Changeset 708277 for src/Atom

Timestamp:

Apr 17, 2013, 6:56:32 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:

691318

Parents:

79d0b9

git-author:

Frederik Heber <heber@…> (03/18/13 18:34:02)

git-committer:

Frederik Heber <heber@…> (04/17/13 18:56:32)

Message:

FIX: Using fixed Observer in CodePatterns 1.2.6.

• we now require CodePatterns 1.2.6.
• Notifications now use subjectKilled() when the Observable they are associated with is destroyed. This allows Observers that are just sign on to a single channel safely sign off.
• also, derived Observable classes must not remove their Channels and Notifications by themselves. This is done by the Observable base class. Otherwise, subjectKilled() is not called.
• changed AtomObserver: Is directly connected to the atom class, AtomInserted and AtomRemoved called in its cstor and dstor. The World has nothing to do with it. However, we have to make sure AtomObserver is purged after World.
• Fixed also some faulty uses of ObserverLog and we always insert into NotificationChannels with static_cast to Observable for clarity.

Location:

src/Atom

Files:

• AtomObserver.cpp (modified) (2 diffs)
• AtomObserver.hpp (modified) (3 diffs)
• atom.cpp (modified) (4 diffs)
• atom_observable.cpp (modified) (2 diffs)
• unittests/AtomObserverUnitTest.cpp (modified) (1 diff)

src/Atom/AtomObserver.cpp

@@ -50 +50 @@
 {
   Channels *OurChannel = new Channels();
-  NotificationChannels.insert( std::make_pair(this, OurChannel) );
+  NotificationChannels.insert( std::make_pair(static_cast<Observable *>(this), OurChannel) );
   OurChannel->addChannel(AtomObservable::PositionChanged);
   OurChannel->addChannel(AtomObservable::ElementChanged);
@@ -71 +71 @@
 }
 
+/** Function to call when an atom is about to get deleted.
+ *
+ * @param res
+ */
+void AtomObserver::AtomRemoved(atom *res)
+{
+  res->signOff(this, AtomObservable::PositionChanged);
+  res->signOff(this, AtomObservable::ElementChanged);
+}
+
 CONSTRUCT_SINGLETON(AtomObserver)

src/Atom/AtomObserver.hpp

@@ -18 +18 @@
 
 class atom;
-class World;
 
 /** The AtomObserver is a central instance to all changes occuring within atoms.
@@ -26 +25 @@
  * keeps him updated in case of removed or added atoms.
  *
+ * \warning AtomObserver must get purged \b after World as we do not keep an
+ * an internal list of all atoms. Hence, each atom must get destroyed while
+ * the AtomObserver instance is still intact or segfault will occur.
+ *
  */
 class AtomObserver : public Singleton<AtomObserver>, public Relay
@@ -32 +35 @@
   friend class Singleton<AtomObserver>;
 
-  //!> grant World access to AtomInserted.
-  friend class World;
+  //!> grant atom access
+  friend class atom;
 public:
 
 private:
   void AtomInserted(atom *res);
+  void AtomRemoved(atom *res);
 
   // private constructor and destructor due to singleton
   AtomObserver();
-  ~AtomObserver();
+  virtual ~AtomObserver();
 };
 

src/Atom/atom.cpp

@@ -35 +35 @@
 
 #include "atom.hpp"
+#include "AtomObserver.hpp"
 #include "Bond/bond.hpp"
 #include "CodePatterns/Log.hpp"
@@ -54 +55 @@
   sort(&Nr),
   mol(0)
-{};
+{
+  // sign on to global atom change tracker
+  AtomObserver::getInstance().AtomInserted(this);
+}
 
 atom::atom(atom *pointer) :
@@ -66 +70 @@
   AtomicVelocity = pointer->AtomicVelocity; // copy trajectory of velocity
   AtomicForce = pointer->AtomicForce;
+  // sign on to global atom change tracker
+  AtomObserver::getInstance().AtomInserted(this);
 };
 
@@ -80 +86 @@
 {
   removeFromMolecule();
-};
+  // sign off from global atom change tracker
+  AtomObserver::getInstance().AtomRemoved(this);
+}
 
 

src/Atom/atom_observable.cpp

@@ -46 +46 @@
 {
   Channels *OurChannel = new Channels;
-  NotificationChannels.insert( std::make_pair(this, OurChannel) );
+  NotificationChannels.insert( std::make_pair(static_cast<Observable *>(this), OurChannel) );
   // add instance for each notification type
   for (size_t type = 0; type < NotificationType_MAX; ++type)
@@ -53 +53 @@
 
 AtomObservable::~AtomObservable()
-{
-  std::map<Observable *, Channels*>::iterator iter = NotificationChannels.find(this);
-  ASSERT(iter != NotificationChannels.end(),
-      "~AtomObservable() - cannot find myself in NotificationChannels.");
-  delete iter->second;
-  NotificationChannels.erase(iter);
-}
+{}

src/Atom/unittests/AtomObserverUnitTest.cpp

@@ -95 +95 @@
   delete observer2;
 
+  World::purgeInstance();
   AtomObserver::purgeInstance();
-  World::purgeInstance();
 }