Changeset 27bd2f for src

Timestamp:

Nov 26, 2009, 11:36:44 AM (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:

4fc93f

Parents:

7273fc

Message:

BUGFIX: testcase heptan was not correctly tesselated, as edges of a (degenerated) polygon were not correctly created.

• rename GetCircleofConnectedPoints() -> GetCircleOfSetOfPoints()
• GetCircleOfSetOfPoints() does not call GetAllConnectedPoints() but receives such a list as a parameter, allowing wider user
• Tesselation::FindClosestTrianglesToPoint() now calls GetAllConnectedPoints() before GetCircleOfSetOfPoints()
• Tesselation::AddCandidateTriangle():we use GetCircleOfSetOfPoints() in order to sort the nodes into a circle around a given reference (one of the baseline's nodes)
• Tesselation::AddCandidateTriangle(): using this circle we may easily add the edges and triangles in a correct manner.

Location:

src

Files:

• tesselation.cpp (modified) (11 diffs)
• tesselation.hpp (modified) (1 diff)

src/tesselation.cpp

@@ -42 +42 @@
 {
         Info FunctionInfo(__func__);
-  Log() << Verbose(1) << "Adding at " << *(node->node) << endl;
+  Log() << Verbose(1) << "Adding Node " << *Walker << endl;
 };
 
@@ -593 +593 @@
 {
         Info FunctionInfo(__func__);
-  ost << "[" << (Name) << "|" << this << "]";
+  ost << "[" << (nr) << "|" << this << "]";
   return ost;
 };
@@ -2075 +2075 @@
         Info FunctionInfo(__func__);
   Vector Center;
-  BoundaryLineSet *BaseLine = CandidateLine.BaseLine;
-
-  // go through all candidates (in degenerate n-nodes case we may have to add multiple triangles)
-  for (TesselPointList::iterator Runner = CandidateLine.pointlist.begin(); Runner != CandidateLine.pointlist.end(); Runner++) {
-    Log() << Verbose(2) << "BaseLine is :" << *(BaseLine) << " with current candidate " << *(*Runner) << "." << endl;
+  TesselPoint * const TurningPoint = CandidateLine.BaseLine->endpoints[0]->node;
+
+  // fill the set of neighbours
+  Center.CopyVector(CandidateLine.BaseLine->endpoints[1]->node->node);
+  Center.SubtractVector(TurningPoint->node);
+  set<TesselPoint*> SetOfNeighbours;
+  SetOfNeighbours.insert(CandidateLine.BaseLine->endpoints[1]->node);
+  for (TesselPointList::iterator Runner = CandidateLine.pointlist.begin(); Runner != CandidateLine.pointlist.end(); Runner++)
+    SetOfNeighbours.insert(*Runner);
+  TesselPointList *connectedClosestPoints = GetCircleOfSetOfPoints(&SetOfNeighbours, TurningPoint, &Center);
+
+  // go through all angle-sorted candidates (in degenerate n-nodes case we may have to add multiple triangles)
+  TesselPointList::iterator Runner = connectedClosestPoints->begin();
+  TesselPointList::iterator Sprinter = Runner;
+  Sprinter++;
+  while(Sprinter != connectedClosestPoints->end()) {
     // add the points
-    AddTesselationPoint(BaseLine->endpoints[0]->node, 0);
-    AddTesselationPoint(BaseLine->endpoints[1]->node, 1);
-    AddTesselationPoint((*Runner), 2);
+    AddTesselationPoint(TurningPoint, 0);
+    AddTesselationPoint((*Runner), 1);
+    AddTesselationPoint((*Sprinter), 2);
 
     Center.CopyVector(&CandidateLine.OptCenter);
     // add the lines
-    AddTesselationLine(TPS[2], TPS[0], 0);
-    AddTesselationLine(TPS[2], TPS[1], 1);
-    AddTesselationLine(TPS[0], TPS[1], 2);
+    AddTesselationLine(TPS[0], TPS[1], 0);
+    AddTesselationLine(TPS[0], TPS[2], 1);
+    AddTesselationLine(TPS[1], TPS[2], 2);
 
