Changeset 8cc22f for src/Atom/atom.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.cpp (modified) (2 diffs)

src/Atom/atom.cpp

@@ -90 +90 @@
 
 
-void atom::UpdateSteps()
-{
-  LOG(4,"atom::UpdateSteps() called.");
+void atom::UpdateStep(const unsigned int _step)
+{
+  LOG(4,"atom::UpdateStep() called.");
   // append to position, velocity and force vector
-  AtomInfo::AppendTrajectoryStep();
+  AtomInfo::AppendTrajectoryStep(WorldTime::getTime()+1);
   // append to ListOfBonds vector
-  BondedParticleInfo::AppendTrajectoryStep();
-}
-
-void atom::removeSteps()
-{
-  LOG(4,"atom::removeSteps() called.");
+  BondedParticleInfo::AppendTrajectoryStep(WorldTime::getTime()+1);
+}
+
+void atom::removeStep(const unsigned int _step)
+{
+  LOG(4,"atom::removeStep() called.");
   // append to position, velocity and force vector
-  AtomInfo::removeTrajectoryStep();
+  AtomInfo::removeTrajectoryStep(_step);
   // append to ListOfBonds vector
-  BondedParticleInfo::removeTrajectoryStep();
+  BondedParticleInfo::removeTrajectoryStep(_step);
 }
 
@@ -310 +310 @@
 atom* NewAtom(atomId_t _id){
   atom * res = new atom();
-  // extent trajectory to current time step
-  const size_t CurrentTime = WorldTime::getTime();
-  for (size_t step = res->getTrajectorySize(); step <= CurrentTime; ++step)
-    res->UpdateSteps();
   res->setId(_id);
   return res;