Changeset e3e52a for src/Graph

Timestamp:

Jan 31, 2016, 12:43:17 PM (9 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:

e39e7a

Parents:

a063787

git-author:

Frederik Heber <heber@…> (01/30/16 17:46:50)

git-committer:

Frederik Heber <heber@…> (01/31/16 12:43:17)

Message:

FIX: BondGraph::Createdjacency compare atoms on position in memory.

• this caused every and again failures in tests as an atom with an earlier id might end up at a "later" memory position resulting in flipped positions in e.g. PDB CONECT entries (regression tests molecules remove failed).

File:

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

src/Graph/BondGraph.hpp

@@ -221 +221 @@
               neighboriter != ListOfNeighbors.end();
               ++neighboriter) {
-            if ((*neighboriter) > Walker) {  // just to not add bonds from both sides
-              const atom * const OtherWalker = dynamic_cast<const atom *>(*neighboriter);
-              ASSERT(OtherWalker != NULL,
-                  "BondGraph::CreateAdjacency() - TesselPoint "
-                  +(*neighboriter)->getName()+" that was not an atom retrieved from LinkedList");
+            const atom * const OtherWalker = dynamic_cast<const atom *>(*neighboriter);
+            ASSERT(OtherWalker != NULL,
+                "BondGraph::CreateAdjacency() - TesselPoint "
+                +(*neighboriter)->getName()+" that was not an atom retrieved from LinkedList");
+            if (OtherWalker->getId() > Walker->getId()) {  // just to not add bonds from both sides
               LOG(4, "INFO: Current other atom is " << *OtherWalker << ".");
 
@@ -245 +245 @@
               }
             } else {
-              LOG(5, "REJECT: Not Adding: Wrong order.");
+              LOG(4, "REJECT: Not Adding: Wrong order.");
             }
           }