Ignore:
Timestamp:
May 8, 2010, 12:47:57 PM (15 years ago)
Author:
Tillmann Crueger <crueger@…>
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:
6d789df
Parents:
6f646d
Message:

FIX: Memory corruption in particleInfo class

File:
1 edited

Legend:

Unmodified
Added
Removed

  • src/molecule_graph.cpp

    r6f646d r68f03d  
    317317    Walker->GraphNr = DFS.CurrentGraphNr;
    318318    Walker->LowpointNr = DFS.CurrentGraphNr;
    319     DoLog(1) && (Log() << Verbose(1) << "Setting Walker[" << Walker->Name << "]'s number to " << Walker->GraphNr << " with Lowpoint " << Walker->LowpointNr << "." << endl);
     319    DoLog(1) && (Log() << Verbose(1) << "Setting Walker[" << Walker->getName() << "]'s number to " << Walker->GraphNr << " with Lowpoint " << Walker->LowpointNr << "." << endl);
    320320    DFS.AtomStack->Push(Walker);
    321321    DFS.CurrentGraphNr++;
    … …  
    348348    Binder->MarkUsed(black);
    349349    OtherAtom = Binder->GetOtherAtom(Walker);
    350     DoLog(2) && (Log() << Verbose(2) << "(4) OtherAtom is " << OtherAtom->Name << "." << endl);
     350    DoLog(2) && (Log() << Verbose(2) << "(4) OtherAtom is " << OtherAtom->getName() << "." << endl);
    351351    if (OtherAtom->GraphNr != -1) {
    352352      // (4a) ... if "other" atom has been visited (GraphNr != 0), set lowpoint to minimum of both, go to (3)
    … …  
    354354      DFS.BackEdgeStack->Push(Binder);
    355355      Walker->LowpointNr = (Walker->LowpointNr < OtherAtom->GraphNr) ? Walker->LowpointNr : OtherAtom->GraphNr;
    356       DoLog(3) && (Log() << Verbose(3) << "(4a) Visited: Setting Lowpoint of Walker[" << Walker->Name << "] to " << Walker->LowpointNr << "." << endl);
     356      DoLog(3) && (Log() << Verbose(3) << "(4a) Visited: Setting Lowpoint of Walker[" << Walker->getName() << "] to " << Walker->LowpointNr << "." << endl);
    357357    } else {
    358358      // (4b) ... otherwise set OtherAtom as Ancestor of Walker and Walker as OtherAtom, go to (2)
    … …  
    360360      OtherAtom->Ancestor = Walker;
    361361      Walker = OtherAtom;
    362       DoLog(3) && (Log() << Verbose(3) << "(4b) Not Visited: OtherAtom[" << OtherAtom->Name << "]'s Ancestor is now " << OtherAtom->Ancestor->Name << ", Walker is OtherAtom " << OtherAtom->Name << "." << endl);
     362      DoLog(3) && (Log() << Verbose(3) << "(4b) Not Visited: OtherAtom[" << OtherAtom->getName() << "]'s Ancestor is now " << OtherAtom->Ancestor->getName() << ", Walker is OtherAtom " << OtherAtom->getName() << "." << endl);
    363363      break;
    364364    }
    … …  
    382382
    383383  // (5) if Ancestor of Walker is ...
