Changeset 7d82a5 for src/Fragmentation

Timestamp:

Feb 13, 2013, 3:47:38 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:

b4b364

Parents:

c8302f3

git-author:

Frederik Heber <heber@…> (11/02/12 13:38:08)

git-committer:

Frederik Heber <heber@…> (02/13/13 15:47:38)

Message:

Changed bond::ptr into boost::shared_ptr.

Changes:

• refactored some BondedParticle functions, cleaning up the interface in terms of private and public functionality, added some helper functions to find bonds.
• ptr = NULL --> .reset().
• now initialising to NULL.
• BondsPerSP is now list of boost::shared_ptr as well.
• some include of bond.hpp instead of forward references necessary.
• leftatom and rightatom are now set to NULL on UnregisterBond().
• bonds are not deleted anymore but simply unregistered.
• FIX: BondedParticleInfo did unrequiredly inherit AtomObservable.
• removed UnregisterAllBonds(), code is now in RemoveAllBonds() where UnregisterBond is called for both bond partners. This ensures that the bond is correctly released and shared_ptr free'd.

Location:

src/Fragmentation

Files:

• BondsPerShortestPath.cpp (modified) (4 diffs)
• BondsPerShortestPath.hpp (modified) (3 diffs)
• PowerSetGenerator.cpp (modified) (1 diff)

src/Fragmentation/BondsPerShortestPath.cpp

@@ -90 +90 @@
     BondsPerSPCount[i] = 0;
   BondsPerSPCount[0] = 1;
-  bond::ptr Binder = new bond(_Root, _Root);
+  bond::ptr Binder(new bond(_Root, _Root));
   BondsPerSPList[0].push_back(Binder);
 };
@@ -110 +110 @@
       (*iter)->leftatom = NULL;
       (*iter)->rightatom = NULL;
-      // now delete it, there we unregister but this checks for NULL
-      delete(*iter);
     }
     BondsPerSPList[i].clear();
@@ -138 +136 @@
   atom *OtherWalker = NULL;
   atom *Predecessor = NULL;
-  bond::ptr Binder = NULL;
+  bond::ptr Binder;
   int RootKeyNr = _RootKeyNr;
   int RemainingWalkers = -1;
@@ -180 +178 @@
           if ((OtherWalker != Predecessor) && (OtherWalker->GetTrueFather()->getNr() > RootKeyNr)) { // only pass through those with label bigger than Root's
             // add the bond in between to the SP list
-            Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
+            Binder.reset(new bond(Walker, OtherWalker)); // create a new bond in such a manner, that bond::rightatom is always the one more distant
             BondsPerSPList[SP+1].push_back(Binder);
             BondsPerSPCount[SP+1]++;

src/Fragmentation/BondsPerShortestPath.hpp

@@ -14 +14 @@
 #endif
 
+#include "Bond/bond.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 
@@ -20 +21 @@
 
 class atom;
-class bond;
 class KeySet;
 
@@ -39 +39 @@
   int getOrder() const;
 
-  typedef std::list<bond*> BondsPerSP;
+  typedef std::list<bond::ptr> BondsPerSP;
   typedef std::vector< BondsPerSP > AllSPBonds;
 

src/Fragmentation/PowerSetGenerator.cpp

@@ -220 +220 @@
 
     // prepare the subset and call the generator
-    std::vector<bond*> BondsList;
+    std::vector<bond::ptr> BondsList;
     BondsList.resize(BondsPerSPList.BondsPerSPCount[0]);
     ASSERT(BondsPerSPList.BondsPerSPList[0].size() != 0,