
+    if (fabs(RelativeOldSphereCenter.ScalarProduct(&CirclePlaneNormal)) > HULLEPSILON) {
+      eLog() << Verbose(1) << "Something's very wrong here: RelativeOldSphereCenter is not on the band's plane as desired by " << fabs(RelativeOldSphereCenter.ScalarProduct(&CirclePlaneNormal)) << "!" << endl;
+      RelativeOldSphereCenter.ProjectOntoPlane(&CirclePlaneNormal);
+    }
+    radius = RelativeOldSphereCenter.NormSquared();
     if (fabs(radius - CircleRadius) < HULLEPSILON) {
-      //Log() << Verbose(1) << "INFO: OldSphereCenter is at " << OldSphereCenter << "." << endl;
+      Log() << Verbose(1) << "INFO: RelativeOldSphereCenter is at " << RelativeOldSphereCenter << "." << endl;
 
       // check SearchDirection
-      //Log() << Verbose(1) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
-      if (fabs(OldSphereCenter.ScalarProduct(&SearchDirection)) > HULLEPSILON) {  // rotated the wrong way!
+      Log() << Verbose(1) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
+      if (fabs(RelativeOldSphereCenter.ScalarProduct(&SearchDirection)) > HULLEPSILON) {  // rotated the wrong way!
         eLog() << Verbose(1) << "SearchDirection and RelativeOldSphereCenter are not orthogonal!" << endl;
       }
@@ -2832 +2846 @@
 
                 // check for three unique points
-                Log() << Verbose(2) << "INFO: Current Candidate is " << *Candidate << " at " << *(Candidate->node) << "." << endl;
+                Log() << Verbose(2) << "INFO: Current Candidate is " << *Candidate << " for BaseLine " << *CandidateLine.BaseLine << " with OldSphereCenter " << OldSphereCenter << "." << endl;
                 if ((Candidate != CandidateLine.BaseLine->endpoints[0]->node) && (Candidate != CandidateLine.BaseLine->endpoints[1]->node) ){
 
-                  // construct both new centers
-                  GetCenterofCircumcircle(&NewSphereCenter, *CandidateLine.BaseLine->endpoints[0]->node->node, *CandidateLine.BaseLine->endpoints[1]->node->node, *Candidate->node);
-                  OtherNewSphereCenter.CopyVector(&NewSphereCenter);
-
-                  if ((NewNormalVector.MakeNormalVector(CandidateLine.BaseLine->endpoints[0]->node->node, CandidateLine.BaseLine->endpoints[1]->node->node, Candidate->node))
-                  && (fabs(NewNormalVector.ScalarProduct(&NewNormalVector)) > HULLEPSILON)
+                  // find center on the plane
+                  GetCenterofCircumcircle(&NewPlaneCenter, *CandidateLine.BaseLine->endpoints[0]->node->node, *CandidateLine.BaseLine->endpoints[1]->node->node, *Candidate->node);
+                  Log() << Verbose(1) << "INFO: NewPlaneCenter is " << NewPlaneCenter << "." << endl;
+
+                  if (NewNormalVector.MakeNormalVector(CandidateLine.BaseLine->endpoints[0]->node->node, CandidateLine.BaseLine->endpoints[1]->node->node, Candidate->node)
+                  && (fabs(NewNormalVector.NormSquared()) > HULLEPSILON)
                   ) {
-                    helper.CopyVector(&NewNormalVector);
                     Log() << Verbose(1) << "INFO: NewNormalVector is " << NewNormalVector << "." << endl;
-                    radius = CandidateLine.BaseLine->endpoints[0]->node->node->DistanceSquared(&NewSphereCenter);
+                    radius = CandidateLine.BaseLine->endpoints[0]->node->node->DistanceSquared(&NewPlaneCenter);
+                    Log() << Verbose(1) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
+                    Log() << Verbose(1) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
+                    Log() << Verbose(1) << "INFO: Radius of CircumCenterCircle is " << radius << "." << endl;
                     if (radius < RADIUS*RADIUS) {
+                      otherradius = CandidateLine.BaseLine->endpoints[1]->node->node->DistanceSquared(&NewPlaneCenter);
+                      if (fabs(radius - otherradius) > HULLEPSILON) {
+                        eLog() << Verbose(1) << "Distance to center of circumcircle is not the same from each corner of the triangle: " << fabs(radius-otherradius) << endl;
+                      }
+                      // construct both new centers
+                      NewSphereCenter.CopyVector(&NewPlaneCenter);
+                      OtherNewSphereCenter.CopyVector(&NewPlaneCenter);
+                      helper.CopyVector(&NewNormalVector);
                       helper.Scale(sqrt(RADIUS*RADIUS - radius));
-                      Log() << Verbose(2) << "INFO: Distance of NewCircleCenter to NewSphereCenter is " << helper.Norm() << " with sphere radius " << RADIUS << "." << endl;
+                      Log() << Verbose(2) << "INFO: Distance of NewPlaneCenter " << NewPlaneCenter << " to either NewSphereCenter is " << helper.Norm() << " of vector " << helper << " with sphere radius " << RADIUS << "." << endl;
                       NewSphereCenter.AddVector(&helper);
-                      NewSphereCenter.SubtractVector(&CircleCenter);
                       Log() << Verbose(2) << "INFO: NewSphereCenter is at " << NewSphereCenter << "." << endl;
-
                       // OtherNewSphereCenter is created by the same vector just in the other direction
                       helper.Scale(-1.);
                       OtherNewSphereCenter.AddVector(&helper);
-                      OtherNewSphereCenter.SubtractVector(&CircleCenter);
                       Log() << Verbose(2) << "INFO: OtherNewSphereCenter is at " << OtherNewSphereCenter << "." << endl;
 
