Changeset 8dbcaf for src/Graph/DepthFirstSearchAnalysis.cpp

Timestamp:

Oct 14, 2013, 11:42:03 PM (11 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:

fe0cb8

Parents:

fb9f6d

git-author:

Frederik Heber <heber@…> (09/24/13 12:32:02)

git-committer:

Frederik Heber <heber@…> (10/14/13 23:42:03)

Message:

FIX: CyclicStructureAnalysis did not work correctly.

• many errors with local variables that probably should have been in the class.
• we use OtherAtom in subsequent RetrieveCycleMembers() but we have not given CyclicBFSFromRootToRoot() its ref.
• the idea now is to use first get all cycles (CyclicBFSFromRootToRoot(). RetrieveCycleMembers()) and then to assign all remaining atoms via AssignRingSizetoNonCycleMembers() with BFSToNextCycle() where we make use of locality property of BFS.

File:

• src/Graph/DepthFirstSearchAnalysis.cpp (modified) (3 diffs)

src/Graph/DepthFirstSearchAnalysis.cpp

@@ -130 +130 @@
     return false;
   }
-  bond::ptr Binder = BackEdgeStack.front();
-  bond::ptr FirstBond = Binder; // mark the first bond, so that we don't loop through the stack indefinitely
-  atom *Walker = NULL, *OtherAtom = NULL;
+  std::deque<bond::ptr > MyBackEdgeStack = BackEdgeStack;
 
   do { // go through all bonds and push local ones
+    const bond::ptr &Binder = MyBackEdgeStack.front(); // loop the stack for next item
+    MyBackEdgeStack.pop_front();
+    LOG(3, "INFO: Current candidate edge " << *Binder << ".");
     const ListOfLocalAtoms_t::const_iterator leftiter = ListOfLocalAtoms.find(Binder->leftatom->getNr());
     ASSERT( leftiter != ListOfLocalAtoms.end(),
         "DepthFirstSearchAnalysis::PickLocalBackEdges() - could not find atom id "
         +toString(Binder->leftatom->getNr())+" in ListOfLocalAtoms.");
-    Walker = leftiter->second; // get one atom in the reference molecule
+    atom * const Walker = leftiter->second; // get one atom in the reference molecule
     if (Walker != NULL) { // if this Walker exists in the subgraph ...
       const BondList& ListOfBonds = Walker->getListOfBonds();
@@ -145 +146 @@
           Runner != ListOfBonds.end();
           ++Runner) {
-        OtherAtom = (*Runner)->GetOtherAtom(Walker);
+        atom * const OtherAtom = (*Runner)->GetOtherAtom(Walker);
         const ListOfLocalAtoms_t::const_iterator rightiter = ListOfLocalAtoms.find((*Runner)->rightatom->getNr());
         if (OtherAtom == rightiter->second) { // found the bond
@@ -154 +155 @@
       }
     }
-    ASSERT(!BackEdgeStack.empty(), "DepthFirstSearchAnalysis::PickLocalBackEdges() - ReferenceStack is empty!");
-    Binder = BackEdgeStack.front(); // loop the stack for next item
-    LOG(3, "Current candidate edge " << Binder << ".");
-  } while (FirstBond != Binder);
+  } while (!MyBackEdgeStack.empty());
 
   return status;