Changeset c54da3

Timestamp:

Jun 3, 2009, 4:16:37 PM (16 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:

a5b2c3a

Parents:

ca2587

git-author:

Frederik Heber <heber@…> (06/03/09 16:05:22)

git-committer:

Frederik Heber <heber@…> (06/03/09 16:16:37)

Message:

BUGFIX: RemoveAtom() would remove the iterator, molecule::RemoveAtom() did not decrease AtomCount

• used two pointer construction, so that the next pointer is already secured before removing the current from the list.
• RemoveAtom() decreases AtomCount if Elements-array-check is ok

Location:

src

Files:

• builder.cpp (modified) (2 diffs)
• molecules.cpp (modified) (1 diff)

src/builder.cpp

@@ -436 +436 @@
 static void RemoveAtoms(molecule *mol)
 {
-        atom *first, *second;
+        atom *first, *second, *third;
         int axis;
         double tmp1, tmp2;
@@ -459 +459 @@
                         break;
                 case 'b':
-                        second = mol->AskAtom("Enter number of atom as reference point: ");
+                  third = mol->AskAtom("Enter number of atom as reference point: ");
                         cout << Verbose(0) << "Enter radius: ";
                         cin >> tmp1;
                         first = mol->start;
-                        while(first->next != mol->end) {
-                                first = first->next;
-                                if (first->x.DistanceSquared((const Vector *)&second->x) > tmp1*tmp1) // distance to first above radius ...
+      second = first->next;
+                        while(second != mol->end) {
+                                first = second;
+        second = first->next;
+                                if (first->x.DistanceSquared((const Vector *)&third->x) > tmp1*tmp1) // distance to first above radius ...
                                         mol->RemoveAtom(first);
                         }

src/molecules.cpp

@@ -1209 +1209 @@
 bool molecule::RemoveAtom(atom *pointer)
 {
-        if (ElementsInMolecule[pointer->type->Z] != 0)  // this would indicate an error
+        if (ElementsInMolecule[pointer->type->Z] != 0)  { // this would indicate an error
                 ElementsInMolecule[pointer->type->Z]--; // decrease number of atom of this element
-        else
+          AtomCount--;
+        } else
                 cerr << "ERROR: Atom " << pointer->Name << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl;
         if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?