Changeset d0b375b

Timestamp:

Oct 25, 2011, 12:08:03 PM (13 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:

212c179

Parents:

f67817f

git-author:

Frederik Heber <heber@…> (10/18/11 13:28:37)

git-committer:

Frederik Heber <heber@…> (10/25/11 12:08:03)

Message:

Removed ShortestPathList.

• there have been references in the code that ShortestPathList is probably obsolete meanwhile (seemingly it is).

Location:

src

Files:

• Fragmentation/UniqueFragments.cpp (modified) (8 diffs)
• Fragmentation/UniqueFragments.hpp (modified) (2 diffs)
• molecule.hpp (modified) (1 diff)
• molecule_fragmentation.cpp (modified) (2 diffs)

src/Fragmentation/UniqueFragments.cpp

@@ -81 +81 @@
 
 /** Sets FragmenSearch to initial value.
- * Sets UniqueFragments::ShortestPathList entries to zero, UniqueFragments::BondsPerSPCount to zero (except zero level to 1) and
- * adds initial bond UniqueFragments::Root to UniqueFragments::Root to UniqueFragments::BondsPerSPList
+ * Sets UniqueFragments::BondsPerSPCount to zero (except zero level to 1) and adds initial bond
+ * UniqueFragments::Root to UniqueFragments::Root to UniqueFragments::BondsPerSPList
  * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
  * \sa UniqueFragments::FreeSPList()
@@ -88 +88 @@
 void UniqueFragments::SetSPList(int Order)
 {
-  // prepare Label and SP arrays of the BFS search
-  ShortestPathList[Root->getNr()] = 0;
-
   // prepare root level (SP = 0) and a loop bond denoting Root
   for (int i=Order;i--;)
@@ -99 +96 @@
 };
 
-/** Resets UniqueFragments::ShortestPathList and cleans bonds from UniqueFragments::BondsPerSPList.
+/** Cleans bonds from UniqueFragments::BondsPerSPList.
  * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
  * \sa UniqueFragments::InitialiseSPList()
@@ -108 +105 @@
   for(int i=Order;i--;) {
     DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << ": ");
-    for (UniqueFragments::BondsPerSP::const_iterator iter = BondsPerSPList[i].begin();
-        iter != BondsPerSPList[i].end();
-        ++iter) {
-      // Log() << Verbose(0) << "Removing atom " << Binder->leftatom->getNr() << " and " << Binder->rightatom->getNr() << "." << endl; // make sure numbers are local
-      ShortestPathList[(*iter)->leftatom->getNr()] = -1;
-      ShortestPathList[(*iter)->rightatom->getNr()] = -1;
-    }
     // delete added bonds
     for (UniqueFragments::BondsPerSP::iterator iter = BondsPerSPList[i].begin();
@@ -183 +173 @@
           // set the label if not set (and push on root stack as well)
           if ((OtherWalker != Predecessor) && (OtherWalker->GetTrueFather()->getNr() > RootKeyNr)) { // only pass through those with label bigger than Root's
-            ShortestPathList[OtherWalker->getNr()] = SP+1;
-            DoLog(3) && (Log() << Verbose(3) << "Set Shortest Path to " << ShortestPathList[OtherWalker->getNr()] << "." << endl);
             // add the bond in between to the SP list
             Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
@@ -239 +227 @@
  * \param AtomCount number of nodes/atoms
  */
-void UniqueFragments::Init(atom *_Root, size_t AtomCount)
+void UniqueFragments::Init(atom *_Root)
 {
   // initialise the fragments structure
@@ -245 +233 @@
   FragmentSet = new KeySet;
   Root = _Root;
-  ShortestPathList = new int[AtomCount];
-  for (int i=AtomCount;i--;) {
-    ShortestPathList[i] = -1;
-  }
 }
 
@@ -256 +240 @@
 void UniqueFragments::Cleanup()
 {
-  delete[](ShortestPathList);
   delete(FragmentSet);
 }

src/Fragmentation/UniqueFragments.hpp

@@ -42 +42 @@
   void OutputSPList(int Order);
   int CountNumbersInBondsList(int Order);
-  void Init(atom *_Root, size_t AtomCount);
+  void Init(atom *_Root);
   void Cleanup();
 
@@ -62 +62 @@
   int ANOVAOrder;
   int CurrentIndex;
-  int *ShortestPathList;
   bool **UsedList;
 };

src/molecule.hpp

@@ -225 +225 @@
   void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack);
   molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
-  int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
   int GuesstimateFragmentCount(int order);
 

src/molecule_fragmentation.cpp

@@ -516 +516 @@
 };
 
-
-
-/** Looks through a std::deque<atom *> and returns the likeliest removal candiate.
- * \param *out output stream for debugging messages
- * \param *&Leaf KeySet to look through
- * \param *&ShortestPathList list of the shortest path to decide which atom to suggest as removal candidate in the end
- * \param index of the atom suggested for removal
- */
-int molecule::LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList)
-{
-  atom *Runner = NULL;
-  int SP, Removal;
-
-  DoLog(2) && (Log() << Verbose(2) << "Looking for removal candidate." << endl);
-  SP = -1; //0;  // not -1, so that Root is never removed
-  Removal = -1;
-  for (KeySet::iterator runner = Leaf->begin(); runner != Leaf->end(); runner++) {
-    Runner = FindAtom((*runner));
-    if (Runner->getType()->getAtomicNumber() != 1) { // skip all those added hydrogens when re-filling snake stack
-      if (ShortestPathList[(*runner)] > SP) {  // remove the oldest one with longest shortest path
-        SP = ShortestPathList[(*runner)];
-        Removal = (*runner);
-      }
-    }
-  }
-  return Removal;
-};
 
 /** Initializes some value for putting fragment of \a *mol into \a *Leaf.
@@ -702 +675 @@
   }
 
-  FragmentSearch.Init(FindAtom(RootKeyNr), getAtomCount());
+  FragmentSearch.Init(FindAtom(RootKeyNr));
 
   // Construct the complete KeySet which we need for topmost level only (but for all Roots)