@@ -2861 +2882 @@
                       Otheralpha = GetPathLengthonCircumCircle(CircleCenter, CirclePlaneNormal, CircleRadius, OtherNewSphereCenter, OldSphereCenter, NormalVector, SearchDirection);
                       alpha = min(alpha, Otheralpha);
+
                       // if there is a better candidate, drop the current list and add the new candidate
                       // otherwise ignore the new candidate and keep the list
@@ -2892 +2914 @@
                         }
                       }
-
                     } else {
                       Log() << Verbose(1) << "REJECT: NewSphereCenter " << NewSphereCenter << " for " << *Candidate << " is too far away: " << radius << "." << endl;
@@ -4127 +4148 @@
   Info FunctionInfo(__func__);
 
-  /// 1. Find all simply degenerated triangles and sort into a list with each endpoint as key
-  map<int, int> * SimplyDegeneratedTriangles = FindAllDegeneratedTriangles();
-
-  /// 2. Go through all lines not contained in degenerated triangles.
-  UniquePolygonSet ListofFours;
-  UniquePolygonSet TestedPolygons;
-  for (LineMap::const_iterator LineRunner = LinesOnBoundary.begin(); LineRunner != LinesOnBoundary.end(); LineRunner++) {
-    Log() << Verbose(1) << "Current Line is: " << *(LineRunner->second) << endl;
-
-    BoundaryPolygonSet *Four = new BoundaryPolygonSet;
-
-    /// 2a. Get all four endpoints of the two connected triangles.
-    Four->FillPolygonFromTrianglesOfLine((LineRunner->second));
-    if (Four->endpoints.size() != 4) {
-      Log() << Verbose(0) << "REJECT: There were no four endpoints:" << *Four << endl;
-      delete(Four);
-      continue;
-    }
-
-    /// 2b. Get the triangles of all those endpoints
-    TriangleSet *T = Four->GetAllContainedTrianglesFromEndpoints();
-
-    /// 2c1. Check whether all triangles have (besides sign) same normal vector)
-    TriangleSet::const_iterator Runner = T->begin();
-    Vector NormalVector;
-    NormalVector.CopyVector(&(*Runner)->NormalVector);
-    Runner++;
-    bool IsPlanar = true;
-    for (; Runner != T->end(); Runner++) {
-      if (fabs(fabs(NormalVector.ScalarProduct(&(*Runner)->NormalVector)) - 1.) > MYEPSILON)  // check whether all NormalVectors are parallel
-        IsPlanar = false;
-    }
-
-    /// 2c2. check whether triangles are not already simply degenerated.
-    size_t DegeneratedCount = 0;
-    for (TriangleSet::const_iterator Runner = T->begin(); Runner != T->end(); Runner++) {
-      if (SimplyDegeneratedTriangles->find((*Runner)->Nr) != SimplyDegeneratedTriangles->end())
-        DegeneratedCount++;
-    }
-    Log() << Verbose(1) << "Found " << DegeneratedCount << " degenerated triangles." << endl;
-
-    if (IsPlanar) {
-      if(DegeneratedCount == 0) {
-        /// 2c. Find all pairs of those triangles that contain the four endpoints
-        const int counter = CountTrianglePairContainingPolygon(Four, T);
-        Log() << Verbose(1) << "There are " << counter << " pairs for this polygon of four." << endl;
-        if (counter %3 == 0) {
-          /// 2d. Check the number of pairs, if greater 1, we have a degenerated polygon (mark down for later use)
-          pair < UniquePolygonSet::iterator, bool > Tester = ListofFours.insert(Four);
-          if (Tester.second) {
-            Log() << Verbose(0) << "ACCEPT: We have a degenerated polygon." << *Four << endl;
-          } else {
-            Log() << Verbose(0) << "REJECT: Degenerated polygon already present." << *Four << endl;
-            delete(Four);
+  /// 2. Go through all BoundaryPointSet's, check their triangles' NormalVector
+  map <int, int> *DegeneratedTriangles = FindAllDegeneratedTriangles();
+  set < BoundaryPointSet *> EndpointCandidateList;
+  pair < set < BoundaryPointSet *>::iterator, bool > InsertionTester;
+  pair < map < int, Vector *>::iterator, bool > TriangleInsertionTester;
+  for (PointMap::const_iterator Runner = PointsOnBoundary.begin(); Runner != PointsOnBoundary.end(); Runner++) {
+    Log() << Verbose(0) << "Current point is " << *Runner->second << "." << endl;
+    map < int, Vector *> TriangleVectors;
+    // gather all NormalVectors
+    Log() << Verbose(1) << "Gathering triangles ..." << endl;
+    for (LineMap::const_iterator LineRunner = (Runner->second)->lines.begin(); LineRunner != (Runner->second)->lines.end(); LineRunner++)
+      for (TriangleMap::const_iterator TriangleRunner = (LineRunner->second)->triangles.begin(); TriangleRunner != (LineRunner->second)->triangles.end(); TriangleRunner++) {
+        if (DegeneratedTriangles->find(TriangleRunner->second->Nr) == DegeneratedTriangles->end()) {
+          TriangleInsertionTester = TriangleVectors.insert( pair< int, Vector *> ((TriangleRunner->second)->Nr, &((TriangleRunner->second)->NormalVector)) );
+          if (TriangleInsertionTester.second)
+            Log() << Verbose(1) << " Adding triangle " << *(TriangleRunner->second) << " to triangles to check-list." << endl;
+        } else {
+          Log() << Verbose(1) << " NOT adding triangle " << *(TriangleRunner->second) << " as it's a simply degenerated one." << endl;
+        }
+      }
+    // check whether there are two that are parallel
+    Log() << Verbose(1) << "Finding two parallel triangles ..." << endl;
