Changeset 87e2735 for src

Timestamp:

Jul 28, 2008, 2:18:25 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:

683914

Parents:

b61043

Message:

CyclicStructureAnalysis: BUGFIX - MinimumRingSize was not set correctly

• During BFS search from non-loop members to loops, Walker was pushed instead of Root at start of BFS
• if Backedge lead to a terminal hydrogen, this hydrogen ended up with AtomCount MinimumRingSize instead of correct one.

File:

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

src/molecules.cpp

@@ -1888 +1888 @@
       // walk through all and set MinimumRingSize
       Walker = Root;
+      MinimumRingSize[Walker->GetTrueFather()->nr] = RingSize;
       while (Walker != BackEdge->rightatom) {
         Walker = PredecessorList[Walker->nr];
@@ -1914 +1915 @@
       
       if (MinimumRingSize[Root->GetTrueFather()->nr] == AtomCount) { // check whether MinimumRingSize is set, if not BFS to next where it is
+        Walker = Root;
         ShortestPathList[Walker->nr] = 0;
         BFSStack->ClearStack();  // start with empty BFS stack
@@ -1920 +1922 @@
         //*out << Verbose(1) << "---------------------------------------------------------------------------------------------------------" << endl;
         OtherAtom = Walker;
-        while ((Walker != Root) && (OtherAtom != NULL)) {  // look for Root
+        while (OtherAtom != NULL) {  // look for Root
           Walker = BFSStack->PopFirst();
           //*out << Verbose(2) << "Current Walker is " << *Walker << ", we look for SP to Root " << *Root << "." << endl;
           for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) {
             Binder = ListOfBondsPerAtom[Walker->nr][i];
-            if (Binder != BackEdge) { // only walk along DFS spanning tree (otherwise we always find SP of one being backedge Binder)
+            if ((Binder != BackEdge) || (NumberOfBondsPerAtom[Walker->nr] == 1)) { // only walk along DFS spanning tree (otherwise we always find SP of 1 being backedge Binder), but terminal hydrogens may be connected via backedge, hence extra check
               OtherAtom = Binder->GetOtherAtom(Walker);
               //*out << Verbose(2) << "Current OtherAtom is: " << OtherAtom->Name << " for bond " << *Binder << "." << endl;