Changeset 8cc22f for src/Atom/atom_bondedparticleinfo.cpp

Timestamp:

Sep 18, 2014, 6:24:51 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:

46ce1c

Parents:

7a7b34

git-author:

Frederik Heber <heber@…> (08/16/14 22:56:59)

git-committer:

Frederik Heber <heber@…> (09/18/14 18:24:51)

Message:

Changed how trajectories are stored, not as vecor but as map.

• AtomInfo and atom_bondedparticleinfo now store map<unsigned int, ...> instead of vector<...>.
• UpdateSteps() -> UpdateStep(unsigned int), same with RemoveSteps() and AppendTrajectorySteps() and RemoveTrajectorySteps().
• made changes necessary to UndoRedoHelpers and two Actions.
• TESTFIX: AtomObserverUnitTest failed as we longer "notify" in case already set element is set again. We now check that setType() sets to different element.

File:

• src/Atom/atom_bondedparticleinfo.cpp (modified) (2 diffs)

src/Atom/atom_bondedparticleinfo.cpp

@@ -57 +57 @@
 {}
 
-void BondedParticleInfo::AppendTrajectoryStep()
+void BondedParticleInfo::AppendTrajectoryStep(const unsigned int _step)
 {
-  ListOfBonds.push_back(BondList());
+  ListOfBonds.insert( std::make_pair(_step, emptyList) );
   LOG(5,"BondedParticleInfo::AppendTrajectoryStep() called, size is " << ListOfBonds.size());
 }
 
-void BondedParticleInfo::removeTrajectoryStep()
+void BondedParticleInfo::removeTrajectoryStep(const unsigned int _step)
 {
-  ListOfBonds.pop_back();
+  ListOfBonds.erase(_step);
   LOG(5,"BondedParticleInfo::removeTrajectoryStep() called, size is " << ListOfBonds.size());
 }
@@ -71 +71 @@
 const BondList& BondedParticleInfo::getListOfBonds() const
 {
-  if(WorldTime::getTime() < ListOfBonds.size())
-    return ListOfBonds[WorldTime::getTime()];
-  else
-    return emptyList;
+  return getListOfBondsAtStep(WorldTime::getTime());
 }
-
-//BondList& BondedParticleInfo::getListOfBonds()
-//{
-//  // todo: here we actually need a container on whose destruction notifiy is emitted, i.e.
-//  // similar or simply an ObservedContainer.
-//  OBSERVE;
-//  NOTIFY(AtomObservable::BondsAdded);
-//  const unsigned int size = ListOfBonds.size();
-//  ASSERT(WorldTime::getTime() <= size,
-//      "BondedParticleInfo::getBondsAtStep() - Access out of range: "
-//      +toString(WorldTime::getTime())
-//      +" not in [0,"+toString(size)+"].");
-//  if (WorldTime::getTime() == size) {
-//    UpdateSteps();
-//  }
-//  return ListOfBonds[WorldTime::getTime()];
-//}
 
 const BondList& BondedParticleInfo::getListOfBondsAtStep(unsigned int _step) const
 {
-  if(_step < ListOfBonds.size())
-    return ListOfBonds[_step];
-  else
-    return emptyList;
+  BondTrajectory_t::const_iterator iter =
+    ListOfBonds.find(_step);
+  if (iter != ListOfBonds.end())
+    return iter->second;
+  return emptyList;
 }
-
-//BondList& BondedParticleInfo::getListOfBondsAtStep(unsigned int _step)
-//{
-//  const unsigned int size = ListOfBonds.size();
-//  ASSERT(_step <= size,
-//      "BondedParticleInfo::getBondsAtStep() - Access out of range: "
-//      +toString(_step)
-//      +" not in [0,"+toString(size)+"].");
-//  if (_step == size) {
-//    UpdateSteps();
-//  }
-//  return ListOfBonds[_step];
-//}