+    for (map < int, Vector *>::iterator VectorWalker = TriangleVectors.begin(); VectorWalker != TriangleVectors.end(); VectorWalker++)
+      for (map < int, Vector *>::iterator VectorRunner = VectorWalker; VectorRunner != TriangleVectors.end(); VectorRunner++)
+        if (VectorWalker != VectorRunner) { // skip equals
+          const double SCP = VectorWalker->second->ScalarProduct(VectorRunner->second);  // ScalarProduct should result in -1. for degenerated triangles
+          Log() << Verbose(1) << "Checking " << *VectorWalker->second<< " against " << *VectorRunner->second << ": " << SCP << endl;
+          if (fabs(SCP + 1.) < ParallelEpsilon) {
+            InsertionTester = EndpointCandidateList.insert((Runner->second));
+            if (InsertionTester.second)
+              Log() << Verbose(0) << " Adding " << *Runner->second << " to endpoint candidate list." << endl;
+            // and break out of both loops
+            VectorWalker = TriangleVectors.end();
+            VectorRunner = TriangleVectors.end();
+            break;
           }
+        }
+  }
+
+  /// 3. Find connected endpoint candidates and put them into a polygon
+  UniquePolygonSet ListofDegeneratedPolygons;
+  BoundaryPointSet *Walker = NULL;
+  BoundaryPointSet *OtherWalker = NULL;
+  BoundaryPolygonSet *Current = NULL;
+  stack <BoundaryPointSet*> ToCheckConnecteds;
+  while (!EndpointCandidateList.empty()) {
+    Walker = *(EndpointCandidateList.begin());
+    if (Current == NULL) {  // create a new polygon with current candidate
+      Log() << Verbose(0) << "Starting new polygon set at point " << *Walker << endl;
+      Current = new BoundaryPolygonSet;
+      Current->endpoints.insert(Walker);
+      EndpointCandidateList.erase(Walker);
+      ToCheckConnecteds.push(Walker);
+    }
+
+    // go through to-check stack
+    while (!ToCheckConnecteds.empty()) {
+      Walker = ToCheckConnecteds.top(); // fetch ...
+      ToCheckConnecteds.pop(); // ... and remove
+      for (LineMap::const_iterator LineWalker = Walker->lines.begin(); LineWalker != Walker->lines.end(); LineWalker++) {
+        OtherWalker = (LineWalker->second)->GetOtherEndpoint(Walker);
+        Log() << Verbose(1) << "Checking " << *OtherWalker << endl;
+        set < BoundaryPointSet *>::iterator Finder = EndpointCandidateList.find(OtherWalker);
+        if (Finder != EndpointCandidateList.end()) {  // found a connected partner
+          Log() << Verbose(1) << " Adding to polygon." << endl;
+          Current->endpoints.insert(OtherWalker);
+          EndpointCandidateList.erase(Finder);  // remove from candidates
+          ToCheckConnecteds.push(OtherWalker);  // but check its partners too
         } else {
-          Log() << Verbose(0) << "REJECT: Seems to be the edge line of a degenerated polygon only." << *Four << endl;
-          delete(Four);
+          Log() << Verbose(1) << " is not connected to " << *Walker << endl;
         }
-      } else {
-        Log() << Verbose(0) << "REJECT: This polygon contains some simply degenerated triangles." << endl;
-        delete(Four);
       }
-    } else {
-      Log() << Verbose(0) << "REJECT: This polygon does not lay on a plane." << endl;
-      delete(Four);
-    }
-
-    delete(T);
-  }
-
-  /// 3. Combine all edge-connected degenerated polygons
-  {
-    UniquePolygonSet::iterator PolygonWalker;  // is the inner iterator
-    UniquePolygonSet::iterator PolygonSprinter; // is the inner advanced iterator
-    for (UniquePolygonSet::iterator PolygonRunner = ListofFours.begin(); PolygonRunner != ListofFours.end(); PolygonRunner++) {
-      const BoundaryPolygonSet *P1 = *PolygonRunner;
-      Log() << Verbose(1) << "Current Polygon is : " << *P1 << endl;
-      PolygonWalker = PolygonRunner;
-      PolygonWalker++;
-      PolygonSprinter = PolygonWalker;
-      while (PolygonWalker != ListofFours.end()) {
-        BoundaryPolygonSet *P2 = *PolygonWalker;
-        Log() << Verbose(1) << "Current Other Polygon is : " << *P2 << endl;
-        PolygonSprinter++;
-        Log() << Verbose(1) << "Are " << *P1 << " and " << *P2 << " edge-connected?" << endl;
-        if (ArePolygonsEdgeConnected((*PolygonRunner), (P2))) { // if connected
-          Log() << Verbose(0) << "Yes!" << endl;
-          CombinePolygons((*PolygonRunner), (P2)); // combined and ...
-          ListofFours.erase(PolygonWalker); // ... remove from list
-          Log() << Verbose(1) << "  New current Polygon is : " << *P1 << endl;
-        } else {
-          Log() << Verbose(0) << "No." << endl;
-        }
-        PolygonWalker = PolygonSprinter;
-      }
-    }
-  }
-
-  Log() << Verbose(0) << "The following degenerated polygons have been found: " << endl;
-  for (UniquePolygonSet::iterator PolygonRunner = ListofFours.begin(); PolygonRunner != ListofFours.end(); PolygonRunner++)
+    }
+
+    Log() << Verbose(0) << "Final polygon is " << *Current << endl;
+    ListofDegeneratedPolygons.insert(Current);
+    Current = NULL;
+  }
+
+  const int counter = ListofDegeneratedPolygons.size();
+
+  Log() << Verbose(0) << "The following " << counter << " degenerated polygons have been found: " << endl;
+  for (UniquePolygonSet::iterator PolygonRunner = ListofDegeneratedPolygons.begin(); PolygonRunner != ListofDegeneratedPolygons.end(); PolygonRunner++)
     Log() << Verbose(0) << " " << **PolygonRunner << endl;
 
   /// 4. Go through all these degenerated polygons
-  for (UniquePolygonSet::iterator PolygonRunner = ListofFours.begin(); PolygonRunner != ListofFours.end(); PolygonRunner++) {
+  for (UniquePolygonSet::iterator PolygonRunner = ListofDegeneratedPolygons.begin(); PolygonRunner != ListofDegeneratedPolygons.end(); PolygonRunner++) {
     stack <int> TriangleNrs;
     Vector NormalVector;
     /// 4a. Gather all triangles of this polygon
     TriangleSet *T = (*PolygonRunner)->GetAllContainedTrianglesFromEndpoints();
+
+    // check whether number is bigger than 2, otherwise it's just a simply degenerated one and nothing to do.
+    if (T->size() == 2) {
+      Log() << Verbose(1) << " Skipping degenerated polygon, is just a (already simply degenerated) triangle." << endl;
+      delete(T);
+      continue;
+    }
+
+    // check whether number is even
+    // If this case occurs, we have to think about it!
+    // The Problem is probably due to two degenerated polygons being connected by a bridging, non-degenerated polygon, as somehow one node has
+    // connections to either polygon ...
+    if (T->size() % 2 != 0) {
+      eLog() << Verbose(0) << " degenerated polygon contains an odd number of triangles, probably contains bridging non-degenerated ones, too!" << endl;
+      performCriticalExit();
+    }
 
