Changeset abb641 for src

Timestamp:

Aug 9, 2013, 2:26:27 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:

3e93bd4

Parents:

d067e35

git-author:

Frederik Heber <heber@…> (07/11/13 21:19:24)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:26:27)

Message:

FIX: AdjacencyList missed atoms without bonds.

• this caused an arbitrary number of argon atoms to have just a single fragment.

File:

• src/Graph/AdjacencyList.cpp (modified) (1 diff)

src/Graph/AdjacencyList.cpp

@@ -134 +134 @@
         +" is not associated to any of World's atoms.");
     const BondList& ListOfBonds = Walker->getListOfBonds();
-    // go through each of its bonds
-    for (BondList::const_iterator Runner = ListOfBonds.begin();
-        Runner != ListOfBonds.end();
-        ++Runner) {
-      const atomId_t id = (*Runner)->GetOtherAtom(Walker)->getId();
-      ASSERT(id != (size_t)-1,
-          "AdjacencyList::CreateMap() - OtherAtom has not id.");
-      if (std::binary_search(atomids.begin(), atomids.end(), id))
-        atombondmap.insert( std::make_pair(WalkerId, id) );
+    if (ListOfBonds.size() > 0) {
+      // go through each of its bonds
+      for (BondList::const_iterator Runner = ListOfBonds.begin();
+          Runner != ListOfBonds.end();
+          ++Runner) {
+        const atomId_t id = (*Runner)->GetOtherAtom(Walker)->getId();
+        ASSERT(id != (size_t)-1,
+            "AdjacencyList::CreateMap() - OtherAtom has not id.");
+        if (std::binary_search(atomids.begin(), atomids.end(), id))
+          atombondmap.insert( std::make_pair(WalkerId, id) );
+      }
+    } else {
+      // insert self-bond if atom is lonesome cowboy
+      atombondmap.insert( std::make_pair(WalkerId, WalkerId) );
     }
   }