Changeset 6d551c for src/Actions/GraphAction/DepthFirstSearchAction.cpp

Timestamp:

Oct 26, 2012, 1:24:01 PM (12 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:

f96874

Parents:

dbe3b9

git-author:

Frederik Heber <heber@…> (09/07/12 08:47:35)

git-committer:

Frederik Heber <heber@…> (10/26/12 13:24:01)

Message:

ListOfLocalAtoms is now a map, inherited into a distinct class.

• this is preparatory for allowing arbitrary fragmentation of atoms not only of a single molecule.

File:

• src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) (4 diffs)

src/Actions/GraphAction/DepthFirstSearchAction.cpp

@@ -40 +40 @@
 #include "Graph/CyclicStructureAnalysis.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
+#include "Graph/ListOfLocalAtoms.hpp"
 #include "molecule.hpp"
 #include "MoleculeLeafClass.hpp"
@@ -56 +57 @@
 Action::state_ptr GraphDepthFirstSearchAction::performCall() {
   LOG(1, "Depth-First-Search Analysis.");
-  atom **ListOfAtoms = NULL;
+  ListOfLocalAtoms_t ListOfAtoms;
   std::deque<bond *> *LocalBackEdgeStack = NULL;
   DepthFirstSearchAnalysis DFS;
@@ -66 +67 @@
     while (Subgraphs->next != NULL) {
       Subgraphs = Subgraphs->next;
-      ListOfAtoms = NULL;
+      ListOfAtoms.clear();
       Subgraphs->Leaf->FillListOfLocalAtoms(ListOfAtoms, Subgraphs->Leaf->getAtomCount());
       LocalBackEdgeStack = new std::deque<bond *>; // no need to have it Subgraphs->Leaf->BondCount size
@@ -75 +76 @@
       Subgraphs->Leaf = NULL;
       delete(Subgraphs->previous);
-      delete[](ListOfAtoms);  // allocated by FillListOfLocalAtoms
       FragmentCounter++;
     }