Changeset 9d83b6 for src/analysis_bonds.cpp

Timestamp:

Feb 24, 2011, 6:51:32 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, 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/analysis_bonds.cpp (modified) (7 diffs)

src/analysis_bonds.cpp

@@ -43 +43 @@
   int AtomCount = 0;
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    const int count = (*iter)->ListOfBonds.size();
+    const BondList& ListOfBonds = (*iter)->getListOfBonds();
+    const int count = ListOfBonds.size();
     if (Max < count)
       Max = count;
@@ -72 +73 @@
   int AtomNo = 0;
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    if ((*iter)->getType() == type1)
-      for (BondList::const_iterator BondRunner = (*iter)->ListOfBonds.begin(); BondRunner != (*iter)->ListOfBonds.end(); BondRunner++)
+    if ((*iter)->getType() == type1) {
+      const BondList& ListOfBonds = (*iter)->getListOfBonds();
+      for (BondList::const_iterator BondRunner = ListOfBonds.begin();
+          BondRunner != ListOfBonds.end();
+          BondRunner++)
         if ((*BondRunner)->GetOtherAtom((*iter))->getType() == type2) {
           const double distance = (*BondRunner)->GetDistanceSquared();
@@ -83 +87 @@
           AtomNo++;
         }
+    }
   }
   if (Max < 0) {
@@ -161 +166 @@
               InterfaceFlag = (InterfaceElement == NULL);
               Interface2Flag = (Interface2Element == NULL);
-              for (BondList::const_iterator BondRunner = (*Runner)->ListOfBonds.begin(); BondRunner != (*Runner)->ListOfBonds.end(); BondRunner++) {
+              const BondList& ListOfBonds = (*Runner)->getListOfBonds();
+              for (BondList::const_iterator BondRunner = ListOfBonds.begin();
+                  BondRunner != ListOfBonds.end();
+                  BondRunner++) {
                 atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Runner);
                 // if hydrogen, check angle to be greater(!) than 30 degrees
@@ -187 +195 @@
               if (InterfaceFlag && Interface2Flag && OtherHydrogenFlag) {
                 // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
-                for (BondList::const_iterator BondRunner = (*Walker)->ListOfBonds.begin(); BondRunner != (*Walker)->ListOfBonds.end(); BondRunner++) {
+                const BondList& ListOfBonds = (*Walker)->getListOfBonds();
+                for (BondList::const_iterator BondRunner = ListOfBonds.begin();
+                    BondRunner != ListOfBonds.end();
+                    BondRunner++) {
                   atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Walker);
                   if (OtherAtom->getType()->getAtomicNumber() == 1) {
@@ -223 +234 @@
       atom * theAtom = *Walker;
       if ((theAtom->getType() == first) || (theAtom->getType() == second)) {  // first element matches
-        for (BondList::const_iterator BondRunner = theAtom->ListOfBonds.begin(); BondRunner != theAtom->ListOfBonds.end(); BondRunner++) {
+        const BondList& ListOfBonds = theAtom->getListOfBonds();
+        for (BondList::const_iterator BondRunner = ListOfBonds.begin();
+            BondRunner != ListOfBonds.end();
+            BondRunner++) {
           atom * const OtherAtom = (*BondRunner)->GetOtherAtom(theAtom);
           if (((OtherAtom->getType() == first) || (OtherAtom->getType() == second)) && (theAtom->nr < OtherAtom->nr)) {
@@ -261 +275 @@
         for (int i=0;i<2;i++)
           MatchFlag[i] = false;
-        for (BondList::const_iterator BondRunner = theAtom->ListOfBonds.begin(); BondRunner != theAtom->ListOfBonds.end(); BondRunner++) {
+        const BondList& ListOfBonds = theAtom->getListOfBonds();
+        for (BondList::const_iterator BondRunner = ListOfBonds.begin();
+            BondRunner != ListOfBonds.end();
+            BondRunner++) {
           atom * const OtherAtom = (*BondRunner)->GetOtherAtom(theAtom);
           for (int i=0;i<2;i++)