Changeset 539f32

Timestamp:

Oct 20, 2011, 1:20:09 PM (13 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:

fa9d1d

Parents:

9317be

git-author:

Frederik Heber <heber@…> (10/20/11 13:19:21)

git-committer:

Frederik Heber <heber@…> (10/20/11 13:20:09)

Message:

Enhanced BondGraph::CreateAdjacency() a bit.

File:

• src/Graph/BondGraph.cpp (modified) (2 diffs)

src/Graph/BondGraph.cpp

@@ -175 +175 @@
   int n[NDIM];
   Box &domain = World::getInstance().getDomain();
+  size_t CurrentTime = WorldTime::getTime();
 
   unsigned int BondCount = 0;
@@ -202 +203 @@
                         ASSERT(OtherWalker != NULL,
                             "BondGraph::CreateAdjacency() - TesselPoint that was not an atom retrieved from LinkedNode");
-                        const range<double> MinMaxDistanceSquared(
-                            getMinMaxDistanceSquared(Walker, OtherWalker));
-                        const double distance = domain.periodicDistanceSquared(OtherWalker->getPosition(),Walker->getPosition());
-                        LOG(2, "INFO: Checking squared distance " << distance << " against typical bond length of " << MinMaxDistanceSquared << ".");
-                        const bool status = MinMaxDistanceSquared.isInRange(distance);
                         if (OtherWalker->father > Walker->father ) { // just to not add bonds from both sides
+                          const range<double> MinMaxDistanceSquared(
+                              getMinMaxDistanceSquared(Walker, OtherWalker));
+                          const double distance = domain.periodicDistanceSquared(OtherWalker->getPosition(),Walker->getPosition());
+                          LOG(3, "INFO: Checking squared distance " << distance << " against typical bond length of " << MinMaxDistanceSquared << ".");
+                          const bool status = MinMaxDistanceSquared.isInRange(distance);
                           if (status) { // create bond if distance is smaller
                             LOG(1, "ACCEPT: Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << ".");
                             //const bond * Binder =
-                              Walker->father->addBond(WorldTime::getTime(), OtherWalker->father);
+                              Walker->father->addBond(CurrentTime, OtherWalker->father);
                             BondCount++;
                           } else {
-                            LOG(1, "REJECT: Squared distance "
+                            LOG(2, "REJECT: Squared distance "
                                 << distance << " is out of squared covalent bounds "
                                 << MinMaxDistanceSquared << ".");