Changeset 9d83b6 for src/molecule.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.cpp (modified) (5 diffs)

src/molecule.cpp

@@ -26 +26 @@
 #include <gsl/gsl_heapsort.h>
 
-#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
+#include "Box.hpp"
+#include "CodePatterns/enumeration.hpp"
+#include "CodePatterns/Log.hpp"
 #include "config.hpp"
 #include "element.hpp"
+#include "Exceptions/LinearDependenceException.hpp"
 #include "graph.hpp"
 #include "Helpers/helpers.hpp"
 #include "LinearAlgebra/leastsquaremin.hpp"
+#include "LinearAlgebra/Plane.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "linkedcell.hpp"
 #include "lists.hpp"
-#include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
-
 #include "periodentafel.hpp"
 #include "tesselation.hpp"
-#include "LinearAlgebra/Vector.hpp"
-#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "World.hpp"
-#include "Box.hpp"
-#include "LinearAlgebra/Plane.hpp"
-#include "Exceptions/LinearDependenceException.hpp"
-
-#include "CodePatterns/enumeration.hpp"
+#include "WorldTime.hpp"
+
 
 /************************************* Functions for class molecule *********************************/
@@ -383 +382 @@
       break;
     case 2:
-      // determine two other bonds (warning if there are more than two other) plus valence sanity check
-      for (BondList::const_iterator Runner = TopOrigin->ListOfBonds.begin(); Runner != TopOrigin->ListOfBonds.end(); (++Runner)) {
-        if ((*Runner) != TopBond) {
-          if (FirstBond == NULL) {
-            FirstBond = (*Runner);
-            FirstOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
-          } else if (SecondBond == NULL) {
-            SecondBond = (*Runner);
-            SecondOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
-          } else {
-            DoeLog(2) && (eLog()<< Verbose(2) << "Detected more than four bonds for atom " << TopOrigin->getName());
+      {
+        // determine two other bonds (warning if there are more than two other) plus valence sanity check
+        const BondList& ListOfBonds = TopOrigin->getListOfBonds();
+        for (BondList::const_iterator Runner = ListOfBonds.begin();
+            Runner != ListOfBonds.end();
+            ++Runner) {
+          if ((*Runner) != TopBond) {
+            if (FirstBond == NULL) {
+              FirstBond = (*Runner);
+              FirstOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
+            } else if (SecondBond == NULL) {
+              SecondBond = (*Runner);
+              SecondOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
+            } else {
+              DoeLog(2) && (eLog()<< Verbose(2) << "Detected more than four bonds for atom " << TopOrigin->getName());
+            }
           }
         }
@@ -642 +646 @@
 
   // copy all bonds
-  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
-    for(BondList::const_iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
+    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
+    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
+        BondRunner != ListOfBonds.end();
+        ++BondRunner)
       if ((*BondRunner)->leftatom == *AtomRunner) {
         bond *Binder = (*BondRunner);
@@ -660 +667 @@
         NewBond->Type = Binder->Type;
       }
+  }
   // correct fathers
   for_each(atoms.begin(),atoms.end(),mem_fun(&atom::CorrectFather));
@@ -749 +757 @@
   //DoeLog(1) && (eLog()<< Verbose(1) << "molecule::RemoveBond: Function not implemented yet." << endl);
   BondList::const_iterator ForeRunner;
-  while (!BondPartner->ListOfBonds.empty()) {
-    ForeRunner = BondPartner->ListOfBonds.begin();
+  BondList& ListOfBonds = BondPartner->getListOfBonds();
+  while (!ListOfBonds.empty()) {
+    ForeRunner = ListOfBonds.begin();
     RemoveBond(*ForeRunner);
   }