Changeset c0f2fc for src

Timestamp:

Feb 11, 2016, 8:07:50 AM (9 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:

29f7c1

Parents:

eb6552

git-author:

Frederik Heber <heber@…> (12/30/15 09:27:51)

git-committer:

Frederik Heber <heber@…> (02/11/16 08:07:50)

Message:

atom now uses associate... and disassociatedAtomWithMolecule().

• this is used to gather all functions that need to be called when a new atom joins a molecule such as signing on to certain channels or updating certain internal values of the molecule.

Location:

src

Files:

• Atom/atom.cpp (modified) (2 diffs)
• Atom/atom.hpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)
• molecule.hpp (modified) (1 diff)

src/Atom/atom.cpp

@@ -295 +295 @@
   mol = _mol;
   if ((mol) && (!mol->containsAtom(this))) {
-    signOn(mol, AtomObservable::PositionChanged);
-    signOn(mol, AtomObservable::ElementChanged);
-    mol->insert(this);
-  }
-}
-
-void atom::unsetMolecule()
-{
-  OBSERVE;
-  NOTIFY(MoleculeChanged);
-  // take this atom from the old molecule
-  ASSERT(!mol->containsAtom(this),
-      "atom::unsetMolecule() - old molecule "+toString(mol)+" still contains us!");
-  signOff(mol, AtomObservable::PositionChanged);
-  signOff(mol, AtomObservable::ElementChanged);
-  mol = NULL;
+    mol->associateAtomWithMolecule(this);
+  }
 }
 
@@ -320 +306 @@
   if(mol){
     if(mol->containsAtom(this)){
-      signOff(mol, AtomObservable::PositionChanged);
-      signOff(mol, AtomObservable::ElementChanged);
-      mol->erase(this);
+      mol->disassociateAtomWithMolecule(this);
     }
     mol=0;

src/Atom/atom.hpp

@@ -243 +243 @@
     void setMolecule(molecule*);
 
-    /** Makes the atom be contained in the no molecule.
-     * Use atom::removeFromMolecule() to delist from old molecule,
-     * this assume that the molecule already knows about it.
-     */
-    void unsetMolecule();
-
     //!> grant World (only) access to selection state changers
     friend class World;

src/molecule.cpp

@@ -1212 +1212 @@
 }
 
+void molecule::associateAtomWithMolecule(atom *_atom)
+{
+  _atom->signOn(this, AtomObservable::PositionChanged);
+  _atom->signOn(this, AtomObservable::ElementChanged);
+  insert(_atom);
+}
+
+void molecule::disassociateAtomWithMolecule(atom *_atom)
+{
+  _atom->signOff(this, AtomObservable::PositionChanged);
+  _atom->signOff(this, AtomObservable::ElementChanged);
+  erase(_atom);
+}
+
 // construct idpool
 CONSTRUCT_IDPOOL(atomId_t, continuousId)

src/molecule.hpp

@@ -357 +357 @@
       > AtomDistanceMap_t;
   std::vector<AtomDistanceMap_t> BoundingBoxSweepingAxis;
+
+  //!> make setMolecule friend to access associateAtomWithMolecule()
+  friend void atom::setMolecule(molecule *);
+
+  /** Helper function only to be called by specific atom function.
+   *
+   * \param _atom atom to be added to this molecule
+   */
+  void associateAtomWithMolecule(atom *_atom);
+
+  /** Helper function only to be called by specific atom function.
+   *
+   * \param _atom atom to be added to this molecule
+   */
+  void disassociateAtomWithMolecule(atom *_atom);
 
 public: