Changeset 2e4105 for src

Timestamp:

Mar 2, 2011, 9:53:08 PM (14 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:

e73ad9a

Parents:

0d9546

git-author:

Frederik Heber <heber@…> (02/25/11 20:44:07)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:08)

Message:

molecule::erase() is only used by atom::removeFromMolecule().

• everywhere else -- even within molecule -- we call atom::removeFromMolecule().
• molecule::erase() is private, atom is friend to underline this.

Location:

src

Files:

• Actions/MoleculeAction/CopyAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) (2 diffs)
• boundary.cpp (modified) (1 diff)
• molecule.cpp (modified) (5 diffs)
• molecule.hpp (modified) (1 diff)

src/Actions/MoleculeAction/CopyAction.cpp

@@ -69 +69 @@
     }
     atom *Walker = *AtomRunner;
-    state->copy->erase(AtomRunner);
     World::getInstance().destroyAtom(Walker);
   }

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -123 +123 @@
           iter = _mol->begin()) {
         atom *Walker = *iter;
-        _mol->erase(iter);
         World::getInstance().destroyAtom(Walker);
       }

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -105 +105 @@
   for (molecule::iterator iter = filler->begin(); !filler->empty(); iter = filler->begin()) {
     atom *Walker = *iter;
-    filler->erase(iter);
     World::getInstance().destroyAtom(Walker);
   }
@@ -143 +142 @@
           iter = _mol->begin()) {
         atom *Walker = *iter;
-        _mol->erase(iter);
         World::getInstance().destroyAtom(Walker);
       }

src/boundary.cpp

@@ -1185 +1185 @@
     for(molecule::iterator miter = filler->begin(); !filler->empty(); miter = filler->begin()) {
       atom *Walker = *miter;
-      filler->erase(Walker);
       World::getInstance().destroyAtom(Walker);
     }

src/molecule.cpp

@@ -184 +184 @@
   OBSERVE;
   molecule::const_iterator iter = loc;
-  iter--;
+  iter++;
   atom* atom = *loc;
   atomIds.erase( atom->getId() );
@@ -198 +198 @@
   molecule::const_iterator iter = find(key);
   if (iter != end()){
+    iter++;
     atomIds.erase( key->getId() );
     atoms.remove( key );
@@ -822 +823 @@
   OBSERVE;
   RemoveBonds(pointer);
-  erase(pointer);
+  pointer->removeFromMolecule();
   return true;
 };
@@ -834 +835 @@
   if (pointer == NULL)
     return false;
-  erase(pointer);
+  pointer->removeFromMolecule();
   return true;
 };
@@ -844 +845 @@
 {
   for (molecule::iterator iter = begin(); !empty(); iter = begin())
-    erase(*iter);
+    (*iter)->removeFromMolecule();
   return empty();
 };

src/molecule.hpp

@@ -131 +131 @@
   bool empty() const;
   size_t size() const;
-  const_iterator erase(const_iterator loc);
-  const_iterator erase(atom * key);
   const_iterator find(atom * key) const;
   pair<iterator, bool> insert(atom * const key);
   bool containsAtom(atom* key);
+
+private:
+  friend void atom::removeFromMolecule();
+  /** Erase an atom from the list.
+   * \note This should only be called by atom::removeFromMolecule(),
+   * otherwise it is not assured that the atom knows about it.
+   *
+   * @param loc locator to atom in list
+   * @return iterator to just after removed item (compliant with standard)
+   */
+  const_iterator erase(const_iterator loc);
+  /** Erase an atom from the list.
+   * \note This should only be called by atom::removeFromMolecule(),
+   * otherwise it is not assured that the atom knows about it.
+   *
+   * @param *key key to atom in list
+   * @return iterator to just after removed item (compliant with standard)
+   */
+  const_iterator erase(atom * key);
+
+public:
 
   /// remove atoms from molecule.