     TriangleSet::iterator TriangleWalker = T->begin();  // is the inner iterator
@@ -4261 +4280 @@
     TriangleWalker = T->begin();
     while (TriangleWalker != T->end()) {  // go through all front triangles
-      Log() << Verbose(1) << " Re-creating triangle " << **TriangleWalker << " with NormalVector " << BTS->NormalVector << endl;
+      Log() << Verbose(1) << " Re-creating triangle " << **TriangleWalker << " with NormalVector " << (*TriangleWalker)->NormalVector << endl;
       for (int i = 0; i < 3; i++)
         AddTesselationPoint((*TriangleWalker)->endpoints[i]->node, i);
@@ -4267 +4286 @@
       AddTesselationLine(TPS[0], TPS[2], 1);
       AddTesselationLine(TPS[1], TPS[2], 2);
+      if (TriangleNrs.empty())
+        eLog() << Verbose(0) << "No more free triangle numbers!" << endl;
       BTS = new BoundaryTriangleSet(BLS, TriangleNrs.top()); // copy triangle ...
       AddTesselationTriangle(); // ... and add
@@ -4272 +4293 @@
       BTS->NormalVector.CopyVector(&(*TriangleWalker)->NormalVector);
       BTS->NormalVector.Scale(-1.);
-      /// 4d. Add all degenerated triangles to the list of simply degenerated triangles
-      SimplyDegeneratedTriangles->insert(pair <int, int> ((*TriangleWalker)->Nr, BTS->Nr) );
-      SimplyDegeneratedTriangles->insert(pair <int, int> (BTS->Nr, (*TriangleWalker)->Nr) );
       TriangleWalker++;
     }
@@ -4283 +4301 @@
   }
 
+  map<int, int> * SimplyDegeneratedTriangles = FindAllDegeneratedTriangles();
   Log() << Verbose(0) << "Final list of simply degenerated triangles found, containing " << SimplyDegeneratedTriangles->size() << " triangles:" << endl;
   map<int,int>::iterator it;
   for (it = SimplyDegeneratedTriangles->begin(); it != SimplyDegeneratedTriangles->end(); it++)
       Log() << Verbose(0) << (*it).first << " => " << (*it).second << endl;
+  delete(SimplyDegeneratedTriangles);
 
   /// 5. exit
   UniquePolygonSet::iterator PolygonRunner;
-  while (!ListofFours.empty()) {
-    PolygonRunner = ListofFours.begin();
+  while (!ListofDegeneratedPolygons.empty()) {
+    PolygonRunner = ListofDegeneratedPolygons.begin();
     delete(*PolygonRunner);
-    ListofFours.erase(PolygonRunner);
-  }
-
-  const int counter = SimplyDegeneratedTriangles->size();
-  delete(SimplyDegeneratedTriangles);
+    ListofDegeneratedPolygons.erase(PolygonRunner);
+  }
+
   return counter;
 };

src/tesselation.hpp

@@ -47 +47 @@
 #define Raster3DSuffix ".r3d"
 #define VRMLSUffix ".wrl"
+
+#define ParallelEpsilon 1e-3
 
