Changeset 38f991

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

Files:

• Actions/AtomAction/RemoveAction.cpp (modified) (2 diffs)
• Actions/FragmentationAction/FragmentationAction.cpp (modified) (1 diff)
• Parser/FormatParser.cpp (modified) (3 diffs)
• Parser/FormatParser.hpp (modified) (1 diff)
• World.cpp (modified) (4 diffs)
• World.hpp (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.");

src/Parser/FormatParser.cpp

@@ -33 +33 @@
 {
   ChangeTracker::getInstance().signOn(this);
+  World::getInstance().signOn(this, World::getInstance().getChannel(World::AtomInserted));
+  World::getInstance().signOn(this, World::getInstance().getChannel(World::AtomRemoved));
 }
 
@@ -40 +42 @@
 FormatParser::~FormatParser() {
   ChangeTracker::getInstance().signOff(this);
+  World::getInstance().signOff(this, World::getInstance().getChannel(World::AtomInserted));
+  World::getInstance().signOff(this, World::getInstance().getChannel(World::AtomRemoved));
 }
 
@@ -57 +61 @@
 
 /**
+ * With this, each format parser is informed about specific changes in the World.
+ */
+void FormatParser::recieveNotification(Observable *publisher, Notification_ptr notification) {
+  switch (notification->getChannelNo()) {
+    case World::AtomInserted:
+      AtomInserted(World::getInstance().lastChanged<atom>()->getId());
+      break;
+    case World::AtomRemoved:
+      AtomRemoved(World::getInstance().lastChanged<atom>()->getId());
+      break;
+    default:
+      ASSERT(0,
+          "FormatParser::recieveNotification() - unknown notification "
+          +toString(notification->getChannelNo())+" received.");
+      break;
+  }
+}
+
+/**
  * The observable can tell when it dies.
  */

src/Parser/FormatParser.hpp

@@ -31 +31 @@
   virtual void load(std::istream* file)=0;
   void setOstream(std::ostream* file);
+
+protected:
   void update(Observable *publisher);
+  void recieveNotification(Observable *publisher, Notification_ptr notification);
   void subjectKilled(Observable *publisher);
+
+  // these functions are called when atoms are inserted or removed
+  virtual void AtomInserted(atomId_t) {};
+  virtual void AtomRemoved(atomId_t) {};
 
 private:

src/World.cpp

@@ -191 +191 @@
 
 void World::destroyMolecule(moleculeId_t id){
-  OBSERVE;
   molecule *mol = molecules[id];
   ASSERT(mol,"Molecule id that was meant to be destroyed did not exist");
-  _lastchangedmol = mol;
-  NOTIFY(MoleculeRemoved);
+  // give notice about immediate removal
+  {
+    OBSERVE;
+    _lastchangedmol = mol;
+    NOTIFY(MoleculeRemoved);
+  }
   DeleteMolecule(mol);
+  if (isMoleculeSelected(id))
+    selectedMolecules.erase(id);
   molecules.erase(id);
   releaseMoleculeId(id);
@@ -239 +244 @@
   }
   DeleteAtom(atom);
+  if (isAtomSelected(id))
+    selectedAtoms.erase(id);
   atoms.erase(id);
   releaseAtomId(id);
@@ -765 +772 @@
 }
 
+World::AtomSelectionConstIterator World::beginAtomSelection() const{
+  return selectedAtoms.begin();
+}
+
+World::AtomSelectionConstIterator World::endAtomSelection() const{
+  return selectedAtoms.end();
+}
+
 
 World::MoleculeSelectionIterator World::beginMoleculeSelection(){
@@ -771 +786 @@
 
 World::MoleculeSelectionIterator World::endMoleculeSelection(){
+  return selectedMolecules.end();
+}
+
+World::MoleculeSelectionConstIterator World::beginMoleculeSelection() const{
+  return selectedMolecules.begin();
+}
+
+World::MoleculeSelectionConstIterator World::endMoleculeSelection() const{
   return selectedMolecules.end();
 }

src/World.hpp

@@ -356 +356 @@
   AtomSelectionIterator beginAtomSelection();
   AtomSelectionIterator endAtomSelection();
+  typedef AtomSet::const_iterator AtomSelectionConstIterator;
+  AtomSelectionConstIterator beginAtomSelection() const;
+  AtomSelectionConstIterator endAtomSelection() const;
 
   typedef MoleculeSet::iterator MoleculeSelectionIterator;
   MoleculeSelectionIterator beginMoleculeSelection();
   MoleculeSelectionIterator endMoleculeSelection();
+  typedef MoleculeSet::const_iterator MoleculeSelectionConstIterator;
+  MoleculeSelectionConstIterator beginMoleculeSelection() const;
+  MoleculeSelectionConstIterator endMoleculeSelection() const;
 
 protected: