Changeset fe0cb8 for src

Timestamp:

Oct 14, 2013, 11:42:03 PM (11 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.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAction.cpp (modified) (4 diffs)
• Actions/FragmentationAction/FragmentationAction.def (modified) (2 diffs)
• Fragmentation/Fragmentation.cpp (modified) (2 diffs)
• Fragmentation/Fragmentation.hpp (modified) (2 diffs)
• Graph/CyclicStructureAnalysis.cpp (modified) (2 diffs)
• Graph/CyclicStructureAnalysis.hpp (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.");
 

src/Actions/FragmentationAction/FragmentationAction.def

@@ -21 +21 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::string)(double)(unsigned int)(bool)(bool)(std::vector<std::string>)(unsigned int)(unsigned int)
-#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")("grid-level")("inter-order")
-#define paramdescriptions ("prefix of each fragment file")("distance in space up to which fragments are combined")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")("resolution of density sampling multigrid")("up to which order distinct fragments are combined")
-#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(0))
-#define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)(level)(InterOrder)
+#define paramtypes (std::string)(double)(unsigned int)(bool)(bool)(std::vector<std::string>)(unsigned int)(unsigned int)(bool)
+#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")("grid-level")("inter-order")("DoCyclesFull")
+#define paramdescriptions ("prefix of each fragment file")("distance in space up to which fragments are combined")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")("resolution of density sampling multigrid")("up to which order distinct fragments are combined")("always calculate (aromatic) rings fully, even beyond desired order")
+#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(0))(PARAM_DEFAULT(false))
+#define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)(level)(InterOrder)(DoCyclesFull)
 #define paramvalids \
 (DummyValidator< std::string >()) \
@@ -35 +35 @@
 (RangeValidator< unsigned int >(1, 10)) \
 (DummyValidator< unsigned int >()) \
+(DummyValidator< bool >())
 
 #undef statetypes

src/Fragmentation/Fragmentation.cpp

@@ -98 +98 @@
  * \param Order up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme
  * \param prefix prefix string for every fragment file name (may include path)
- * \param &DFS contains bond structure analysis data
  * \return 1 - continue, 2 - stop (no fragmentation occured)
  */
@@ -105 +104 @@
     int Order,
     const std::string &prefix,
-    DepthFirstSearchAnalysis &DFS,
     const Graph &ParsedFragmentList)
 {

src/Fragmentation/Fragmentation.hpp

@@ -14 +14 @@
 #endif
 
-#include "Graph/DepthFirstSearchAnalysis.hpp"
-
 #include "Fragmentation/fragmentation_helpers.hpp"
 #include "Fragmentation/Graph.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
+#include "Graph/ListOfLocalAtoms.hpp"
 #include "types.hpp"
 
@@ -47 +46 @@
   ~Fragmentation();
 
-  int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, const std::string &prefix, DepthFirstSearchAnalysis &DFS, const Graph &ParsedFragmentList);
+  int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, const std::string &prefix, const Graph &ParsedFragmentList);
 
   const Graph& getGraph() const {

src/Graph/CyclicStructureAnalysis.cpp

@@ -208 +208 @@
     Root->GetTrueFather()->IsCyclic = true;
 
-    std::stringstream output;
-    output << "Found ring contains: ";
-    Walker = Root;
-    while (Walker != BackEdge->rightatom) {
-      output << Walker->getName() << " <-> ";
-      Walker = PredecessorList[Walker->getNr()];
-      Walker->GetTrueFather()->IsCyclic = true;
-      RingSize++;
-    }
-    output << Walker->getName() << "  with a length of " << RingSize << ".";
-    LOG(0, "INFO: " << output.str());
+    {
+      CyclicStructureAnalysis::cycle_t currentcycle;
+      std::stringstream output;
+      output << "Found ring contains: ";
+      Walker = Root;
+      currentcycle.insert(Walker->GetTrueFather()->getId());
+      while (Walker != BackEdge->rightatom) { // leftatom is root
+        output << Walker->getName() << " <-> ";
+        Walker = PredecessorList[Walker->getNr()];
+        Walker->GetTrueFather()->IsCyclic = true;
+#ifndef NDEBUG
+        std::pair< cycle_t::iterator, bool > inserter =
+#endif
+            currentcycle.insert(Walker->GetTrueFather()->getId());
+        ASSERT( inserter.second,
+            "CyclicStructureAnalysis::RetrieveCycleMembers() - we already inserted "
+            +toString(Walker->GetTrueFather()->getId())+" into currentcycle.");
+        RingSize++;
+      }
+      output << Walker->getName() << "  with a length of " << RingSize << ".";
+      LOG(0, "INFO: " << output.str());
+      allcycles.push_back(currentcycle);
+    }
 
     // walk through all and set MinimumRingSize
@@ -365 +377 @@
   int MinRingSize = -1;
 
+  // clear cycle container
+  allcycles.clear();
+
   {
     std::stringstream output;

src/Graph/CyclicStructureAnalysis.hpp

@@ -16 +16 @@
 #include <deque>
 #include <map>
+#include <vector>
 
 #include "Bond/bond.hpp"
 #include "Bond/GraphEdge.hpp"
+#include "Fragmentation/KeySet.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Helpers/defs.hpp"
@@ -29 +31 @@
 {
 public:
+  //!> typedef for specifying a cycle
+  typedef KeySet cycle_t;
+  //!> typedef for specifying many cycles
+  typedef std::vector< cycle_t > cycles_t;
+
   explicit CyclicStructureAnalysis(const enum HydrogenTreatment _treatment);
   ~CyclicStructureAnalysis();
@@ -37 +44 @@
   const std::map<atomId_t, int >& getMinimumRingSize() const;
 
+  /** Getter for all found cycles.
+   *
+   */
+  cycles_t getAllCycles() const {
+    return allcycles;
+  }
+
 private:
+
   // init or reset
   void InitNode(atomId_t atom_id);
@@ -59 +74 @@
   atom *Root;
 
+  //!> container for all found cycles, note that these are global ids
+  cycles_t allcycles;
+
   //!> whether to treat hydrogen special or not
   const enum HydrogenTreatment treatment;