Changeset 7294dc for src/Fragmentation

Timestamp:

Jun 21, 2017, 9:51:24 PM (8 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.1, ChangeBugEmailaddress, ChemicalSpaceEvaluator, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph_documentation, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_oldresults, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, StoppableMakroAction, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps

Children:

101d2d

Parents:

9f2071

git-author:

Frederik Heber <heber@…> (03/23/17 17:11:47)

git-committer:

Frederik Heber <frederik.heber@…> (06/21/17 21:51:24)

Message:

FIX: Fixing the use of the trajectories that were changed to maps.

• as the atom's trajectories are now stored inside a map, i.e. not every step necessarily needs to be present, there will still some places in the code that were meant for the old vector storing.
• Atom::UpdateStep() updates the current step, not the future step.
• AtomInfo::append/removeTrajectoryStep() now no longer ASSERT that the step is not the current one. Due to the trajectory in map concept (with current it simply sought by lower_bound()) this is no longer necessary.
• HydrogenPool no longer adds all trajectory steps till current time.
• World has commented out code for also copying the current atom positions in case a new time step is added, but this is not used as so far we do not recognize whether it is a new time step ... and also it is not really necessary.
• TESTS: Removed XFAILs from tests of previous commit. They are all working again.

Location:

src/Fragmentation/Exporters

Files:

• HydrogenPool.cpp (modified) (1 diff)
• HydrogenPool.hpp (modified) (1 diff)

src/Fragmentation/Exporters/HydrogenPool.cpp

@@ -91 +91 @@
       +" from pool is already in use.");
   LOG(3, "DEBUG: Leasing " << *Walker << ".");
-  UpdateSteps(Walker);
   HydrogenInUse.insert( std::make_pair( Walker->getId(), Walker) );
   HydrogenQueue.pop_front();
 
   return Walker;
-}
-
-void HydrogenPool::UpdateSteps(atom * _atom) const
-{
-  // make sure we are up to current time step
-  const size_t CurrentTime = WorldTime::getTime();
-  for (size_t step = _atom->getTrajectorySize(); step <= CurrentTime; ++step)
-    _atom->UpdateStep(step);
 }
 

src/Fragmentation/Exporters/HydrogenPool.hpp

@@ -73 +73 @@
   void cleanup();
 
-  /** Helper function to make sure \a _atom is up to current time step.
-   *
-   * \param _atom atom to bring trajectory size up to speed
-   */
-  void UpdateSteps(atom * _atom) const;
-
-
 private:
   //!> typedef for the deque of available hydrogens.