Changeset 5e2f80 for src/moleculelist.cpp

Timestamp:

Oct 6, 2011, 4:06:10 PM (14 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, Candidate_v1.7.0, 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:

9c18e4

Parents:

37b2575

git-author:

Frederik Heber <heber@…> (09/01/11 17:06:04)

git-committer:

Frederik Heber <heber@…> (10/06/11 16:06:10)

Message:

BondedParticle no more hands out non-const ListOfBonds.

• the few required instances were always for removing all bonds inL
  • GraphCreateAdjacencyAction::performCall(),
  • MoleculeCopyAction::performUndo(),
  • BondGraph::cleanAdjacencyList(),
  • BondGraph::resetBondDegree(),
  • molecule::removeBonds(),
  • MoleculeListClass::AddHydrogenCorrection(),
  • ListOfBondsTest::AddingBondTest().
• added BondedParticle::removeAllBonds().
• added BondedParticle::resetBondDegree().
• BondedParticleInfo::getListOfBonds...() now returns empty list if out of bounds (emptylist is static member variable of the class).
• ListOfBondsUnitTest runs fine.

File:

• src/moleculelist.cpp (modified) (2 diffs)

src/moleculelist.cpp

@@ -283 +283 @@
 bool MoleculeListClass::AddHydrogenCorrection(std::string &path)
 {
-  bond *Binder = NULL;
+  const bond *Binder = NULL;
   double ***FitConstant = NULL, **correction = NULL;
   int a, b;
@@ -395 +395 @@
           //Log() << Verbose(2) << "Runner: " << *(*runner) << " with first bond " << *((*iter)->getListOfBonds().begin()) << "." << endl;
           // 3. take every other hydrogen that is the not the first and not bound to same bonding partner
-          Binder = *((*runner)->getListOfBonds().begin());
+          const BondList &bondlist = (*runner)->getListOfBonds();
+          Binder = *(bondlist.begin());
           if (((*runner)->getType()->getAtomicNumber() == 1) && ((*runner)->getNr() > (*iter)->getNr()) && (Binder->GetOtherAtom((*runner)) != Binder->GetOtherAtom((*iter)))) { // (hydrogens have only one bonding partner!)
             // 4. evaluate the morse potential for each matrix component and add up