Changeset b4bd0e for src/UIElements/Qt4/InstanceBoard

Timestamp:

Apr 20, 2016, 10:58:42 PM (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:

96f14a

Parents:

6af6a62

git-author:

Frederik Heber <heber@…> (03/15/16 10:10:54)

git-committer:

Frederik Heber <heber@…> (04/20/16 22:58:42)

Message:

Added QtObservedBond, managed by QtObservedInstanceBoard.

• QtObservedBond is special because it observes not only a bond, but also two atoms and a molecule in total.
• but the general idea is to rather have information duplicate, i.e. the left atom's position is also available via the QtObservedAtom. But in this way QtObservedBond does not depend on the QtObservedAtom being still or already present.

Location:

src/UIElements/Qt4/InstanceBoard

Files:

• QtObservedBond.cpp (added)
• QtObservedBond.hpp (added)
• QtObservedInstanceBoard.cpp (modified) (11 diffs)
• QtObservedInstanceBoard.hpp (modified) (9 diffs)

src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp

@@ -62 +62 @@
       *this,
       boost::bind(&QtObservedInstanceBoard::atomcountsubjectKilled, this, _1)),
+  bondObservedValues(
+      "bond",
+      *this,
+      boost::bind(&QtObservedInstanceBoard::bondcountsubjectKilled, this, _1)),
   moleculeObservedValues(
       "molecule",
@@ -69 +73 @@
   qRegisterMetaType<ObservedValue_Index_t>("ObservedValue_Index_t");
   qRegisterMetaType<QtObservedAtom::ptr>("QtObservedAtom::ptr");
+  qRegisterMetaType<QtObservedBond::ptr>("QtObservedBond::ptr");
   qRegisterMetaType<QtObservedMolecule::ptr>("QtObservedMolecule::ptr");
 
@@ -83 +88 @@
     World::getInstance().signOff(this, World::MoleculeInserted);
   }
-  // sign off from all remaining molecules and atoms
+  // sign off from all remaining molecules, bonds, and atoms
   for (SignedOn_t::iterator iter = AtomSignedOn.begin(); !AtomSignedOn.empty();
       iter = AtomSignedOn.begin()) {
     (*iter)->signOff(this, atom::IndexChanged);
-    AtomSignedOn.erase(iter);
+    (*iter)->signOff(this, atom::BondsAdded);
+    AtomSignedOn.erase(*iter);
   }
 
@@ -108 +114 @@
   if ( iter != AtomSignedOn.end()) {
     LOG(3, "DEBUG: InstanceBoard got subjectKilled() from atom " << publisher);
-    AtomSignedOn.erase(iter);
+    AtomSignedOn.erase(iter); // only remove one
   } else {
     iter = MoleculeSignedOn.find(publisher);
@@ -176 +182 @@
           LOG(3, "DEBUG: InformationBoard signOn()s to atom " << _id);
           _atom->signOn(this, atom::IndexChanged);
+          _atom->signOn(this, atom::BondsAdded);
+          AtomSignedOn.insert( static_cast<Observable *>(const_cast<atom *>(_atom)) );
           AtomSignedOn.insert( static_cast<Observable *>(const_cast<atom *>(_atom)) );
           emit atomInserted(observedatom);
@@ -232 +240 @@
         break;
       }
+      case AtomObservable::BondsAdded:
+      {
+        const atom * _atom = dynamic_cast<atom *>(publisher);
+        const atomId_t _id = _atom->getId();
+#ifdef LOG_OBSERVER
+      observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that atom "+toString(_id)+" has been inserted.";
+#endif
+        LOG(3, "DEBUG: InformationBoard got bondInserted signal for atom " << _id);
+        if (_atom != NULL) {
+          // find the new bond by simply taking the last added to the list
+          const BondList &ListOfBonds = _atom->getListOfBonds();
+          const bond::ptr bondref = ListOfBonds.back();
+          const bondId_t bondid =
+              std::make_pair( bondref->leftatom->getId(), bondref->rightatom->getId());
+          LOG(3, "DEBUG: InformationBoard initializes QtObservedBond for " << bondid);
+          QtObservedBond::ptr observedbond(
+              new QtObservedBond(bondid, bondref, *this));
+          const ObservedValue_Index_t index = observedbond->getIndex();
+          bondObservedValues.insert(index, observedbond);
+          bondids_lookup.left.insert( std::make_pair(bondid, index) );
+          emit bondInserted(observedbond);
+        } else {
+          ELOG(1, "QtObservedInstanceBoard got BondsAdded for unknown atom id " << _id);
+        }
+        break;
+      }
       default:
         ASSERT(0, "QtObservedInstanceBoard::recieveNotification() - we cannot get here.");
@@ -239 +273 @@
     ASSERT(0, "QtObservedInstanceBoard::recieveNotification() - notification from unknown source.");
   }
-}
-
-void QtObservedInstanceBoard::atomcountsubjectKilled(ObservedValue_Index_t _id)
-{
-  LOG(3, "DEBUG: InstanceBoard emits atomRemoved for " << _id);
-  emit atomRemoved(_id);
-}
-
-void QtObservedInstanceBoard::moleculecountsubjectKilled(ObservedValue_Index_t _id)
-{
-  LOG(3, "DEBUG: InstanceBoard emits moleculeRemoved for " << _id);
-  emit moleculeRemoved(_id);
 }
 
