Changeset 1d9b7aa for src

Timestamp:

Aug 19, 2009, 2:31:29 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:

34e0592

Parents:

99c484

Message:

Smaller fixes, but convex tesselation not working yet

• BoundaryPointSet::value initialized.
• ConvexizeNonconvexEnvelope() - iteratively FlipBaselines() and RemovePointFrom...()
• BoundaryLineSet::CheckConvexityCriterion() returns convex if triangles are missing, reduced verbosity
• Tesselation::IsConvexRectangle() - not working due to buggy GetClosestPoint and ClosestPoint was removed too early
• BUGFIX: GetClosestPointBetweenLine() - NewOffset was wrong, projection to relative to plane offset, NewDirection wrong also, as has to be absolute, not relative for GetIntersection...()
• Tesselation::RemovePointFromTesselatedSurface() - we first gather all removal candidates, then erase them, still memory leaks and warnings from valgrind though

Location:

src

Files:

• boundary.cpp (modified) (3 diffs)
• tesselation.cpp (modified) (13 diffs)

src/boundary.cpp

@@ -624 +624 @@
 
   // First step: RemovePointFromTesselatedSurface
-  PointRunner = TesselStruct->PointsOnBoundary.begin();
-  PointAdvance = PointRunner; // we need an advanced point, as the PointRunner might get removed
-  while (PointRunner != TesselStruct->PointsOnBoundary.end()) {
-    PointAdvance++;
-    point = PointRunner->second;
-    *out << Verbose(1) << "INFO: Current point is " << *point << "." << endl;
-    Concavity = true;
-    for (LineMap::iterator LineRunner = point->lines.begin(); LineRunner != point->lines.end(); LineRunner++) {
+  do {
+    Concavity = false;
+    PointRunner = TesselStruct->PointsOnBoundary.begin();
+    PointAdvance = PointRunner; // we need an advanced point, as the PointRunner might get removed
+    while (PointRunner != TesselStruct->PointsOnBoundary.end()) {
+      PointAdvance++;
+      point = PointRunner->second;
+      *out << Verbose(1) << "INFO: Current point is " << *point << "." << endl;
+      for (LineMap::iterator LineRunner = point->lines.begin(); LineRunner != point->lines.end(); LineRunner++) {
+        line = LineRunner->second;
+        *out << Verbose(2) << "INFO: Current line of point " << *point << " is " << *line << "." << endl;
+      }
+      if (!line->CheckConvexityCriterion(out)) {
+        *out << Verbose(1) << "... point " << *point << " cannot be on convex envelope." << endl;
+        // remove the point
+        Concavity = true;
+        TesselStruct->RemovePointFromTesselatedSurface(out, point);
+      }
+      PointRunner = PointAdvance;
+    }
+
+    //CalculateConcavityPerBoundaryPoint(out, TesselStruct);
+    //StoreTrianglesinFile(out, mol, filename, "-second");
+
+    // second step: PickFarthestofTwoBaselines
+    LineRunner = TesselStruct->LinesOnBoundary.begin();
+    LineAdvance = LineRunner;  // we need an advanced line, as the LineRunner might get removed
+    while (LineRunner != TesselStruct->LinesOnBoundary.end()) {
+      LineAdvance++;
       line = LineRunner->second;
-      *out << Verbose(2) << "INFO: Current line of point " << *point << " is " << *line << "." << endl;
-      Concavity = Concavity && (!line->CheckConvexityCriterion(out));
-    }
-    if (Concavity) {
-      *out << Verbose(1) << "... point " << *point << " cannot be on convex envelope." << endl;
-      // remove the point
-      TesselStruct->RemovePointFromTesselatedSurface(out, point);
-    }
-    PointRunner = PointAdvance;
-  }
-
-  //CalculateConcavityPerBoundaryPoint(out, TesselStruct);
-  StoreTrianglesinFile(out, mol, filename, "-second");
-
-  // second step: PickFarthestofTwoBaselines
-  LineRunner = TesselStruct->LinesOnBoundary.begin();
-  LineAdvance = LineRunner;  // we need an advanced line, as the LineRunner might get removed
-  while (LineRunner != TesselStruct->LinesOnBoundary.end()) {
-    LineAdvance++;
-    line = LineRunner->second;
-    *out << Verbose(1) << "INFO: Picking farthest baseline for line is " << *line << "." << endl;
-    // take highest of both lines
-    if (TesselStruct->IsConvexRectangle(out, line) == NULL)
-      TesselStruct->PickFarthestofTwoBaselines(out, line);
-    LineRunner = LineAdvance;
-  }
-
-  //CalculateConcavityPerBoundaryPoint(out, TesselStruct);
+      *out << Verbose(1) << "INFO: Picking farthest baseline for line is " << *line << "." << endl;
+      // take highest of both lines
+      if (TesselStruct->IsConvexRectangle(out, line) == NULL) {
+        TesselStruct->PickFarthestofTwoBaselines(out, line);
+        Concavity = true;
+      }
+      LineRunner = LineAdvance;
+    }
+  } while (Concavity);
+  CalculateConcavityPerBoundaryPoint(out, TesselStruct);
   StoreTrianglesinFile(out, mol, filename, "-third");
 
