Changeset 6fe4f7 for src/UIElements/Views

Timestamp:

Aug 5, 2015, 5:32:13 PM (9 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:

d07a38

Parents:

ec8471

git-author:

Frederik Heber <heber@…> (08/04/15 13:53:52)

git-committer:

Frederik Heber <heber@…> (08/05/15 17:32:13)

Message:

FIX: updateBoundingBox() must not call molecule::getBoundingBox() on every update.

• this is O(N^{2). We now update by using the current center and radius and looking at the last changed atom's position. This diverges with respect to the radius after some time. Hence, a true getBoundingBox() should be called after a while.}

Location:

src/UIElements/Views/Qt4/Qt3D

Files:

• GLMoleculeObject_molecule.cpp (modified) (3 diffs)
• GLMoleculeObject_molecule.hpp (modified) (1 diff)

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp

@@ -143 +143 @@
       BoundingBoxUpdater,
       "MoleculeBoundingBox_"+toString(_molid),
-      updateBoundingBox(),
+      initBoundingBox(),
       BoundingBoxChannels),
   PresentAtoms(
@@ -220 +220 @@
       BoundingBoxUpdater,
       "MoleculeBoundingBox_"+toString(_molid),
-      updateBoundingBox(),
+      initBoundingBox(),
       BoundingBoxChannels),
   PresentAtoms(
@@ -403 +403 @@
 }
 
+GLMoleculeObject_molecule::BoundingBoxInfo GLMoleculeObject_molecule::initBoundingBox() const
+{
+  BoundingBoxInfo info;
+  info.position = zeroVec;
+  info.radius = 0.;
+  return info;
+}
+
 GLMoleculeObject_molecule::BoundingBoxInfo GLMoleculeObject_molecule::updateBoundingBox() const
 {
-  BoundingBoxInfo info;
+  BoundingBoxInfo info = BoundingBox.get();
   const molecule * const _molecule = getMolecule(MolIndex.get());
   if (_molecule != NULL) {
-    Shape shape = _molecule->getBoundingSphere();
-    info.position = shape.getCenter();
-    info.radius = shape.getRadius();
+    // just update the position and radius by looking at the last atom
+    int atomcount = _molecule->getAtomCount();
+    atomId_t lastatomid = _molecule->lastChangedAtomId();
+    const atom * const lastatom =
+        const_cast<const World &>(World::getInstance()).getAtom(AtomById(lastatomid));
+    if (lastatom != NULL) {
+      const Vector oldcenter = info.position;
+      const double oldradius = info.radius;
+      // update position: center is exactly updated
+      Vector newcenter = (double)(atomcount-1) * oldcenter;
+      newcenter += lastatom->getPosition();
+      newcenter *= 1./(double)atomcount;
+      info.position = newcenter;
+      // update radius: radius is always larger than exact update
+      double newradius = newcenter.DistanceSquared(lastatom->getPosition());
+      double oldupdatedradius = oldradius*oldradius + (newcenter - oldcenter).NormSquared();
+      info.radius = sqrt( std::max(newradius, oldupdatedradius) );
+    }
   } else
     ELOG(2, "GLMoleculeObject_molecule cannot updateBoundingBox, molecule with "

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp

@@ -125 +125 @@
   };
 
+  BoundingBoxInfo initBoundingBox() const;
+
   QGeometryData updateTesselationHull() const;
   BoundingBoxInfo updateBoundingBox() const;