Changeset a67a04

Timestamp:

Nov 16, 2012, 2:13:43 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:

a3a382

Parents:

8b58ac

git-author:

Frederik Heber <heber@…> (08/02/12 19:42:36)

git-committer:

Frederik Heber <heber@…> (11/16/12 14:13:43)

Message:

IndexedVector's cstor ignores -1 as indices.

• this is to allow for ignoring the saturated hydrogens whose index is -1 in Force-Factors.dat and also to mark certain vectors as to drop.
• -1 has been enumerated as DropIndex.
• FragmentationAutomationAction now correctly parses forces also for the contained hydrogens due to specifically created IndexedVectors with index sets that also incorporate hydrogens.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (2 diffs)
• Fragmentation/SetValues/IndexedVectors.cpp (modified) (1 diff)
• Fragmentation/SetValues/IndexedVectors.hpp (modified) (3 diffs)
• Fragmentation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) (1 diff)
• Fragmentation/SetValues/unittests/IndexedVectorsUnitTest.hpp (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -296 +296 @@
   }
 
-  // forces need different keysets: they must include hydrogen
-  // (though without ones added by saturation)
+  /// prepare for OrthogonalSummation
 
   // convert KeySetContainer to IndexSetContainer
   IndexSetContainer::ptr container(new IndexSetContainer(KeySet));
-
   // create the map of all keysets
   SubsetMap::ptr subsetmap(new SubsetMap(*container));
+
+// we probably don't need this, it suffices if IndexedVectors has some extra indices
+//  // forces need different keysets: they must include hydrogen
+//  // (though without ones added by saturation)
+//  IndexSetContainer::ptr forceindices(new IndexSetContainer(ForceKeySet));
+//  // create the map of all keysets
+//  SubsetMap::ptr subsetmapforces(new SubsetMap(*forceindices));
 
   /// convert all MPQCData to MPQCDataMap_t
@@ -328 +333 @@
 
     // forces
-    const IndexSetContainer::Container_t &indices = container->getContainer();
-    ASSERT( indices.size() == fragmentData.size(),
-        "FragmentationAutomationAction::performCall() - indices and fragmentData differ in size.");
+    ASSERT( ForceKeySet.KeySets.size() == fragmentData.size(),
+        "FragmentationAutomationAction::performCall() - ForceKeySet's KeySets and fragmentData differ in size.");
     std::vector<MPQCDataForceMap_t> MPQCData_Force_fused;
     MPQCData_Force_fused.reserve(fragmentData.size());
     std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
-    IndexSetContainer::Container_t::const_iterator indexiter = indices.begin();
-    for(;dataiter != fragmentData.end(); ++dataiter, ++indexiter) {
+    KeySetsContainer::ArrayOfIntVectors::const_iterator arrayiter = ForceKeySet.KeySets.begin();
+    for(;dataiter != fragmentData.end(); ++dataiter, ++arrayiter) {
       const MPQCData &extractedData = *dataiter;
       LOG(2, "DEBUG: Current extracted Data is " << extractedData << ".");
       MPQCDataForceMap_t instance;
+      // must convert int to index_t
+      IndexedVectors::indices_t indices(arrayiter->begin(), arrayiter->end());
       boost::fusion::at_key<MPQCDataFused::forces>(instance) =
-          IndexedVectors(**indexiter, extractedData.forces);
+          IndexedVectors(indices, extractedData.forces);
       MPQCData_Force_fused.push_back(instance);
     }

src/Fragmentation/SetValues/IndexedVectors.cpp

@@ -57 +57 @@
         +toString(vectoriter->size())+" different to FixedSize "
         +toString(FixedSize)+".");
+    if (*indexiter != (size_t)DropIndex) { // skip all force vectors associated to -1
 #ifndef NDEBUG
-    std::pair<indexedvectors_t::iterator, bool> inserter =
+      std::pair<indexedvectors_t::iterator, bool> inserter =
 #endif
-    vectors.insert( std::make_pair( *indexiter, *vectoriter) );
-    ASSERT( inserter.second,
-        "IndexedVectors::IndexedVectors() - index "
-        +toString(inserter.first->first)+" already present with vector "
-        +toString(inserter.first->second)+".");
+      vectors.insert( std::make_pair( *indexiter, *vectoriter) );
+      ASSERT( inserter.second,
+          "IndexedVectors::IndexedVectors() - index "
+          +toString(inserter.first->first)+" already present with vector "
+          +toString(inserter.first->second)+".");
+    }
   }
 }

src/Fragmentation/SetValues/IndexedVectors.hpp

@@ -16 +16 @@
 #include <iosfwd>
 #include <map>
-#include <set>
 #include <vector>
 
@@ -41 +40 @@
   typedef std::vector<vector_t> vectors_t;
   //!> typedef for the ordered indices matching the bunch of vectors
-  typedef std::set<index_t> indices_t;
+  typedef std::vector<index_t> indices_t;
   //!> typedef for a bunch of indexed vectors
   typedef std::map<index_t, vector_t> indexedvectors_t;
+
+  enum SpecificIndices_t {
+    DropIndex = -1
+  };
 
   /** Default constructor for class IndexedVectors.
@@ -52 +55 @@
   /** Constructor for class IndexedVectors.
    *
-   * We construct the internal map from \a _indices and \a _vectors.
+   * We construct the internal map from \a _indices and \a _vectors. For
+   * every index -1 contained in \a _indices the respective vector in
+   * \a _vectors is \b not added but silently dropped.
    *
    * \param _indices index to each vector

src/Fragmentation/SetValues/unittests/IndexedVectorsUnitTest.cpp

@@ -101 +101 @@
 }
 
+
+/** UnitTest for cstor's
+ */
+void IndexedVectorsTest::Constructor_Test()
+{
+  // check whether -1 is dropped
+  IndexedVectors::indices_t indices;
+  indices += 1,-1,3;
+  IndexedVectors::vectors_t vectors;
+  vectors.push_back(ones);
+  vectors.push_back(twos);
+  vectors.push_back(threes);
+  IndexedVectors testivectors(indices, vectors);
+
+  CPPUNIT_ASSERT_EQUAL( (size_t)2, testivectors.vectors.size() );
+  CPPUNIT_ASSERT_EQUAL( ones, testivectors.vectors[1] );
+  CPPUNIT_ASSERT_EQUAL( threes, testivectors.vectors[3] );
+  CPPUNIT_ASSERT( testivectors.vectors.find(-1) == testivectors.vectors.end() );
+}
+
 /** UnitTest for operator+=()
  */

src/Fragmentation/SetValues/unittests/IndexedVectorsUnitTest.hpp

@@ -24 +24 @@
 {
     CPPUNIT_TEST_SUITE( IndexedVectorsTest) ;
+    CPPUNIT_TEST ( Constructor_Test );
     CPPUNIT_TEST ( operatorPlusEqual_Test );
     CPPUNIT_TEST ( operatorMinusEqual_Test );
@@ -31 +32 @@
       void setUp();
       void tearDown();
+      void Constructor_Test();
       void operatorPlusEqual_Test();
       void operatorMinusEqual_Test();