Changeset 7dea7c for src/boundary.cpp

Timestamp:

Oct 2, 2009, 3:19:51 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:

a33931, aba92d

Parents:

e4a379

Message:

Fixes to the (Non)ConvexTesselation, working with 1_2_dimethoxyethylene

minor changes:

• BoundaryLineSet::CheckConvexityCriterion() reduced verbosity
• CalculateConcavityPerBoundaryPoint() moved to tesselationhelpers.cpp
• FindNonConvexBorder(): flag -> OneLoopWithoutSuccessFlag, failflag -> TesselationFailFlag, N removed
• FindNonConvexBorder() - CheckListOfBaseline() used before and after insertion of straddling points
• BoundaryTriangleSet::ContainsBoundaryPoint() overloaded function to check also for TesselPoint
• Tesselation::InsertStraddlingPoints() - LinkedCell only redone when point was added
• Tesselation::AddTesselationTriangle() - overloaded function to set index of triangle directly.
• new function CheckListOfBaselines() - outsourced from FindNonConvexBorder()

major changes:

• BUGFIX: FindNonConvexBorder() - increment of baseline was missing
• third step (Flipping baselines) removed from ConvexizeNonconvexEnvelope()
• BUGFIX: BoundaryTriangleSet::GetIntersectionInsideTriangle() < should have been > in final if-statement to check whether in- or outside
• Tesselation::InsertStraddlingPoints() - behavior of FindClosestTriangle() changed, hence we have to check whether returned triangle does not contain the point in question.
• BUGFIX: Tesselation::FlipBaseline() - did not change LastTriangle which caused crashes on writing envelope, as it pointed to delete memory

File:

• src/boundary.cpp (modified) (8 diffs)

src/boundary.cpp

@@ -572 +572 @@
 
   // third step: IsConvexRectangle
-  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: Current line is " << *line << "." << 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;
-
-      // take highest of both lines
-      point = TesselStruct->IsConvexRectangle(out, line);
-      if (point != NULL)
-        volume += TesselStruct->RemovePointFromTesselatedSurface(out, point);
-    }
-    LineRunner = LineAdvance;
-  }
+//  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: Current line is " << *line << "." << 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;
+//
+//      // take highest of both lines
+//      point = TesselStruct->IsConvexRectangle(out, line);
+//      if (point != NULL)
+//        volume += TesselStruct->RemovePointFromTesselatedSurface(out, point);
+//    }
+//    LineRunner = LineAdvance;
+//  }
 
   CalculateConcavityPerBoundaryPoint(out, TesselStruct);
@@ -600 +600 @@
 };
 
-/** Calculates the concavity for each of the BoundaryPointSet's in a Tesselation.
- * Sets BoundaryPointSet::value equal to the number of connected lines that are not convex.
- * \param *out output stream for debugging
- * \param *TesselStruct pointer to Tesselation structure
- */
-void CalculateConcavityPerBoundaryPoint(ofstream *out, class Tesselation *TesselStruct)
-{
-  class BoundaryPointSet *point = NULL;
-  class BoundaryLineSet *line = NULL;
-  // calculate remaining concavity
-  for (PointMap::iterator PointRunner = TesselStruct->PointsOnBoundary.begin(); PointRunner != TesselStruct->PointsOnBoundary.end(); PointRunner++) {
-    point = PointRunner->second;
-    *out << Verbose(1) << "INFO: Current point is " << *point << "." << endl;
-    point->value = 0;
-    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))
-        point->value += 1;
-    }
-  }
-};
-
-/** Stores triangles to file.
- * \param *out output stream for debugging
- * \param *mol molecule with atoms and bonds
- * \param *filename prefix of filename
- * \param *extraSuffix intermediate suffix
- */
-void StoreTrianglesinFile(ofstream *out, molecule *mol, const char *filename, const char *extraSuffix)
-{
-  // 4. Store triangles in tecplot file
-  if (filename != NULL) {
-    if (DoTecplotOutput) {
-      string OutputName(filename);
-      OutputName.append(extraSuffix);
-      OutputName.append(TecplotSuffix);
-      ofstream *tecplot = new ofstream(OutputName.c_str());
-      WriteTecplotFile(out, tecplot, mol->TesselStruct, mol, 0);
-      tecplot->close();
-      delete(tecplot);
-    }
-    if (DoRaster3DOutput) {
-      string OutputName(filename);
-      OutputName.append(extraSuffix);
-      OutputName.append(Raster3DSuffix);
-      ofstream *rasterplot = new ofstream(OutputName.c_str());
-      WriteRaster3dFile(out, rasterplot, mol->TesselStruct, mol);
-      rasterplot->close();
-      delete(rasterplot);
-    }
-  }
-};
 
