Changeset 9b3262b for src

Timestamp:

Jul 24, 2015, 4:44:34 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:

270bdf

Parents:

d12d818

git-author:

Frederik Heber <heber@…> (06/02/15 10:43:49)

git-committer:

Frederik Heber <heber@…> (07/24/15 16:44:34)

Message:

FIX: molecule's Formula is not changed when atom changes element.

Location:

src

Files:

• Atom/atom.cpp (modified) (3 diffs)
• molecule.cpp (modified) (2 diffs)
• molecule.hpp (modified) (1 diff)

src/Atom/atom.cpp ¶

@@ -289 +289 @@
   if ((mol) && (!mol->containsAtom(this))) {
     signOn(mol, AtomObservable::PositionChanged);
+    signOn(mol, AtomObservable::ElementChanged);
     mol->insert(this);
   }
@@ -299 +300 @@
       "atom::unsetMolecule() - old molecule "+toString(mol)+" still contains us!");
   signOff(mol, AtomObservable::PositionChanged);
+  signOff(mol, AtomObservable::ElementChanged);
   mol = NULL;
 }
@@ -310 +312 @@
     if(mol->containsAtom(this)){
       signOff(mol, AtomObservable::PositionChanged);
+      signOff(mol, AtomObservable::ElementChanged);
       mol->erase(this);
     }

src/molecule.cpp ¶

@@ -1044 +1044 @@
         break;
       }
+      case AtomObservable::ElementChanged:
+      {
+        // emit others about one of our atoms moved
+        _lastchangedatom = const_cast<atom *>(_atom);
+        OBSERVE;
+        NOTIFY(FormulaChanged);
+        resetFormula();
+        break;
+      }
       default:
         ASSERT( 0, "molecule::recieveNotification() - we did not sign up for channel "
@@ -1057 +1066 @@
 }
 
+void molecule::resetFormula()
+{
+  // clear
+  formula.clear();
+
+  for (molecule::const_iterator iter = const_cast<const molecule *>(this)->begin();
+      iter != const_cast<const molecule *>(this)->end(); ++iter)
+    formula+=(*iter)->getType();
+}
 
 // construct idpool

src/molecule.hpp ¶

@@ -249 +249 @@
    */
   void setAtomName(atom *_atom) const;
+
+  /** Resets the formula for this molecule.
+   *
+   * This is required in case an atom changes its element as we then don't
+   * have any knowledge about its previous element anymore.
+   */
+  void resetFormula();
 
 public: