Changeset 11f0fa for src/Fragmentation

Timestamp:

Jul 9, 2013, 6:21:28 AM (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:

bcb593

Parents:

f73351

git-author:

Frederik Heber <heber@…> (06/18/13 14:33:06)

git-committer:

Frederik Heber <heber@…> (07/09/13 06:21:28)

Message:

FIX: Newly created atoms must have trajectories reaching out till CurrentTime.

• this became apparent when fragmenting on next time step in molecular dynamics run because atoms in hydrogen pool did not have fitting trajectories.
• now, newly created atoms have automatically trajectories extended till CurrentTime.
• also, HydrogenPool makes sure that hydrogens used from pool are up to date.

Location:

src/Fragmentation/Exporters

Files:

• HydrogenPool.cpp (modified) (2 diffs)
• HydrogenPool.hpp (modified) (1 diff)

src/Fragmentation/Exporters/HydrogenPool.cpp

@@ -46 +46 @@
 #include "Element/periodentafel.hpp"
 #include "World.hpp"
+#include "WorldTime.hpp"
 
 HydrogenPool::HydrogenPool() :
@@ -90 +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->UpdateSteps();
 }
 

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.