Changeset c27778 for src/molecule_graph.cpp

Timestamp:

Jul 3, 2010, 2:02:26 PM (15 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:

2a374e

Parents:

b9c847

git-author:

Frederik Heber <heber@…> (07/03/10 13:24:25)

git-committer:

Frederik Heber <heber@…> (07/03/10 14:02:26)

Message:

MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not free'd correctly.

• FragmentationDepthFirstSearchAction::performCall() - uses now just ListOfAtoms, free'd and set to NULL in while loop
• changed signature: FillBondStructureFromReference(), FillListOfLocalAtoms() do not get FragmentCounter and ListOfLocalAtoms is now atom (i.e. directly the local list of this fragment not the global one)
• MoleculeLeafClass::FillListOfLocalAtoms() - simplified a lot due to the above
• no more removal of global list if this is the first fragment in MoleculeLeafClass::FillBondStructureFromReference(), MoleculeLeafClass::AssignKeySetsToFragment()
• molecule::FragmentMolecule() - for one we just use ListOfAtoms and around AssignKeySetstoFragments() call we properly allocate, set each component to NULL and free it afterwards.

NOTE: All of these lists and maps are hard to understand and make the code very confusing. It's really high time for refactoring.

Signed-off-by: Frederik Heber <heber@…>

File:

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

src/molecule_graph.cpp

@@ -664 +664 @@
   BFS.ColorList = new enum Shading[AtomCount];
   BFS.BFSStack = new StackClass<atom *> (AtomCount);
+  BFS.TouchedStack = new StackClass<atom *> (AtomCount);
 
   for (int i = AtomCount; i--;) {
     BFS.ShortestPathList[i] = -1;
     BFS.PredecessorList[i] = 0;
+    BFS.ColorList[i] = white;
   }
 };
@@ -681 +683 @@
   delete[](BFS.ColorList);
   delete (BFS.BFSStack);
+  delete (BFS.TouchedStack);
   BFS.AtomCount = 0;
 };
@@ -825 +828 @@
       MinRingSize = RingSize;
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "No ring containing " << *BFS.Root << " with length equal to or smaller than " << MinimumRingSize[Walker->GetTrueFather()->nr] << " found." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "No ring containing " << *BFS.Root << " with length equal to or smaller than " << MinimumRingSize[BFS.Root->GetTrueFather()->nr] << " found." << endl);
   }
 };