    384   DoLog(1) && (Log() << Verbose(1) << "(5) Number of Walker[" << Walker->Name << "]'s Ancestor[" << Walker->Ancestor->Name << "] is " << Walker->Ancestor->GraphNr << "." << endl);
     384  DoLog(1) && (Log() << Verbose(1) << "(5) Number of Walker[" << Walker->getName() << "]'s Ancestor[" << Walker->Ancestor->getName() << "] is " << Walker->Ancestor->GraphNr << "." << endl);
    385385
    386386  if (Walker->Ancestor->GraphNr != DFS.Root->GraphNr) {
    … …  
    389389      // (6a) set Ancestor's Lowpoint number to minimum of of its Ancestor and itself, go to Step(8)
    390390      Walker->Ancestor->LowpointNr = (Walker->Ancestor->LowpointNr < Walker->LowpointNr) ? Walker->Ancestor->LowpointNr : Walker->LowpointNr;
    391       DoLog(2) && (Log() << Verbose(2) << "(6) Setting Walker[" << Walker->Name << "]'s Ancestor[" << Walker->Ancestor->Name << "]'s Lowpoint to " << Walker->Ancestor->LowpointNr << "." << endl);
     391      DoLog(2) && (Log() << Verbose(2) << "(6) Setting Walker[" << Walker->getName() << "]'s Ancestor[" << Walker->Ancestor->getName() << "]'s Lowpoint to " << Walker->Ancestor->LowpointNr << "." << endl);
    392392    } else {
    393393      // (7) (Ancestor of Walker is a separating vertex, remove all from stack till Walker (including), these and Ancestor form a component
    394394      Walker->Ancestor->SeparationVertex = true;
    395       DoLog(2) && (Log() << Verbose(2) << "(7) Walker[" << Walker->Name << "]'s Ancestor[" << Walker->Ancestor->Name << "]'s is a separating vertex, creating component." << endl);
     395      DoLog(2) && (Log() << Verbose(2) << "(7) Walker[" << Walker->getName() << "]'s Ancestor[" << Walker->Ancestor->getName() << "]'s is a separating vertex, creating component." << endl);
    396396      mol->SetNextComponentNumber(Walker->Ancestor, DFS.ComponentNumber);
    397       DoLog(3) && (Log() << Verbose(3) << "(7) Walker[" << Walker->Name << "]'s Ancestor's Compont is " << DFS.ComponentNumber << "." << endl);
     397      DoLog(3) && (Log() << Verbose(3) << "(7) Walker[" << Walker->getName() << "]'s Ancestor's Compont is " << DFS.ComponentNumber << "." << endl);
    398398      mol->SetNextComponentNumber(Walker, DFS.ComponentNumber);
    399       DoLog(3) && (Log() << Verbose(3) << "(7) Walker[" << Walker->Name << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
     399      DoLog(3) && (Log() << Verbose(3) << "(7) Walker[" << Walker->getName() << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
    400400      do {
    401401        OtherAtom = DFS.AtomStack->PopLast();
    402402        LeafWalker->Leaf->AddCopyAtom(OtherAtom);
    403403        mol->SetNextComponentNumber(OtherAtom, DFS.ComponentNumber);
    404         DoLog(3) && (Log() << Verbose(3) << "(7) Other[" << OtherAtom->Name << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
     404        DoLog(3) && (Log() << Verbose(3) << "(7) Other[" << OtherAtom->getName() << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
    405405      } while (OtherAtom != Walker);
    406406      DFS.ComponentNumber++;
    407407    }
    408408    // (8) Walker becomes its Ancestor, go to (3)
    409     DoLog(2) && (Log() << Verbose(2) << "(8) Walker[" << Walker->Name << "] is now its Ancestor " << Walker->Ancestor->Name << ", backstepping. " << endl);
     409    DoLog(2) && (Log() << Verbose(2) << "(8) Walker[" << Walker->getName() << "] is now its Ancestor " << Walker->Ancestor->getName() << ", backstepping. " << endl);
    410410    Walker = Walker->Ancestor;
    411411    DFS.BackStepping = true;
    … …  
    431431    //DFS.AtomStack->Output(out);
    432432    mol->SetNextComponentNumber(DFS.Root, DFS.ComponentNumber);
    433     DoLog(3) && (Log() << Verbose(3) << "(9) Root[" << DFS.Root->Name << "]'s Component is " << DFS.ComponentNumber << "." << endl);
     433    DoLog(3) && (Log() << Verbose(3) << "(9) Root[" << DFS.Root->getName() << "]'s Component is " << DFS.ComponentNumber << "." << endl);
    434434    mol->SetNextComponentNumber(Walker, DFS.ComponentNumber);
