Changeset fad93c for src/tesselation.cpp


Ignore:
Timestamp:
Nov 28, 2009, 6:01:00 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:
a8eb4a
Parents:
856098
git-author:
Frederik Heber <heber@…> (11/28/09 17:52:05)
git-committer:
Frederik Heber <heber@…> (11/28/09 18:01:00)
Message:

The finding of the degenerated polygons' endpoints was not yet correct, fixed.

  • PROBLEM: we always looked for quadragons as atomic units of degenerated polygons, however for aromatic rings there may actually be no quadrons sub parts but only a a hexagon to be found.
  • Tesselation::CorrectAllDegeneratedPolygons(): rename ListofFourse -> ListofDegeneratedPolygons
  • FIX: Tesselation::CorrectAllDegeneratedPolygons(): Number of simply degenerated polygons was returned instead of number of degenerated polygons
  • Rewritten Tesselation::CorrectAllDegeneratedPolygons() in the following manner (which is also a lot faster than before):
    1. Go through all BoundaryPoints
    2. Check whether they have two triangles with anti-parallel NormalVectors, indicating that this point is part of a degenerated polygon.
    3. Combine endpoint candidates based on whether there is a BoundaryLineSet in between, then put them into the same polygon.
    4. Proceed with 3. until all candidates have been put into BoundaryPolygonSets
    5. continue with the unchanged remainder on this new "ListofFours" (our list of degenerated polygons).
File:
1 edited

Legend:

Unmodified
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Removed

  • src/tesselation.cpp

    r856098 rfad93c  
    41274127  Info FunctionInfo(__func__);
    41284128
    4129   /// 1. Find all simply degenerated triangles and sort into a list with each endpoint as key
    4130   map<int, int> * SimplyDegeneratedTriangles = FindAllDegeneratedTriangles();
    4131 
    4132   /// 2. Go through all lines not contained in degenerated triangles.
    4133   UniquePolygonSet ListofFours;
    4134   UniquePolygonSet TestedPolygons;
    4135   for (LineMap::const_iterator LineRunner = LinesOnBoundary.begin(); LineRunner != LinesOnBoundary.end(); LineRunner++) {
    4136     Log() << Verbose(1) << "Current Line is: " << *(LineRunner->second) << endl;
    4137 
    4138     BoundaryPolygonSet *Four = new BoundaryPolygonSet;
    4139 
    4140     /// 2a. Get all four endpoints of the two connected triangles.
    4141     Four->FillPolygonFromTrianglesOfLine((LineRunner->second));
    4142     if (Four->endpoints.size() != 4) {
    4143       Log() << Verbose(0) << "REJECT: There were no four endpoints:" << *Four << endl;
    4144       delete(Four);
    4145       continue;
    4146     }
    4147 
    4148     /// 2b. Get the triangles of all those endpoints
    4149     TriangleSet *T = Four->GetAllContainedTrianglesFromEndpoints();
    4150 
    4151     /// 2c1. Check whether all triangles have (besides sign) same normal vector)
    4152     TriangleSet::const_iterator Runner = T->begin();
    4153     Vector NormalVector;
    4154     NormalVector.CopyVector(&(*Runner)->NormalVector);
    4155     Runner++;
    4156     bool IsPlanar = true;
    4157     for (; Runner != T->end(); Runner++) {
    4158       if (fabs(fabs(NormalVector.ScalarProduct(&(*Runner)->NormalVector)) - 1.) > MYEPSILON)  // check whether all NormalVectors are parallel
    4159         IsPlanar = false;
    4160     }
    4161 
    4162     /// 2c2. check whether triangles are not already simply degenerated.
    4163     size_t DegeneratedCount = 0;
    4164     for (TriangleSet::const_iterator Runner = T->begin(); Runner != T->end(); Runner++) {
    4165       if (SimplyDegeneratedTriangles->find((*Runner)->Nr) != SimplyDegeneratedTriangles->end())
    4166         DegeneratedCount++;
    4167     }
    4168     Log() << Verbose(1) << "Found " << DegeneratedCount << " degenerated triangles." << endl;
    4169 
    4170     if (IsPlanar) {
    4171       if(DegeneratedCount == 0) {
    4172         /// 2c. Find all pairs of those triangles that contain the four endpoints
    4173         const int counter = CountTrianglePairContainingPolygon(Four, T);
    4174         Log() << Verbose(1) << "There are " << counter << " pairs for this polygon of four." << endl;
    4175         if (counter %3 == 0) {
    4176           /// 2d. Check the number of pairs, if greater 1, we have a degenerated polygon (mark down for later use)
    4177           pair < UniquePolygonSet::iterator, bool > Tester = ListofFours.insert(Four);
    4178           if (Tester.second) {
    4179             Log() << Verbose(0) << "ACCEPT: We have a degenerated polygon." << *Four << endl;
    4180           } else {
    4181             Log() << Verbose(0) << "REJECT: Degenerated polygon already present." << *Four << endl;
    4182             delete(Four);
     4129  /// 2. Go through all BoundaryPointSet's, check their triangles' NormalVector
     4130  set < BoundaryPointSet *> EndpointCandidateList;
     4131  pair < set < BoundaryPointSet *>::iterator, bool > InsertionTester;
     4132  pair < map < int, Vector *>::iterator, bool > TriangleInsertionTester;
     4133  for (PointMap::const_iterator Runner = PointsOnBoundary.begin(); Runner != PointsOnBoundary.end(); Runner++) {
     4134    Log() << Verbose(0) << "Current point is " << *Runner->second << "." << endl;
     4135    map < int, Vector *> TriangleVectors;
     4136    // gather all NormalVectors
     4137    Log() << Verbose(1) << "Gathering triangles ..." << endl;
     4138    for (LineMap::const_iterator LineRunner = (Runner->second)->lines.begin(); LineRunner != (Runner->second)->lines.end(); LineRunner++)
     4139      for (TriangleMap::const_iterator TriangleRunner = (LineRunner->second)->triangles.begin(); TriangleRunner != (LineRunner->second)->triangles.end(); TriangleRunner++) {
     4140        TriangleInsertionTester = TriangleVectors.insert( pair< int, Vector *> ((TriangleRunner->second)->Nr, &((TriangleRunner->second)->NormalVector)) );
     4141        if (TriangleInsertionTester.second)
     4142          Log() << Verbose(1) << " Adding triangle " << *(TriangleRunner->second) << " to triangles to check-list." << endl;
     4143      }
