Changeset 683914

Timestamp:

Jul 28, 2008, 2:41:22 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:

41baaf

Parents:

87e2735

Message:

CyclicStructureAnalysis: BUGFIX - MinimumRingSize of non-loop atoms was wrong

• new bool atom:IsCyclic states whether atoms is part of a cycle or not, this is set in CyclicStructureAnalysis()
• MinimumRingSize was set to MinimumRingSize plus ShortestPath thereto. This gives correct results only if this goes to a loop-member. However the if-condition was phrased in such a manner, that it became possible that non-loop members (with MinimumRingSize set below AtomCount) would now also be regarded als loop members. This is sort of a triangle inequality problem :), path of A to B plus path from B to C is probably not the same as path from A to C in terms of length

Location:

src

Files:

• atom.cpp (modified) (1 diff)
• molecules.cpp (modified) (2 diffs)
• molecules.hpp (modified) (1 diff)

src/atom.cpp

@@ -24 +24 @@
   GraphNr = -1;
   ComponentNr = NULL;
+  IsCyclic = false;
   SeparationVertex = false;
   LowpointNr = -1;

src/molecules.cpp

@@ -1878 +1878 @@
       NumCycles++;
       RingSize = 1;
-      Walker = Root;
+      Root->GetTrueFather()->IsCyclic = true;
       *out << Verbose(1) << "Found ring contains: ";
       while (Walker != BackEdge->rightatom) {
         *out << Walker->Name << " <-> ";
         Walker = PredecessorList[Walker->nr];
+        Walker->GetTrueFather()->IsCyclic = true;
         RingSize++;
       }
@@ -1936 +1937 @@
                 ShortestPathList[OtherAtom->nr] = ShortestPathList[Walker->nr]+1;
                 //*out << Verbose(2) << "Coloring OtherAtom " << OtherAtom->Name << " lightgray, its predecessor is " << Walker->Name << " and its Shortest Path is " << ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl;
-                if (MinimumRingSize[OtherAtom->GetTrueFather()->nr] != AtomCount) { // if the other atom is connected to a ring
+                if (OtherAtom->GetTrueFather()->IsCyclic) { // if the other atom is connected to a ring
                   MinimumRingSize[Root->GetTrueFather()->nr] = ShortestPathList[OtherAtom->nr]+MinimumRingSize[OtherAtom->GetTrueFather()->nr];
                   OtherAtom = NULL; //break;

src/molecules.hpp

@@ -100 +100 @@
     int *ComponentNr;//!< belongs to this nonseparable components, given in DepthFirstSearchAnalysis() (if more than one, then is SeparationVertex)
     int LowpointNr; //!< needed in DepthFirstSearchAnalysis() to detect nonseparable components, is the lowest possible number of an atom to reach via tree edges only followed by at most one back edge.
-    bool SeparationVertex; //!< whether this atom separates off subsets of atoms or not, given in DepthFirstSearchAnalysis()
+    bool SeparationVertex; //!< whether this atom separates off subsets of atoms or not, determined in DepthFirstSearchAnalysis()
+    bool IsCyclic;        //!< whether atom belong to as cycle or not, determined in DepthFirstSearchAnalysis()
     unsigned char AdaptiveOrder;  //!< current present bond order at site (0 means "not set")