Changeset c1d837 for src

Timestamp:

Feb 10, 2015, 2:09:10 PM (10 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:

329cf3

Parents:

c26617

git-author:

Frederik Heber <heber@…> (02/10/15 12:18:33)

git-committer:

Frederik Heber <heber@…> (02/10/15 14:09:10)

Message:

FIX: [push/pop][Atom/Molecule]Selection would store ptrs instead of ids.

• this is potentially risky as popping a selection may occur at a later stage where the ptrs has been deallocated. Hence, we now store only ids and these get reselected on popping.
• also fixed some faulty message with respect to associated Actions.

Location:

src

Files:

• Actions/ActionSequence.hpp (modified) (2 diffs)
• Actions/MakroAction.hpp (modified) (2 diffs)
• Actions/SelectionAction/Atoms/PopAtomsAction.cpp (modified) (1 diff)
• Actions/SelectionAction/Atoms/PushAtomsAction.cpp (modified) (1 diff)
• Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) (1 diff)
• Actions/unittests/ActionSequenceUnitTest.cpp (modified) (1 diff)
• World.cpp (modified) (5 diffs)
• World.hpp (modified) (2 diffs)

src/Actions/ActionSequence.hpp

@@ -19 +19 @@
 #include <deque>
 
+class ActionSequenceTest;
+
 namespace MoleCuilder {
 
@@ -27 +29 @@
 {
   friend class MakroAction;
+  //!> grant unit test access to private sequence
+  friend class ::ActionSequenceTest;
 public:
   typedef std::deque<Action*> actionSet;

src/Actions/MakroAction.hpp

@@ -19 +19 @@
 #include "Actions/Action.hpp"
 
+class ActionSequenceTest;
+
 namespace MoleCuilder {
   class ActionRegistry;
@@ -30 +32 @@
 class MakroAction : public Action
 {
+  //!> grant unit test access to sequence
+  friend class ::ActionSequenceTest;
 public:
   MakroAction(const ActionTrait &_trait,ActionSequence& _actions);

src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp

@@ -63 +63 @@
 ActionState::ptr SelectionPopAtomsAction::performUndo(ActionState::ptr _state) {
   SelectionPopAtomsState *state = static_cast<SelectionPopAtomsState *>(_state.get());
-  LOG(1, "Popping atom selection.");
+  LOG(1, "Pushing atom selection.");
   World::getInstance().pushAtomSelection();
 

src/Actions/SelectionAction/Atoms/PushAtomsAction.cpp

@@ -54 +54 @@
 
 ActionState::ptr SelectionPushAtomsAction::performUndo(ActionState::ptr _state) {
-  LOG(1, "Pushing atom selection.");
+  LOG(1, "Popping atom selection.");
   World::getInstance().popAtomSelection();
 

src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp

@@ -55 +55 @@
 ActionState::ptr SelectionMoleculeOfAtomAction::performCall() {
   std::vector<molecule *> selectedMolecules = World::getInstance().getSelectedMolecules();
-  LOG(1, "Selecting molecule to currently selected atoms.");
+  LOG(1, "Selecting molecule to currently selected atoms: " << World::getInstance().countSelectedAtoms());
   World::getInstance().selectAllMolecules(MoleculesByAtomSelection());
   LOG(0, World::getInstance().countSelectedMolecules() << " molecules selected.");

src/Actions/unittests/ActionSequenceUnitTest.cpp

@@ -301 +301 @@
   ActionSequence *sequence = new ActionSequence();
   ActionTrait wasCalledTrait("wasCalledActionStub");
-  wasCalledActionStub *wasCalled1 = new wasCalledActionStub(wasCalledTrait);
-  wasCalledActionStub *wasCalled2 = new wasCalledActionStub(wasCalledTrait);
-  sequence->addAction(wasCalled1);
-  sequence->addAction(wasCalled2);
+  sequence->addAction(new wasCalledActionStub(wasCalledTrait));
+  sequence->addAction(new wasCalledActionStub(wasCalledTrait));
 
