Changeset 59fff1 for src/Fragmentation

Timestamp:

Dec 28, 2011, 3:25:49 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:

afa9d8

Parents:

30c753

git-author:

Frederik Heber <heber@…> (12/23/11 10:09:37)

git-committer:

Frederik Heber <heber@…> (12/28/11 15:25:49)

Message:

Replaced the molecule::const_iterator by a true const version of the transform_iterator.

• lots of places used const_iterator where it made no sense, atom some others one could have sensibly done so but details prevented it, e.g.
  • FormatParserStorage::save() requires vector<atom*> not const atom *,
  • Boundaries (and most of Tesselation for that) requires atom *, not const atom *.
• Added new function molecule::isInMolecule() to check whether atomic id is in molecule::atomIds.
• Added const version of atom::GetTrueFather().

File:

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

src/Fragmentation/Fragmentation.cpp

@@ -595 +595 @@
 
     // set atom values
-    for(molecule::const_iterator iter=mol->begin();iter!=mol->end();++iter){
+    for(molecule::iterator iter=mol->begin();iter!=mol->end();++iter){
       (*iter)->AdaptiveOrder = OrderArray[(*iter)->getNr()];
       (*iter)->MaxOrder = MaxArray[(*iter)->getNr()];
@@ -676 +676 @@
 
   // we increment the iter just before skipping the hydrogen
-  for (molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end();) {
+  // as we use AddBond, we cannot have a const_iterator here
+  for (molecule::iterator iter = Leaf->begin(); iter != Leaf->end();) {
     LonelyFlag = true;
     FatherOfRunner = (*iter)->father;