@@ -262 +284 @@
 }
 
+const QtObservedInstanceBoard::bondId_t
+QtObservedInstanceBoard::getBondIdToIndex(ObservedValue_Index_t _id) const
+{
+  typename IdtoIndex_t<bondId_t>::right_const_iterator iter = bondids_lookup.right.find(_id);
+  ASSERT( iter != bondids_lookup.right.end(),
+      "QtObservedInstanceBoard::getBondIdToIndex() - index "
+      +toString(_id)+" is unknown.");
+  return iter->second;
+}
+
 const moleculeId_t QtObservedInstanceBoard::getMoleculeIdToIndex(ObservedValue_Index_t _id) const
 {
@@ -271 +303 @@
 }
 
+void QtObservedInstanceBoard::atomcountsubjectKilled(ObservedValue_Index_t _id)
+{
+  LOG(3, "DEBUG: InstanceBoard emits atomRemoved for " << getAtomIdToIndex(_id));
+  emit atomRemoved(_id);
+}
+
+void QtObservedInstanceBoard::bondcountsubjectKilled(ObservedValue_Index_t _id)
+{
+  LOG(3, "DEBUG: InstanceBoard emits bondRemoved for " << getBondIdToIndex(_id));
+  emit bondRemoved(_id);
+}
+
+void QtObservedInstanceBoard::moleculecountsubjectKilled(ObservedValue_Index_t _id)
+{
+  LOG(3, "DEBUG: InstanceBoard emits moleculeRemoved for " << getMoleculeIdToIndex(_id));
+  emit moleculeRemoved(_id);
+}
+
 QtObservedAtom::ptr QtObservedInstanceBoard::getObservedAtom(const atomId_t _id)
 {
@@ -279 +329 @@
 {
   return atomObservedValues.get(_id);
+}
+
+QtObservedBond::ptr QtObservedInstanceBoard::getObservedBond(const bondId_t _id)
+{
+  return bondObservedValues.get(bondids_lookup.left.at(_id));
+}
+
+QtObservedBond::ptr QtObservedInstanceBoard::getObservedBond(ObservedValue_Index_t _id)
+{
+  return bondObservedValues.get(_id);
 }
 
@@ -307 +367 @@
 }
 
+void QtObservedInstanceBoard::markObservedBondAsConnected(ObservedValue_Index_t _id)
+{
+  bondObservedValues.markObservedValuesAsConnected(_id);
+}
+
+void QtObservedInstanceBoard::markObservedBondAsDisconnected(ObservedValue_Index_t _id)
+{
+  bondObservedValues.markObservedValuesAsDisconnected(_id);
+}
+
+void QtObservedInstanceBoard::markObservedBondForErase(ObservedValue_Index_t _id)
+{
+  bondObservedValues.eraseObservedValues(_id);
+  bondids_lookup.right.erase(_id);
+}
+
 void QtObservedInstanceBoard::markObservedMoleculeAsConnected(ObservedValue_Index_t _id)
 {

src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp

@@ -18 +18 @@
 
 #include "UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp"
+#include "UIElements/Qt4/InstanceBoard/QtObservedBond.hpp"
 #include "UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp"
 
@@ -64 +65 @@
 
 public:
+  //!> copy bond id type from QtObservedBond
+  typedef QtObservedBond::bondId_t bondId_t;
+
   /** Cstor of QtObservedInstanceBoard.
    *
@@ -81 +85 @@
 
   const atomId_t getAtomIdToIndex(ObservedValue_Index_t _id) const;
+  const bondId_t getBondIdToIndex(ObservedValue_Index_t _id) const;
   const moleculeId_t getMoleculeIdToIndex(ObservedValue_Index_t _id) const;
 
   QtObservedAtom::ptr getObservedAtom(const atomId_t _id);
   QtObservedAtom::ptr getObservedAtom(ObservedValue_Index_t _id);
+  QtObservedBond::ptr getObservedBond(const bondId_t _id);
+  QtObservedBond::ptr getObservedBond(ObservedValue_Index_t _id);
   QtObservedMolecule::ptr getObservedMolecule(const moleculeId_t _id);
   QtObservedMolecule::ptr getObservedMolecule(ObservedValue_Index_t _id);
@@ -90 +97 @@
   void markObservedAtomAsDisconnected(ObservedValue_Index_t _id);
   void markObservedAtomForErase(ObservedValue_Index_t _id);
+  void markObservedBondAsConnected(ObservedValue_Index_t _id);
+  void markObservedBondAsDisconnected(ObservedValue_Index_t _id);
+  void markObservedBondForErase(ObservedValue_Index_t _id);
   void markObservedMoleculeAsConnected(ObservedValue_Index_t _id);
   void markObservedMoleculeAsDisconnected(ObservedValue_Index_t _id);
@@ -98 +108 @@
   void atomRemoved(ObservedValue_Index_t _atomid);
   void atomIndexChanged(const atomId_t _oldid, const atomId_t _newid);
+  void bondInserted(QtObservedBond::ptr _bond);
+  void bondRemoved(ObservedValue_Index_t _bondid);
+  void bondIndexChanged(const bondId_t _oldid, const bondId_t _newid);
   void moleculeInserted(QtObservedMolecule::ptr _mol);
   void moleculeRemoved(ObservedValue_Index_t _molid);
@@ -111 +124 @@
   bool WorldSignedOn;
 
-  typedef std::set<Observable *> SignedOn_t;
+  typedef std::multiset<Observable *> SignedOn_t;
   //!> map indicating to which atom we are currently signed on
   SignedOn_t AtomSignedOn;
@@ -121 +134 @@
   struct IdtoIndex_t : boost::bimap<id, ObservedValue_Index_t> {};
   IdtoIndex_t<atomId_t> atomids_lookup;
+  IdtoIndex_t<bondId_t> bondids_lookup;
   IdtoIndex_t<moleculeId_t> moleculeids_lookup;
 
@@ -132 +146 @@
    */
   void atomcountsubjectKilled(ObservedValue_Index_t _id);
+
+  /** Counts how many bond's ObservedValues got subjectKilled.
+   *
+   * This is used to give removal signal only when each and every
+   * ObservedValue (and the instance itself) has been subjectKilled by the
+   * monitored Observable. Only then can we safely remove the instance.
+   *
+   * \param _bondid id of the bond
+   */
+  void bondcountsubjectKilled(ObservedValue_Index_t _bondid);
 
   /** Counts how many molecule's ObservedValues got subjectKilled.
@@ -145 +169 @@
   //!> container with all ObservedValues for each atom, associated by id
   ObservedValuesContainer<QtObservedAtom, ObservedValue_Index_t> atomObservedValues;
+  //!> container with all ObservedValues for each bond, associated by id pairs
+  ObservedValuesContainer<QtObservedBond, ObservedValue_Index_t> bondObservedValues;
   //!> container with all ObservedValues for each molecule, associated by id
   ObservedValuesContainer<QtObservedMolecule, ObservedValue_Index_t> moleculeObservedValues;