Changeset bf1d1b for src

Timestamp:

Aug 9, 2013, 2:20:36 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:

e355b31

Parents:

ff09f3

git-author:

Frederik Heber <heber@…> (07/04/13 08:49:28)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:20:36)

Message:

HomologyContainer now stores full struct as value to HomologyGraph key.

• this structure does not only contain fragment and energy but also the sampled charge and potential distribution.
• added version handling to HomologyContainer::value_t serialization.
• added option "store-grids" to AnalyseFragmentationResultsAction.
• TESTFIX: adapted HomologyContainerUnitTest such that new values are correctly constructed.

Location:

src

Files:

• Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (6 diffs)
• Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) (1 diff)
• Actions/FragmentationAction/FitPotentialAction.cpp (modified) (2 diffs)
• Fragmentation/Homology/HomologyContainer.cpp (modified) (1 diff)
• Fragmentation/Homology/HomologyContainer.hpp (modified) (3 diffs)
• Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) (3 diffs)
• Fragmentation/Homology/unittests/Makefile.am (modified) (1 diff)
• FunctionApproximation/TrainingData.cpp (modified) (2 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -222 +222 @@
 void appendToHomologies(
     const FragmentationShortRangeResults &shortrangeresults,
-    const FragmentationLongRangeResults &longrangeresults
+    const FragmentationLongRangeResults &longrangeresults,
+    const bool storeGrids
     )
 {
@@ -246 +247 @@
     LOG(2, "DEBUG: Created graph " << graph << ".");
     const IndexSet::ptr &index = *iter;
+
+    /// we fill the value structure
     HomologyContainer::value_t value;
-
-    // obtain fragment as key
+    value.containsGrids = storeGrids;
+    // obtain fragment
     std::map<IndexSet::ptr, std::pair< MPQCDataFragmentMap_t, MPQCDataFragmentMap_t> >::const_iterator fragmentiter
         = longrangeresults.Result_perIndexSet_Fragment.find(index);
@@ -254 +257 @@
         "appendToHomologyFile() - cannot find index "+toString(*index)
         +" in FragmentResults.");
-    value.first = boost::fusion::at_key<MPQCDataFused::fragment>(fragmentiter->second.first);
-
-    // obtain energy as value
+    value.fragment = boost::fusion::at_key<MPQCDataFused::fragment>(fragmentiter->second.first);
+
+    // obtain energy
     std::map<IndexSet::ptr, std::pair< MPQCDataEnergyMap_t, MPQCDataEnergyMap_t> >::const_iterator energyiter
         = shortrangeresults.Result_perIndexSet_Energy.find(index);
@@ -262 +265 @@
         "appendToHomologyFile() - cannot find index "+toString(*index)
         +" in FragmentResults.");
-    // value.second = boost::fusion::at_key<MPQCDataFused::energy_total>(energyiter->second.first); // values
-    value.second = boost::fusion::at_key<MPQCDataFused::energy_total>(energyiter->second.second); // contributions
+    value.energy = boost::fusion::at_key<MPQCDataFused::energy_total>(energyiter->second.second); // contributions
+
+    // only store sampled grids if desired
+    if (storeGrids) {
+      // obtain charge distribution
+      std::map<IndexSet::ptr, std::pair< MPQCDataGridMap_t, MPQCDataGridMap_t> >::const_iterator chargeiter
+          = longrangeresults.Result_perIndexSet_Grid.find(index);
+      ASSERT( chargeiter != longrangeresults.Result_perIndexSet_Grid.end(),
+          "appendToHomologyFile() - cannot find index "+toString(*index)
+          +" in FragmentResults.");
+      value.charge_distribution = boost::fusion::at_key<MPQCDataFused::sampled_grid>(chargeiter->second.second); // contributions
+
+      // obtain potential distribution
+      std::map<IndexSet::ptr, std::pair< VMGDataMap_t, VMGDataMap_t> >::const_iterator potentialiter
+          = longrangeresults.Result_perIndexSet_LongRange.find(index);
+      ASSERT( potentialiter != longrangeresults.Result_perIndexSet_LongRange.end(),
+          "appendToHomologyFile() - cannot find index "+toString(*index)
+          +" in FragmentResults.");
+      value.potential_distribution = boost::fusion::at_key<VMGDataFused::sampled_potential>(potentialiter->second.second); // contributions
+    }
     values.insert( std::make_pair( graph, value) );
   }
@@ -282 +303 @@
     for (HomologyContainer::container_t::const_iterator iter =
         homology_container.begin(); iter != homology_container.end(); ++iter) {
-      LOG(2, "DEBUG: graph " << iter->first << " has Fragment "
-          << iter->second.first << " and associated energy " << iter->second.second << ".");
+      LOG(2, "DEBUG: graph " << iter->first
+          << " has Fragment " << iter->second.fragment
+          << ", associated energy " << iter->second.energy
+          << ", and sampled grid integral " << iter->second.charge_distribution.integral()
+          << ".");
     }
   }
@@ -383 +407 @@
 
