Changeset efe516 for src/Graph

Timestamp:

Mar 2, 2011, 9:53:09 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:

7d8aa0

Parents:

2fa1dc

git-author:

Frederik Heber <heber@…> (03/01/11 14:16:44)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:09)

Message:

Removed bond::nr.

• has only been used by BreadthFirstSearchAdd.
• changed BreadthFirstSearchAdd::AddedBonds into map<bond*,bond*>.

Location:

src/Graph

Files:

• BondGraph.hpp (modified) (1 diff)
• BreadthFirstSearchAdd.cpp (modified) (3 diffs)
• BreadthFirstSearchAdd.hpp (modified) (1 diff)

src/Graph/BondGraph.hpp

@@ -230 +230 @@
 
       LOG(3, "INFO: Creating bond between atoms " << atom1 << " and " << atom2 << ".");
-      bond * const Binder = new bond(Walker, OtherWalker, 1, -1);
+      bond * const Binder = new bond(Walker, OtherWalker, 1);
       Walker->RegisterBond(WorldTime::getTime(), Binder);
       OtherWalker->RegisterBond(WorldTime::getTime(), Binder);

src/Graph/BreadthFirstSearchAdd.cpp

@@ -75 +75 @@
       AddedAtomList[OtherAtom->getNr()] = Mol->AddCopyAtom(OtherAtom);
       DoLog(0) && (Log() << Verbose(0) << "Added OtherAtom " << OtherAtom->getName());
-      AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
-      DoLog(0) && (Log() << Verbose(0) << " and bond " << *(AddedBondList[Binder->nr]) << ", ");
+      AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
+      DoLog(0) && (Log() << Verbose(0) << " and bond " << *(AddedBondList[Binder]) << ", ");
     } else { // this code should actually never come into play (all GraphEdge::white atoms are not yet present in BondMolecule, that's why they are GraphEdge::white in the first place)
       DoLog(0) && (Log() << Verbose(0) << "Not adding OtherAtom " << OtherAtom->getName());
-      if (AddedBondList[Binder->nr] == NULL) {
-        AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
-        DoLog(0) && (Log() << Verbose(0) << ", added Bond " << *(AddedBondList[Binder->nr]));
+      if (AddedBondList[Binder] == NULL) {
+        AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
+        DoLog(0) && (Log() << Verbose(0) << ", added Bond " << *(AddedBondList[Binder]));
       } else
         DoLog(0) && (Log() << Verbose(0) << ", not added Bond ");
@@ -96 +96 @@
     if (!Binder->Cyclic)
       DoLog(0) && (Log() << Verbose(0) << ", is not part of a cyclic bond, saturating bond with Hydrogen." << endl);
-    if (AddedBondList[Binder->nr] == NULL) {
+    if (AddedBondList[Binder] == NULL) {
       if ((AddedAtomList[OtherAtom->getNr()] != NULL)) { // .. whether we add or saturate
-        AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
+        AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
       } else {
 #ifdef ADDHYDROGEN
@@ -114 +114 @@
   DoLog(3) && (Log() << Verbose(3) << "Not Adding, has already been visited." << endl);
   // This has to be a cyclic bond, check whether it's present ...
-  if (AddedBondList[Binder->nr] == NULL) {
+  if (AddedBondList[Binder] == NULL) {
     if ((Binder != Bond) && (Binder->Cyclic) && (((ShortestPathList[Walker->getNr()] + 1) < BondOrder))) {
-      AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
+      AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
     } else { // if it's root bond it has to broken (otherwise we would not create the fragments)
 #ifdef ADDHYDROGEN

src/Graph/BreadthFirstSearchAdd.hpp

@@ -69 +69 @@
   int ComponentNr;
   std::map<atomId_t, atom *> AddedAtomList;
-  std::map<int, bond *> AddedBondList;
+  std::map<bond *, bond *> AddedBondList; //!< maps from father bond to son
 
   bool IsAngstroem;