Changeset ad85c2 for src

Timestamp:

Oct 10, 2008, 1:32:33 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:

fcbfc8

Parents:

df793a

Message:

BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in output even if no candidate had been found

+ If no Candidate has been found, output message would declare to be unable to correct bond degree for a unspecified bond (CandidateBondNo set to no sensible value)

File:

• src/molecules.cpp (modified) (2 diffs)

src/molecules.cpp

@@ -2470 +2470 @@
           if ((int)(Walker->type->NoValenceOrbitals) > NoBonds) { // we have a mismatch, check all bonding partners for mismatch
             Candidate = NULL;
+            CandidateBondNo = -1;
             for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) { // go through each of its bond partners
               OtherWalker = ListOfBondsPerAtom[Walker->nr][i]->GetOtherAtom(Walker);
@@ -2485 +2486 @@
                     }
                   }
-            if (Candidate != NULL) {
+            if ((Candidate != NULL) && (CandidateBondNo != -1)) {
               ListOfBondsPerAtom[Walker->nr][CandidateBondNo]->BondDegree++;
               *out << Verbose(2) << "Increased bond degree for bond " << *ListOfBondsPerAtom[Walker->nr][CandidateBondNo] << "." << endl;
             } else
-              *out << Verbose(2) << "Could not find correct degree for bond " << *ListOfBondsPerAtom[Walker->nr][CandidateBondNo] << "." << endl;
+              *out << Verbose(2) << "Could not find correct degree for atom " << *Walker << "." << endl;
               FalseBondDegree++;
           }