Changeset 326000 for src

Timestamp:

Apr 17, 2013, 6:56:55 PM (12 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:

4f04ab8

Parents:

378fc6b

git-author:

Frederik Heber <heber@…> (03/19/13 13:32:21)

git-committer:

Frederik Heber <heber@…> (04/17/13 18:56:55)

Message:

BondGraph::CorrectBondDegree() now allows for incrementing only on a subset.

• is used to first increment backedges, then treeedges.

Location:

src/Graph

Files:

• BondGraph.cpp (modified) (6 diffs)
• BondGraph.hpp (modified) (4 diffs)

src/Graph/BondGraph.cpp

@@ -35 +35 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <deque>
 #include <iostream>
 
@@ -49 +50 @@
 #include "Element/periodentafel.hpp"
 #include "Fragmentation/MatrixContainer.hpp"
+#include "Graph/DepthFirstSearchAnalysis.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"
@@ -226 +228 @@
 
 /** Corrects the bond degree by one at most if necessary.
+ *
+ * We are constraint to bonds in \a egdes, if the candidate bond is in edges, we
+ * just don't increment its bond degree. We do not choose an alternative for this
+ * atom.
+ *
+ * \param edges only these edges can be updated
  * \return number of corrections done
  */
-int BondGraph::CorrectBondDegree(atom *_atom) const
+int BondGraph::CorrectBondDegree(atom *_atom, const std::set<bond::ptr>& edges) const
 {
   int NoBonds = 0;
@@ -260 +268 @@
     }
     if ((CandidateBond != NULL)) {
-      CandidateBond->setDegree(CandidateBond->getDegree()+1);
-      LOG(2, "Increased bond degree for bond " << *CandidateBond << ".");
+      if (edges.find(CandidateBond) != edges.end()) {
+        CandidateBond->setDegree(CandidateBond->getDegree()+1);
+        LOG(2, "Increased bond degree for bond " << *CandidateBond << ".");
+      } else
+        LOG(2, "Bond " << *CandidateBond << " is not in edges.");
     } else {
       ELOG(2, "Could not find correct degree for atom " << *_atom << ".");
@@ -268 +279 @@
   }
   return FalseBondDegree;
-};
+}
 
 /** Sets the weight of all connected bonds to one.
@@ -279 +290 @@
       ++BondRunner)
     (*BondRunner)->setDegree(1);
-};
-
+}
+
+std::set<bond::ptr> BondGraph::getBackEdges() const
+{
+  DepthFirstSearchAnalysis DFS;
+  DFS();
+
+  const std::deque<bond::ptr>& backedgestack = DFS.getBackEdgeStack();
+  std::set<bond::ptr> backedges(backedgestack.begin(), backedgestack.end());
+
+  return backedges;
+}
+
+std::set<bond::ptr> BondGraph::getTreeEdges() const
+{
+  const std::set<bond::ptr> backedges = getBackEdges();
+  std::set<bond::ptr> alledges;
+  const World& world = World::getInstance();
+  for(World::AtomConstIterator iter = world.getAtomIter();
+      iter != world.atomEnd(); ++iter) {
+    const BondList &ListOfBonds = (*iter)->getListOfBonds();
+    alledges.insert(ListOfBonds.begin(), ListOfBonds.end());
+  }
+  std::set<bond::ptr> treeedges;
+  std::set_difference(
+      alledges.begin(), alledges.end(),
+      backedges.begin(), backedges.end(),
+      std::inserter(treeedges, treeedges.begin()));
+  return treeedges;
+}

src/Graph/BondGraph.hpp

@@ -473 +473 @@
             class iterator_type,
             class const_iterator_type>
-  void resetBondDegree(
+  void resetBondDegree (
       AtomSetMixin<container_type,iterator_type,const_iterator_type> &Set) const
   {
@@ -493 +493 @@
       AtomSetMixin<container_type,iterator_type,const_iterator_type> &Set) const
   {
+    const std::set<bond::ptr> backedges = getBackEdges();
+    const std::set<bond::ptr> treeedges = getTreeEdges();
+
     //LOG(1, "Correcting Bond degree of each bond ... ");
     int No = 0, OldNo = -1;
@@ -499 +502 @@
       No=0;
       for(iterator_type AtomRunner = Set.begin(); AtomRunner != Set.end(); ++AtomRunner) {
-        No+=CorrectBondDegree(*AtomRunner);
+        No+=CorrectBondDegree(*AtomRunner, backedges);
+      }
+      for(iterator_type AtomRunner = Set.begin(); AtomRunner != Set.end(); ++AtomRunner) {
+        No+=CorrectBondDegree(*AtomRunner, treeedges);
       }
     } while (OldNo != No);
@@ -512 +518 @@
   }
 
-  int CorrectBondDegree(atom *_atom) const;
+  std::set<bond::ptr> getBackEdges() const;
+  std::set<bond::ptr> getTreeEdges() const;
+
+  int CorrectBondDegree(atom *_atom, const std::set<bond::ptr>& skipedges) const;
 
   void resetBondDegree(atom *_atom) const;