Changeset 7d82a5 for src/Bond

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/Bond

Files:

• bond.cpp (modified) (3 diffs)
• bond.hpp (modified) (4 diffs)

src/Bond/bond.cpp

@@ -81 +81 @@
     NOTIFY(BondRemoved);
   }
-  // remove this node from the list structure
-  if (leftatom != NULL)
-    leftatom->removeBond(this);
-  // there might be self-bonds
-  if ((leftatom != rightatom) && (rightatom != NULL))
-    rightatom->removeBond(this);
+  // atoms should have been destroyed and NULL'd their entry already
+  ASSERT (leftatom == NULL,
+      "~bond() - leftatom is not NULL.");
+  ASSERT (rightatom == NULL,
+      "~bond() - rightatom is not NULL.");
 };
 
@@ -101 +100 @@
 atom * bond::GetOtherAtom(const ParticleInfo * const Atom) const
 {
+  ASSERT( (leftatom != NULL) && (rightatom != NULL),
+      "bond::GetOtherAtom() - one of the atoms refs is NULL.");
   if(leftatom == Atom) 
     return rightatom;
@@ -143 +144 @@
   return (leftatom->DistanceSquared(*rightatom));
 };
+
+/** Sets either leftatom or rightatom to NULL.
+ *
+ * \param Atom atom to remove
+ */
+void bond::removeAtom(const ParticleInfo * const Atom)
+{
+  if (static_cast<const ParticleInfo *>(leftatom) == Atom)
+    leftatom = NULL;
+  if (static_cast<const ParticleInfo *>(rightatom) == Atom)
+    rightatom = NULL;
+}

src/Bond/bond.hpp

@@ -18 +18 @@
 #endif
 
+#include <boost/shared_ptr.hpp>
+
 #include "Bond/bond_observable.hpp"
 #include "Bond/GraphEdge.hpp"
@@ -24 +26 @@
 
 class atom;
+class BondedParticle;
 class ParticleInfo;
 
@@ -39 +42 @@
 public:
   //!> typedef for a bond ptr
-  typedef bond* ptr;
+  typedef boost::shared_ptr<bond> ptr;
 
   atom *leftatom;    //!< first bond partner
@@ -56 +59 @@
   bond(atom *left, atom *right, const int degree=1);
   ~bond();
+
+private:
+  //!> grant atom_bondedparticle access to unregister function
+  friend class BondedParticle;
+  void removeAtom(const ParticleInfo * const Atom);
 };