Changeset 19c50e for src/Fragmentation/Summation

Timestamp:

Dec 10, 2012, 10:10:58 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:

d4f31f

Parents:

4f056e

git-author:

Frederik Heber <heber@…> (09/04/12 08:26:23)

git-committer:

Frederik Heber <heber@…> (12/10/12 10:10:58)

Message:

IndexSetContainer now treats super set specially.

• The super set must not gather its subsets via the gatherSubsets() as by construction all other sets are its subsets! As the super set is very large the power set way is no good idea.
• added default cstor for SortedVector
• removed SubsetMap::getMaximumSubsetLevel() as is replaced by ::getMaximumSetLevel() which is the level to sum up to.
• changed all uses of getMaximumSubsetLevel() to getMaximumSetLevel().
• TESTFIX: Changed unit test function on getMaximumSubsetLevel() to check on getMaximumSetLevel()
• removed OrthogonalFullSummator as is fully replacable by OrthogonalSummator.
• changed IndexSetContainer::createSuperSet a bit.
• IndexSetContainer::AllIndices is now no more static convenience entity but truely contains the super set (non-statically). ::createSuperSet() is for convenience to be called in cstor for AllIndices.

Location:

src/Fragmentation/Summation

Files:

• AllLevelOrthogonalSummator.hpp (modified) (2 diffs)
• AllLevelSummator.hpp (modified) (2 diffs)
• IndexSetContainer.cpp (modified) (3 diffs)
• IndexSetContainer.hpp (modified) (1 diff)
• Makefile.am (modified) (1 diff)
• OrthogonalFullSummator.hpp (deleted)
• OrthogonalSumUpPerLevel.hpp (modified) (1 diff)
• SortedVector.hpp (modified) (1 diff)
• SubsetMap.cpp (modified) (3 diffs)
• SubsetMap.hpp (modified) (1 diff)
• SumUpPerLevel.hpp (modified) (1 diff)
• unittests/SubsetMapUnitTest.cpp (modified) (3 diffs)
• unittests/SubsetMapUnitTest.hpp (modified) (2 diffs)

src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp

@@ -52 +52 @@
     results(_results)
   {
-    ASSERT( results.size() >= subsetmap->getMaximumSubsetLevel(),
+    ASSERT( results.size() >= subsetmap->getMaximumSetLevel(),
         "AllLevelOrthogonalSummator() - result vector is not large enough.");
   }
@@ -69 +69 @@
         subsetmap, data, container, MatrixNrLookup
         );
-    const size_t MaxLevel = subsetmap->getMaximumSubsetLevel();
+    const size_t MaxLevel = subsetmap->getMaximumSetLevel();
     for (size_t level=1; level <= MaxLevel; ++level) {
       MapType &LevelResults = results[level-1];

src/Fragmentation/Summation/AllLevelSummator.hpp

@@ -52 +52 @@
     results(_results)
   {
-    ASSERT( results.size() >= subsetmap->getMaximumSubsetLevel(),
+    ASSERT( results.size() >= subsetmap->getMaximumSetLevel(),
         "AllLevelSummator() - result vector is not large enough.");
   }
@@ -69 +69 @@
         subsetmap, data, container, MatrixNrLookup
         );
-    const size_t MaxLevel = subsetmap->getMaximumSubsetLevel();
+    const size_t MaxLevel = subsetmap->getMaximumSetLevel();
     for (size_t level=1; level <= MaxLevel; ++level) {
       MapType &LevelResults = results[level-1];

src/Fragmentation/Summation/IndexSetContainer.cpp

@@ -45 +45 @@
 #include "Fragmentation/KeySetsContainer.hpp"
 
-IndexSet::ptr IndexSetContainer::AllIndices(new IndexSet);
-
-IndexSet::ptr& IndexSetContainer::createSuperSet(const KeySetsContainer &_keysets) const
+IndexSet::ptr IndexSetContainer::createSuperSet(const KeySetsContainer &_keysets) const
 {
   // create superset
-  //IndexSet::ptr AllIndices(new IndexSet);
+  IndexSet::ptr _AllIndices(new IndexSet);
   for (KeySetsContainer::ArrayOfIntVectors::const_iterator iter = _keysets.KeySets.begin();
       iter != _keysets.KeySets.end(); ++iter)
@@ -56 +54 @@
         keyiter != (*iter).end(); ++keyiter) {
       if (*keyiter != -1)
-        AllIndices->insert((Index_t)*keyiter);
+        _AllIndices->insert((Index_t)*keyiter);
     }
-  LOG(1, "INFO: AllIndices is " << *AllIndices << ".");
+  LOG(1, "INFO: AllIndices is " << *_AllIndices << ".");
 
