Changeset 00b59d5

Timestamp:

Feb 4, 2011, 6:56:38 PM (14 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:

038713

Parents:

1d5afa5

git-author:

Frederik Heber <heber@…> (01/17/11 14:05:30)

git-committer:

Frederik Heber <heber@…> (02/04/11 18:56:38)

Message:

FIX: molecule::FragmentMolecule() did not remove copied atoms and molecules.

• Subgraph copies molecules, are now removed in MoleculeLeafClass dstor.
• BondFragments's molecules, i.e. the created fragments, are not removed, hence the output file got a lot bigger ...

Location:

src

Files:

• molecule_fragmentation.cpp (modified) (2 diffs)
• moleculelist.cpp (modified) (1 diff)

src/molecule_fragmentation.cpp

@@ -752 +752 @@
   // free subgraph memory again
   FragmentCounter = 0;
-  if (Subgraphs != NULL) {
-    while (Subgraphs->next != NULL) {
-      Subgraphs = Subgraphs->next;
-      delete(FragmentList[FragmentCounter++]);
-      delete(Subgraphs->previous);
-    }
+  while (Subgraphs != NULL) {
+    // remove entry in fragment list
+    // remove subgraph fragment
+    MolecularWalker = Subgraphs->next;
     delete(Subgraphs);
-  }
+    Subgraphs = MolecularWalker;
+  }
+  // free fragment list
+  for (int i=0; i< FragmentCounter; ++i )
+    delete(FragmentList[i]);
   delete[](FragmentList);
+
+  DoLog(0) && (Log() << Verbose(0) << FragmentCounter-1 << " subgraph fragments have been removed." << std::endl);
 
   // ===== 8b. gather keyset lists (graphs) from all subgraphs and transform into MoleculeListClass =====
@@ -813 +817 @@
   } else {
     DoLog(1) && (Log() << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl);
+  }
+  // remove all create molecules again from the World including their atoms
+  for (MoleculeList::iterator iter = BondFragments->ListOfMolecules.begin();
+      !BondFragments->ListOfMolecules.empty();
+      iter = BondFragments->ListOfMolecules.begin()) {
+    // remove copied atoms and molecule again
+    molecule *mol = *iter;
+    mol->removeAtomsinMolecule();
+    World::getInstance().destroyMolecule(mol);
+    BondFragments->ListOfMolecules.erase(iter);
   }
   delete(BondFragments);

src/moleculelist.cpp

@@ -741 +741 @@
   // remove the leaf itself
   if (Leaf != NULL) {
+    Leaf->removeAtomsinMolecule();
     World::getInstance().destroyMolecule(Leaf);
     Leaf = NULL;