Changeset b32dbb for src/tesselation.cpp

Timestamp:

May 29, 2010, 12:59:31 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, Candidate_v1.7.0, 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:

a7c344

Parents:

bfd839

git-author:

Frederik Heber <heber@…> (05/27/10 11:04:42)

git-committer:

Frederik Heber <heber@…> (05/29/10 12:59:31)

Message:

Fixes and changes to tesselation and concavity measurements.

Here, we implement two attempts for a concavity measure:

1. Measure concavity per point by looking at neighbouring triangles
   • BoundaryLineSet::CheckConvexityCriterion() split up (calculation of angle outsourced to CalculateConvexity())
   • CHANGE: CalculateConcavityPerBoundaryPoint() uses new concavity measure per BoundaryPointSet containing:
     • concavity per line uses angle instead of +/-1 for line, averaged by number of lines
     • also concavity over all attached triangles uses area of triangle and only in case of concavity, averaged by total area
   • new functions
     • BoundaryLineSet::CalculateConvexity() - calculates the angle between two triangles.
     • BoundaryLineSet::GetOtherTriangle() - for a closed line returns the other triangle for a given one
     • BoundaryTriangleSet::GetThirdLine() - for a given boundary point returns the line of the three which does not contain it (opposite line to a point)
     • CalculateAreaofGeneralTriangle() - calculates area of arbitrary triangle

2. Measure concavity by the distance to a more convex envelope (i.e. created with bigger sphere radius)
   • ParseCommandLineOptions(): case 'N' - two envelopes are created and the distance used as concavity measure via CalculateConstrictionPerBoundaryPoint()
   • FIX: CandidateForTesselation::CheckValidity() - checked against OptCenter instead of (*VRunner), animate_sphere line is printed as error, hence always visible
   • FIX: Tesselation::FindThirdPointForTesselation() - error if circumcenter is not the equidistant from each triangle node is now an error mesage
   • BUGFIX: Tesselation::RemoveDegeneratedTriangles() - would fail for more than two degenerate triangles to remove due to faulty loop construction and break instead of continue
   • BUGFIX: GetCenterofCircumcircle() - is numerically unstable (>1e-10) for big sphere radii, there are two other variants, not using angles.
   • FindNonConvexBorder() - RemoveDegeneratedTriangles() commented-out as runs into infinite loop for small radii (<5) for L-shaped cluster

Other unrelated stuff:

• DOCUFIX: CalculateVolumeofGeneralTetraeder() - four times "first vector"
• FIX: Tesselation::FindAllDegeneratedTriangles() - iterator integrated into for-loop statement

Signed-off-by: Frederik Heber <heber@…>

File:

• src/tesselation.cpp (modified) (10 diffs)

src/tesselation.cpp

@@ -229 +229 @@
 {
   Info FunctionInfo(__func__);
+  double angle = CalculateConvexity();
+  if (angle > -MYEPSILON) {
+    DoLog(0) && (Log() << Verbose(0) << "ACCEPT: Angle is greater than pi: convex." << endl);
+    return true;
+  } else {
+    DoLog(0) && (Log() << Verbose(0) << "REJECT: Angle is less than pi: concave." << endl);
+    return false;
+  }
+}
+
+
+/** Calculates the angle between two triangles with respect to their normal vector.
+ * We sum the two angles of each height vector with respect to the center of the baseline.
+ * \return angle > 0 then convex, if < 0 then concave
+ */
+double BoundaryLineSet::CalculateConvexity() const
+{
+  Info FunctionInfo(__func__);
   Vector BaseLineCenter, BaseLineNormal, BaseLine, helper[2], NormalCheck;
   // get the two triangles
@@ -277 +295 @@
   BaseLineNormal.Scale(-1.);
   double angle = GetAngle(helper[0], helper[1], BaseLineNormal);
-  if ((angle - M_PI) > -MYEPSILON) {
-    DoLog(0) && (Log() << Verbose(0) << "ACCEPT: Angle is greater than pi: convex." << endl);
-    return true;
-  } else {
-    DoLog(0) && (Log() << Verbose(0) << "REJECT: Angle is less than pi: concave." << endl);
-    return false;
-  }
+  return (angle - M_PI);
 }
 
