Changeset b119a0 for src/Actions

Timestamp:

Oct 19, 2014, 5:10:16 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:

5c8807

Parents:

9e1bfb (diff), 46ce1c (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'DynamicMolecules' into Candidate_v1.4.9

Location:

src/Actions

Files:

• MoleculeAction/ForceAnnealingAction.cpp (modified) (1 diff)
• MoleculeAction/VerletIntegrationAction.cpp (modified) (3 diffs)
• UndoRedoHelpers.cpp (modified) (1 diff)
• UndoRedoHelpers.hpp (modified) (3 diffs)

src/Actions/MoleculeAction/ForceAnnealingAction.cpp

@@ -79 +79 @@
         ++iter) {
       atom * const Walker = iter->second;
-      Walker->UpdateSteps();
       Walker->setPositionAtStep(CurrentStep+1,
           Walker->getPositionAtStep(CurrentStep));

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

src/Actions/UndoRedoHelpers.cpp

@@ -181 +181 @@
 }
 
-void MoleCuilder::removeLastStep(const std::vector<atomId_t> &_atoms)
+void MoleCuilder::removeLastStep(const std::vector<atomId_t> &_atoms, const unsigned int _step)
 {
   for (size_t i=0; i<_atoms.size(); ++i) {
     atom * const _atom = World::getInstance().getAtom(AtomById(_atoms[i]));
-    _atom->removeSteps();
-  }
-}
-
-void MoleCuilder::addNewStep(const std::vector<AtomicInfo> &_movedatoms)
+    _atom->removeStep(_step);
+  }
+}
+
+void MoleCuilder::addNewStep(const std::vector<AtomicInfo> &_movedatoms, const unsigned int _step)
 {
   for(size_t i=0; i< _movedatoms.size(); ++i) {
     atom * const _atom = World::getInstance().getAtom(AtomById(_movedatoms[i].getId()));
-    _atom->UpdateSteps();
-  }
-}
-
-void MoleCuilder::addNewStep(const std::vector<atomId_t> &_ids)
+    _atom->UpdateStep(_step);
+  }
+}
+
+void MoleCuilder::addNewStep(const std::vector<atomId_t> &_ids, const unsigned int _step)
 {
   for(size_t i=0; i< _ids.size(); ++i) {
     atom * const _atom = World::getInstance().getAtom(AtomById(_ids[i]));
-    _atom->UpdateSteps();
+    _atom->UpdateStep(_step);
   }
 }

src/Actions/UndoRedoHelpers.hpp

@@ -107 +107 @@
    *
    * @param movedatoms atoms whose last step in time to remove
+   * @param _step which trajectory to remove
    */
-  void removeLastStep(const std::vector<atomId_t> &movedatoms);
+  void removeLastStep(const std::vector<atomId_t> &movedatoms, const unsigned int _step);
 
   /** Adds another time step to all \a movedatoms.
@@ -115 +116 @@
    *
    * @param _ids atoms whose last step in time to remove
+   * @param _step which trajectory to insert/assign
    */
-  void addNewStep(const std::vector<atomId_t> &_ids);
+  void addNewStep(const std::vector<atomId_t> &_ids, const unsigned int _step);
 
   /** Adds another time step to all \a movedatoms.
@@ -124 +126 @@
    *
    * @param _movedatoms atoms whose last step in time to remove
+   * @param _step which trajectory to insert/assign
    */
-  void addNewStep(const std::vector<AtomicInfo> &_movedatoms);
+  void addNewStep(const std::vector<AtomicInfo> &_movedatoms, const unsigned int _step);
 
   /** Helper function to extract id information from vector of AtomicInfo.