Changeset e1589e for src

Timestamp:

Jul 28, 2009, 1:02:51 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:

2319ed

Parents:

d4d0dd

Message:

Convex tesselation is now working also for heptan. But the convex hull of the bigger molecules is too small.

• GetBoundaryPoints(): Replaced Norm() by NormSquared where possible
• GetBoundaryPoints(): When throwing out points, comparison between height and MinDistance now takes MYEPSILON environment into account.
• Tesselation::TesselateOnBoundary(): BUGFIX - BaseLineCenter was calculated twice the sum of one endpoint not of either endpoint.
• Tesselation::TesselateOnBoundary(): We check if target and winner have same angle which of the two has angle close to desired propagation direction.

File:

• src/boundary.cpp (modified) (9 diffs)

src/boundary.cpp

@@ -319 +319 @@
     AngleReferenceNormalVector.x[(axis + 2) % NDIM] = 1.;
 
-    //*out << Verbose(1) << "Axisvector is " << AxisVector << " and AngleReferenceVector is " << AngleReferenceVector << ", and AngleReferenceNormalVector is " << AngleReferenceNormalVector << "." << endl;
+    *out << Verbose(1) << "Axisvector is " << AxisVector << " and AngleReferenceVector is " << AngleReferenceVector << ", and AngleReferenceNormalVector is " << AngleReferenceNormalVector << "." << endl;
 
     // 3b. construct set of all points, transformed into cylindrical system and with left and right neighbours
@@ -331 +331 @@
 
       // correct for negative side
-      radius = ProjectedVector.Norm();
+      radius = ProjectedVector.NormSquared();
       if (fabs(radius) > MYEPSILON)
         angle = ProjectedVector.Angle(&AngleReferenceVector);
@@ -341 +341 @@
         angle = 2. * M_PI - angle;
       }
-      //*out << Verbose(2) << "Inserting " << *Walker << ": (r, alpha) = (" << radius << "," << angle << "): " << ProjectedVector << endl;
-      BoundaryTestPair = BoundaryPoints[axis].insert(BoundariesPair(angle,
-          DistancePair (radius, Walker)));
-      if (BoundaryTestPair.second) { // successfully inserted
-      } else { // same point exists, check first r, then distance of original vectors to center of gravity
+      *out << Verbose(2) << "Inserting " << *Walker << ": (r, alpha) = (" << radius << "," << angle << "): " << ProjectedVector << endl;
+      BoundaryTestPair = BoundaryPoints[axis].insert(BoundariesPair(angle, DistancePair (radius, Walker)));
+      if (!BoundaryTestPair.second) { // same point exists, check first r, then distance of original vectors to center of gravity
         *out << Verbose(2) << "Encountered two vectors whose projection onto axis " << axis << " is equal: " << endl;
-        *out << Verbose(2) << "Present vector: " << BoundaryTestPair.first->second.second->x << endl;
-        *out << Verbose(2) << "New vector: " << Walker << endl;
-        double tmp = ProjectedVector.Norm();
-        if (tmp > BoundaryTestPair.first->second.first) {
+        *out << Verbose(2) << "Present vector: " << *BoundaryTestPair.first->second.second << endl;
+        *out << Verbose(2) << "New vector: " << *Walker << endl;
+        double tmp = ProjectedVector.NormSquared();
+        if ((tmp - BoundaryTestPair.first->second.first) > MYEPSILON) {
           BoundaryTestPair.first->second.first = tmp;
           BoundaryTestPair.first->second.second = Walker;
-          *out << Verbose(2) << "Keeping new vector." << endl;
-        } else if (tmp == BoundaryTestPair.first->second.first) {
+          *out << Verbose(2) << "Keeping new vector due to larger projected distance " << tmp << "." << endl;
+        } else if (fabs(tmp - BoundaryTestPair.first->second.first) < MYEPSILON) {
           helper.CopyVector(&Walker->x);
           helper.SubtractVector(MolCenter);
-          if (BoundaryTestPair.first->second.second->x.ScalarProduct(&BoundaryTestPair.first->second.second->x) < helper.ScalarProduct(&helper)) { // Norm() does a sqrt, which makes it a lot slower
+          tmp = helper.NormSquared();
+          helper.CopyVector(&BoundaryTestPair.first->second.second->x);
+          helper.SubtractVector(MolCenter);
+          if (helper.NormSquared() < tmp) {
             BoundaryTestPair.first->second.second = Walker;
-            *out << Verbose(2) << "Keeping new vector." << endl;
+            *out << Verbose(2) << "Keeping new vector due to larger distance to molecule center " << helper.NormSquared() << "." << endl;
           } else {
-            *out << Verbose(2) << "Keeping present vector." << endl;
+            *out << Verbose(2) << "Keeping present vector due to larger distance to molecule center " << tmp << "." << endl;
           }
         } else {
-          *out << Verbose(2) << "Keeping present vector." << endl;
+          *out << Verbose(2) << "Keeping present vector due to larger projected distance " << tmp << "." << endl;
         }
       }
@@ -446 +447 @@
           double MinDistance = a * sin(beta) / (sin(delta)) * (((alpha < M_PI / 2.) || (gamma < M_PI / 2.)) ? 1. : -1.);
           //*out << Verbose(2) << " I calculated: a = " << a << ", h = " << h << ", beta(" << left->second.second->Name << "," << left->second.second->Name << "-" << right->second.second->Name << ") = " << beta << ", delta(" << left->second.second->Name << "," << runner->second.second->Name << ") = " << delta << ", Min = " << MinDistance << "." << endl;
-          //*out << Verbose(1) << "Checking CoG distance of runner " << *runner->second.second << " " << h << " against triangle's side length spanned by (" << *left->second.second << "," << *right->second.second << ") of " << MinDistance << "." << endl;
-          if ((fabs(h / fabs(h) - MinDistance / fabs(MinDistance)) < MYEPSILON) && (h < MinDistance)) {
+          *out << Verbose(1) << "Checking CoG distance of runner " << *runner->second.second << " " << h << " against triangle's side length spanned by (" << *left->second.second << "," << *right->second.second << ") of " << MinDistance << "." << endl;
+          if ((fabs(h / fabs(h) - MinDistance / fabs(MinDistance)) < MYEPSILON) && ((h - MinDistance)) < -MYEPSILON) {
             // throw out point
-            //*out << Verbose(1) << "Throwing out " << *runner->second.second << "." << endl;
+            *out << Verbose(1) << "Throwing out " << *runner->second.second << "." << endl;
             BoundaryPoints[axis].erase(runner);
             flag = true;
@@ -1191 +1192 @@
   class BoundaryPointSet *peak = NULL;
   double SmallestAngle, TempAngle;
-  Vector NormalVector, VirtualNormalVector, CenterVector, TempVector, PropagationVector, *MolCenter = NULL;
+  Vector NormalVector, VirtualNormalVector, CenterVector, TempVector, helper, PropagationVector, *MolCenter = NULL;
   LineMap::iterator LineChecker[2];
 
@@ -1213 +1214 @@
         Vector BaseLineCenter, BaseLine;
         BaseLineCenter.CopyVector(&baseline->second->endpoints[0]->node->x);
-        BaseLineCenter.AddVector(&baseline->second->endpoints[0]->node->x);
+        BaseLineCenter.AddVector(&baseline->second->endpoints[1]->node->x);
         BaseLineCenter.Scale(1. / 2.); // points now to center of base line
         BaseLine.CopyVector(&baseline->second->endpoints[0]->node->x);
@@ -1253 +1254 @@
             VirtualNormalVector.ProjectOntoPlane(&NormalVector);
             TempAngle = VirtualNormalVector.Angle(&PropagationVector);
+            *out << Verbose(4) << "VirtualNormalVector is " << VirtualNormalVector << " and PropagationVector is " << PropagationVector << "." << endl;
             if (TempAngle > (M_PI/2.)) { // no bends bigger than Pi/2 (90 degrees)
               *out << Verbose(4) << "Angle on triangle plane between propagation direction and base line to " << *(target->second) << " is " << TempAngle << ", bad direction!" << endl;
@@ -1274 +1276 @@
             if ((((LineChecker[0] != baseline->second->endpoints[0]->lines.end()) && (LineChecker[1] != baseline->second->endpoints[1]->lines.end()) && (GetCommonEndpoint(LineChecker[0]->second, LineChecker[1]->second) == peak)))) {
               *out << Verbose(4) << "Current target is peak!" << endl;
+              continue;
+            }
+
+            // check for linear dependence
+            TempVector.CopyVector(&baseline->second->endpoints[0]->node->x);
+            TempVector.SubtractVector(&target->second->node->x);
+            helper.CopyVector(&baseline->second->endpoints[1]->node->x);
+            helper.SubtractVector(&target->second->node->x);
+            helper.ProjectOntoPlane(&TempVector);
+            if (fabs(helper.NormSquared()) < MYEPSILON) {
+              *out << Verbose(4) << "Chosen set of vectors is linear dependent." << endl;
               continue;
             }
@@ -1291 +1304 @@
             TempAngle = NormalVector.Angle(&VirtualNormalVector);
             *out << Verbose(4) << "NormalVector is " << VirtualNormalVector << " and the angle is " << TempAngle << "." << endl;
-            if (SmallestAngle > TempAngle) { // set to new possible winner
+            if ((SmallestAngle - TempAngle) > MYEPSILON) { // set to new possible winner
               SmallestAngle = TempAngle;
               winner = target;
-            }
+              *out << Verbose(4) << "New winner " << *winner->second->node << " due to smaller angle between normal vectors." << endl;
+            } else if (fabs(SmallestAngle - TempAngle) < MYEPSILON) { // check the angle to propagation, both possible targets are in one plane! (their normals have same angle)
+              // hence, check the angles to some normal direction from our base line but in this common plane of both targets...
+              helper.CopyVector(&target->second->node->x);
+              helper.SubtractVector(&BaseLineCenter);
+              helper.ProjectOntoPlane(&BaseLine);
+              // ...the one with the smaller angle is the better candidate
+              TempVector.CopyVector(&target->second->node->x);
+              TempVector.SubtractVector(&BaseLineCenter);
+              TempVector.ProjectOntoPlane(&VirtualNormalVector);
+              TempAngle = TempVector.Angle(&helper);
+              TempVector.CopyVector(&winner->second->node->x);
+              TempVector.SubtractVector(&BaseLineCenter);
+              TempVector.ProjectOntoPlane(&VirtualNormalVector);
+              if (TempAngle < TempVector.Angle(&helper)) {
+                TempAngle = NormalVector.Angle(&VirtualNormalVector);
+                SmallestAngle = TempAngle;
+                winner = target;
+                *out << Verbose(4) << "New winner " << *winner->second->node << " due to smaller angle " << TempAngle << " to propagation direction." << endl;
+              } else
+                *out << Verbose(4) << "Keeping old winner " << *winner->second->node << " due to smaller angle to propagation direction." << endl;
+            } else
+              *out << Verbose(4) << "Keeping old winner " << *winner->second->node << " due to smaller angle between normal vectors." << endl;
           }
         } // end of loop over all boundary points