Changeset f3b597 for src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp

Timestamp:

Jul 24, 2015, 4:44:35 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:

e7341e

Parents:

fac58f

git-author:

Frederik Heber <heber@…> (06/02/15 10:41:40)

git-committer:

Frederik Heber <heber@…> (07/24/15 16:44:35)

Message:

FIX: GLMoleculeObject_molecule() may overlap with atomInserted() signal.

• this is because GLMoleculeObject_molecule takes some time till init() is called and its runs in a separate thread (hence, further atoms may be loaded into the just created atoms). As we first signOn() and then call init(), we may end up initializing atoms whose atomInserted signal then also comes in but lateron. This causes the AtomsInSceneMap to have double entries and the assertion to fail. We now keep book of all atomic ids inserted during init() and these are ok to appear doubly and their signal is skipped.

File:

• src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) (2 diffs)

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

@@ -266 +266 @@
       atomicid = (*atomiter)->getId();
       atomInserted(atomicid);
+      InitAtomNodesSet.insert(atomicid);
 
       // create bond objects in scene
@@ -542 +543 @@
 {
   LOG(3, "INFO: GLWorldScene: Received signal atomInserted for atom "+toString(_id)+".");
-  GLMoleculeObject_atom *atomObject = new GLMoleculeObject_atom(GLMoleculeObject::meshSphere, this, _id);
-  ASSERT( atomObject != NULL,
-      "GLMoleculeObject_molecule::atomInserted - could not create atom object for "+toString(_id));
-  AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
-  ASSERT(iter == AtomsinSceneMap.end(),
-      "GLMoleculeObject_molecule::atomInserted - same atom with id "+toString(_id)+" added again.");
-  AtomsinSceneMap.insert( make_pair(_id, atomObject) );
-
-  qRegisterMetaType<atomId_t>("atomId_t");
-  qRegisterMetaType<bond::ptr>("bond::ptr");
-  qRegisterMetaType<GLMoleculeObject_bond::SideOfBond>("GLMoleculeObject_bond::SideOfBond");
-  connect (atomObject, SIGNAL(clicked(atomId_t)), this, SIGNAL(atomClicked(atomId_t)));
-  connect (atomObject, SIGNAL(changed()), this, SIGNAL(changed()));
-  connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SIGNAL(changed()));
-  connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SLOT(hoverChangedSignalled(GLMoleculeObject *)));
-  connect (atomObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
-  connect (atomObject, SIGNAL(BondsInserted(const bond::ptr , const GLMoleculeObject_bond::SideOfBond)), this, SLOT(bondInserted(const bond::ptr , const GLMoleculeObject_bond::SideOfBond)));
-  connect (atomObject, SIGNAL(indexChanged(GLMoleculeObject_atom*, int, int)), this, SIGNAL(changeAtomId(GLMoleculeObject_atom*, int, int)));
-
-  isBoundingBoxUptodate = false;
-
-  if (m_objectId  == -1)
-    setObjectId(_id);
+  // remove ids if second insertion via update comes in
+  if ((!InitAtomNodesSet.empty()) && (InitAtomNodesSet.find(_id) != InitAtomNodesSet.end())) {
+    // the problem is as follows:
+    // In order to get really all atoms, we first signOn to molecule and then call init()
+    // however, in init() further atoms may have been loaded which are then also
+    // instantiated by init(). Note only that but we also obtain an update() from
+    // molecule itself (because we signOn'd before) that a new atom is to be inserted
+    // hence, this would cause double insertion of the same atom and this has to be
+    // caught
+    InitAtomNodesSet.erase(_id);
+    LOG(4, "Atom with " << _id << " has already been added.");
+  } else {
+    GLMoleculeObject_atom *atomObject = new GLMoleculeObject_atom(GLMoleculeObject::meshSphere, this, _id);
+    ASSERT( atomObject != NULL,
+        "GLMoleculeObject_molecule::atomInserted - could not create atom object for "+toString(_id));
+    AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
+    ASSERT(iter == AtomsinSceneMap.end(),
+        "GLMoleculeObject_molecule::atomInserted - same atom with id "+toString(_id)+" added again.");
+    AtomsinSceneMap.insert( make_pair(_id, atomObject) );
+
+    qRegisterMetaType<atomId_t>("atomId_t");
+    qRegisterMetaType<bond::ptr>("bond::ptr");
+    qRegisterMetaType<GLMoleculeObject_bond::SideOfBond>("GLMoleculeObject_bond::SideOfBond");
+    connect (atomObject, SIGNAL(clicked(atomId_t)), this, SIGNAL(atomClicked(atomId_t)));
+    connect (atomObject, SIGNAL(changed()), this, SIGNAL(changed()));
+    connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SIGNAL(changed()));
+    connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SLOT(hoverChangedSignalled(GLMoleculeObject *)));
+    connect (atomObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
+    connect (atomObject, SIGNAL(BondsInserted(const bond::ptr , const GLMoleculeObject_bond::SideOfBond)), this, SLOT(bondInserted(const bond::ptr , const GLMoleculeObject_bond::SideOfBond)));
+    connect (atomObject, SIGNAL(indexChanged(GLMoleculeObject_atom*, int, int)), this, SIGNAL(changeAtomId(GLMoleculeObject_atom*, int, int)));
+
+    isBoundingBoxUptodate = false;
+
+    if (m_objectId  == -1)
+      setObjectId(_id);
+  }
 
   // add all bonds