@@ -302 +314 @@
 /** Returns other endpoint of the line.
  * \param *point other endpoint
- * \return NULL - if endpoint not contained in BoundaryLineSet, or pointer to BoundaryPointSet otherwise
+ * \return NULL - if endpoint not contained in BoundaryLineSet::lines, or pointer to BoundaryPointSet otherwise
  */
 class BoundaryPointSet *BoundaryLineSet::GetOtherEndpoint(const BoundaryPointSet * const point) const
@@ -313 +325 @@
   else
     return NULL;
+}
+;
+
+/** Returns other triangle of the line.
+ * \param *point other endpoint
+ * \return NULL - if triangle not contained in BoundaryLineSet::triangles, or pointer to BoundaryTriangleSet otherwise
+ */
+class BoundaryTriangleSet *BoundaryLineSet::GetOtherTriangle(const BoundaryTriangleSet * const triangle) const
+{
+  Info FunctionInfo(__func__);
+  if (triangles.size() == 2) {
+    for (TriangleMap::const_iterator TriangleRunner = triangles.begin(); TriangleRunner != triangles.end(); ++TriangleRunner)
+      if (TriangleRunner->second != triangle)
+        return TriangleRunner->second;
+  }
+  return NULL;
 }
 ;
@@ -669 +697 @@
 ;
 
+/** Returns the baseline which does not contain the given boundary point \a *point.
+ * \param *point endpoint which is neither endpoint of the desired line
+ * \return pointer to desired third baseline
+ */
+class BoundaryLineSet *BoundaryTriangleSet::GetThirdLine(const BoundaryPointSet * const point) const
+{
+  Info FunctionInfo(__func__);
+  // sanity check
+  if (!ContainsBoundaryPoint(point))
+    return NULL;
+  for (int i = 0; i < 3; i++)
+    if (!lines[i]->ContainsBoundaryPoint(point))
+      return lines[i];
+  // actually, that' impossible :)
+  return NULL;
+}
+;
+
 /** Calculates the center point of the triangle.
  * Is third of the sum of all endpoints.
@@ -1106 +1152 @@
     TesselPointList *ListofPoints = LC->GetPointsInsideSphere(RADIUS, (*VRunner));
 
-    DoLog(1) && (Log() << Verbose(1) << "The following atoms are inside sphere at " << OtherOptCenter << ":" << endl);
+    DoLog(1) && (Log() << Verbose(1) << "The following atoms are inside sphere at " << (*VRunner) << ":" << endl);
     for (TesselPointList::const_iterator Runner = ListofPoints->begin(); Runner != ListofPoints->end(); ++Runner)
-      DoLog(1) && (Log() << Verbose(1) << "  " << *(*Runner) << " with distance " << (*Runner)->node->distance(OtherOptCenter) << "." << endl);
+      DoLog(1) && (Log() << Verbose(1) << "  " << *(*Runner) << " with distance " << (*Runner)->node->distance(*(*VRunner)) << "." << endl);
 
     // remove baseline's endpoints and candidates
@@ -1124 +1170 @@
       DoeLog(1) && (eLog() << Verbose(1) << "External atoms inside of sphere at " << *(*VRunner) << ":" << endl);
       for (TesselPointList::const_iterator Runner = ListofPoints->begin(); Runner != ListofPoints->end(); ++Runner)
-        DoeLog(1) && (eLog() << Verbose(1) << "  " << *(*Runner) << endl);
+        DoeLog(1) && (eLog() << Verbose(1) << "  " << *(*Runner) << " at distance " << setprecision(13) << (*Runner)->node->distance(*(*VRunner)) << setprecision(6) << "." << endl);
+
+      // check with animate_sphere.tcl VMD script
+      if (ThirdPoint != NULL) {
+        DoeLog(1) && (eLog() << Verbose(1) << "Check by: animate_sphere 0 " << BaseLine->endpoints[0]->Nr + 1 << " " << BaseLine->endpoints[1]->Nr + 1 << " " << ThirdPoint->Nr + 1 << " " << RADIUS << " " << OldCenter[0] << " " << OldCenter[1] << " " << OldCenter[2] << " " << (*VRunner)->at(0) << " " << (*VRunner)->at(1) << " " << (*VRunner)->at(2) << endl);
+      } else {
+        DoeLog(1) && (eLog() << Verbose(1) << "Check by: ... missing third point ..." << endl);
+        DoeLog(1) && (eLog() << Verbose(1) << "Check by: animate_sphere 0 " << BaseLine->endpoints[0]->Nr + 1 << " " << BaseLine->endpoints[1]->Nr + 1 << " ??? " << RADIUS << " " << OldCenter[0] << " " << OldCenter[1] << " " << OldCenter[2] << " " << (*VRunner)->at(0) << " " << (*VRunner)->at(1) << " " << (*VRunner)->at(2) << endl);
+      }
     }
     delete (ListofPoints);
 