   ActionTrait MakroTrait("Test MakroAction");
   MakroAction act(MakroTrait,*sequence);
+  wasCalledActionStub *wasCalled1 =
+      static_cast<wasCalledActionStub *>(act.actions.actions.front());
+  wasCalledActionStub *wasCalled2 =
+      static_cast<wasCalledActionStub *>(act.actions.actions.back());
 
   act.call();

src/World.cpp

@@ -48 +48 @@
 #include "Descriptors/AtomDescriptor.hpp"
 #include "Descriptors/AtomDescriptor_impl.hpp"
+#include "Descriptors/AtomIdDescriptor.hpp"
 #include "Descriptors/AtomSelectionDescriptor.hpp"
 #include "Descriptors/MoleculeDescriptor.hpp"
 #include "Descriptors/MoleculeDescriptor_impl.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "Descriptors/MoleculeSelectionDescriptor.hpp"
 #include "Descriptors/SelectiveConstIterator_impl.hpp"
@@ -559 +561 @@
   OBSERVE;
   NOTIFY(SelectionChanged);
-  selectedAtoms = selectedAtoms_Stack.top();
+  const atomIdsVector_t atomids = selectedAtoms_Stack.top();
+  boost::function<void (const atomId_t)> IdSelector =
+      boost::bind(static_cast<void (World::*)(const atomId_t)>(&World::selectAtom), this, _1);
+  selectedAtoms.clear();
+  std::for_each(atomids.begin(),atomids.end(), IdSelector);
   selectedAtoms_Stack.pop();
 }
@@ -566 +572 @@
   OBSERVE;
   NOTIFY(SelectionChanged);
-  selectedAtoms_Stack.push( selectedAtoms );
+  atomIdsVector_t atomids(countSelectedAtoms(), (atomId_t)-1);
+  std::copy(
+      MapKeyIterator<AtomSelectionConstIterator>(beginAtomSelection()),
+      MapKeyIterator<AtomSelectionConstIterator>(endAtomSelection()),
+      atomids.begin());
+  selectedAtoms_Stack.push( atomids );
   selectedAtoms.clear();
 }
@@ -703 +714 @@
   OBSERVE;
   NOTIFY(SelectionChanged);
-  selectedMolecules = selectedMolecules_Stack.top();
+  const moleculeIdsVector_t moleculeids = selectedMolecules_Stack.top();
+  boost::function<void (const moleculeId_t)> IdSelector =
+      boost::bind(static_cast<void (World::*)(const moleculeId_t)>(&World::selectMolecule), this, _1);
+  selectedMolecules.clear();
+  std::for_each(moleculeids.begin(),moleculeids.end(), IdSelector);
   selectedMolecules_Stack.pop();
 }
@@ -710 +725 @@
   OBSERVE;
   NOTIFY(SelectionChanged);
-  selectedMolecules_Stack.push( selectedMolecules );
+  moleculeIdsVector_t moleculeids(countSelectedMolecules(), (moleculeId_t)-1);
+  boost::function<moleculeId_t (const molecule*)> IdRetriever =
+      boost::bind(&molecule::getId, _1);
+  std::copy(
+      MapKeyIterator<MoleculeSelectionConstIterator>(beginMoleculeSelection()),
+      MapKeyIterator<MoleculeSelectionConstIterator>(endMoleculeSelection()),
+      moleculeids.begin());
+  selectedMolecules_Stack.push( moleculeids );
   selectedMolecules.clear();
 }

src/World.hpp

@@ -491 +491 @@
   AtomSet atoms;
   AtomSet selectedAtoms;
-  std::stack<AtomSet> selectedAtoms_Stack;
+  typedef std::vector<atomId_t> atomIdsVector_t;
+  std::stack<atomIdsVector_t> selectedAtoms_Stack;
   /**
    * stores the pool for all available AtomIds below currAtomId
@@ -501 +502 @@
   MoleculeSet molecules;
   MoleculeSet selectedMolecules;
-  std::stack<MoleculeSet> selectedMolecules_Stack;
+  typedef std::vector<moleculeId_t> moleculeIdsVector_t;
+  std::stack<moleculeIdsVector_t> selectedMolecules_Stack;
   /**
    * stores the pool for all available AtomIds below currAtomId