     // append all keysets to homology file
-    appendToHomologies(shortrangeresults, longrangeresults);
+    appendToHomologies(shortrangeresults, longrangeresults, params.DoStoreGrids.get());
   }
 #else

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def

@@ -14 +14 @@
 // 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 (boost::filesystem::path)
-#define paramtokens ("fragment-resultfile")
-#define paramdescriptions ("parse fragment results from the given file")
-#define paramdefaults (PARAM_DEFAULT(""))
-#define paramreferences (resultsfile)
+#define paramtypes (boost::filesystem::path)(bool)
+#define paramtokens ("fragment-resultfile")("store-grids")
+#define paramdescriptions ("parse fragment results from the given file")("whether to store sampled grids in homology files")
+#define paramdefaults (PARAM_DEFAULT(""))(PARAM_DEFAULT("0"))
+#define paramreferences (resultsfile)(DoStoreGrids)
 #define paramvalids \
-(DummyValidator< boost::filesystem::path >())
+(DummyValidator< boost::filesystem::path >()) \
+(DummyValidator< bool >())
 
 #undef statetypes

src/Actions/FragmentationAction/FitPotentialAction.cpp

@@ -191 +191 @@
   for (HomologyContainer::container_t::const_iterator iter =
       homologies.begin(); iter != homologies.end(); ++iter) {
-    LOG(1, "INFO: graph " << iter->first << " has Fragment " << iter->second.first
-        << " and associated energy " << iter->second.second << ".");
+    LOG(1, "INFO: graph " << iter->first
+        << " has Fragment " << iter->second.fragment
+        << ", associated energy " << iter->second.energy
+        << ", and sampled grid integral " << iter->second.charge_distribution.integral()
+        << ".");
   }
 
@@ -289 +292 @@
         iter != fragmentrange.second;
         ++iter) {
-      const Fragment& fragment = iter->second.first;
-      const double &energy = iter->second.second;
+      const Fragment& fragment = iter->second.fragment;
+      const double &energy = iter->second.energy;
 
       // create arguments from the fragment

src/Fragmentation/Homology/HomologyContainer.cpp

@@ -62 +62 @@
       iter != homologycontainer.container.end(); ++iter) {
     out << "Graph: " << iter->first
-        << ", (Fragment " << iter->second.first
-        << ":" << iter->second.second << ")\n";
+        << ", (Fragment " << iter->second.fragment
+        << ":" << iter->second.energy
+        << ":" << iter->second.charge_distribution.integral()
+        << ")\n";
   }
   return out;
+}
+
+bool HomologyContainer::value_t::operator==(const value_t &othervalue) const
+{
+  if (fragment != othervalue.fragment)
+    return false;
+  if (energy != othervalue.energy)
+    return false;
+  if (charge_distribution != othervalue.charge_distribution)
+    return false;
+  if (potential_distribution != othervalue.potential_distribution)
+    return false;
+  return true;
 }
 

src/Fragmentation/Homology/HomologyContainer.hpp

@@ -29 +29 @@
 #include "Fragmentation/Homology/HomologyGraph.hpp"
 #include "Fragmentation/Summation/SetValues/Fragment.hpp"
+#include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
 