     // add the triangles
@@ -2098 +2109 @@
 
     Log() << Verbose(0) << "--> New triangle with " << *BTS << " and normal vector " << BTS->NormalVector << "." << endl;
-    BaseLine = BLS[0];  // go to next baseline, in order to add in star formation from CandidateLine.BaseLine->endpoints[0]->node
+    Runner = Sprinter;
+    Sprinter++;
   }
 };
@@ -2739 +2751 @@
     }
   } else {
-    list<TesselPoint*> *connectedClosestPoints = GetCircleOfConnectedPoints(trianglePoints[0], x);
+    set<TesselPoint*> *connectedPoints = GetAllConnectedPoints(trianglePoints[0]);
+    TesselPointList *connectedClosestPoints = GetCircleOfSetOfPoints(connectedPoints, trianglePoints[0], x);
+    delete(connectedPoints);
     if (connectedClosestPoints != NULL) {
       trianglePoints[1] = connectedClosestPoints->front();
@@ -2917 +2931 @@
  *
  * @param *out output stream for debugging
+ * @param *SetOfNeighbours all points for which the angle should be calculated
  * @param *Point of which get all connected points
  * @param *Reference Reference vector for zero angle or NULL for no preference
  * @return list of the all points linked to the provided one
  */
-list<TesselPoint*> * Tesselation::GetCircleOfConnectedPoints(const TesselPoint* const Point, const Vector * const Reference) const
+list<TesselPoint*> * Tesselation::GetCircleOfSetOfPoints(set<TesselPoint*> *SetOfNeighbours, const TesselPoint* const Point, const Vector * const Reference) const
 {
         Info FunctionInfo(__func__);
   map<double, TesselPoint*> anglesOfPoints;
-  set<TesselPoint*> *connectedPoints = GetAllConnectedPoints(Point);
   list<TesselPoint*> *connectedCircle = new list<TesselPoint*>;
   Vector center;
@@ -2933 +2947 @@
   Vector helper;
 
-  if (connectedPoints == NULL) {
+  if (SetOfNeighbours == NULL) {
     eLog() << Verbose(2) << "Could not find any connected points!" << endl;
     delete(connectedCircle);
@@ -2940 +2954 @@
 
   // calculate central point
-  for (set<TesselPoint*>::const_iterator TesselRunner = connectedPoints->begin(); TesselRunner != connectedPoints->end(); TesselRunner++)
+  for (set<TesselPoint*>::const_iterator TesselRunner = SetOfNeighbours->begin(); TesselRunner != SetOfNeighbours->end(); TesselRunner++)
     center.AddVector((*TesselRunner)->node);
   //Log() << Verbose(0) << "Summed vectors " << center << "; number of points " << connectedPoints.size()
   //  << "; scale factor " << 1.0/connectedPoints.size();
-  center.Scale(1.0/connectedPoints->size());
+  center.Scale(1.0/SetOfNeighbours->size());
   Log() << Verbose(1) << "INFO: Calculated center of all circle points is " << center << "." << endl;
 
@@ -2960 +2974 @@
   }
   if ((Reference == NULL) || (AngleZero.NormSquared() < MYEPSILON )) {
-    Log() << Verbose(1) << "Using alternatively " << *(*connectedPoints->begin())->node << " as angle 0 referencer." << endl;
-    AngleZero.CopyVector((*connectedPoints->begin())->node);
+    Log() << Verbose(1) << "Using alternatively " << *(*SetOfNeighbours->begin())->node << " as angle 0 referencer." << endl;
+    AngleZero.CopyVector((*SetOfNeighbours->begin())->node);
     AngleZero.SubtractVector(Point->node);
     AngleZero.ProjectOntoPlane(&PlaneNormal);
@@ -2977 +2991 @@
 
   // go through all connected points and calculate angle
-  for (set<TesselPoint*>::iterator listRunner = connectedPoints->begin(); listRunner != connectedPoints->end(); listRunner++) {
+  for (set<TesselPoint*>::iterator listRunner = SetOfNeighbours->begin(); listRunner != SetOfNeighbours->end(); listRunner++) {
     helper.CopyVector((*listRunner)->node);
     helper.SubtractVector(Point->node);
@@ -2989 +3003 @@
     connectedCircle->push_back(AngleRunner->second);
   }
-
-  delete(connectedPoints);
 
   return connectedCircle;

src/tesselation.hpp

@@ -251 +251 @@
     list<list<TesselPoint*> *> * GetPathsOfConnectedPoints(const TesselPoint* const Point) const;
     list<list<TesselPoint*> *> * GetClosedPathsOfConnectedPoints(const TesselPoint* const Point) const;
-    list<TesselPoint*> * GetCircleOfConnectedPoints(const TesselPoint* const Point, const Vector * const Reference = NULL) const;
+    list<TesselPoint*> * GetCircleOfSetOfPoints(set<TesselPoint*> *SetOfNeighbours, const TesselPoint* const Point, const Vector * const Reference = NULL) const;
     class BoundaryPointSet *GetCommonEndpoint(const BoundaryLineSet * line1, const BoundaryLineSet * line2) const;
     list<BoundaryTriangleSet*> *FindTriangles(const TesselPoint* const Points[3]) const;