Changeset c27778 for src/molecule_fragmentation.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_fragmentation.cpp (modified) (4 diffs)

src/molecule_fragmentation.cpp

@@ -629 +629 @@
     MinimumRingSize[i] = getAtomCount();
   MolecularWalker = Subgraphs;
+  const int LeafCount = Subgraphs->next->Count();
   FragmentCounter = 0;
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
     // fill the bond structure of the individually stored subgraphs
-    MolecularWalker->FillBondStructureFromReference(this, FragmentCounter, ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
+    ListOfAtoms = NULL;
+    MolecularWalker->FillBondStructureFromReference(this, ListOfAtoms, false);  // we want to keep the created ListOfLocalAtoms
     DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
     LocalBackEdgeStack = new StackClass<bond *> (MolecularWalker->Leaf->BondCount);
@@ -644 +646 @@
 //        Log() << Verbose(0) << "\t" << ListOfLocalAtoms[FragmentCounter][i]->Name;
     DoLog(0) && (Log() << Verbose(0) << "Gathering local back edges for subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
-    MolecularWalker->Leaf->PickLocalBackEdges(ListOfLocalAtoms[FragmentCounter++], BackEdgeStack, LocalBackEdgeStack);
+    MolecularWalker->Leaf->PickLocalBackEdges(ListOfAtoms, BackEdgeStack, LocalBackEdgeStack);
     DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
     MolecularWalker->Leaf->CyclicStructureAnalysis(LocalBackEdgeStack, MinimumRingSize);
     DoLog(0) && (Log() << Verbose(0) << "Done with Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
     delete(LocalBackEdgeStack);
+    delete(ListOfAtoms);
+    FragmentCounter++;
   }
   delete(BackEdgeStack);
@@ -660 +664 @@
   // =================================== Begin of FRAGMENTATION ===============================
   // ===== 6a. assign each keyset to its respective subgraph =====
-  Subgraphs->next->AssignKeySetsToFragment(this, ParsedFragmentList, ListOfLocalAtoms, FragmentList, (FragmentCounter = 0), true);
+  ListOfLocalAtoms = new atom **[LeafCount];
+  for (int i=0;i<LeafCount;i++)
+    ListOfLocalAtoms[i] = NULL;
+  FragmentCounter = 0;
+  Subgraphs->next->AssignKeySetsToFragment(this, ParsedFragmentList, ListOfLocalAtoms, FragmentList, FragmentCounter, true);
+  delete[](ListOfLocalAtoms);
 
   // ===== 6b. prepare and go into the adaptive (Order<0), single-step (Order==0) or incremental (Order>0) cycle
@@ -695 +704 @@
   delete(ParsedFragmentList);
   delete[](MinimumRingSize);
-
 
   // ==================================== End of FRAGMENTATION ============================================