Changeset 6cabaac for src/Fragmentation

Timestamp:

Apr 8, 2013, 11:56:08 AM (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:

c39675

Parents:

7d5fcd

git-author:

Frederik Heber <heber@…> (03/03/13 10:26:14)

git-committer:

Frederik Heber <heber@…> (04/08/13 11:56:08)

Message:

Extended ExportGraph to spill our molecular fragments one by one.

• the biggest scaling issue with fragmentation is the number of hydrogen atoms that are created to saturate all (e.g. 200.000 fragments frm 3.000 atoms at order 6!) the molecular fragments.
• hence, create one by one and have a controlled pool of hydrogens that are re-used.

Location:

src/Fragmentation/Exporters

Files:

• ExportGraph.cpp (modified) (2 diffs)
• ExportGraph.hpp (modified) (4 diffs)

src/Fragmentation/Exporters/ExportGraph.cpp

@@ -59 +59 @@
   const enum HydrogenSaturation _saturation) :
   TotalGraph(_graph),
+  CurrentKeySet(TotalGraph.begin()),
   BondFragments(World::getPointer()),
   treatment(_treatment),
@@ -86 +87 @@
   if (BondFragments.ListOfMolecules.size() == 0)
     prepareMolecule();
+}
+
+void ExportGraph::reset()
+{
+  CurrentKeySet = TotalGraph.begin();
+}
+
+ExportGraph::SaturatedFragment_ptr ExportGraph::getNextFragment()
+{
+  // if a fragment is still leased, return zero ptr.
+  if (!KeySetsInUse.empty()) {
+    ELOG(1, "Leasing KeySet while old one is not returned.");
+    return SaturatedFragment_ptr();
+  }
+
+  // else return current fragment or indicate end
+  if (CurrentKeySet != TotalGraph.end()) {
+    const KeySet &set = (CurrentKeySet++)->first;
+    return leaseFragment(set);
+  } else {
+    return leaseFragment(EmptySet);
+  }
+}
+
+ExportGraph::SaturatedFragment_ptr ExportGraph::leaseFragment(const KeySet &_set)
+{
+  // create the saturation which adds itself to KeySetsInUse
+  SaturatedFragment_ptr _ptr(new SaturatedFragment(_set, KeySetsInUse, hydrogens));
+  // and return
+  return _ptr;
+}
+
+void ExportGraph::releaseFragment(SaturatedFragment_ptr &_ptr)
+{
+  ASSERT(_ptr != NULL,
+      "ExportGraph::releaseFragment() - pointer is NULL.");
+  SaturatedFragment::KeySetsInUse_t::iterator iter = KeySetsInUse.find(_ptr->getKeySet());
+  if (iter == KeySetsInUse.end()) {
+    ASSERT(0,
+        "ExportGraph::releaseFragment() - returning unknown set "
+        +toString(_ptr->getKeySet())+".");
+    return;
+  } else {
+    // release instance which removes itself in KeySetsInUse
+    _ptr.reset();
+  }
 }
 

src/Fragmentation/Exporters/ExportGraph.hpp

@@ -14 +14 @@
 #endif
 
+#include <boost/shared_ptr.hpp>
+
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Fragmentation/Exporters/ExportGraph.hpp"
+#include "Fragmentation/Exporters/HydrogenPool.hpp"
+#include "Fragmentation/Exporters/SaturatedFragment.hpp"
 #include "MoleculeListClass.hpp"
 
@@ -38 +42 @@
       const enum HydrogenTreatment _treatment,
       const enum HydrogenSaturation _saturation);
-        virtual ~ExportGraph();
+  virtual ~ExportGraph();
 
-        virtual void operator()();
+  typedef boost::shared_ptr<SaturatedFragment> SaturatedFragment_ptr;
+
+  virtual void operator()();
+
+  /** Returns a saturated fragment for immediate use only.
+   *
+   * An empty KeySet indicates the end of all possible fragments
+   * A shared_ptr containing NULL indicate an error
+   *
+   * \return RAII instance of a saturated fragment, NULL - failure, empty set - end
+   */
+  SaturatedFragment_ptr getNextFragment();
+
+  /** Sets the next fragment to the first graph again.
+   *
+   */
+  void reset();
 
 private:
+
+  /** Helper function to create a fragment from a keyset and note down its in use.
+   *
+   * \param _set KeySet to create saturated fragment from
+   * \return RAII instance of a saturated fragment
+   */
+   SaturatedFragment_ptr leaseFragment(const KeySet &_set);
+
+  /** Helper function to create a fragment from a keyset and note down its in use.
+   *
+   * \param _ptr RAII instance of a saturated fragment to release again
+   */
+  void releaseFragment(SaturatedFragment_ptr &_ptr);
 
   void prepareMolecule();
@@ -50 +83 @@
 
 protected:
+  //!> empty set to indicate last and one fragment
+  const KeySet EmptySet;
+
+protected:
+  //!> set of all KeySets that are leased as saturated fragments
+  SaturatedFragment::KeySetsInUse_t KeySetsInUse;
+
+  //!> pool containing hydrogens for saturation
+  HydrogenPool hydrogens;
+
+  //!> graph containing all keysets
   const Graph &TotalGraph;
   //!> internal list of created molecules
@@ -57 +101 @@
   //!> whether to saturate dangling bonds or not
   const enum HydrogenSaturation saturation;
+
+private:
+  //!> iterator pointing at the CurrentKeySet to be exported
+  Graph::const_iterator CurrentKeySet;
 };