Changeset 8cc22f for src/Actions/MoleculeAction/VerletIntegrationAction.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, 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/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) (3 diffs)

src/Actions/MoleculeAction/VerletIntegrationAction.cpp

@@ -56 +56 @@
 using namespace MoleCuilder;
 
-enum {
+enum VectorIndexType {
   PositionIndex=0,
   VelocityIndex=1,
   ForceIndex=2,
   MAXINDEX
-} VectorIndexType;
+};
 
 // and construct the stuff
@@ -134 +134 @@
 
   // remove current step for all modified atoms
-  removeLastStep(getIdsFromAtomicInfo(state->UndoInfo));
+  removeLastStep(getIdsFromAtomicInfo(state->UndoInfo), CurrentStep);
 
   // and set back the old step (forces have been changed)
@@ -151 +151 @@
 
   // set stored new state
-  addNewStep(state->UndoInfo);
+  size_t CurrentStep = WorldTime::getInstance().getTime()+1;
+  addNewStep(state->UndoInfo, CurrentStep);
 
   // add a new time step
-  size_t CurrentStep = WorldTime::getInstance().getTime();
-  World::getInstance().setTime(CurrentStep+1);
+  World::getInstance().setTime(CurrentStep);
 
   // and set positions of the new step