Changeset 53731f

Timestamp:

Mar 18, 2010, 3:40:37 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

24725c

Parents:

f2bb0f

Message:

Fixed two unittests by forcibly assigning numbers on Atoms in CreateAdjacencyList

File:

• src/molecule_graph.cpp (modified) (4 diffs)

src/molecule_graph.cpp

@@ -102 +102 @@
   atom *Walker = NULL;
   atom *OtherWalker = NULL;
-  vector<atom*> AtomMap;
   int n[NDIM];
   double MinDistance, MaxDistance;
@@ -135 +134 @@
     // create a list to map Tesselpoint::nr to atom *
     Log() << Verbose(2) << "Creating TesselPoint to atom map ... " << endl;
-    //AtomMap = Calloc<atom *> (AtomCount, "molecule::CreateAdjacencyList - **AtomCount");
-    //for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-    //  std::cout << "!!!!!!!!!!!!Copying pointer to Atom number: " << (*iter)->nr << std::endl;
-    //  AtomMap[(*iter)->nr] = (*iter);
-    //}
-
-    copy(atoms.begin(),atoms.end(),back_inserter(AtomMap));
+
+    // set numbers for atoms that can later be used
+    int i=0;
+    for(internal_iterator iter = atoms.begin();iter!= atoms.end(); ++iter){
+      (*iter)->nr = i++;
+    }
 
     // 3a. go through every cell
@@ -152 +150 @@
           if (List != NULL) {
             for (LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
-              //Walker = AtomMap[(*Runner)->nr];
               Walker = dynamic_cast<atom*>(*Runner);
               ASSERT(Walker,"Tesselpoint that was not an atom retrieved from LinkedNode");
@@ -165 +162 @@
                       for (LinkedNodes::const_iterator OtherRunner = OtherList->begin(); OtherRunner != OtherList->end(); OtherRunner++) {
                         if ((*OtherRunner)->nr > Walker->nr) {
-                          //OtherWalker = AtomMap[(*OtherRunner)->nr];
                           OtherWalker = dynamic_cast<atom*>(*OtherRunner);
                           ASSERT(OtherWalker,"TesselPoint that was not an atom retrieved from LinkedNode");