Changeset d05088 for src/Atom

Timestamp:

Jan 27, 2015, 5:18:28 PM (10 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:

24edfe

Parents:

910a5d

git-author:

Frederik Heber <heber@…> (01/17/15 16:45:07)

git-committer:

Frederik Heber <heber@…> (01/27/15 17:18:28)

Message:

FIX: Atom is notified when its father dies and resets father to itself then.

• this caused a segfault with FormatParser::save() when a copied molecule's atoms is stored.

Location:

src/Atom

Files:

• AtomicInfo.cpp (modified) (1 diff)
• atom.cpp (modified) (5 diffs)
• atom.hpp (modified) (3 diffs)
• atom_observable.cpp (modified) (1 diff)
• atom_observable.hpp (modified) (1 diff)

src/Atom/AtomicInfo.cpp

@@ -88 +88 @@
   bool status = true;
   if (_atom.getId() != Id)
-    status = _atom.changeId(Id);
+    status &= _atom.changeId(Id);
 
   // set its father
-  atom * const _father = World::getInstance().getAtom(AtomById(FatherId));
-  if (_father == NULL)
-    _atom.father = &_atom;
-  else
-    _atom.father = _father;
+  if (status) {
+    atom * const _father = World::getInstance().getAtom(AtomById(FatherId));
+    if ((_father == NULL) || (Id == FatherId)) {
+      _atom.father = &_atom;
+      // don't sign on
+    } else {
+      _atom.father = _father;
+      _father->signOn(&_atom);
+    }
 
-  // setting molecule
-  molecule * const _mol = World::getInstance().getMolecule(MoleculeById(MolId));
-  if (_mol != NULL)
-    _atom.setMolecule(_mol); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
-  _atom.changeNr(Nr);
+    // setting molecule
+    molecule * const _mol = World::getInstance().getMolecule(MoleculeById(MolId));
+    if (_mol != NULL)
+      _atom.setMolecule(_mol); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
+    _atom.changeNr(Nr);
+  }
 
   return status;

src/Atom/atom.cpp

@@ -58 +58 @@
   mol(0)
 {
-  // sign on to global atom change tracker
+  // note AtomObserver about inserted atom
   AtomObserver::getInstance().AtomInserted(this);
 }
@@ -69 +69 @@
     mol(0)
 {
-  // sign on to global atom change tracker
+  // sign on to father atom to be notified when it is removed
+  father->signOn(this);
+
+  // note AtomObserver about inserted atom
   AtomObserver::getInstance().AtomInserted(this);
 };
@@ -84 +87 @@
 atom::~atom()
 {
+  // sign off from possible father
+  if ((father != this) && (father != NULL))
+    father->signOff(this);
+
   removeFromMolecule();
-  // sign off from global atom change tracker
+  // note AtomObserver about removed atom
   AtomObserver::getInstance().AtomRemoved(this);
 }
@@ -129 +136 @@
 void atom::setFather(atom * const _father)
 {
+  // sign off from old father
+  if ((father != this) && (father != NULL))
+    father->signOff(this);
+
   father = _father;
+  father->signOn(this);
 }
 
@@ -330 +342 @@
   return atom1->getType()->getAtomicNumber() < atom2->getType()->getAtomicNumber();
 }
+/*
+void atom::update(Observable *publisher)
+{}
+
+void atom::recieveNotification(Observable *publisher, Notification_ptr notification)
+{
+  ASSERT(0, "atom::recieveNotification() - we are not signed on to any notifications.");
+}
+*/
+void atom::subjectKilled(Observable *publisher)
+{
+  // as publisher has been half-deallocated (Observable is one of the base classes, hence
+  // becomes destroyed latest), we cannot senibly cast it anymore.
+  // Hence, we simply have to check here whether it is NOT one of the other instances
+  // we are signed on to.
+  father = this;
+  // no need to sign off
+}

src/Atom/atom.hpp

@@ -25 +25 @@
 #include "atom_bondedparticle.hpp"
 #include "atom_graphnode.hpp"
+#include "atom_observable.hpp"
 #include "atom_particleinfo.hpp"
 #include "Atom/TesselPoint.hpp"
 #include "types.hpp"
 
+#include "CodePatterns/Observer/Observer.hpp"
 #include "CodePatterns/enumeration.hpp"
 
@@ -44 +46 @@
  * Class incorporates position, type
  */
-class atom : public GraphNode, public BondedParticle, public TesselPoint {
+class atom :
+            public GraphNode,
+            public BondedParticle,
+            public TesselPoint
+{
   friend atom* NewAtom(atomId_t);
   friend void  DeleteAtom(atom*);
@@ -243 +249 @@
     void unsetMolecule();
 
+//    virtual void update(Observable *publisher);
+//    virtual void recieveNotification(Observable *publisher, Notification_ptr notification);
+    virtual void subjectKilled(Observable *publisher);
 
   private:

src/Atom/atom_observable.cpp

@@ -55 +55 @@
 AtomObservable::~AtomObservable()
 {}
+
+void AtomObservable::subjectKilled(Observable *publisher)
+{}

src/Atom/atom_observable.hpp

@@ -41 +41 @@
   AtomObservable();
   virtual ~AtomObservable();
+
+protected:
+
+  virtual void subjectKilled(Observable *publisher);
 };