Changeset 41f151 for src/moleculelist.cpp

Timestamp:

Oct 9, 2008, 6:29:34 PM (17 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:

4158ba

Parents:

795a54

git-author:

Frederik Heber <heber@…> (10/09/08 18:27:56)

git-committer:

Frederik Heber <heber@…> (10/09/08 18:29:34)

Message:

BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected subgraphs, AssignKeySetsToFragment() and FillBondStructureFromReference() memory cleanup corrected

+ molecule::DepthFirstSearchAnalysis() now just returns BackEdgeStack, not MinimumRingSize. CyclicStructureAnalysis() is called during FragmentMolecule(), after subgraphs bonds list have been filled by FillBondStructureFromReference().
+ new function molecule::PickLocalBackEdges(), as the BackEdgeStack returned by DepthFirstSearchAnalysis() co
ntains only global bonds, not the local ones for the subgraph, we have to step through it and pick the right
ones out.
+ molecule::FragmentMolecule() now calls molecule::CyclicStructureAnalysis() separately for each subgraph, along with a BackEdgeStack filled by PickLocalBackEdges(), and allocates&initialises MinimumRingSize array. Als
o AssignKeySetsToFragment() frees the LocalListOfAtoms now (FreeList=true), now longer after the following wh
ile
+ molecule::CyclicStructureAnalysis() takes a local BackEdgeStack and analysis the subgraphs cycles, returnin
g minimum ring size
+ MoleculeLeafClass::AssignKeySetsToFragment() now frees memory for ListOfLocalAtoms when FreeList is set. BUGFIX: test of first key was testing against ..->nr != -1. However, LocalListOfAtoms was not even initialised correctly to NULL, hence ...->nr pointed in some cases to nowhere. Now it test atom* against NULL.
+ MoleculeLeafClass::FillBondStructureFromReference() now frees memory for ListOfLocalAtoms when FreeList is set correctly (only free initial pointer when FragmentCounter == 0, also it was decreased not before but after freeing, hence we free'd the wrong list). Also, father replaced by GetTrueFather() (makes the function moregenerally useable, was not a bug).
+ ParseCommandLineOptions() option 'D': adapted to changes in DepthFirstSearchAnalysis() in a similar manner
to FragmentMolecule()
+ molecule::CountCyclicBonds() adapted but does not perform CyclicStructureAnalysis()
+ molecule::CreateAdjacencyList() counts the bonds that could not be brought to covalently corrected degree (i.e. the remaining ionic atoms)
+ molecule::CreateListOfBondsPerAtom() prints atom names and number, which is helpful as name contains global

and number contains local number (helped in finding above bugs)

+ CreateFatherLookupTable(): BUGFIX: LookupTable was not initialised to NULL (see above)

File:

• src/moleculelist.cpp (modified) (5 diffs)

src/moleculelist.cpp

@@ -589 +589 @@
     while (Walker->next != Leaf->end) {
       Walker = Walker->next;
-      AtomNo = Walker->father->nr;  // global id of the current walker
+      AtomNo = Walker->GetTrueFather()->nr;  // global id of the current walker
       for(int i=0;i<reference->NumberOfBondsPerAtom[AtomNo];i++) { // go through father's bonds and copy them all
         Binder = reference->ListOfBondsPerAtom[AtomNo][i];
-        OtherWalker = ListOfLocalAtoms[FragmentCounter][Binder->GetOtherAtom(Walker->father)->nr];    // local copy of current bond partner of walker
+        OtherWalker = ListOfLocalAtoms[FragmentCounter][Binder->GetOtherAtom(Walker->GetTrueFather())->nr];    // local copy of current bond partner of walker
         if (OtherWalker != NULL) {
           if (OtherWalker->nr > Walker->nr)
           Leaf->AddBond(Walker, OtherWalker, Binder->BondDegree);
         } else {
-          *out << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << Binder->GetOtherAtom(Walker->father)->nr << "] is NULL!" << endl;
+          *out << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << Binder->GetOtherAtom(Walker->GetTrueFather())->nr << "] is NULL!" << endl;
           status = false;
         }
@@ -608 +608 @@
   }
   
+  FragmentCounter--;
   if (FreeList) {
     // free the index lookup list
     Free((void **)&ListOfLocalAtoms[FragmentCounter], "MoleculeLeafClass::FillBondStructureFromReference - **ListOfLocalAtoms[]");
-    if (ListOfLocalAtoms[FragmentCounter] == NULL)
+    if (FragmentCounter == 0) // first fragments frees the initial pointer to list
       Free((void **)&ListOfLocalAtoms, "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
   }
@@ -661 +662 @@
  * \param *out output stream fro debugging
  * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
- * \param &FragmentCounter counts the fragments as we move along the list
+ * \param FragmentCounter counts the fragments as we move along the list
  * \param GlobalAtomCount number of atoms in the complete molecule
  * \param &FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
  * \return true - succes, false - failure
  */
-bool MoleculeLeafClass::FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, int &FragmentCounter, int GlobalAtomCount, bool &FreeList)
+bool MoleculeLeafClass::FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList)
 {
   bool status = true;
@@ -726 +727 @@
     KeySet *TempSet = new KeySet;
     for(Graph::iterator runner = KeySetList->begin();runner != KeySetList->end(); runner++) { // key sets contain global numbers!
-      if ( ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*((*runner).first.begin()))->nr]->nr != -1) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
+      if ( ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*((*runner).first.begin()))->nr] != NULL) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
         // translate keyset to local numbers
         for(KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
@@ -744 +745 @@
     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) {
+    // free the index lookup list
+    Free((void **)&ListOfLocalAtoms[FragmentCounter], "MoleculeLeafClass::AssignKeySetsToFragment - **ListOfLocalAtoms[]");
+    if (FragmentCounter == 0) // first fragments frees the initial pointer to list
+      Free((void **)&ListOfLocalAtoms, "MoleculeLeafClass::AssignKeySetsToFragment - ***ListOfLocalAtoms");
+  }
   return status;
 };