Changeset a7aebd

Timestamp:

Jan 11, 2015, 4:41:14 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:

f115cc

Parents:

7b93f9

git-author:

Frederik Heber <heber@…> (12/03/14 19:20:31)

git-committer:

Frederik Heber <heber@…> (01/11/15 16:41:14)

Message:

World removes empty molecules.

• on destroyAtom() of molecule's last atom, destroyMolecule() is called.
• FIX: destroyMolecule(molecule *) did use OBSERVE unncessarily. This caused seg'fault.
• extracted removeAtomsinMolecule from molecule class. This is necessary since World will automatically remove empty molecules.

Location:

src

Files:

• Actions/UndoRedoHelpers.cpp (modified) (1 diff)
• Actions/WorldAction/RepeatBoxAction.cpp (modified) (1 diff)
• Fragmentation/Exporters/ExportGraph.cpp (modified) (1 diff)
• Graph/unittests/AdjacencyListUnitTest.cpp (modified) (1 diff)
• MoleculeLeafClass.cpp (modified) (1 diff)
• World.cpp (modified) (4 diffs)
• molecule.cpp (modified) (1 diff)
• molecule.hpp (modified) (2 diffs)

src/Actions/UndoRedoHelpers.cpp

@@ -173 +173 @@
   for (std::vector<moleculeId_t>::const_iterator iter = ids.begin();
       iter != ids.end(); ++iter) {
-    molecule * const mol = World::getInstance().getMolecule(MoleculeById(*iter));
+    molecule * mol = World::getInstance().getMolecule(MoleculeById(*iter));
     if (mol != NULL) {
-      mol->removeAtomsinMolecule();
-      World::getInstance().destroyMolecule(mol);
+      removeAtomsinMolecule(mol);
+      // molecules are automatically removed when empty
     }
   }

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -147 +147 @@
       iter != allmolecules.end();
       ++iter) {
-    if (state->oldmolecules.find(*iter) == state->oldmolecules.end()) {
-      (*iter)->removeAtomsinMolecule();
-      // TODO: Remove this when World don't has deprecated MoleculeListClass anymore
-      molecules->erase(*iter);
-      World::getInstance().destroyMolecule(*iter);
-    }
+    if (state->oldmolecules.find(*iter) == state->oldmolecules.end())
+      removeAtomsinMolecule(*iter);
   }
 

src/Fragmentation/Exporters/ExportGraph.cpp

@@ -80 +80 @@
     // remove copied atoms and molecule again
     molecule *mol = *iter;
-    mol->removeAtomsinMolecule();
-    World::getInstance().destroyMolecule(mol);
     BondFragments.ListOfMolecules.erase(iter);
+    removeAtomsinMolecule(mol);
   }
 }

src/Graph/unittests/AdjacencyListUnitTest.cpp

@@ -153 +153 @@
 
   // destroy molecule and contained atoms
-  TestMolecule->removeAtomsinMolecule();
-  World::getInstance().destroyMolecule(TestMolecule);
+  removeAtomsinMolecule(TestMolecule);
   // destroy World
   World::purgeInstance();

src/MoleculeLeafClass.cpp

@@ -85 +85 @@
   //  }
   // remove the leaf itself
-  if (Leaf != NULL) {
-    Leaf->removeAtomsinMolecule();
-    World::getInstance().destroyMolecule(Leaf);
-    Leaf = NULL;
-  }
+  if (Leaf != NULL)
+    removeAtomsinMolecule(Leaf);
   // remove this Leaf from level list
   if (previous != NULL)

src/World.cpp

@@ -304 +304 @@
 
 void World::destroyMolecule(molecule* mol){
-  OBSERVE;
   ASSERT(mol,"Molecule that was meant to be destroyed did not exist");
   destroyMolecule(mol->getId());
@@ -319 +318 @@
   }
   mol->signOff(this);
+  // TODO: removed when depcreated MoleculeListClass is gone
+  molecules_deprecated->erase(mol);
   DeleteMolecule(mol);
   if (isMoleculeSelected(id))
@@ -365 +366 @@
     NOTIFY(AtomRemoved);
   }
+  // check if it's the last atom
+  molecule *_mol = atom->getMolecule();
+  if ((_mol == NULL) || (_mol->getAtomCount() > (size_t)1))
+    _mol = NULL;
   DeleteAtom(atom);
   if (isAtomSelected(id))
@@ -370 +375 @@
   atoms.erase(id);
   atomIdPool.releaseId(id);
+  // remove molecule if empty
+  if (_mol != NULL)
+    destroyMolecule(_mol);
 }
 

src/molecule.cpp

@@ -646 +646 @@
 /** Destroys all atoms inside this molecule.
  */
-void molecule::removeAtomsinMolecule()
+void removeAtomsinMolecule(molecule *&_mol)
 {
   // remove each atom from world
-  for(iterator AtomRunner = begin(); !empty(); AtomRunner = begin())
+  for(molecule::iterator AtomRunner = _mol->begin(); !_mol->empty(); AtomRunner = _mol->begin())
     World::getInstance().destroyAtom(*AtomRunner);
+  // make sure that pointer os not usable
+  _mol = NULL;
 };
 

src/molecule.hpp

@@ -57 +57 @@
 /************************************* Class definitions ****************************************/
 
+/** External function to remove all atoms since this will also delete the molecule
+ *
+ * \param _mol ref pointer to molecule to destroy
+ */
+void removeAtomsinMolecule(molecule *&_mol);
+
 /** The complete molecule.
  * Class incorporates number of types
@@ -262 +268 @@
   bool UnlinkAtom(atom *pointer);
   bool CleanupMolecule();
-  void removeAtomsinMolecule();
 
   /// Add/remove atoms to/from molecule.