Changeset fe0cb8 for src/Actions/FragmentationAction/FragmentationAction.cpp

Timestamp:

Oct 14, 2013, 11:42:03 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:

adb51ab

Parents:

8dbcaf

git-author:

Frederik Heber <heber@…> (09/25/13 08:49:20)

git-committer:

Frederik Heber <heber@…> (10/14/13 23:42:03)

Message:

Added option DoCyclesFull to FragmentationAction.

• FIX: Fragmentation::Fragmentation() has no need for a ref to DFS anymore.
• DFS in FragmentationAction is now used for Cycle detection only.
• CyclicStructureAnalysis::RetrieveCycleMembers() also fills internal vector with all found cycles (as KeySet's), with a getter.

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (4 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -50 +50 @@
 #include "Graph/AdjacencyList.hpp"
 #include "Graph/BondGraph.hpp"
+#include "Graph/CyclicStructureAnalysis.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
 #include "Helpers/defs.hpp"
@@ -128 +129 @@
   }
 
-  // we require the current bond graph
-  DepthFirstSearchAnalysis DFS;
-
   // we parse in the keysets from last time if present
   Graph StoredGraph;
@@ -162 +160 @@
     {
       Graph StoredLocalGraph(StoredGraph.getLocalGraph(mol));
-      const int tempFlag = Fragmenter.FragmentMolecule(mols_atomids, params.order.get(), params.prefix.get(), DFS, StoredLocalGraph);
+      const int tempFlag = Fragmenter.FragmentMolecule(mols_atomids, params.order.get(), params.prefix.get(), StoredLocalGraph);
       if ((ExitFlag == 2) && (tempFlag != 2))
         ExitFlag = tempFlag; // if there is one molecule that needs further fragmentation, it overrides others
@@ -175 +173 @@
 
   }
+  // add full cycles if desired
+  if (params.DoCyclesFull.get()) {
+    // get the BackEdgeStack from somewhere
+    DepthFirstSearchAnalysis DFS;
+    DFS();
+    std::deque<bond::ptr> BackEdgeStack = DFS.getBackEdgeStack();
+    // then we analyse the cycles and get them
+    CyclicStructureAnalysis CycleAnalysis(params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen);
+    CycleAnalysis(&BackEdgeStack);
+    CyclicStructureAnalysis::cycles_t cycles = CycleAnalysis.getAllCycles();
+    LOG(0, "STATUS: Adding " << cycles.size() << " cycles.");
+    // Create graph and insert into TotalGraph
+    {
+      Graph CycleGraph;
+      for (CyclicStructureAnalysis::cycles_t::const_iterator iter = cycles.begin();
+          iter != cycles.end(); ++iter) {
+        const CyclicStructureAnalysis::cycle_t &currentcycle = *iter;
+        LOG(2, "INFO: Inserting cycle " << currentcycle << ".");
+#ifndef NDEBUG
+        std::pair< Graph::iterator, bool > inserter =
+#endif
+        CycleGraph.insert( std::make_pair(currentcycle, NumberValuePair(1,1.)) );
+        ASSERT( inserter.second,
+            "FragmentationFragmentationAction::performCall() - keyset "
+            +toString(currentcycle)+" inserted twice into CycleGraph.");
+      }
+      TotalGraph.InsertGraph(CycleGraph, keysetcounter);
+    }
+  }
+
   LOG(0, "STATUS: There are " << TotalGraph.size() << " fragments.");