@@ -670 +673 @@
     line = LineRunner->second;
     *out << Verbose(1) << "INFO: Current line is " << *line << "." << endl;
-    if (LineAdvance != TesselStruct->LinesOnBoundary.end())
-      *out << Verbose(1) << "INFO: Next line will be " << *(LineAdvance->second) << "." << endl;
+    //if (LineAdvance != TesselStruct->LinesOnBoundary.end())
+      //*out << Verbose(1) << "INFO: Next line will be " << *(LineAdvance->second) << "." << endl;
     if (!line->CheckConvexityCriterion(out)) {
       *out << Verbose(1) << "... line " << *line << " is concave, flipping it." << endl;
@@ -684 +687 @@
 
   CalculateConcavityPerBoundaryPoint(out, TesselStruct);
+  StoreTrianglesinFile(out, mol, filename, "-fourth");
 
   // end

src/tesselation.cpp

@@ -16 +16 @@
   LinesCount = 0;
   Nr = -1;
+  value = 0.;
 };
 
@@ -26 +27 @@
   LinesCount = 0;
   Nr = Walker->nr;
+  value = 0.;
 };
 
@@ -148 +150 @@
 void BoundaryLineSet::AddTriangle(class BoundaryTriangleSet *triangle)
 {
-  cout << Verbose(6) << "Add " << triangle->Nr << " to line " << *this << "."
-      << endl;
+  cout << Verbose(6) << "Add " << triangle->Nr << " to line " << *this << "." << endl;
   triangles.insert(TrianglePair(triangle->Nr, triangle));
 };
@@ -177 +178 @@
   if (triangles.size() != 2) {
     *out << Verbose(1) << "ERROR: Baseline " << *this << " is connect to less than two triangles, Tesselation incomplete!" << endl;
-    return false;
+    return true;
   }
   // check normal vectors
   // have a normal vector on the base line pointing outwards
-  *out << Verbose(3) << "INFO: " << *this << " has vectors at " << *(endpoints[0]->node->node) << " and at " << *(endpoints[1]->node->node) << "." << endl;
+  //*out << Verbose(3) << "INFO: " << *this << " has vectors at " << *(endpoints[0]->node->node) << " and at " << *(endpoints[1]->node->node) << "." << endl;
   BaseLineCenter.CopyVector(endpoints[0]->node->node);
   BaseLineCenter.AddVector(endpoints[1]->node->node);
@@ -187 +188 @@
   BaseLine.CopyVector(endpoints[0]->node->node);
   BaseLine.SubtractVector(endpoints[1]->node->node);
-  *out << Verbose(3) << "INFO: Baseline is " << BaseLine << " and its center is at " << BaseLineCenter << "." << endl;
+  //*out << Verbose(3) << "INFO: Baseline is " << BaseLine << " and its center is at " << BaseLineCenter << "." << endl;
 
   BaseLineNormal.Zero();
@@ -195 +196 @@
   class BoundaryPointSet *node = NULL;
   for(TriangleMap::iterator runner = triangles.begin(); runner != triangles.end(); runner++) {
-    *out << Verbose(3) << "INFO: NormalVector of " << *(runner->second) << " is " << runner->second->NormalVector << "." << endl;
+    //*out << Verbose(3) << "INFO: NormalVector of " << *(runner->second) << " is " << runner->second->NormalVector << "." << endl;
     NormalCheck.AddVector(&runner->second->NormalVector);
     NormalCheck.Scale(sign);
@@ -202 +203 @@
     node = runner->second->GetThirdEndpoint(this);
     if (node != NULL) {
-      *out << Verbose(3) << "INFO: Third node for triangle " << *(runner->second) << " is " << *node << " at " << *(node->node->node) << "." << endl;
+      //*out << Verbose(3) << "INFO: Third node for triangle " << *(runner->second) << " is " << *node << " at " << *(node->node->node) << "." << endl;
       helper[i].CopyVector(node->node->node);
       helper[i].SubtractVector(&BaseLineCenter);
       helper[i].MakeNormalVector(&BaseLine);  // we want to compare the triangle's heights' angles!
-      *out << Verbose(4) << "INFO: Height vector with respect to baseline is " << helper[i] << "." << endl;
+      //*out << Verbose(4) << "INFO: Height vector with respect to baseline is " << helper[i] << "." << endl;
       i++;
     } else {
-      *out << Verbose(2) << "WARNING: I cannot find third node in triangle, something's wrong." << endl;
+      //*out << Verbose(2) << "WARNING: I cannot find third node in triangle, something's wrong." << endl;
       return true;
     }
   }
-  *out << Verbose(3) << "INFO: BaselineNormal is " << BaseLineNormal << "." << endl;
+  //*out << Verbose(3) << "INFO: BaselineNormal is " << BaseLineNormal << "." << endl;
   if (NormalCheck.NormSquared() < MYEPSILON) {
-    *out << Verbose(3) << "Normalvectors of both triangles are the same: convex." << endl;
+    *out << Verbose(2) << "ACCEPT: Normalvectors of both triangles are the same: convex." << endl;
     return true;
   }
   double angle = getAngle(helper[0], helper[1], BaseLineNormal);
-  if ((angle - M_PI) > -MYEPSILON)
+  if ((angle - M_PI) > -MYEPSILON) {
+    *out << Verbose(2) << "ACCEPT: Angle is greater than pi: convex." << endl;
     return true;
-  else
+  } else {
+    *out << Verbose(2) << "REJECT: Angle is less than pi: concave." << endl;
     return false;
+  }
 }
 
