Changeset 388ddd for src/World.cpp

Timestamp:

Sep 8, 2014, 9:36:29 PM (10 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:

dc798d

Parents:

553c54

git-author:

Frederik Heber <heber@…> (08/15/14 00:00:21)

git-committer:

Frederik Heber <heber@…> (09/08/14 21:36:29)

Message:

World::setTime() now only copies bond graph, does not re-create it.

• this gives us more flexibility when doing MD/Opt because we may decice for ourselves whether we want to remain (within the fragmentation scheme) in the structure governed by the same bond graph ... or seek even for a different structure (although that's not so easy due to charge neutrality).

File:

• src/World.cpp (modified) (2 diffs)

src/World.cpp

@@ -194 +194 @@
 }
 
+bool areBondsPresent(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->getListOfBondsAtStep(_step).empty();
+  }
+
+  return status;
+}
+
+void copyBondgraph(const unsigned int _srcstep, const unsigned int _deststep)
+{
+  // gather all bonds from _srcstep
+  std::set<bond *> SetOfBonds;
+  for (World::AtomConstIterator iter = const_cast<const World &>(World::getInstance()).getAtomIter();
+      iter != const_cast<const World &>(World::getInstance()).atomEnd(); ++iter) {
+    const atom * const Walker = *iter;
+    const BondList bonds = Walker->getListOfBondsAtStep(_srcstep);
+    BOOST_FOREACH( bond::ptr bondptr, bonds) {
+      SetOfBonds.insert(bondptr.get());
+    }
+  }
+  LOG(4, "DEBUG: We gathered " << SetOfBonds.size() << " bonds in total.");
+
+  // copy bond to new time step
+  for (std::set<bond *>::const_iterator bonditer = SetOfBonds.begin();
+      bonditer != SetOfBonds.end(); ++bonditer) {
+    const atom * const Walker = (*bonditer)->leftatom;
+    const atom * const OtherWalker = (*bonditer)->rightatom;
+    const_cast<atom *>(Walker)->addBond(_deststep, const_cast<atom *>(OtherWalker));
+  }
+}
+
 void World::setTime(const unsigned int _step)
 {
   if (_step != WorldTime::getTime()) {
+    const unsigned int oldstep = WorldTime::getTime();
     // set new time
     WorldTime::getInstance().setTime(_step);
@@ -207 +244 @@
       destroyMolecule(*iter);
     }
-    // 2. (re-)create bondgraph
-    AtomComposite Set = getAllAtoms();
-    BG->CreateAdjacency(Set);
+    // 2. copy bond graph
+    if (!areBondsPresent(_step)) {
+//      AtomComposite Set = getAllAtoms();
+//      BG->cleanAdjacencyList(Set);
+      copyBondgraph(oldstep, _step);
+    }
 
     // 3. scan for connected subgraphs => molecules