-  return AllIndices;
+  return _AllIndices;
 }
 
 IndexSetContainer::IndexSetContainer(const KeySetsContainer &_keysets) :
-  SortedVector<IndexSet>(createSuperSet(_keysets))
+     AllIndices(createSuperSet(_keysets))
 {
-  const size_t SupersetSize = getContainer()[0]->size();
+  const size_t SupersetSize = AllIndices->size();
   // create container with all keysets
   for (KeySetsContainer::ArrayOfIntVectors::const_iterator iter = _keysets.KeySets.begin();
       iter != _keysets.KeySets.end(); ++iter) {
+    // create the IndexSets ...
     IndexSet tempset;
     for(KeySetsContainer::IntVector::const_iterator keyiter = (*iter).begin();
@@ -75 +74 @@
       if (*keyiter != -1)
         tempset.insert((Index_t)*keyiter);
-    if (tempset.size() < SupersetSize)  // only insert if not super set
+    // ... and insert, making sure that super set is AllIndices when present
+    if (tempset.size() < SupersetSize)
       insert(tempset);
+    else
+      insert(AllIndices);
   }
 }

src/Fragmentation/Summation/IndexSetContainer.hpp

@@ -83 +83 @@
   size_t countSetsTillLevel(const size_t level) const;
 
+  /** Getter to the super set.
+   *
+   * @return AllIndices
+   */
+  const IndexSet::ptr getSuperSet() const
+  {
+    return AllIndices;
+  }
+
 private:
-  /** Helper function to get the super set out of a KeySetsContainer.
+  /** Helper function to create the super set out of a KeySetsContainer.
    *
    * @param _keysets keysets to construct super set for
-   * @return IndexSet that contains each index once that appears in the sets of \a _keysets
+   * @return super set created from all keysets in \a _keysets
    */
-  IndexSet::ptr& createSuperSet(const KeySetsContainer &_keysets) const;
+  IndexSet::ptr createSuperSet(const KeySetsContainer &_keysets) const;
 
-  //!> static instance for AllIndices such that createSuperSet may return a reference.
-  static IndexSet::ptr AllIndices;
+  //!> super set that contains all present index sets
+  IndexSet::ptr AllIndices;
 };
 

src/Fragmentation/Summation/Makefile.am

@@ -13 +13 @@
         Fragmentation/Summation/IndexSet.hpp \
         Fragmentation/Summation/IndexSetContainer.hpp \
-        Fragmentation/Summation/OrthogonalFullSummator.hpp \
         Fragmentation/Summation/OrthogonalSummation.hpp \
         Fragmentation/Summation/OrthogonalSummation_impl.hpp \

src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp

@@ -39 +39 @@
   convertDataTo<TypeData, TypeMap>(fragmentData, Data_fused);
   // instantiate summator
-  std::vector<TypeMap> Result_fused(subsetmap->getMaximumSubsetLevel());
+  std::vector<TypeMap> Result_fused(subsetmap->getMaximumSetLevel());
   AllLevelOrthogonalSummator<TypeMap> Summer(
               subsetmap,

src/Fragmentation/Summation/SortedVector.hpp

@@ -84 +84 @@
   }
 
+  /** Default constructor.
+   *
+   * An empty vector is automatically sorted.
+   *
+   * @return
+   */
+  SortedVector() :
+    ContainerSorted(true)
+  {}
+
   /** Getter to sorted container.
    *

src/Fragmentation/Summation/SubsetMap.cpp

@@ -40 +40 @@
 #include <boost/bind.hpp>
 #include <boost/foreach.hpp>
+#include <boost/lambda/lambda.hpp>
 #include <algorithm>
 #include <bitset>
 #include <set>
 
+#include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
 
@@ -49 +51 @@
   tempset(new IndexSet())
 {
+  /// go through all IndexSets
   const IndexSetContainer::Container_t &container = _container.getContainer();
-
-// we don't need this level-wise sorting as this is automatically achieved by specific sorting
-//  /// place in level-wise multimap
-//  typedef size_t level_t;
-//  // note: We use an IndexSetContainer as it is not accessed while filling it
-//  // also, as insert uses push_back, the IndexSetContainer is actually created
-//  // as sorted. Hence, the call to sort() just needs linear time (and does
-//  // nothing)
-//  typedef std::map<level_t, IndexSetContainer > IndexSetPerLevel_t;
-//  IndexSetPerLevel_t IndexSetPerLevel;
-//  for(IndexSetContainer::Container_t::const_iterator iter = container.begin();
-//      iter != container.end(); ++iter) {
-//    // key present in map?
-//    const size_t level = (*iter)->size();
-//    LOG(1, "INFO: Current set is " << **iter << " with size " << level << ".");
-//    IndexSetPerLevel_t::iterator leveliter = IndexSetPerLevel.find(level);
-//    // we have to explicitly copy the shared_ptr for insertion due to const container
-//    IndexSet_ptr ptr(*iter);
-//    if (leveliter == IndexSetPerLevel.end()) {
-//      LOG(2, "DEBUG: Level not present in Lookup, creating new container");
-//      IndexSetPerLevel.insert( std::make_pair( level, IndexSetContainer(ptr)) );
-//    } else {
-//      LOG(2, "DEBUG: Level present in Lookup, appending to container");
-//      leveliter->second.insert(ptr);
-//    }
-//  }
-
-  /// go through all IndexSets
-  std::for_each( container.begin(), container.end(),
-      boost::bind(&SubsetMap::gatherSubsets, this, _1));
+  for (IndexSetContainer::Container_t::const_iterator iter = container.begin();
+      iter != container.end(); ++iter) {
+    // check whether its the super set
+    if (*iter == _container.getSuperSet()) {
+      // place all other sets as its subsets
+      std::vector<IndexSet> returnsets;
+      returnsets.reserve(container.size());
+      for (IndexSetContainer::Container_t::const_iterator insertiter = container.begin();
+            insertiter != container.end(); ++insertiter)
+        if (iter != insertiter) {
+          LOG(2, "INFO: Current subset is " << **insertiter << " for super set.");
+          ASSERT( _container.getSuperSet()->contains(**insertiter),
+              "SubsetMap::SubsetMap() - "+toString(**insertiter)+" is not contained in super set "
+              +toString(*_container.getSuperSet())+".");
+          returnsets.push_back(**insertiter);
+        }
+      Lookup.insert( std::make_pair(*iter, IndexSetContainer::ptr(new IndexSetContainer(returnsets))) );
+    } else {
+      gatherSubsets(*iter);
+    }
+  }
 }
 