     4144    // check whether there are two that are parallel
     4145    Log() << Verbose(1) << "Finding two parallel triangles ..." << endl;
     4146    for (map < int, Vector *>::iterator VectorWalker = TriangleVectors.begin(); VectorWalker != TriangleVectors.end(); VectorWalker++)
     4147      for (map < int, Vector *>::iterator VectorRunner = VectorWalker; VectorRunner != TriangleVectors.end(); VectorRunner++)
     4148        if (VectorWalker != VectorRunner) { // skip equals
     4149          const double SCP = VectorWalker->second->ScalarProduct(VectorRunner->second);  // ScalarProduct should result in -1. for degenerated triangles
     4150          Log() << Verbose(1) << "Checking " << *VectorWalker->second<< " against " << *VectorRunner->second << ": " << SCP << endl;
     4151          if (fabs(SCP + 1.) < ParallelEpsilon) {
     4152            InsertionTester = EndpointCandidateList.insert((Runner->second));
     4153            if (InsertionTester.second)
     4154              Log() << Verbose(0) << " Adding " << *Runner->second << " to endpoint candidate list." << endl;
     4155            // and break out of both loops
     4156            VectorWalker = TriangleVectors.end();
     4157            VectorRunner = TriangleVectors.end();
     4158            break;
    41834159          }
     4160        }
     4161  }
     4162
     4163  /// 3. Find connected endpoint candidates and put them into a polygon
     4164  UniquePolygonSet ListofDegeneratedPolygons;
     4165  BoundaryPointSet *Walker = NULL;
     4166  BoundaryPointSet *OtherWalker = NULL;
     4167  BoundaryPolygonSet *Current = NULL;
     4168  stack <BoundaryPointSet*> ToCheckConnecteds;
     4169  while (!EndpointCandidateList.empty()) {
     4170    Walker = *(EndpointCandidateList.begin());
     4171    if (Current == NULL) {  // create a new polygon with current candidate
     4172      Log() << Verbose(0) << "Starting new polygon set at point " << *Walker << endl;
     4173      Current = new BoundaryPolygonSet;
     4174      Current->endpoints.insert(Walker);
     4175      EndpointCandidateList.erase(Walker);
     4176      ToCheckConnecteds.push(Walker);
     4177    }
     4178
     4179    // go through to-check stack
     4180    while (!ToCheckConnecteds.empty()) {
     4181      Walker = ToCheckConnecteds.top(); // fetch ...
     4182      ToCheckConnecteds.pop(); // ... and remove
     4183      for (LineMap::const_iterator LineWalker = Walker->lines.begin(); LineWalker != Walker->lines.end(); LineWalker++) {
     4184        OtherWalker = (LineWalker->second)->GetOtherEndpoint(Walker);
     4185        Log() << Verbose(1) << "Checking " << *OtherWalker << endl;
     4186        set < BoundaryPointSet *>::iterator Finder = EndpointCandidateList.find(OtherWalker);
     4187        if (Finder != EndpointCandidateList.end()) {  // found a connected partner
     4188          Log() << Verbose(1) << " Adding to polygon." << endl;
     4189          Current->endpoints.insert(OtherWalker);
     4190          EndpointCandidateList.erase(Finder);  // remove from candidates
     4191          ToCheckConnecteds.push(OtherWalker);  // but check its partners too
    41844192        } else {
    4185           Log() << Verbose(0) << "REJECT: Seems to be the edge line of a degenerated polygon only." << *Four << endl;
    4186           delete(Four);
     4193          Log() << Verbose(1) << " is not connected to " << *Walker << endl;
    41874194        }
    4188       } else {
    4189         Log() << Verbose(0) << "REJECT: This polygon contains some simply degenerated triangles." << endl;
    4190         delete(Four);
    41914195      }
    4192     } else {
    4193       Log() << Verbose(0) << "REJECT: This polygon does not lay on a plane." << endl;
    4194       delete(Four);
    4195     }
    4196 
    4197     delete(T);
    4198   }
    4199 
    4200   /// 3. Combine all edge-connected degenerated polygons
    4201   {
    4202     UniquePolygonSet::iterator PolygonWalker;  // is the inner iterator
    4203     UniquePolygonSet::iterator PolygonSprinter; // is the inner advanced iterator
    4204     for (UniquePolygonSet::iterator PolygonRunner = ListofFours.begin(); PolygonRunner != ListofFours.end(); PolygonRunner++) {
    4205       const BoundaryPolygonSet *P1 = *PolygonRunner;
    4206       Log() << Verbose(1) << "Current Polygon is : " << *P1 << endl;
    4207       PolygonWalker = PolygonRunner;
    4208       PolygonWalker++;
    4209       PolygonSprinter = PolygonWalker;
    4210       while (PolygonWalker != ListofFours.end()) {
    4211         BoundaryPolygonSet *P2 = *PolygonWalker;
    4212         Log() << Verbose(1) << "Current Other Polygon is : " << *P2 << endl;
    4213         PolygonSprinter++;