 class HomologyContainerTest;
@@ -49 +50 @@
   //!> grant unit test access
   friend class HomologyContainerTest;
+
 public:
-  typedef double energy_t;
-  typedef std::pair<Fragment, energy_t> value_t;
+  /** This structure represents all values associated to a specific homology
+   * that we wish to store in this container for later reference.
+   */
+  struct value_t {
+    Fragment fragment;
+    double energy;
+    bool containsGrids;
+    SamplingGrid charge_distribution;
+    SamplingGrid potential_distribution;
+
+    value_t() :
+      energy(0.),
+      containsGrids(false)
+    {}
+
+    bool operator==(const value_t &othervalue) const;
+
+  private:
+    friend class boost::serialization::access;
+    // serialization
+    template <typename Archive>
+    void serialize(Archive& ar, const unsigned int version)
+    {
+      ar & fragment;
+      ar & energy;
+      if (version > 0) {
+        ar & containsGrids;
+        if (containsGrids) {
+          ar & charge_distribution;
+          ar & potential_distribution;
+        }
+      }
+    }
+  };
+
+public:
   typedef std::multimap< HomologyGraph, value_t> container_t;
   typedef container_t::const_iterator const_iterator;
@@ -176 +212 @@
 BOOST_CLASS_EXPORT_KEY(HomologyContainer)
 
+// version for serialized information associated to HomologyGraph
+BOOST_CLASS_VERSION(HomologyContainer::value_t, 1)
 
 #endif /* HOMOLOGYCONTAINER_HPP_ */

src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp

@@ -100 +100 @@
   positions[0][0] = 2.;
   Fragment dummy2(positions, charges);
+  HomologyContainer::value_t value1;
+  value1.fragment = dummy1;
+  value1.energy = 1.;
+  HomologyContainer::value_t value2;
+  value2.fragment = dummy2;
+  value2.energy = 1.5;
+  HomologyContainer::value_t value3;
+  value3.fragment = dummy;
+  value3.energy = 2.;
   container +=
-      std::make_pair( graph, std::make_pair(dummy1, 1.) ),
-      std::make_pair( graph, std::make_pair(dummy2, 1.5) ),
-      std::make_pair( othergraph, std::make_pair(dummy, 2.) );
+      std::make_pair( graph, value1 ),
+      std::make_pair( graph, value2 ),
+      std::make_pair( othergraph, value3 );
   // create HomologyContainer
   Keys = new HomologyContainer(container);
@@ -126 +135 @@
   Fragment::charges_t charges(1,1.);
   Fragment dummy(positions, charges);
+  HomologyContainer::value_t value;
+  value.fragment = dummy;
+  value.energy = 1.;
   newcontainer +=
-      std::make_pair( graph, std::make_pair(dummy, 1.) );
+      std::make_pair( graph, value );
 
   Keys->insert(newcontainer);
@@ -148 +160 @@
   Fragment::charges_t charges(1,1.);
   Fragment dummy(positions, charges);
+  HomologyContainer::value_t value;
+  value.fragment = dummy;
+  value.energy = 1.;
   newcontainer +=
-      std::make_pair( graph, std::make_pair(dummy, 1.) );
+      std::make_pair( graph, value );
 
   HomologyContainer other(newcontainer);

src/Fragmentation/Homology/unittests/Makefile.am

@@ -25 +25 @@
 
 FRAGMENTATIONHOMOLOGYLIBS = \
+        ../libMolecuilderFragmentationSetValues.la \
         ../libMolecuilderFragmentation.la \
         ../libMolecuilderFragmentation_getFromKeysetStub.la \

src/FunctionApproximation/TrainingData.cpp

@@ -54 +54 @@
 void TrainingData::operator()(const range_t &range) {
   for (HomologyContainer::const_iterator iter = range.first; iter != range.second; ++iter) {
-    const Fragment &fragment = iter->second.first;
+    const Fragment &fragment = iter->second.fragment;
     // create internal list of arguments
     FunctionModel::arguments_t all_args = Extractors::gatherAllSymmetricDistances(
@@ -62 +62 @@
         );
     DistanceVector.push_back( all_args );
-    const double &energy = iter->second.second;
+    const double &energy = iter->second.energy;
     EnergyVector.push_back( FunctionModel::results_t(1, energy) );
     // filter distances out of list of all arguments