-    // check with animate_sphere.tcl VMD script
-    if (ThirdPoint != NULL) {
-      DoLog(1) && (Log() << Verbose(1) << "Check by: animate_sphere 0 " << BaseLine->endpoints[0]->Nr + 1 << " " << BaseLine->endpoints[1]->Nr + 1 << " " << ThirdPoint->Nr + 1 << " " << RADIUS << " " << OldCenter[0] << " " << OldCenter[1] << " " << OldCenter[2] << " " << (*VRunner)->at(0) << " " << (*VRunner)->at(1) << " " << (*VRunner)->at(2) << endl);
-    } else {
-      DoLog(1) && (Log() << Verbose(1) << "Check by: ... missing third point ..." << endl);
-      DoLog(1) && (Log() << Verbose(1) << "Check by: animate_sphere 0 " << BaseLine->endpoints[0]->Nr + 1 << " " << BaseLine->endpoints[1]->Nr + 1 << " ??? " << RADIUS << " " << OldCenter[0] << " " << OldCenter[1] << " " << OldCenter[2] << " " << (*VRunner)->at(0) << " " << (*VRunner)->at(1) << " " << (*VRunner)->at(2) << endl);
-    }
   }
   return flag;
@@ -3313 +3360 @@
                         }
                       } else {
-                        DoLog(1) && (Log() << Verbose(1) << "REJECT: Distance to center of circumcircle is not the same from each corner of the triangle: " << fabs(radius - otherradius) << endl);
+                        DoeLog(0) && (eLog() << Verbose(1) << "REJECT: Distance to center of circumcircle is not the same from each corner of the triangle: " << fabs(radius - otherradius) << endl);
                       }
                     } else {
@@ -4613 +4660 @@
 
   DoLog(0) && (Log() << Verbose(0) << "FindAllDegeneratedTriangles() found " << DegeneratedTriangles->size() << " triangles:" << endl);
-  IndexToIndex::iterator it;
-  for (it = DegeneratedTriangles->begin(); it != DegeneratedTriangles->end(); it++)
+  for (IndexToIndex::iterator it = DegeneratedTriangles->begin(); it != DegeneratedTriangles->end(); it++)
     DoLog(0) && (Log() << Verbose(0) << (*it).first << " => " << (*it).second << endl);
 
@@ -4632 +4678 @@
   int count = 0;
 
-  for (IndexToIndex::iterator TriangleKeyRunner = DegeneratedTriangles->begin(); TriangleKeyRunner != DegeneratedTriangles->end(); ++TriangleKeyRunner) {
+  // iterate over all degenerated triangles
+  for (IndexToIndex::iterator TriangleKeyRunner = DegeneratedTriangles->begin(); !DegeneratedTriangles->empty(); TriangleKeyRunner = DegeneratedTriangles->begin()) {
+    DoLog(0) && (Log() << Verbose(0) << "Checking presence of triangles " << TriangleKeyRunner->first << " and " << TriangleKeyRunner->second << "." << endl);
+    // both ways are stored in the map, only use one
+    if (TriangleKeyRunner->first > TriangleKeyRunner->second)
+      continue;
+
+    // determine from the keys in the map the two _present_ triangles
     finder = TrianglesOnBoundary.find(TriangleKeyRunner->first);
     if (finder != TrianglesOnBoundary.end())
       triangle = finder->second;
     else
-      break;
+      continue;
     finder = TrianglesOnBoundary.find(TriangleKeyRunner->second);
     if (finder != TrianglesOnBoundary.end())
       partnerTriangle = finder->second;
     else
-      break;
-
+      continue;
+
+    // determine which lines are shared by the two triangles
     bool trianglesShareLine = false;
     for (int i = 0; i < 3; ++i)