Changeset bdb143 for src/tesselation.cpp

Timestamp:

Jun 28, 2010, 3:38:05 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:

13892b, 51a5c8

Parents:

b2531f (diff), c39cc4 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (06/28/10 14:53:18)

git-committer:

Frederik Heber <heber@…> (06/28/10 15:38:05)

Message:

Merge branch 'StructureRefactoring' into stable

Conflicts:

molecuilder/src/analysis_bonds.cpp
molecuilder/src/analysis_bonds.hpp
molecuilder/src/builder.cpp
molecuilder/src/unittests/Makefile.am
molecuilder/src/unittests/TestRunnerMain.cpp

• TESTFIX: Tesselations/heptan - Due to different implementations of GetCircumCenter() sequence of triangles nodes has changed in degenerate case
• TESTFIX: Tesselation/1-3 - Due to convexity criterion fourth argument (i.e. the value at the node) has changed.

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

File:

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

src/tesselation.cpp

@@ -231 +231 @@
 {
   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
@@ -279 +297 @@
   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);
 }
 
@@ -304 +316 @@
 /** 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
@@ -315 +327 @@
   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;
 }
 ;
@@ -661 +689 @@
 ;
 
+/** 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.
@@ -1110 +1156 @@
     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
@@ -1128 +1174 @@
       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;
@@ -3290 +3337 @@
                         }
                       } 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 {
@@ -4590 +4637 @@
 
   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);
 
@@ -4609 +4655 @@
   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)