Changeset 917659

Timestamp:

Sep 29, 2013, 11:40:49 AM (11 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:

c60665

Parents:

beadd0

git-author:

Frederik Heber <heber@…> (09/05/13 07:07:45)

git-committer:

Frederik Heber <heber@…> (09/29/13 11:40:49)

Message:

FIX: GLMoleculeObject_atom just stores the atom's id, now ptr.

Location:

src/UIElements/Views/Qt4/Qt3D

Files:

• GLMoleculeObject_atom.cpp (modified) (11 diffs)
• GLMoleculeObject_atom.hpp (modified) (3 diffs)
• GLWorldScene.cpp (modified) (1 diff)

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp

@@ -53 +53 @@
 #include "WorldTime.hpp"
 
-GLMoleculeObject_atom::GLMoleculeObject_atom(QGLSceneNode *mesh[], QObject *parent, const atom *atomref) :
+GLMoleculeObject_atom::GLMoleculeObject_atom(QGLSceneNode *mesh[], QObject *parent, const atomId_t _id) :
   GLMoleculeObject(mesh, parent),
-  Observer(std::string("GLMoleculeObject_atom")+toString(atomref->getId())),
-  _atom(atomref)
+  Observer(std::string("GLMoleculeObject_atom")+toString(_id)),
+  atomicid(_id)
 {
   // sign on as observer (obtain non-const instance before)
-  atomref->signOn(this, AtomObservable::IndexChanged);
-  atomref->signOn(this, AtomObservable::PositionChanged);
-  atomref->signOn(this, AtomObservable::ElementChanged);
-  atomref->signOn(this, AtomObservable::BondsAdded);
+  const atom *_atom = World::getInstance().getAtom(AtomById(atomicid));
+  if (_atom != NULL) {
+    _atom->signOn(this, AtomObservable::IndexChanged);
+    _atom->signOn(this, AtomObservable::PositionChanged);
+    _atom->signOn(this, AtomObservable::ElementChanged);
+    _atom->signOn(this, AtomObservable::BondsAdded);
+  } else {
+    ELOG(2, "Atom with id "+toString(atomicid)+" is already gone.");
+  }
   World::getInstance().signOn(this, World::SelectionChanged);
   WorldTime::getInstance().signOn(this, WorldTime::TimeChanged);
@@ -69 +74 @@
   resetProperties();
 
-  LOG(2, "INFO: Created sphere for atom " << _atom->getId() << ".");
+  LOG(2, "INFO: Created sphere for atom " << atomicid << ".");
 
   connect( this, SIGNAL(clicked()), this, SLOT(wasClicked()));
@@ -76 +81 @@
 GLMoleculeObject_atom::~GLMoleculeObject_atom()
 {
-  if (_atom){
+  const atom *_atom = World::getInstance().getAtom(AtomById(atomicid));
+  if (_atom != NULL){
     _atom->signOff(this, AtomObservable::IndexChanged);
     _atom->signOff(this, AtomObservable::PositionChanged);
@@ -89 +95 @@
 {
 #ifdef LOG_OBSERVER
-  observerLog().addMessage() << "++ Update of Observer " << observerLog().getName(static_cast<Observer *>(this)) << " from atom "+toString(_atom->getId())+".";
+  observerLog().addMessage() << "++ Update of Observer " << observerLog().getName(static_cast<Observer *>(this)) << " from atom "+toString(atomicid)+".";
 #endif
   resetProperties();
@@ -96 +102 @@
 void GLMoleculeObject_atom::resetPosition()
 {
-  const Vector Position = _atom->getPosition();
-  LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new position is "+toString(Position)+".");
-  setPosition(QVector3D(Position[0], Position[1], Position[2]));
+  const atom *_atom = World::getInstance().getAtom(AtomById(atomicid));
+  if (_atom != NULL) {
+    const Vector Position = _atom->getPosition();
+    LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new position is "+toString(Position)+".");
+    setPosition(QVector3D(Position[0], Position[1], Position[2]));
+  } else {
+    ELOG(2, "Atom with id "+toString(atomicid)+" is already gone.");
+  }
 }
 