    435     DoLog(3) && (Log() << Verbose(3) << "(9) Walker[" << Walker->Name << "]'s Component is " << DFS.ComponentNumber << "." << endl);
     435    DoLog(3) && (Log() << Verbose(3) << "(9) Walker[" << Walker->getName() << "]'s Component is " << DFS.ComponentNumber << "." << endl);
    436436    do {
    437437      OtherAtom = DFS.AtomStack->PopLast();
    438438      LeafWalker->Leaf->AddCopyAtom(OtherAtom);
    439439      mol->SetNextComponentNumber(OtherAtom, DFS.ComponentNumber);
    440       DoLog(3) && (Log() << Verbose(3) << "(7) Other[" << OtherAtom->Name << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
     440      DoLog(3) && (Log() << Verbose(3) << "(7) Other[" << OtherAtom->getName() << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
    441441    } while (OtherAtom != Walker);
    442442    DFS.ComponentNumber++;
    … …  
    445445    Walker = DFS.Root;
    446446    Binder = mol->FindNextUnused(Walker);
    447     DoLog(1) && (Log() << Verbose(1) << "(10) Walker is Root[" << DFS.Root->Name << "], next Unused Bond is " << Binder << "." << endl);
     447    DoLog(1) && (Log() << Verbose(1) << "(10) Walker is Root[" << DFS.Root->getName() << "], next Unused Bond is " << Binder << "." << endl);
    448448    if (Binder != NULL) { // Root is separation vertex
    449449      DoLog(1) && (Log() << Verbose(1) << "(11) Root is a separation vertex." << endl);
    … …  
    692692        if (OtherAtom->type->Z != 1) {
    693693#endif
    694         DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->Name << " for bond " << *(*Runner) << "." << endl);
     694        DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
    695695        if (BFS.ColorList[OtherAtom->nr] == white) {
    696696          BFS.TouchedStack->Push(OtherAtom);
    … …  
    698698          BFS.PredecessorList[OtherAtom->nr] = Walker; // Walker is the predecessor
    699699          BFS.ShortestPathList[OtherAtom->nr] = BFS.ShortestPathList[Walker->nr] + 1;
    700           DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->Name << " lightgray, its predecessor is " << Walker->Name << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl);
     700          DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->getName() << " lightgray, its predecessor is " << Walker->getName() << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl);
    701701          //if (BFS.ShortestPathList[OtherAtom->nr] < MinimumRingSize[Walker->GetTrueFather()->nr]) { // Check for maximum distance
    702702          DoLog(3) && (Log() << Verbose(3) << "Putting OtherAtom into queue." << endl);
    … …  
    719719    }
    720720    BFS.ColorList[Walker->nr] = black;
    721     DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->Name << " black." << endl);
     721    DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " black." << endl);
    722722    if (OtherAtom == BFS.Root) { // if we have found the root, check whether this cycle wasn't already found beforehand
    723723      // step through predecessor list
    … …  
    770770    Walker = BFS.Root;
    771771    while (Walker != BackEdge->rightatom) {
    772       DoLog(0) && (Log() << Verbose(0) << Walker->Name << " <-> ");
     772      DoLog(0) && (Log() << Verbose(0) << Walker->getName() << " <-> ");
    773773      Walker = BFS.PredecessorList[Walker->nr];
    774774      Walker->GetTrueFather()->IsCyclic = true;
    775775      RingSize++;
    776776    }
    777     DoLog(0) && (Log() << Verbose(0) << Walker->Name << "  with a length of " << RingSize << "." << endl << endl);
     777    DoLog(0) && (Log() << Verbose(0) << Walker->getName() << "  with a length of " << RingSize << "." << endl << endl);
    778778    // walk through all and set MinimumRingSize
    779779    Walker = BFS.Root;
    … …  
    12331233  BFS.PredecessorList[OtherAtom->nr] = Walker; // Walker is the predecessor
    12341234  BFS.ShortestPathList[OtherAtom->nr] = BFS.ShortestPathList[Walker->nr] + 1;
