Changeset b32dbb for src/tesselationhelpers.cpp

Timestamp:

May 29, 2010, 12:59:31 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, 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/tesselationhelpers.cpp (modified) (6 diffs)

src/tesselationhelpers.cpp

@@ -10 +10 @@
 #include "info.hpp"
 #include "linkedcell.hpp"
+#include "linearsystemofequations.hpp"
 #include "log.hpp"
 #include "tesselation.hpp"
@@ -182 +183 @@
   beta = M_PI - SideC.Angle(SideA);
   gamma = M_PI - SideA.Angle(SideB);
-  //Log() << Verbose(1) << "INFO: alpha = " << alpha/M_PI*180. << ", beta = " << beta/M_PI*180. << ", gamma = " << gamma/M_PI*180. << "." << endl;
+  Log() << Verbose(1) << "INFO: alpha = " << alpha/M_PI*180. << ", beta = " << beta/M_PI*180. << ", gamma = " << gamma/M_PI*180. << "." << endl;
   if (fabs(M_PI - alpha - beta - gamma) > HULLEPSILON) {
     DoeLog(2) && (eLog()<< Verbose(2) << "GetCenterofCircumcircle: Sum of angles " << (alpha+beta+gamma)/M_PI*180. << " > 180 degrees by " << fabs(M_PI - alpha - beta - gamma)/M_PI*180. << "!" << endl);
@@ -195 +196 @@
   (*Center) += helper;
   Center->Scale(1./(sin(2.*alpha) + sin(2.*beta) + sin(2.*gamma)));
+  Log() << Verbose(1) << "INFO: Center (1st algo) is at " << *Center << "." << endl;
+
+//  LinearSystemOfEquations LSofEq(NDIM,NDIM);
+//  double *matrix = new double[NDIM*NDIM];
+//  matrix[0] = 0.;
+//  matrix[1] = a.DistanceSquared(b);
+//  matrix[2] = a.DistanceSquared(c);
+//  matrix[3] = a.DistanceSquared(b);
+//  matrix[4] = 0.;
+//  matrix[5] = b.DistanceSquared(c);
+//  matrix[6] = a.DistanceSquared(c);
+//  matrix[7] = b.DistanceSquared(c);
+//  matrix[8] = 0.;
+//  cout << "Matrix is: ";
+//  for (int i=0;i<NDIM*NDIM;i++)
+//    cout << matrix[i] << "\t";
+//  cout << endl;
+//  LSofEq.SetA(matrix);
+//  delete[](matrix);
+//  LSofEq.Setb(new Vector(1.,1.,1.));
+//  LSofEq.SetSymmetric(true);
+//  helper.Zero();
+//  if (!LSofEq.GetSolutionAsVector(helper)) {
+//    DoLog(0) && (eLog()<< Verbose(0) << "Could not solve the linear system in GetCenterofCircumCircle()!" << endl);
+//  }
+//  cout << "Solution is " << helper << endl;
+  // is equivalent to the three lines below
+  helper[0] = SideA.NormSquared()*(SideB.NormSquared()+SideC.NormSquared() - SideA.NormSquared());
+  helper[1] = SideB.NormSquared()*(SideC.NormSquared()+SideA.NormSquared() - SideB.NormSquared());
+  helper[2] = SideC.NormSquared()*(SideA.NormSquared()+SideB.NormSquared() - SideC.NormSquared());
+
+  Center->Zero();
+  *Center += helper[0] * a;
+  *Center += helper[1] * b;
+  *Center += helper[2] * c;
+  Center->Scale(1./(helper[0]+helper[1]+helper[2]));
+  Log() << Verbose(1) << "INFO: Center (2nd algo) is at " << *Center << "." << endl;
 };
 
@@ -416 +454 @@
 /** Calculates the volume of a general tetraeder.
  * \param *a first vector
- * \param *a first vector
- * \param *a first vector
- * \param *a first vector
+ * \param *b second vector
+ * \param *c third vector
+ * \param *d fourth vector
  * \return \f$ \frac{1}{6} \cdot ((a-d) \times (a-c) \cdot  (a-b)) \f$
  */
@@ -436 +474 @@
   volume = 1./6. * fabs(Point.ScalarProduct(TetraederVector[2]));
   return volume;
+};
+
+/** Calculates the area of a general triangle.
+ * We use the Heron's formula of area, [Bronstein, S. 138]
+ * \param &A first vector
+ * \param &B second vector
+ * \param &C third vector
+ * \return \f$ \frac{1}{6} \cdot ((a-d) \times (a-c) \cdot  (a-b)) \f$
+ */
+double CalculateAreaofGeneralTriangle(const Vector &A, const Vector &B, const Vector &C)
+{
+  Info FunctionInfo(__func__);
+
+  const double sidea = B.distance(C);
+  const double sideb = A.distance(C);
+  const double sidec = A.distance(B);
+  const double s = (sidea+sideb+sidec)/2.;
+
+  const double area = sqrt(s*(s-sidea)*(s-sideb)*(s-sidec));
+  return area;
 };
 