@@ -104 +115 @@
 {
   size_t elementno = 0;
-  if (_atom->getType() != NULL) {
-    elementno = _atom->getType()->getAtomicNumber();
-  } else { // if no element yet, set to hydrogen
-    elementno = 1;
-  }
-  LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new element number is "+toString(elementno)+".");
-
-  // set materials
-  QGLMaterial *elementmaterial = getMaterial(elementno);
-  ASSERT(elementmaterial != NULL,
-      "GLMoleculeObject_atom::GLMoleculeObject_atom() - QGLMaterial ref from getter function is NULL.");
-  setMaterial(elementmaterial);
-
-  // set scale
-  double radius = 0.;
-  if (_atom->getType() != NULL) {
-    radius = _atom->getType()->getVanDerWaalsRadius();
-  } else {
-    radius = 0.5;
-  }
-  setScale( radius / 4. );
+  const atom *_atom = World::getInstance().getAtom(AtomById(atomicid));
+  if (_atom != NULL) {
+    const element *_type = _atom->getType();
+    if (_type != NULL) {
+      elementno = _type->getAtomicNumber();
+    } else { // if no element yet, set to hydrogen
+      elementno = 1;
+    }
+    LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new element number is "+toString(elementno)+".");
+
+    // set materials
+    QGLMaterial *elementmaterial = getMaterial(elementno);
+    ASSERT(elementmaterial != NULL,
+        "GLMoleculeObject_atom::GLMoleculeObject_atom() - QGLMaterial ref from getter function is NULL.");
+    setMaterial(elementmaterial);
+
+    // set scale
+    double radius = 0.;
+    if (_type != NULL) {
+      radius = _type->getVanDerWaalsRadius();
+    } else {
+      radius = 0.5;
+    }
+    setScale( radius / 4. );
+  } else {
+    ELOG(2, "Atom with id "+toString(atomicid)+" is already gone.");
+  }
 }
 
@@ -130 +147 @@
 {
   int oldId = objectId();
-  const size_t atomno = _atom->getId();
-  LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new index is "+toString(atomno)+".");
-  setObjectId(atomno);
-
-  emit indexChanged(this, oldId, atomno);
+  LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new index is "+toString(atomicid)+".");
+  setObjectId(atomicid);
+
+  emit indexChanged(this, oldId, atomicid);
 }
 
@@ -149 +165 @@
 
   // selected?
-  setSelected(World::getInstance().isSelected(_atom));
+  setSelected(World::getInstance().isAtomSelected(atomicid));
 }
 
 void GLMoleculeObject_atom::subjectKilled(Observable *publisher)
 {
-  _atom = NULL;
+  // remove id such that we don't sign off accidentally from a different atom
+  const_cast<atomId_t &>(atomicid) = -1;
 }
 
 void GLMoleculeObject_atom::recieveNotification(Observable *publisher, Notification_ptr notification)
 {
+  const atom *_atom = World::getInstance().getAtom(AtomById(atomicid));
   if (publisher == dynamic_cast<const Observable*>(_atom)){
     // notofication from atom
@@ -180 +198 @@
       case AtomObservable::BondsAdded:
       {
+        const atom *_atom = World::getInstance().getAtom(AtomById(atomicid));
+        if (_atom != NULL) {
           ASSERT(!_atom->getListOfBonds().empty(),
               "GLMoleculeObject_atom::recieveNotification() - received BondsAdded but ListOfBonds is empty.");
@@ -186 +206 @@
               GLMoleculeObject_bond::left : GLMoleculeObject_bond::right;
           emit BondsInserted(_bond, side);
-          break;
+        } else {
+          ELOG(2, "Atom with id "+toString(atomicid)+" is already gone.");
         }
+        break;
+      }
       default:
         //setProperties();
@@ -226 +249 @@
 void GLMoleculeObject_atom::wasClicked()
 {
-  LOG(4, "INFO: GLMoleculeObject_atom: atom " << _atom->getId() << " has been clicked");
-  emit clicked(_atom->getId());
-}
+  LOG(4, "INFO: GLMoleculeObject_atom: atom " << atomicid << " has been clicked");
+  emit clicked(atomicid);
+}

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp

@@ -19 +19 @@
 
 #include "Bond/bond.hpp"
-#include "GLMoleculeObject_bond.hpp"
-
-class atom;
+#include "UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp"
+#include "types.hpp"
 
 class GLMoleculeObject_atom : public GLMoleculeObject, public Observer
@@ -27 +26 @@
   Q_OBJECT
 public:
-  GLMoleculeObject_atom(QGLSceneNode *mesh[], QObject *parent, const atom *atomref);
+  GLMoleculeObject_atom(QGLSceneNode *mesh[], QObject *parent, const atomId_t id);
   virtual ~GLMoleculeObject_atom();
 
@@ -51 +50 @@
   void resetProperties();
 
-  const atom *_atom;
+  const atomId_t atomicid;
 };
 

src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp

@@ -145 +145 @@
 {
   LOG(3, "INFO: GLWorldScene: Received signal atomInserted for atom "+toString(_id)+".");
-  const atom *_atom = World::getInstance().getAtom(AtomById(_id));
-  GLMoleculeObject_atom *atomObject = new GLMoleculeObject_atom(meshSphere, this, _atom);
+  GLMoleculeObject_atom *atomObject = new GLMoleculeObject_atom(meshSphere, this, _id);
   AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
   ASSERT(iter == AtomsinSceneMap.end(),
-      "GLWorldScene::atomAdded() - same atom "+_atom->getName()+" added again.");
+      "GLWorldScene::atomAdded() - same atom "+toString(_id)+" added again.");
   AtomsinSceneMap.insert( make_pair(_id, atomObject) );