Changeset 7294dc for src/World.cpp

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.

File:

• src/World.cpp (modified) (4 diffs)

src/World.cpp

@@ -221 +221 @@
 }
 
-bool areBondsPresent(const unsigned int _step)
+static bool areBondsPresent(const unsigned int _step)
 {
   bool status = false;
@@ -229 +229 @@
     const atom * const Walker = *iter;
     status |= !Walker->getListOfBondsAtStep(_step).empty();
+  }
+
+  return status;
+}
+
+static bool areAtomsPresent(const unsigned int _step)
+{
+  bool status = false;
+
+  for (World::AtomConstIterator iter = const_cast<const World &>(World::getInstance()).getAtomIter();
+      (!status) && (iter != const_cast<const World &>(World::getInstance()).atomEnd()); ++iter) {
+    const atom * const Walker = *iter;
+    status |= (Walker->getTrajectorySize() >= _step);
   }
 
@@ -259 +272 @@
 }
 
-static void copyAtoms(const unsigned int _srcstep, const unsigned int _deststep)
-{
-  for (World::AtomIterator iter = World::getInstance().getAtomIter();
-      iter != World::getInstance().atomEnd(); ++iter) {
-    atom * const Walker = *iter;
-    Walker->UpdateStep(_deststep);
-    Walker->setPositionAtStep(_deststep, Walker->getPositionAtStep(_srcstep));
-    Walker->setAtomicVelocityAtStep(_deststep, Walker->getAtomicVelocityAtStep(_srcstep));
-    Walker->setAtomicForceAtStep(_deststep, Walker->getAtomicForceAtStep(_srcstep));
-  }
-}
+//static void copyAtoms(const unsigned int _srcstep, const unsigned int _deststep)
+//{
+//  for (World::AtomIterator iter = World::getInstance().getAtomIter();
+//      iter != World::getInstance().atomEnd(); ++iter) {
+//    atom * const Walker = *iter;
+//    Walker->UpdateStep(_deststep);
+//    Walker->setPositionAtStep(_deststep, Walker->getPositionAtStep(_srcstep));
+//    Walker->setAtomicVelocityAtStep(_deststep, Walker->getAtomicVelocityAtStep(_srcstep));
+//    Walker->setAtomicForceAtStep(_deststep, Walker->getAtomicForceAtStep(_srcstep));
+//  }
+//}
 
 void World::setTime(const unsigned int _step)
@@ -276 +289 @@
     const unsigned int oldstep = WorldTime::getTime();
 
-    copyAtoms(oldstep, _step);
+//    if (!areAtomsPresent(_step))
+//      copyAtoms(oldstep, _step);
+
     // 1. copy bond graph (such not each addBond causes GUI update)
     if (!areBondsPresent(_step)) {