@@ -870 +928 @@
   class BoundaryPointSet *point = NULL;
   class BoundaryLineSet *line = NULL;
-
-  // calculate remaining concavity
+  class BoundaryTriangleSet *triangle = NULL;
+  double ConcavityPerLine = 0.;
+  double ConcavityPerTriangle = 0.;
+  double area = 0.;
+  double totalarea = 0.;
+
   for (PointMap::const_iterator PointRunner = TesselStruct->PointsOnBoundary.begin(); PointRunner != TesselStruct->PointsOnBoundary.end(); PointRunner++) {
     point = PointRunner->second;
     DoLog(1) && (Log() << Verbose(1) << "INFO: Current point is " << *point << "." << endl);
-    point->value = 0;
+
+    // calculate mean concavity over all connected line
+    ConcavityPerLine = 0.;
     for (LineMap::iterator LineRunner = point->lines.begin(); LineRunner != point->lines.end(); LineRunner++) {
       line = LineRunner->second;
       //Log() << Verbose(1) << "INFO: Current line of point " << *point << " is " << *line << "." << endl;
-      if (!line->CheckConvexityCriterion())
-        point->value += 1;
-    }
-  }
-};
-
+      ConcavityPerLine -= line->CalculateConvexity();
+    }
+    ConcavityPerLine /= point->lines.size();
+
+    // weigh with total area of the surrounding triangles
+    totalarea  = 0.;
+    TriangleSet *triangles = TesselStruct->GetAllTriangles(PointRunner->second);
+    for (TriangleSet::iterator TriangleRunner = triangles->begin(); TriangleRunner != triangles->end(); ++TriangleRunner) {
+      totalarea += CalculateAreaofGeneralTriangle(*(*TriangleRunner)->endpoints[0]->node->node, *(*TriangleRunner)->endpoints[1]->node->node, *(*TriangleRunner)->endpoints[2]->node->node);
+    }
+    ConcavityPerLine *= totalarea;
+
+    // calculate mean concavity over all attached triangles
+    ConcavityPerTriangle = 0.;
+    for (TriangleSet::const_iterator TriangleRunner = triangles->begin(); TriangleRunner != triangles->end(); ++TriangleRunner) {
+      line = (*TriangleRunner)->GetThirdLine(PointRunner->second);
+      triangle = line->GetOtherTriangle(*TriangleRunner);
+      area = CalculateAreaofGeneralTriangle(*triangle->endpoints[0]->node->node, *triangle->endpoints[1]->node->node, *triangle->endpoints[2]->node->node);
+      area += CalculateAreaofGeneralTriangle(*(*TriangleRunner)->endpoints[0]->node->node, *(*TriangleRunner)->endpoints[1]->node->node, *(*TriangleRunner)->endpoints[2]->node->node);
+      area *= -line->CalculateConvexity();
+      if (area > 0)
+        ConcavityPerTriangle += area;
+//      else
+//        ConcavityPerTriangle -= area;
+    }
+    ConcavityPerTriangle /= triangles->size()/totalarea;
+    delete(triangles);
+
+    // add up
+    point->value = ConcavityPerLine + ConcavityPerTriangle;
+  }
+};
+
+
+
+/** Calculates the concavity for each of the BoundaryPointSet's in a Tesselation.
+ * Sets BoundaryPointSet::value equal to the nearest distance to convex envelope.
+ * \param *out output stream for debugging
+ * \param *TesselStruct pointer to Tesselation structure
+ * \param *Convex pointer to convex Tesselation structure as reference
+ */
+void CalculateConstrictionPerBoundaryPoint(const Tesselation * const TesselStruct, const Tesselation * const Convex)
+{
+  Info FunctionInfo(__func__);
+  double distance = 0.;
+
+  for (PointMap::const_iterator PointRunner = TesselStruct->PointsOnBoundary.begin(); PointRunner != TesselStruct->PointsOnBoundary.end(); PointRunner++) {
+    DoeLog(1) && (eLog() << Verbose(1) << "INFO: Current point is " << * PointRunner->second << "." << endl);
+
+    distance = 0.;
+    for (TriangleMap::const_iterator TriangleRunner = Convex->TrianglesOnBoundary.begin(); TriangleRunner != Convex->TrianglesOnBoundary.end(); TriangleRunner++) {
+      const double CurrentDistance = Convex->GetDistanceSquaredToTriangle(*PointRunner->second->node->node, TriangleRunner->second);
+      if (CurrentDistance < distance)
+        distance = CurrentDistance;
+    }
+
+    PointRunner->second->value = distance;
+  }
+};
 
 /** Checks whether each BoundaryLineSet in the Tesselation has two triangles.