Changeset 28e203 for src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp

Timestamp:

Dec 14, 2012, 5:39:42 PM (13 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

91a565

Parents:

d058e6

git-author:

Frederik Heber <heber@…> (09/28/12 16:22:03)

git-committer:

Frederik Heber <heber@…> (12/14/12 17:39:42)

Message:

FIX: nodes_t and edges_t in HomologyGraph must be a map.

• there may be multiples of the same node or edge. Hence, now we store the count in a map.
• changed operator<<() accordingly.

File:

• src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) (3 diffs)

src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp

@@ -58 +58 @@
   for (typename std::set<T>::const_iterator iter = keyset.begin();
       iter != keyset.end(); ++iter) {
+//    LOG(2, "DEBUG: Current global id is " << *iter << ".");
     const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
     if (Walker != NULL) {
+      size_t NoBonds = 0;
       const BondList& ListOfBonds = Walker->getListOfBonds();
-#ifndef NDEBUG
+      for (BondList::const_iterator bonditer = ListOfBonds.begin();
+          bonditer != ListOfBonds.end(); ++bonditer) {
+        const atom *OtherWalker = (*bonditer)->GetOtherAtom(Walker);
+        if (keyset.count(OtherWalker->getId()))
+          ++NoBonds;
+      }
+//      LOG(2, "DEBUG: Adding node " << Walker->getId() << " with element "
+//          << Walker->getElementNo() << " and " << NoBonds << " bonds.");
     std::pair<HomologyGraph::nodes_t::iterator,bool> inserter =
-#endif
-        nodes.insert( FragmentNode(Walker->getElementNo(), ListOfBonds.size()) );
+        nodes.insert( std::make_pair(FragmentNode(Walker->getElementNo(), NoBonds), (size_t)1) );
+    if (!inserter.second)
+      inserter.first->second += (size_t)1;
     } else {
-      ELOG(0, "Id " << *iter << " is not associated with any atom.");
+      ELOG(3, "Skipping id " << *iter << ", is not associated with any atom.");
     }
   }
@@ -78 +88 @@
   for (typename std::set<T>::const_iterator iter = keyset.begin();
       iter != keyset.end(); ++iter) {
+//    LOG(2, "DEBUG: Current global id is " << *iter << ".");
     const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
     if (Walker != NULL) {
@@ -84 +95 @@
           bonditer != ListOfBonds.end(); ++bonditer) {
         const atom *OtherWalker = (*bonditer)->GetOtherAtom(Walker);
-        if (Walker->getId() < OtherWalker->getId())
-          edges.insert( FragmentEdge( Walker->getElementNo(), OtherWalker->getElementNo()) );
+//        LOG(2, "DEBUG: Neighbor is " << OtherWalker->getId() << ".");
+        if ((keyset.count(OtherWalker->getId())) && (Walker->getId() < OtherWalker->getId())) {
+//          LOG(1, "DEBUG: Adding edge " << Walker->getId() << " and " << OtherWalker->getId() << ".");
+          std::pair<HomologyGraph::edges_t::iterator,bool> inserter =
+              edges.insert( std::make_pair(FragmentEdge( Walker->getElementNo(), OtherWalker->getElementNo()), (size_t)1) );
+          if (!inserter.second)
+            inserter.first->second += (size_t)1;
+        }
       }
     } else {
-      ELOG(0, "Id " << *iter << " is not associated with any atom.");
+      ELOG(3, "Skipping id " << *iter << ", is not associated with any atom.");
     }
   }