    4214         Log() << Verbose(1) << "Are " << *P1 << " and " << *P2 << " edge-connected?" << endl;
    4215         if (ArePolygonsEdgeConnected((*PolygonRunner), (P2))) { // if connected
    4216           Log() << Verbose(0) << "Yes!" << endl;
    4217           CombinePolygons((*PolygonRunner), (P2)); // combined and ...
    4218           ListofFours.erase(PolygonWalker); // ... remove from list
    4219           Log() << Verbose(1) << "  New current Polygon is : " << *P1 << endl;
    4220         } else {
    4221           Log() << Verbose(0) << "No." << endl;
    4222         }
    4223         PolygonWalker = PolygonSprinter;
    4224       }
    4225     }
    4226   }
    4227 
    4228   Log() << Verbose(0) << "The following degenerated polygons have been found: " << endl;
    4229   for (UniquePolygonSet::iterator PolygonRunner = ListofFours.begin(); PolygonRunner != ListofFours.end(); PolygonRunner++)
     4196    }
     4197
     4198    Log() << Verbose(0) << "Final polygon is " << *Current << endl;
     4199    ListofDegeneratedPolygons.insert(Current);
     4200    Current = NULL;
     4201  }
     4202
     4203  const int counter = ListofDegeneratedPolygons.size();
     4204
     4205  Log() << Verbose(0) << "The following " << counter << " degenerated polygons have been found: " << endl;
     4206  for (UniquePolygonSet::iterator PolygonRunner = ListofDegeneratedPolygons.begin(); PolygonRunner != ListofDegeneratedPolygons.end(); PolygonRunner++)
    42304207    Log() << Verbose(0) << " " << **PolygonRunner << endl;
    42314208
    42324209  /// 4. Go through all these degenerated polygons
    4233   for (UniquePolygonSet::iterator PolygonRunner = ListofFours.begin(); PolygonRunner != ListofFours.end(); PolygonRunner++) {
     4210  for (UniquePolygonSet::iterator PolygonRunner = ListofDegeneratedPolygons.begin(); PolygonRunner != ListofDegeneratedPolygons.end(); PolygonRunner++) {
    42344211    stack <int> TriangleNrs;
    42354212    Vector NormalVector;
    … …  
    42614238    TriangleWalker = T->begin();
    42624239    while (TriangleWalker != T->end()) {  // go through all front triangles
    4263       Log() << Verbose(1) << " Re-creating triangle " << **TriangleWalker << " with NormalVector " << BTS->NormalVector << endl;
     4240      Log() << Verbose(1) << " Re-creating triangle " << **TriangleWalker << " with NormalVector " << (*TriangleWalker)->NormalVector << endl;
    42644241      for (int i = 0; i < 3; i++)
    42654242        AddTesselationPoint((*TriangleWalker)->endpoints[i]->node, i);
    … …  
    42674244      AddTesselationLine(TPS[0], TPS[2], 1);
    42684245      AddTesselationLine(TPS[1], TPS[2], 2);
     4246      if (TriangleNrs.empty())
     4247        eLog() << Verbose(0) << "No more free triangle numbers!" << endl;
    42694248      BTS = new BoundaryTriangleSet(BLS, TriangleNrs.top()); // copy triangle ...
    42704249      AddTesselationTriangle(); // ... and add
    … …  
    42724251      BTS->NormalVector.CopyVector(&(*TriangleWalker)->NormalVector);
    42734252      BTS->NormalVector.Scale(-1.);
    4274       /// 4d. Add all degenerated triangles to the list of simply degenerated triangles
    4275       SimplyDegeneratedTriangles->insert(pair <int, int> ((*TriangleWalker)->Nr, BTS->Nr) );
    4276       SimplyDegeneratedTriangles->insert(pair <int, int> (BTS->Nr, (*TriangleWalker)->Nr) );
    42774253      TriangleWalker++;
    42784254    }
    … …  
    42834259  }
    42844260
     4261  map<int, int> * SimplyDegeneratedTriangles = FindAllDegeneratedTriangles();
    42854262  Log() << Verbose(0) << "Final list of simply degenerated triangles found, containing " << SimplyDegeneratedTriangles->size() << " triangles:" << endl;
    42864263  map<int,int>::iterator it;
    42874264  for (it = SimplyDegeneratedTriangles->begin(); it != SimplyDegeneratedTriangles->end(); it++)
    42884265      Log() << Verbose(0) << (*it).first << " => " << (*it).second << endl;
     4266  delete(SimplyDegeneratedTriangles);
    42894267
    42904268  /// 5. exit
    42914269  UniquePolygonSet::iterator PolygonRunner;
    4292   while (!ListofFours.empty()) {
    4293     PolygonRunner = ListofFours.begin();
     4270  while (!ListofDegeneratedPolygons.empty()) {
     4271    PolygonRunner = ListofDegeneratedPolygons.begin();
    42944272    delete(*PolygonRunner);
    4295     ListofFours.erase(PolygonRunner);
    4296   }
    4297 
    4298   const int counter = SimplyDegeneratedTriangles->size();
    4299   delete(SimplyDegeneratedTriangles);
     4273    ListofDegeneratedPolygons.erase(PolygonRunner);
     4274  }
     4275
    43004276  return counter;
    43014277};
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