Changeset fc1309 for src

Timestamp:

May 8, 2008, 12:45:52 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:

d2a294

Parents:

4a54f3

Message:

MoleculeLeafClass::FillRootStackForSubgraphs used to remove filling of root stack (abstraction)

File:

• src/molecules.cpp (modified) (1 diff)

src/molecules.cpp

@@ -2217 +2217 @@
     *out << Verbose(0) << "Bond order " << Order << " greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed." << endl;
   } else {
-    FragmentList = (Graph **) Malloc(sizeof(Graph *)*FragmentCounter, "molecule::FragmentMolecule - **BondFragments");
+    FragmentList = (Graph **) Malloc(sizeof(Graph *)*Subgraphs->next->Count(), "molecule::FragmentMolecule - **BondFragments");
     
     // ===== 6a. fill RootStack for each subgraph (second adaptivity check) ===== 
     // NOTE: (keep this extern of following while loop, as lateron we may here look for which site to add to which subgraph)
     // fill the root stack
-    KeyStack RootStack[FragmentCounter];
-
-    if (Order == -1) {  // means we want to increase order adaptively
-      cerr << "Adaptive chosing of sites not yet implemented!" << endl;
-    } else {  // means we just want to increase it at every site by one
-      FragmentCounter = 0;
-      MolecularWalker = Subgraphs;
-      // count subgraphs and allocate fragments
-      while (MolecularWalker->next != NULL) {
-        MolecularWalker = MolecularWalker->next;
-        // find first root candidates  
-        RootStack[FragmentCounter].clear();  
-        Walker = MolecularWalker->Leaf->start;
-        while (Walker->next != MolecularWalker->Leaf->end) { // go through all (non-hydrogen) atoms
-          Walker = Walker->next;
-      #ifdef ADDHYDROGEN
-          if (Walker->type->Z != 1) // skip hydrogen
-      #endif
-            if (Walker->GetTrueFather()->AdaptiveOrder < Order) // only if Order is still greater
-              RootStack[FragmentCounter].push_front(Walker->nr);
-        }
-        FragmentCounter++;
-      }
-    }
+    KeyStack *RootStack = new KeyStack[Subgraphs->next->Count()];
+    Subgraphs->next->FillRootStackForSubgraphs(out, RootStack, Order, (FragmentCounter = 0));
 
    // ===== 6b. assign each keyset to its respective subgraph =====