@@ -1767 +1771 @@
 
   // delete the temporary other base line
-  delete(ClosestPoint);
   delete(OtherBase);
 
@@ -1780 +1783 @@
     distance[i] = BaseLine.ScalarProduct(&DistanceToIntersection[i]);
   }
-  if ((distance[0] * distance[1]) > MYEPSILON)  { // have same sign?
-    *out << Verbose(3) << "REJECT: Both SKPs have same sign: " << distance[0] << " and " << distance[1]  << ". " << *Base << " is concave." << endl;
+  delete(ClosestPoint);
+  if ((distance[0] * distance[1]) > 0)  { // have same sign?
+    *out << Verbose(3) << "REJECT: Both SKPs have same sign: " << distance[0] << " and " << distance[1]  << ". " << *Base << "' rectangle is concave." << endl;
     if (distance[0] < distance[1]) {
       Spot = Base->endpoints[0];
@@ -1903 +1907 @@
   Vector NewOffset;
   NewOffset.CopyVector(OtherBase->endpoints[0]->node->node);
+  NewOffset.SubtractVector(Base->endpoints[0]->node->node);
   NewOffset.ProjectOntoPlane(&Normal);
   NewOffset.AddVector(Base->endpoints[0]->node->node);
+  Vector NewDirection;
+  NewDirection.CopyVector(&NewOffset);
+  NewDirection.AddVector(&OtherBaseline);
 
   // calculate the intersection between this projected baseline and Base
   Vector *Intersection = new Vector;
-  Intersection->GetIntersectionOfTwoLinesOnPlane(out, Base->endpoints[0]->node->node, Base->endpoints[1]->node->node, &NewOffset, &OtherBaseline, &Normal);
+  Intersection->GetIntersectionOfTwoLinesOnPlane(out, Base->endpoints[0]->node->node, Base->endpoints[1]->node->node, &NewOffset, &NewDirection, &Normal);
   Normal.CopyVector(Intersection);
   Normal.SubtractVector(Base->endpoints[0]->node->node);
@@ -2622 +2630 @@
   int i;
 
+  if (point == NULL) {
+    *out << Verbose(1) << "ERROR: Cannot remove the point " << point << ", it's NULL!" << endl;
+    return 0.;
+  } else
+    *out << Verbose(2) << "Removing point " << *point << " from tesselated boundary ..." << endl;
+
   // copy old location for the volume
   OldPoint.CopyVector(point->node->node);
@@ -2636 +2650 @@
     count+=LineRunner->second->triangles.size();
   numbers = new int[count];
+  class BoundaryTriangleSet **Candidates = new BoundaryTriangleSet*[count];
   i=0;
   for (LineMap::iterator LineRunner = point->lines.begin(); (point != NULL) && (LineRunner != point->lines.end()); LineRunner++) {
@@ -2641 +2656 @@
     for (TriangleMap::iterator TriangleRunner = line->triangles.begin(); TriangleRunner != line->triangles.end(); TriangleRunner++) {
       triangle = TriangleRunner->second;
-      *out << Verbose(2) << "Erasing triangle " << *triangle << "." << endl;
+      Candidates[i] = triangle;
       numbers[i++] = triangle->Nr;
-      RemoveTesselationTriangle(triangle);
-      triangle = NULL;
-    }
-  }
+    }
+  }
+  for (int j=0;j<i;j++) {
+    RemoveTesselationTriangle(Candidates[j]);
+  }
+  delete[](Candidates);
   *out << Verbose(1) << i << " triangles were removed." << endl;