 /** Determines the volume of a cluster.
@@ -699 +646 @@
 
   return volume;
-}
-;
+};
+
+/** Stores triangles to file.
+ * \param *out output stream for debugging
+ * \param *mol molecule with atoms and bonds
+ * \param *filename prefix of filename
+ * \param *extraSuffix intermediate suffix
+ */
+void StoreTrianglesinFile(ofstream *out, molecule *mol, const char *filename, const char *extraSuffix)
+{
+  // 4. Store triangles in tecplot file
+  if (filename != NULL) {
+    if (DoTecplotOutput) {
+      string OutputName(filename);
+      OutputName.append(extraSuffix);
+      OutputName.append(TecplotSuffix);
+      ofstream *tecplot = new ofstream(OutputName.c_str());
+      WriteTecplotFile(out, tecplot, mol->TesselStruct, mol, 0);
+      tecplot->close();
+      delete(tecplot);
+    }
+    if (DoRaster3DOutput) {
+      string OutputName(filename);
+      OutputName.append(extraSuffix);
+      OutputName.append(Raster3DSuffix);
+      ofstream *rasterplot = new ofstream(OutputName.c_str());
+      WriteRaster3dFile(out, rasterplot, mol->TesselStruct, mol);
+      rasterplot->close();
+      delete(rasterplot);
+    }
+  }
+};
 
 /** Creates multiples of the by \a *mol given cluster and suspends them in water with a given final density.
@@ -990 +967 @@
 void FindNonConvexBorder(ofstream *out, molecule* mol, class LinkedCell *LCList, const double RADIUS, const char *filename = NULL)
 {
-  int N = 0;
   bool freeLC = false;
 
@@ -1005 +981 @@
   LineMap::iterator testline;
   *out << Verbose(0) << "Begin of FindNonConvexBorder\n";
-  bool flag = false;  // marks whether we went once through all baselines without finding any without two triangles
-  bool failflag = false;
+  bool OneLoopWithoutSuccessFlag = false;  // marks whether we went once through all baselines without finding any without two triangles
+  bool TesselationFailFlag = false;
 
   // initialise Linked Cell
@@ -1020 +996 @@
   baseline = mol->TesselStruct->LinesOnBoundary.begin();
   baseline++; // skip first line
-  while ((baseline != mol->TesselStruct->LinesOnBoundary.end()) || (flag)) {
+  while ((baseline != mol->TesselStruct->LinesOnBoundary.end()) || (OneLoopWithoutSuccessFlag)) {
     if (baseline->second->triangles.size() == 1) {
       // 3. find next triangle
-      failflag = mol->TesselStruct->FindNextSuitableTriangle(out, *(baseline->second), *(((baseline->second->triangles.begin()))->second), RADIUS, LCList); //the line is there, so there is a triangle, but only one.
-      flag = flag || failflag;
-      if (!failflag)
+      TesselationFailFlag = mol->TesselStruct->FindNextSuitableTriangle(out, *(baseline->second), *(((baseline->second->triangles.begin()))->second), RADIUS, LCList); //the line is there, so there is a triangle, but only one.
+      OneLoopWithoutSuccessFlag = OneLoopWithoutSuccessFlag || TesselationFailFlag;
+      if (!TesselationFailFlag)
         cerr << "WARNING: FindNextSuitableTriangle failed." << endl;
 
       // write temporary envelope
       if (filename != NULL) {
-        if ((DoSingleStepOutput && ((mol->TesselStruct->TrianglesOnBoundary.size() % SingleStepWidth == 0) || (mol->TesselStruct->TrianglesOnBoundary.size() > 8520 && mol->TesselStruct->TrianglesOnBoundary.size() <= 8530)))) { // if we have a new triangle and want to output each new triangle configuration
+        if ((DoSingleStepOutput && ((mol->TesselStruct->TrianglesOnBoundary.size() % SingleStepWidth == 0)))) { // if we have a new triangle and want to output each new triangle configuration
           mol->TesselStruct->Output(out, filename, mol);
         }
       }
       baseline = mol->TesselStruct->LinesOnBoundary.end();
+      *out << Verbose(2) << "Baseline set to end." << endl;
     } else {
       //cout << Verbose(1) << "Line " << *baseline->second << " has " << baseline->second->triangles.size() << " triangles adjacent" << endl;
@@ -1041 +1018 @@
     }
 
-    N++;
-    if ((baseline == mol->TesselStruct->LinesOnBoundary.end()) && (flag)) {
+    if ((baseline == mol->TesselStruct->LinesOnBoundary.end()) && (OneLoopWithoutSuccessFlag)) {
       baseline = mol->TesselStruct->LinesOnBoundary.begin();   // restart if we reach end due to newly inserted lines
-      baseline++;
-      flag = false;
-    }
-  }
+      OneLoopWithoutSuccessFlag = false;
+    }
+    baseline++;
+  }
+  // check envelope for consistency
+  CheckListOfBaselines(out, mol->TesselStruct);
+
   // look whether all points are inside of the convex envelope, otherwise add them via degenerated triangles
   mol->TesselStruct->InsertStraddlingPoints(out, mol, LCList);
@@ -1067 +1046 @@
   mol->TesselStruct->RemoveDegeneratedTriangles();
 
-  cout << Verbose(2) << "Check: List of Baselines with not two connected triangles:" << endl;
-  int counter = 0;
-  for (testline = mol->TesselStruct->LinesOnBoundary.begin(); testline != mol->TesselStruct->LinesOnBoundary.end(); testline++) {
-    if (testline->second->triangles.size() != 2) {
-      cout << Verbose(2) << *testline->second << "\t" << testline->second->triangles.size() << endl;
-      counter++;
-    }
-  }
-  if (counter == 0)
-    *out << Verbose(2) << "None." << endl;
+  // check envelope for consistency
+  CheckListOfBaselines(out, mol->TesselStruct);
 
   // write final envelope