 // ======================================================= some template functions =========================================
@@ -156 +158 @@
     class BoundaryLineSet *lines[3];
     Vector NormalVector;
+    Vector SphereCenter;
     int Nr;
 };

src/tesselationhelpers.cpp

@@ -226 +226 @@
   Vector helper;
   double radius, alpha;
-
-  helper.CopyVector(&NewSphereCenter);
+  Vector RelativeOldSphereCenter;
+  Vector RelativeNewSphereCenter;
+
+  RelativeOldSphereCenter.CopyVector(&OldSphereCenter);
+  RelativeOldSphereCenter.SubtractVector(&CircleCenter);
+  RelativeNewSphereCenter.CopyVector(&NewSphereCenter);
+  RelativeNewSphereCenter.SubtractVector(&CircleCenter);
+  helper.CopyVector(&RelativeNewSphereCenter);
   // test whether new center is on the parameter circle's plane
   if (fabs(helper.ScalarProduct(&CirclePlaneNormal)) > HULLEPSILON) {
@@ -233 +239 @@
     helper.ProjectOntoPlane(&CirclePlaneNormal);
   }
-  radius = helper.ScalarProduct(&helper);
+  radius = helper.NormSquared();
   // test whether the new center vector has length of CircleRadius
   if (fabs(radius - CircleRadius) > HULLEPSILON)
     eLog() << Verbose(1) << "The projected center of the new sphere has radius " << radius << " instead of " << CircleRadius << "." << endl;
-  alpha = helper.Angle(&OldSphereCenter);
+  alpha = helper.Angle(&RelativeOldSphereCenter);
   // make the angle unique by checking the halfplanes/search direction
   if (helper.ScalarProduct(&SearchDirection) < -HULLEPSILON)  // acos is not unique on [0, 2.*M_PI), hence extra check to decide between two half intervals
     alpha = 2.*M_PI - alpha;
-  //Log() << Verbose(1) << "INFO: RelativeNewSphereCenter is " << helper << ", RelativeOldSphereCenter is " << OldSphereCenter << " and resulting angle is " << alpha << "." << endl;
-  radius = helper.Distance(&OldSphereCenter);
+  Log() << Verbose(1) << "INFO: RelativeNewSphereCenter is " << helper << ", RelativeOldSphereCenter is " << RelativeOldSphereCenter << " and resulting angle is " << alpha << "." << endl;
+  radius = helper.Distance(&RelativeOldSphereCenter);
   helper.ProjectOntoPlane(&NormalVector);
   // check whether new center is somewhat away or at least right over the current baseline to prevent intersecting triangles
   if ((radius > HULLEPSILON) || (helper.Norm() < HULLEPSILON)) {
-    //Log() << Verbose(1) << "INFO: Distance between old and new center is " << radius << " and between new center and baseline center is " << helper.Norm() << "." << endl;
+    Log() << Verbose(1) << "INFO: Distance between old and new center is " << radius << " and between new center and baseline center is " << helper.Norm() << "." << endl;
     return alpha;
   } else {
-    //Log() << Verbose(1) << "INFO: NewSphereCenter " << helper << " is too close to OldSphereCenter" << OldSphereCenter << "." << endl;
+    Log() << Verbose(1) << "INFO: NewSphereCenter " << RelativeNewSphereCenter << " is too close to RelativeOldSphereCenter" << RelativeOldSphereCenter << "." << endl;
     return 2.*M_PI;
   }

src/vector.cpp

@@ -480 +480 @@
   else
     return false;
+};
+
+/** Checks whether vector is normal to \a *normal.
+ * @return true - vector is normalized, false - vector is not
+ */
+bool Vector::IsEqualTo(const Vector * const a) const
+{
+  bool status = true;
+  for (int i=0;i<NDIM;i++) {
+    if (fabs(x[i] - a->x[i]) > MYEPSILON)
+      status = false;
+  }
+  return status;
 };
 

src/vector.hpp

@@ -42 +42 @@
   bool IsOne() const;
   bool IsNormalTo(const Vector * const normal) const;
+  bool IsEqualTo(const Vector * const a) const;
 
   void AddVector(const Vector * const y);