Changeset 9d83b6 for src/boundary.cpp

Timestamp:

Feb 24, 2011, 6:51:32 PM (15 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:

a2bdbe

Parents:

c0d9eb

git-author:

Frederik Heber <heber@…> (02/24/11 14:41:13)

git-committer:

Frederik Heber <heber@…> (02/24/11 18:51:32)

Message:

BondedParticleInfo now has vector<BondList>

• vector<BondList> ListOfBonds is private, getter for (non-)const access.
• Access everywhere to ListOfBonds replaced by respective getter.
• Access is as of now always to time step zero.
• greatest impact is on molecule... files, and ListOfBondsUnitTest.

File:

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

src/boundary.cpp

@@ -818 +818 @@
   const int FillerCount = filler->getAtomCount();
   DoLog(2) && (Log() << Verbose(2) << "INFO: Filler molecule has the following bonds:" << endl);
-  for(molecule::iterator AtomRunner = filler->begin(); AtomRunner != filler->end(); ++AtomRunner)
-    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+  for(molecule::iterator AtomRunner = filler->begin(); AtomRunner != filler->end(); ++AtomRunner) {
+    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
+    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
+        BondRunner != ListOfBonds.end();
+        ++BondRunner) {
       if ((*BondRunner)->leftatom == *AtomRunner)
         DoLog(2) && (Log() << Verbose(2) << "  " << *(*BondRunner) << endl);
+    }
+  }
 
   atom * CopyAtoms[FillerCount];
@@ -912 +917 @@
         }
         // go through all bonds and add as well
-        for(molecule::iterator AtomRunner = filler->begin(); AtomRunner != filler->end(); ++AtomRunner)
-          for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+        for(molecule::iterator AtomRunner = filler->begin(); AtomRunner != filler->end(); ++AtomRunner) {
+          const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
+          for(BondList::const_iterator BondRunner = ListOfBonds.begin();
+              BondRunner != ListOfBonds.end();
+              ++BondRunner)
             if ((*BondRunner)->leftatom == *AtomRunner) {
               Binder = (*BondRunner);
@@ -921 +929 @@
               }
             }
+        }
       }
   for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++) {
@@ -1084 +1093 @@
   //const int FillerCount = filler->getAtomCount();
   DoLog(2) && (Log() << Verbose(2) << "INFO: Filler molecule has the following bonds:" << endl);
-  for(molecule::iterator AtomRunner = filler->begin(); AtomRunner != filler->end(); ++AtomRunner)
-    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+  for(molecule::iterator AtomRunner = filler->begin(); AtomRunner != filler->end(); ++AtomRunner) {
+    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
+    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
+        BondRunner != ListOfBonds.end();
+        ++BondRunner)
       if ((*BondRunner)->leftatom == *AtomRunner)
         DoLog(2) && (Log() << Verbose(2) << "  " << *(*BondRunner) << endl);
+  }
 
   // calculate filler grid in [0,1]^3