Changeset df793a for src/builder.cpp

Timestamp:

Oct 9, 2008, 6:27:56 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:

ad85c2

Parents:

ba4432

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/builder.cpp (modified) (3 diffs)

src/builder.cpp

@@ -953 +953 @@
                 cout << Verbose(1) << "Depth-First-Search Analysis." << endl;
                 MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
-                int *MinimumRingSize = NULL;
+                int *MinimumRingSize = new int[mol->AtomCount];
+                atom ***ListOfLocalAtoms = NULL;
+                int FragmentCounter = 0;
+                class StackClass<bond *> *BackEdgeStack = NULL;
+                class StackClass<bond *> *LocalBackEdgeStack = NULL;
                 mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr]), configuration.GetIsAngstroem());
                 mol->CreateListOfBondsPerAtom((ofstream *)&cout);
-                Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, MinimumRingSize);
-                delete[](MinimumRingSize);
+                Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, BackEdgeStack);
                 if (Subgraphs != NULL) {
+                  Subgraphs->next->FillBondStructureFromReference((ofstream *)&cout, mol, (FragmentCounter = 0), ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
                   while (Subgraphs->next != NULL) {
                     Subgraphs = Subgraphs->next;
+                    LocalBackEdgeStack = new StackClass<bond *> (Subgraphs->Leaf->BondCount);
+                    Subgraphs->Leaf->PickLocalBackEdges((ofstream *)&cout, ListOfLocalAtoms[FragmentCounter++], BackEdgeStack, LocalBackEdgeStack);
+                    Subgraphs->Leaf->CyclicStructureAnalysis((ofstream *)&cout, BackEdgeStack, MinimumRingSize);
+                    delete(LocalBackEdgeStack);
                     delete(Subgraphs->previous);
                   }
                   delete(Subgraphs);
+                  for (int i=0;i<FragmentCounter;i++)
+                    Free((void **)&ListOfLocalAtoms[FragmentCounter], "ParseCommandLineOptions: **ListOfLocalAtoms[]");
+                  Free((void **)&ListOfLocalAtoms, "ParseCommandLineOptions: ***ListOfLocalAtoms");
                 }
+                delete(BackEdgeStack);
+                delete[](MinimumRingSize);
               }
               argptr+=1;
@@ -1255 +1268 @@
   int Z;
   int j, axis, count, faktor;
-  int *MinimumRingSize = NULL;
+  clock_t start,end;
+//  int *MinimumRingSize = NULL;
   MoleculeLeafClass *Subgraphs = NULL;
-  clock_t start,end;
+//  class StackClass<bond *> *BackEdgeStack = NULL;
   element **Elements;
   Vector **vectors;
@@ -1423 +1437 @@
        
       case 'o': // create the connection matrix
-        cout << Verbose(0) << "What's the maximum bond distance: ";
-        cin >> tmp1;
-        start = clock();
-        mol->CreateAdjacencyList((ofstream *)&cout, tmp1, configuration.GetIsAngstroem());
-        //mol->CreateListOfBondsPerAtom((ofstream *)&cout);
-        Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, MinimumRingSize);
-        while (Subgraphs->next != NULL) {
-          Subgraphs = Subgraphs->next;
-          delete(Subgraphs->previous);
+        {
+          cout << Verbose(0) << "What's the maximum bond distance: ";
+          cin >> tmp1;
+          start = clock();
+          mol->CreateAdjacencyList((ofstream *)&cout, tmp1, configuration.GetIsAngstroem());
+          mol->CreateListOfBondsPerAtom((ofstream *)&cout);
+//          Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, BackEdgeStack);
+//          while (Subgraphs->next != NULL) {
+//            Subgraphs = Subgraphs->next;
+//            Subgraphs->Leaf->CyclicStructureAnalysis((ofstream *)&cout, BackEdgeStack, MinimumRingSize);
+//            delete(Subgraphs->previous);
+//          }
+//          delete(Subgraphs);    // we don't need the list here, so free everything
+//          delete[](MinimumRingSize);
+//          Subgraphs = NULL;
+          end = clock();
+          cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
         }
-        delete(Subgraphs);    // we don't need the list here, so free everything
-        delete[](MinimumRingSize);
-        Subgraphs = NULL;
-        end = clock();
-        cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
         break;