@@ -184 +178 @@
 }
 
-size_t SubsetMap::getMaximumSubsetLevel() const
-{
-  // last one is super set, hence, the one before has largest subset size
-  Lookup_t::const_iterator iter = --Lookup.end();
-  --iter;
-  return iter->first->size();
-}
-
 size_t SubsetMap::getMaximumSetLevel() const
 {

src/Fragmentation/Summation/SubsetMap.hpp

@@ -58 +58 @@
     return lookupiter->second;
   }
-
-  /** Returns the size of the largest \b sub set.
-   *
-   * This would be \f${\cal O}(n)\f$ if we had to look at each set. However, due
-   * to the specific sorting we just have to check the last sets.
-   *
-   * @return number of indices in largest subset, -1 if SubsetMap contains no IndexSet's
-   */
-  size_t getMaximumSubsetLevel() const;
 
   /** Returns the size of the largest set.

src/Fragmentation/Summation/SumUpPerLevel.hpp

@@ -38 +38 @@
   convertDataTo<TypeData, TypeMap>(fragmentData, Data_fused);
   // instantiate summator
-  std::vector<TypeMap> Result_fused(subsetmap->getMaximumSubsetLevel());
+  std::vector<TypeMap> Result_fused(subsetmap->getMaximumSetLevel());
   AllLevelSummator<TypeMap> Summer(
               subsetmap,

src/Fragmentation/Summation/unittests/SubsetMapUnitTest.cpp

@@ -301 +301 @@
 }
 
-/** UnitTest for getMaximumSubsetLevel()
- */
-void SubsetMapTest::getMaximumSubsetLevelTest()
+/** UnitTest for getMaximumSetLevel()
+ */
+void SubsetMapTest::getMaximumSetLevelTest()
 {
   // create small container
@@ -323 +323 @@
     CPPUNIT_ASSERT( SM != NULL );
 
-    CPPUNIT_ASSERT_EQUAL( (size_t)1, SM->getMaximumSubsetLevel() );
-    // we are strictly less than super set (last one)
-    CPPUNIT_ASSERT( SM->getMaximumSubsetLevel() < (--SM->Lookup.end())->first->size() );
+    CPPUNIT_ASSERT_EQUAL( (size_t)2, SM->getMaximumSetLevel() );
+    // we are strictly the last set
+    CPPUNIT_ASSERT( SM->getMaximumSetLevel() == (--SM->Lookup.end())->first->size() );
   }
 
@@ -335 +335 @@
     CPPUNIT_ASSERT( SM != NULL );
 
-    CPPUNIT_ASSERT_EQUAL( (size_t)3, SM->getMaximumSubsetLevel() );
-    CPPUNIT_ASSERT( SM->getMaximumSubsetLevel() < (--SM->Lookup.end())->first->size() );
+    CPPUNIT_ASSERT_EQUAL( (size_t)4, SM->getMaximumSetLevel() );
+    CPPUNIT_ASSERT( SM->getMaximumSetLevel() == (--SM->Lookup.end())->first->size() );
   }
 }

src/Fragmentation/Summation/unittests/SubsetMapUnitTest.hpp

@@ -31 +31 @@
     CPPUNIT_TEST ( getSubsetTest );
     CPPUNIT_TEST ( gatherSubsetTest );
-    CPPUNIT_TEST ( getMaximumSubsetLevelTest );
+    CPPUNIT_TEST ( getMaximumSetLevelTest );
     CPPUNIT_TEST_SUITE_END();
 
@@ -41 +41 @@
       void getSubsetTest();
       void gatherSubsetTest();
-      void getMaximumSubsetLevelTest();
+      void getMaximumSetLevelTest();
 
 private: