Changeset 65de9b

Timestamp:

Oct 17, 2008, 1:24:10 PM (16 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:

450d63

Parents:

4ee3df

Message:

molecule::PickLocalBackEdges(): BUGFIX: if Walker as not in subgraph, next candidate wasn't popped from stack due to wrong brackets of if clause.

This caused to loop to run indefinitely (hence, the new output messages for the functions in molecule::FragmentMolecule(). It is fixed.

File:

• src/molecules.cpp (modified) (3 diffs)

src/molecules.cpp

@@ -2942 +2942 @@
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
-    *out << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     LocalBackEdgeStack = new StackClass<bond *> (MolecularWalker->Leaf->BondCount);
 //    // check the list of local atoms for debugging
@@ -2951 +2950 @@
 //      else
 //        *out << "\t" << ListOfLocalAtoms[FragmentCounter][i]->Name;
+    *out << Verbose(0) << "Gathering local back edges for subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     MolecularWalker->Leaf->PickLocalBackEdges(out, ListOfLocalAtoms[FragmentCounter++], BackEdgeStack, LocalBackEdgeStack);
+    *out << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     MolecularWalker->Leaf->CyclicStructureAnalysis(out, LocalBackEdgeStack, MinimumRingSize);
+    *out << Verbose(0) << "Done with Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     delete(LocalBackEdgeStack);
   }
@@ -3094 +3096 @@
   do {  // go through all bonds and push local ones
     Walker = ListOfLocalAtoms[Binder->leftatom->nr];  // get one atom in the reference molecule
-    if (Walker == NULL) // if this Walker exists in the subgraph ... 
-      continue;
-    for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) {    // go through the local list of bonds
-      OtherAtom = ListOfBondsPerAtom[Walker->nr][i]->GetOtherAtom(Walker);
-      if (OtherAtom == ListOfLocalAtoms[Binder->rightatom->nr]) { // found the bond
-        LocalStack->Push(ListOfBondsPerAtom[Walker->nr][i]);
-        break;
-      }
-    }
+    if (Walker != NULL) // if this Walker exists in the subgraph ... 
+        for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) {    // go through the local list of bonds
+        OtherAtom = ListOfBondsPerAtom[Walker->nr][i]->GetOtherAtom(Walker);
+              if (OtherAtom == ListOfLocalAtoms[Binder->rightatom->nr]) { // found the bond
+              LocalStack->Push(ListOfBondsPerAtom[Walker->nr][i]);
+                                        *out << Verbose(3) << "Found local edge " << *(ListOfBondsPerAtom[Walker->nr][i]) << "." << endl;
+                break;
+            }
+        }
     Binder = ReferenceStack->PopFirst();  // loop the stack for next item
+                *out << Verbose(3) << "Current candidate edge " << Binder << "." << endl;
     ReferenceStack->Push(Binder);
   } while (FirstBond != Binder);