Changeset b119a0 for src/Atom/atom.cpp

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

File:

• src/Atom/atom.cpp (modified) (3 diffs)

src/Atom/atom.cpp

@@ -69 +69 @@
     mol(0)
 {
-  AtomicPosition = pointer->AtomicPosition; // copy trajectory of coordination
-  AtomicVelocity = pointer->AtomicVelocity; // copy trajectory of velocity
-  AtomicForce = pointer->AtomicForce;
   // sign on to global atom change tracker
   AtomObserver::getInstance().AtomInserted(this);
@@ -93 +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);
 }
 
@@ -313 +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;