Changeset 88c8ec for src/Graph/DepthFirstSearchAnalysis.cpp

Timestamp:

Jan 17, 2013, 10:59:15 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:

c8302f3

Parents:

d6b6ce

git-author:

Frederik Heber <heber@…> (10/29/12 00:28:46)

git-committer:

Frederik Heber <heber@…> (01/17/13 22:59:15)

Message:

REFACTOR: Replaced all "bond *" appearances by bond::ptr.

• this is preparatory for making bond::ptr a boost::shared_ptr of bond.
• NOTE: We had to remove a const prefix at four or five places and forward declarations had to be replaced by the true inclusion of bond.hpp at tne or so files. Apart from that, the replacement has been very smooth.

File:

• src/Graph/DepthFirstSearchAnalysis.cpp (modified) (8 diffs)

src/Graph/DepthFirstSearchAnalysis.cpp

@@ -77 +77 @@
 
 
-bond * DepthFirstSearchAnalysis::FindNextUnused(atom *vertex) const
+bond::ptr DepthFirstSearchAnalysis::FindNextUnused(atom *vertex) const
 {
   const BondList& ListOfBonds = vertex->getListOfBonds();
@@ -122 +122 @@
 
 
-bool DepthFirstSearchAnalysis::PickLocalBackEdges(const ListOfLocalAtoms_t &ListOfLocalAtoms, std::deque<bond *> *&LocalStack) const
+bool DepthFirstSearchAnalysis::PickLocalBackEdges(const ListOfLocalAtoms_t &ListOfLocalAtoms, std::deque<bond::ptr > *&LocalStack) const
 {
   bool status = true;
@@ -129 +129 @@
     return false;
   }
-  bond *Binder = BackEdgeStack.front();
-  bond *FirstBond = Binder; // mark the first bond, so that we don't loop through the stack indefinitely
+  bond::ptr Binder = BackEdgeStack.front();
+  bond::ptr FirstBond = Binder; // mark the first bond, so that we don't loop through the stack indefinitely
   atom *Walker = NULL, *OtherAtom = NULL;
 
@@ -183 +183 @@
         ++BondRunner)
       if ((*BondRunner)->leftatom == *AtomRunner) {
-        const bond *Binder = *BondRunner;
+        const bond::ptr Binder = *BondRunner;
         if (DoLog(2)) {
           std::stringstream output;
@@ -235 +235 @@
 
 
-void DepthFirstSearchAnalysis::ProbeAlongUnusedBond(atom *&Walker, bond *&Binder)
+void DepthFirstSearchAnalysis::ProbeAlongUnusedBond(atom *&Walker, bond::ptr &Binder)
 {
   atom *OtherAtom = NULL;
@@ -308 +308 @@
 
 
-void DepthFirstSearchAnalysis::CleanRootStackDownTillWalker(atom *&Walker, bond *&Binder, ConnectedSubgraph &Subgraph)
+void DepthFirstSearchAnalysis::CleanRootStackDownTillWalker(atom *&Walker, bond::ptr &Binder, ConnectedSubgraph &Subgraph)
 {
   atom *OtherAtom = NULL;
@@ -343 +343 @@
 
 
-const std::deque<bond *>& DepthFirstSearchAnalysis::getBackEdgeStack() const
+const std::deque<bond::ptr >& DepthFirstSearchAnalysis::getBackEdgeStack() const
 {
   return BackEdgeStack;
@@ -355 +355 @@
   int OldGraphNr = 0;
   atom *Walker = NULL;
-  bond *Binder = NULL;
+  bond::ptr Binder = NULL;
 
   if (World::getInstance().numAtoms() == 0)