Changeset 38f991 for src/Actions

Timestamp:

Oct 10, 2011, 2:25:37 PM (13 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:

6bc86c

Parents:

ab4a33

git-author:

Frederik Heber <heber@…> (09/05/11 17:23:16)

git-committer:

Frederik Heber <heber@…> (10/10/11 14:25:37)

Message:

FormatParser now listens to World::AtomRemoved and ::AtomInserted notifications.

• World now has const iterators for selectedAtoms and selectedMolecules.
• FIX: RemoveAction was broken in usage of beginSelectedAtoms() for removing them! This is fixed. Same for FragmentAction() where non-const iterator had been used for fragmenting.
• The above was caused by the following (we would stumble over receiveNotifications() going into void):
• new virtual functions AtomRemoved() and AtomInserted() which the specific parsers overwrite, e.g. to remove additional information when the associated atom is removed.

Location:

src/Actions

Files:

• AtomAction/RemoveAction.cpp (modified) (2 diffs)
• FragmentationAction/FragmentationAction.cpp (modified) (1 diff)

src/Actions/AtomAction/RemoveAction.cpp

@@ -40 +40 @@
 /** =========== define the function ====================== */
 Action::state_ptr AtomRemoveAction::performCall() {
-  atom *first = NULL;
-
   // create undo state
   std::vector<AtomicInfo> Walkers;
-  for (World::AtomSelectionIterator iter = World::getInstance().beginAtomSelection(); iter != World::getInstance().endAtomSelection(); ++iter) {
+  for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
+      iter != World::getInstance().endAtomSelection();
+      ++iter) {
     Walkers.push_back(AtomicInfo(*(iter->second)));
   }
@@ -50 +50 @@
 
   // remove all selected atoms
-//  std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
-  for (World::AtomSelectionIterator iter = World::getInstance().beginAtomSelection(); iter != World::getInstance().endAtomSelection(); ++iter) {
-    first = iter->second;
-    DoLog(1) && (Log() << Verbose(1) << "Removing atom " << first->getId() << "." << endl);
-//    // TODO: this is not necessary when atoms and their storing to file are handled by the World
-//    // simply try to erase in every molecule found
-//    for (std::vector<molecule *>::iterator iter = molecules.begin();iter != molecules.end(); ++iter) {
-//      (*iter)->erase(first);
-//    }
-    World::getInstance().destroyAtom(first);
+  for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
+      iter != World::getInstance().endAtomSelection();
+      iter = World::getInstance().beginAtomSelection()) {
+    DoLog(1) && (Log() << Verbose(1) << "Removing atom " << (iter->second)->getId() << "." << endl);
+    World::getInstance().destroyAtom((iter->second));
   }
   return Action::state_ptr(UndoState);

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -50 +50 @@
 
   DepthFirstSearchAnalysis DFS;
-  for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
+  for (World::MoleculeSelectionConstIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     mol = iter->second;
     ASSERT(mol != NULL, "No molecule has been picked for fragmentation.");