Changeset af2c7ec for src/FunctionApproximation

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:

b5f548

Parents:

31a2be

git-author:

Frederik Heber <heber@…> (06/25/13 13:08:43)

git-committer:

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

Message:

TrainingData now generates internal list of all arguments.

• InputVector is now the filtered sequence.
• TrainingData's cstor now expects filter instead of extractor.
• adapted FitPotentialAction.
• Extended TrainingData documentation on generation of all pair-wise distances.

Location:

src/FunctionApproximation

Files:

• TrainingData.cpp (modified) (5 diffs)
• TrainingData.hpp (modified) (5 diffs)

src/FunctionApproximation/TrainingData.cpp

@@ -50 +50 @@
 #include "Fragmentation/Summation/SetValues/Fragment.hpp"
 #include "FunctionApproximation/FunctionModel.hpp"
+#include "FunctionApproximation/Extractors.hpp"
 
 void TrainingData::operator()(const range_t &range) {
   for (HomologyContainer::const_iterator iter = range.first; iter != range.second; ++iter) {
-    // get distance out of Fragment
     const Fragment &fragment = iter->second.first;
-    FunctionModel::arguments_t args = extractor(
-          fragment,
-          DistanceVector.size()
+    // create internal list of arguments
+    FunctionModel::arguments_t all_args = Extractors::gatherAllSymmetricDistances(
+        fragment.getPositions(),
+        fragment.getCharges(),
+        DistanceVector.size()
         );
-    DistanceVector.push_back( args );
+    DistanceVector.push_back( all_args );
     const double &energy = iter->second.second;
     EnergyVector.push_back( FunctionModel::results_t(1, energy) );
+    // filter distances out of list of all arguments
+    FunctionModel::arguments_t args = filter(all_args);
+    LOG(3, "DEBUG: Filtered arguments are " << args << ".");
+    ArgumentVector.push_back( args );
   }
 }
@@ -69 +75 @@
   double L2sum = 0.;
 
-  FunctionApproximation::inputs_t::const_iterator initer = DistanceVector.begin();
+  FunctionApproximation::inputs_t::const_iterator initer = ArgumentVector.begin();
   FunctionApproximation::outputs_t::const_iterator outiter = EnergyVector.begin();
-  for (; initer != DistanceVector.end(); ++initer, ++outiter) {
+  for (; initer != ArgumentVector.end(); ++initer, ++outiter) {
     const FunctionModel::results_t result = model((*initer));
     const double temp = fabs((*outiter)[0] - result[0]);
@@ -82 +88 @@
 {
   double Lmax = 0.;
-  size_t maxindex = -1;
-  FunctionApproximation::inputs_t::const_iterator initer = DistanceVector.begin();
+//  size_t maxindex = -1;
+  FunctionApproximation::inputs_t::const_iterator initer = ArgumentVector.begin();
   FunctionApproximation::outputs_t::const_iterator outiter = EnergyVector.begin();
-  for (; initer != DistanceVector.end(); ++initer, ++outiter) {
+  for (; initer != ArgumentVector.end(); ++initer, ++outiter) {
     const FunctionModel::results_t result = model((*initer));
     const double temp = fabs((*outiter)[0] - result[0]);
     if (temp > Lmax) {
       Lmax = temp;
-      maxindex = std::distance(
-          const_cast<const FunctionApproximation::inputs_t &>(DistanceVector).begin(),
-          initer
-          );
+//      maxindex = std::distance(
+//          const_cast<const FunctionApproximation::inputs_t &>(ArgumentVector).begin(),
+//          initer
+//          );
     }
   }
@@ -102 +108 @@
 {
   TrainingData::DistanceEnergyTable_t table;
-  const InputVector_t &DistanceVector = getTrainingInputs();
-  const OutputVector_t &EnergyVector = getTrainingOutputs();
 
   /// extract distance member variable from argument_t and first value from results_t
   OutputVector_t::const_iterator ergiter = EnergyVector.begin();
-  for (InputVector_t::const_iterator iter = DistanceVector.begin();
-      iter != DistanceVector.end(); ++iter, ++ergiter) {
+  for (InputVector_t::const_iterator iter = ArgumentVector.begin();
+      iter != ArgumentVector.end(); ++iter, ++ergiter) {
     ASSERT( ergiter != EnergyVector.end(),
         "TrainingData::getDistanceEnergyTable() - less output than input values.");
@@ -149 +153 @@
 std::ostream &operator<<(std::ostream &out, const TrainingData &data)
 {
-  const TrainingData::InputVector_t &DistanceVector = data.getTrainingInputs();
+  const TrainingData::InputVector_t &DistanceVector = data.getAllArguments();
   const TrainingData::OutputVector_t &EnergyVector = data.getTrainingOutputs();
   out << "(" << DistanceVector.size()

src/FunctionApproximation/TrainingData.hpp

@@ -26 +26 @@
  * The data is added piece-wise by calling the operator() with a specific
  * Fragment.
+ *
+ * In TrainingData::operator() we construct first all pair-wise distances as
+ * list of all arguments. Then, these are filtered depending on the specific
+ * FunctionModel's Filter and only these are handed to down to evaluate it.
+ *
  */
 class TrainingData
@@ -45 +50 @@
    *
    */
-  explicit TrainingData(const FunctionModel::extractor_t &_extractor) :
-      extractor(_extractor)
+  explicit TrainingData(const FunctionModel::filter_t &_filter) :
+      filter(_filter)
   {}
+
   /** Destructor for class TrainingData.
    *
@@ -55 +61 @@
 
   /** We go through the given \a range of homologous fragments and call
-   * TrainingData::extractor on them in order to gather the distance and
+   * TrainingData::filter on them in order to gather the distance and
    * the energy value, stored internally.
    *
@@ -67 +73 @@
    */
   const InputVector_t& getTrainingInputs() const {
+    return ArgumentVector;
+  }
+
+  /** Getter for const access to internal list of all pair-wise distances.
+   *
+   * \return const ref to all arguments
+   */
+  const InputVector_t& getAllArguments() const {
     return DistanceVector;
   }
@@ -114 +128 @@
   InputVector_t DistanceVector;
   OutputVector_t EnergyVector;
+  //!> list of all filtered arguments over all tuples
+  InputVector_t ArgumentVector;
   //!> function to be used for training input data extraction from a fragment
-  const FunctionModel::extractor_t extractor;
+  const FunctionModel::filter_t filter;
 };