Changeset 9d83b6 for src/molecule_fragmentation.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/molecule_fragmentation.cpp (modified) (7 diffs)

src/molecule_fragmentation.cpp

@@ -56 +56 @@
   // get maximum bond degree
   for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-    c = ((*iter)->ListOfBonds.size() > c) ? (*iter)->ListOfBonds.size() : c;
+    const BondList& ListOfBonds = (*iter)->getListOfBonds();
+    c = (ListOfBonds.size() > c) ? ListOfBonds.size() : c;
   }
   FragmentCount = NoNonHydrogen*(1 << (c*order));
@@ -670 +671 @@
         atomiter != (*iter)->end();
         ++atomiter) {
-      for (BondList::iterator bonditer = (*atomiter)->ListOfBonds.begin();
-          bonditer != (*atomiter)->ListOfBonds.end();
+      const BondList& ListOfBonds = (*atomiter)->getListOfBonds();
+      for (BondList::const_iterator bonditer = ListOfBonds.begin();
+          bonditer != ListOfBonds.end();
           ++bonditer) {
         (*bonditer)->BondDegree = 1;
@@ -1009 +1011 @@
     if (SonList[FatherOfRunner->nr] != NULL)  {  // check if this, our father, is present in list
       // create all bonds
-      for (BondList::const_iterator BondRunner = FatherOfRunner->ListOfBonds.begin(); BondRunner != FatherOfRunner->ListOfBonds.end(); (++BondRunner)) {
+      const BondList& ListOfBonds = FatherOfRunner->getListOfBonds();
+      for (BondList::const_iterator BondRunner = ListOfBonds.begin();
+          BondRunner != ListOfBonds.end();
+          ++BondRunner) {
         OtherFather = (*BondRunner)->GetOtherAtom(FatherOfRunner);
 //        Log() << Verbose(2) << "Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->nr] << " is bound to " << *OtherFather;
@@ -1416 +1421 @@
       // go through all its bonds
       DoLog(1) && (Log() << Verbose(1) << "Going through all bonds of Walker." << endl);
-      for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
+      const BondList& ListOfBonds = Walker->getListOfBonds();
+      for (BondList::const_iterator Runner = ListOfBonds.begin();
+          Runner != ListOfBonds.end();
+          ++Runner) {
         OtherWalker = (*Runner)->GetOtherAtom(Walker);
         if ((RestrictedKeySet.find(OtherWalker->nr) != RestrictedKeySet.end())
@@ -1811 +1819 @@
     // scan all bonds
     flag = false;
-    for(molecule::iterator AtomRunner = begin(); (!flag) && (AtomRunner != end()); ++AtomRunner)
-      for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); (!flag) && (BondRunner != (*AtomRunner)->ListOfBonds.end()); ++BondRunner) {
+    for(molecule::iterator AtomRunner = begin(); (!flag) && (AtomRunner != end()); ++AtomRunner) {
+      const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
+      for(BondList::const_iterator BondRunner = ListOfBonds.begin();
+          (!flag) && (BondRunner != ListOfBonds.end());
+          ++BondRunner) {
         Binder = (*BondRunner);
         for (int i=NDIM;i--;) {
@@ -1832 +1843 @@
         }
       }
+    }
     //if (flag) {
     if (0) {
@@ -1853 +1865 @@
         ColorList[Walker->nr] = black;    // mark as explored
         *Walker += Translationvector; // translate
-        for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
+        const BondList& ListOfBonds = Walker->getListOfBonds();
+        for (BondList::const_iterator Runner = ListOfBonds.begin();
+            Runner != ListOfBonds.end();
+            ++Runner) {
           if ((*Runner) != Binder) {
             OtherWalker = (*Runner)->GetOtherAtom(Walker);