Changeset 617b53 for src

Timestamp:

Oct 10, 2008, 1:38:46 PM (16 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:

74a65e

Parents:

1e8243

git-author:

Frederik Heber <heber@…> (10/10/08 13:36:06)

git-committer:

Frederik Heber <heber@…> (10/10/08 13:38:46)

Message:

BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong place

+ MoleculeLeafClass::AssignKeySetsToFragment(): FragmentCounter was decreased even when no keyset had been scanned, setting it to -1, bad for the subsequent free. It has to be decreased again right after the recursive call. Begin and end messages added. Free checks for FreeList=true and ListOfLocalAtoms != NULL (safety measure).
+ MoleculeLeafClass::FillBondStructureFromReference(): No BUG here (no keyset check to prevent increase for subsequent decrease), but same changes

File:

• src/moleculelist.cpp (modified) (6 diffs)

src/moleculelist.cpp

@@ -573 +573 @@
   int AtomNo;
 
+  *out << Verbose(1) << "Begin of FillBondStructureFromReference." << endl;
   // fill ListOfLocalAtoms if NULL was given
   if (!FillListOfLocalAtoms(out, ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
@@ -601 +602 @@
     if (next != NULL)
       status = next->FillBondStructureFromReference(out, reference, FragmentCounter, ListOfLocalAtoms);
-  }
-  
-  FragmentCounter--;
-  if (FreeList) {
+    FragmentCounter--;
+  }
+  
+  if ((FreeList) && (ListOfLocalAtoms != NULL)) {
     // free the index lookup list
     Free((void **)&ListOfLocalAtoms[FragmentCounter], "MoleculeLeafClass::FillBondStructureFromReference - **ListOfLocalAtoms[]");
@@ -611 +612 @@
   }
   FragmentCounter--;
+  *out << Verbose(1) << "End of FillBondStructureFromReference." << endl;
   return status;
 };
@@ -701 +703 @@
   int KeySetCounter = 0;
   
+  *out << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl;
   // fill ListOfLocalAtoms if NULL was given
   if (!FillListOfLocalAtoms(out, ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
@@ -740 +743 @@
     if (next != NULL)
       next->AssignKeySetsToFragment(out, reference, KeySetList, ListOfLocalAtoms, FragmentList, FragmentCounter, FreeList);
+    FragmentCounter--;
   } else
     *out << Verbose(1) << "KeySetList is NULL or empty." << endl;
   
-  FragmentCounter--;
-  if (FreeList) {
+  if ((FreeList) && (ListOfLocalAtoms != NULL)) {
     // free the index lookup list
     Free((void **)&ListOfLocalAtoms[FragmentCounter], "MoleculeLeafClass::AssignKeySetsToFragment - **ListOfLocalAtoms[]");
@@ -750 +753 @@
       Free((void **)&ListOfLocalAtoms, "MoleculeLeafClass::AssignKeySetsToFragment - ***ListOfLocalAtoms");
   }
+  *out << Verbose(1) << "End of AssignKeySetsToFragment." << endl;
   return status;
 };