Changeset adb51ab

Timestamp:

Oct 14, 2013, 11:42:04 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:

7d507c

Parents:

fe0cb8

git-author:

Frederik Heber <heber@…> (09/26/13 10:47:57)

git-committer:

Frederik Heber <heber@…> (10/14/13 23:42:04)

Message:

FragmentationAction stores cycles to file and in FragmentationResultContainer.

• added FragmentationResultContainer::addCycles() to add cycle keysets to the present cycle-specific KeySetsContainer. These must be given as KeySetsContainer to avoid dependencing on libMolecuilderFragmentation.so which vector<KeySet> would trigger.
• added CYCLEKEYSETFILE with default file name

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAction.cpp (modified) (2 diffs)
• Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) (1 diff)
• Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) (6 diffs)
• Helpers/defs.cpp (modified) (1 diff)
• Helpers/defs.hpp (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -48 +48 @@
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Fragmentation/Interfragmenter.hpp"
+#include "Fragmentation/KeySetsContainer.hpp"
+#include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
 #include "Graph/AdjacencyList.hpp"
 #include "Graph/BondGraph.hpp"
@@ -183 +185 @@
     CycleAnalysis(&BackEdgeStack);
     CyclicStructureAnalysis::cycles_t cycles = CycleAnalysis.getAllCycles();
+    // sort them according to KeySet::operator<()
+    std::sort(cycles.begin(), cycles.end());
+    // store all found cycles to file
+    {
+      boost::filesystem::path filename(params.prefix.get() + std::string(CYCLEKEYSETFILE));
+      std::ofstream File;
+      LOG(1, "INFO: Storing cycle keysets to " << filename.string() << ".");
+      File.open(filename.string().c_str(), ios::out);
+      for (CyclicStructureAnalysis::cycles_t::const_iterator iter = cycles.begin();
+          iter != cycles.end(); ++iter) {
+        for (CyclicStructureAnalysis::cycle_t::const_iterator cycleiter = (*iter).begin();
+            cycleiter != (*iter).end(); ++cycleiter) {
+          File << *cycleiter << "\t";
+        }
+        File << "\n";
+      }
+      File.close();
+    }
+    // ... and to result container
+    {
+      KeySetsContainer cyclekeys;
+      for (CyclicStructureAnalysis::cycles_t::const_iterator iter = cycles.begin();
+          iter != cycles.end(); ++iter) {
+        const CyclicStructureAnalysis::cycle_t &cycle = *iter;
+        const size_t order = cycle.size();
+        KeySetsContainer::IntVector temp_cycle(cycle.begin(), cycle.end());
+        cyclekeys.insert(temp_cycle, order);
+      }
+      FragmentationResultContainer::getInstance().addCycles(cyclekeys);
+    }
+    // Create graph and insert into TotalGraph
     LOG(0, "STATUS: Adding " << cycles.size() << " cycles.");
-    // Create graph and insert into TotalGraph
     {
       Graph CycleGraph;

src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp

@@ -96 +96 @@
 }
 
-
 #ifdef HAVE_VMG
 const FragmentationResultContainer::longrangedata_t&

src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp

@@ -68 +68 @@
    *
    * \param _keysets
-   * \param _forcekeysets
+   * \param _forcekeysetskeysets
    * \param _shortrangedata
    * \param _longrangedata
@@ -94 +94 @@
       );
 
+  /** Adds given cycles to internal keyset list.
+   *
+   * \param _cycles keysets of cycles to add
+   */
+  void addCycles(const KeySetsContainer &_cycles)
+  { cycles.insert(_cycles); }
+
   /** Clears all internal containers.
    *
@@ -111 +118 @@
 
   const KeySetsContainer &getKeySets() const { return keysets; }
+  const KeySetsContainer &getCycles() const { return cycles; }
   const KeySetsContainer &getForceKeySets() const  { return forcekeysets; }
   const shortrangedata_t& getShortRangeResults() const  { return shortrangedata; }
@@ -131 +139 @@
   //!> container for all short-range results
   std::map<JobId_t, MPQCData> shortrangedata;
+  //! container of all cycle keysets
+  KeySetsContainer cycles;
 
 #ifdef HAVE_VMG
@@ -146 +156 @@
     ar & forcekeysets;
     ar & shortrangedata;
+    if (version > 0)
+      ar & cycles;
 #ifdef HAVE_VMG
     ar & longrangedata;
@@ -152 +164 @@
 };
 
+// version for serialized information associated to FragmentationResultContainer
+BOOST_CLASS_VERSION(FragmentationResultContainer, 1)
+
 #endif /* FRAGMENTATIONRESULTCONTAINER_HPP_ */

src/Helpers/defs.cpp

@@ -57 +57 @@
 const char *CONVEXENVELOPE = "ConvexEnvelope.dat";    //!< default filename of convex envelope tecplot data file
 const char *KEYSETFILE = "KeySets.dat";    //!< default filename of BOSSANOVA key sets file
+const char *CYCLEKEYSETFILE = "Cycles.dat";    //!< default filename of BOSSANOVA adjacancy file
 const char *ADJACENCYFILE = "Adjacency.dat";    //!< default filename of BOSSANOVA adjacancy file
 const char *TEFACTORSFILE = "TE-Factors.dat";    //!< default filename of BOSSANOVA total energy factors file

src/Helpers/defs.hpp

@@ -54 +54 @@
 extern "C" const char *CONVEXENVELOPE;    //!< default filename of convex envelope tecplot data file
 extern "C" const char *KEYSETFILE;    //!< default filename of BOSSANOVA key sets file
+extern "C" const char *CYCLEKEYSETFILE;    //!< default filename of BOSSANOVA cycle key sets file
 extern "C" const char *ADJACENCYFILE;    //!< default filename of BOSSANOVA adjacancy file
 extern "C" const char *TEFACTORSFILE;    //!< default filename of BOSSANOVA total energy factors file