Changeset 8cc22f for src/Atom/atom_bondedparticle.cpp

Timestamp:

Sep 18, 2014, 6:24:51 PM (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, Candidate_v1.7.0, 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_bondedparticle.cpp (modified) (7 diffs)

src/Atom/atom_bondedparticle.cpp

@@ -52 +52 @@
 BondedParticle::BondedParticle()
 {
-  ListOfBonds.push_back(BondList());
+  ListOfBonds.insert( std::make_pair(0, emptyList) );
 };
 
@@ -59 +59 @@
 BondedParticle::~BondedParticle()
 {
-  removeAllBonds();
+  for(BondTrajectory_t::iterator iter = ListOfBonds.begin(); !ListOfBonds.empty();
+      iter = ListOfBonds.begin()) {
+    removeAllBonds(iter->first);
+    ListOfBonds.erase(iter);
+  }
 };
 
@@ -220 +224 @@
 }
 
-/** Removes all bonds in all timesteps and their instances, too.
+/** Removes all bonds in current timestep and their instances, too.
  *
  */
 void BondedParticle::removeAllBonds()
 {
-  for (size_t index = 0; index < ListOfBonds.size(); ++index)
-    removeAllBonds(index);
+  removeAllBonds(WorldTime::getTime());
 }
 
@@ -236 +239 @@
 {
   //LOG(3,"INFO: Clearing all bonds of " << *this << ": " << ListOfBonds[_step]);
-  for (BondList::iterator iter = (ListOfBonds[_step]).begin();
-      !(ListOfBonds[_step]).empty();
-      iter = (ListOfBonds[_step]).begin()) {
-    //LOG(3,"INFO: Clearing bond (" << *iter << ") " << *(*iter) << " of list " << &ListOfBonds);
-    atom * const Other = (*iter)->GetOtherAtom(this);
-    ASSERT( Other != NULL,
-        "BondedParticle::removeAllBonds() - cannot find bond partner for "
-        +toString(**iter)+".");
-    Other->UnregisterBond(_step, *iter);
-    UnregisterBond(_step, *iter);
-  }
+  BondTrajectory_t::iterator listiter = ListOfBonds.find(_step);
+  if (listiter != ListOfBonds.end())
+    for (BondList::iterator iter = listiter->second.begin();
+        !listiter->second.empty();
+        iter = listiter->second.begin()) {
+      //LOG(3,"INFO: Clearing bond (" << *iter << ") " << *(*iter) << " of list " << &ListOfBonds);
+      atom * const Other = (*iter)->GetOtherAtom(this);
+      ASSERT( Other != NULL,
+          "BondedParticle::removeAllBonds() - cannot find bond partner for "
+          +toString(**iter)+".");
+      Other->UnregisterBond(_step, *iter);
+      UnregisterBond(_step, *iter);
+    }
 }
 
@@ -260 +265 @@
     if (Binder->Contains(this)) {
       //LOG(3,"INFO: Registering bond "<< *Binder << " with atom " << *this << " at step " << _step);
-      if (ListOfBonds.size() <= _step)
-        ListOfBonds.resize(_step+1);
-      ListOfBonds[_step].push_back(Binder);
+      std::pair< BondTrajectory_t::iterator, bool> inserter =
+          ListOfBonds.insert( std::make_pair( _step, BondList(1, Binder)) );
+      if (!inserter.second)
+        inserter.first->second.push_back(Binder);
       if (WorldTime::getTime() == _step)
         NOTIFY(AtomObservable::BondsAdded);
@@ -290 +296 @@
       OBSERVE;
       //LOG(0,"INFO: Unregistering bond "<< *Binder << " from list " << &ListOfBonds << " of atom " << *this << " at step " << step);
+      BondTrajectory_t::iterator listiter = ListOfBonds.find(_step);
+      if (listiter != ListOfBonds.end()) {
 #ifndef NDEBUG
-      BondList::const_iterator iter =
-          std::find(ListOfBonds[_step].begin(), ListOfBonds[_step].end(), Binder);
-      ASSERT( iter != ListOfBonds[_step].end(),
-          "BondedParticle::UnregisterBond() - "+toString(*Binder)+" not contained at "
-          +toString(_step));
+        BondList::const_iterator iter =
+            std::find(listiter->second.begin(), listiter->second.end(), Binder);
+        ASSERT( iter != listiter->second.end(),
+            "BondedParticle::UnregisterBond() - "+toString(*Binder)+" not contained at "
+            +toString(_step));
 #endif
-      Binder->removeAtom(this);
-      ListOfBonds[_step].remove(Binder);
-      if (WorldTime::getTime() == _step)
-        NOTIFY(AtomObservable::BondsRemoved);
-      status = true;
+        Binder->removeAtom(this);
+        listiter->second.remove(Binder);
+        if (WorldTime::getTime() == _step)
+          NOTIFY(AtomObservable::BondsRemoved);
+        status = true;
+      }
     } else {
       ELOG(1, *Binder << " does not contain " << *this << ".");
@@ -328 +337 @@
 {
   int step = -1;
-  int tempstep = 0;
-  for(std::vector<BondList>::const_iterator iter = ListOfBonds.begin();
-      iter != ListOfBonds.end();
-      ++iter,++tempstep) {
-    for (BondList::const_iterator bonditer = iter->begin();
-        bonditer != iter->end();
+  for(BondTrajectory_t::const_iterator listiter = ListOfBonds.begin();
+      listiter != ListOfBonds.end();
+      ++listiter) {
+    for (BondList::const_iterator bonditer = listiter->second.begin();
+        bonditer != listiter->second.end();
         ++bonditer) {
       if ((*bonditer) == Binder) {
-        step = tempstep;
+        step = listiter->first;
         break;
       }