    1235   DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->Name << " " << ((BFS.ColorList[OtherAtom->nr] == white) ? "white" : "lightgray") << ", its predecessor is " << Walker->Name << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl);
     1235  DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->getName() << " " << ((BFS.ColorList[OtherAtom->nr] == white) ? "white" : "lightgray") << ", its predecessor is " << Walker->getName() << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl);
    12361236  if ((((BFS.ShortestPathList[OtherAtom->nr] < BFS.BondOrder) && (Binder != Bond)))) { // Check for maximum distance
    12371237    DoLog(3) && (Log() << Verbose(3));
    12381238    if (AddedAtomList[OtherAtom->nr] == NULL) { // add if it's not been so far
    12391239      AddedAtomList[OtherAtom->nr] = Mol->AddCopyAtom(OtherAtom);
    1240       DoLog(0) && (Log() << Verbose(0) << "Added OtherAtom " << OtherAtom->Name);
     1240      DoLog(0) && (Log() << Verbose(0) << "Added OtherAtom " << OtherAtom->getName());
    12411241      AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->nr], AddedAtomList[OtherAtom->nr], Binder);
    12421242      DoLog(0) && (Log() << Verbose(0) << " and bond " << *(AddedBondList[Binder->nr]) << ", ");
    12431243    } else { // this code should actually never come into play (all white atoms are not yet present in BondMolecule, that's why they are white in the first place)
    1244       DoLog(0) && (Log() << Verbose(0) << "Not adding OtherAtom " << OtherAtom->Name);
     1244      DoLog(0) && (Log() << Verbose(0) << "Not adding OtherAtom " << OtherAtom->getName());
    12451245      if (AddedBondList[Binder->nr] == NULL) {
    12461246        AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->nr], AddedAtomList[OtherAtom->nr], Binder);
    … …  
    13221322    // followed by n+1 till top of stack.
    13231323    Walker = BFS.BFSStack->PopFirst(); // pop oldest added
    1324     DoLog(1) && (Log() << Verbose(1) << "Current Walker is: " << Walker->Name << ", and has " << Walker->ListOfBonds.size() << " bonds." << endl);
     1324    DoLog(1) && (Log() << Verbose(1) << "Current Walker is: " << Walker->getName() << ", and has " << Walker->ListOfBonds.size() << " bonds." << endl);
    13251325    for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
    13261326      if ((*Runner) != NULL) { // don't look at bond equal NULL
    13271327        Binder = (*Runner);
    13281328        OtherAtom = (*Runner)->GetOtherAtom(Walker);
    1329         DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->Name << " for bond " << *(*Runner) << "." << endl);
     1329        DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
    13301330        if (BFS.ColorList[OtherAtom->nr] == white) {
    13311331          BreadthFirstSearchAdd_UnvisitedNode(Mol, BFS, Walker, OtherAtom, Binder, Bond, AddedAtomList, AddedBondList, IsAngstroem);
    … …  
    13361336    }
    13371337    BFS.ColorList[Walker->nr] = black;
    1338     DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->Name << " black." << endl);
     1338    DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " black." << endl);
    13391339  }
    13401340  BreadthFirstSearchAdd_Free(BFS);
    … …  
    14031403          OtherAtom = (*Runner)->GetOtherAtom(Walker);
    14041404          if (ParentList[OtherAtom->nr] != NULL) { // if otheratom is also a father of an atom on this molecule, create the bond
    1405             DoLog(4) && (Log() << Verbose(4) << "Endpoints of Bond " << (*Runner) << " are both present: " << ParentList[Walker->nr]->Name << " and " << ParentList[OtherAtom->nr]->Name << "." << endl);
     1405            DoLog(4) && (Log() << Verbose(4) << "Endpoints of Bond " << (*Runner) << " are both present: " << ParentList[Walker->nr]->getName() << " and " << ParentList[OtherAtom->nr]->getName() << "." << endl);
    14061406            mol->AddBond(ParentList[Walker->nr], ParentList[OtherAtom->nr], (*Runner)->BondDegree);
    14071407          }
Note: See TracChangeset for help on using the changeset viewer.