Changeset fad93c

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).

Location:

src

Files:

• tesselation.cpp (modified) (5 diffs)
• tesselation.hpp (modified) (1 diff)

src/tesselation.cpp

@@ -4127 +4127 @@
   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
+  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++) {
+        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;
+      }
+    // 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;
@@ -4261 +4238 @@
     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 +4244 @@
       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 +4251 @@
       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 +4259 @@
   }
 
+  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 =========================================