Changeset 7b019a for src/FunctionApproximation

Timestamp:

Feb 27, 2013, 12:39:03 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:

d52819

Parents:

69fcba

git-author:

Frederik Heber <heber@…> (11/30/12 15:33:58)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:39:03)

Message:

Extended FunctionModel by getFragmentSpecificExtractor() definition.

• shifted extractor_t from TrainingData to FunctionModel.
• implemented function for every specific potential.
• this is preparatory for generalizing function approximation in LevMartester.
• we make use of the newly introduced extractors in the potentials and the required number of charges is ASSERT'd.

Location:

src/FunctionApproximation

Files:

• FunctionModel.hpp (modified) (4 diffs)
• TrainingData.hpp (modified) (4 diffs)

src/FunctionApproximation/FunctionModel.hpp ¶

@@ -14 +14 @@
 #endif
 
+#include <boost/function.hpp>
 #include <vector>
 
 #include "FunctionApproximation/FunctionArgument.hpp"
+
+class Fragment;
 
 /** This class represents the interface for a given function to model a
@@ -39 +42 @@
   //!> typedef for the result vector as returned by the function
   typedef std::vector<result_t> results_t;
+  //!> typedef for a function containing how to extract required information from a Fragment.
+  typedef boost::function< arguments_t (const Fragment &, const size_t)> extractor_t;
+  //!> typedef for a vector of particle tyoes
+  typedef std::vector< double > charges_t;
+
 public:
   FunctionModel() {}
@@ -54 +62 @@
    */
   virtual parameters_t getParameters() const=0;
+
+//  /** Sets the parameter randomly within the sensible range of each parameter.
+//   *
+//   */
+//  virtual void setParametersToRandomInitialValues() const=0;
 
   /** Getter for the number of parameters of this model function.
@@ -99 +112 @@
    */
   virtual parameters_t getUpperBoxConstraints() const=0;
+
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \param charges vector of charges to be extracted
+   * \return bound function extracting distances from a fragment
+   */
+  virtual extractor_t getFragmentSpecificExtractor(const charges_t &charges) const=0;
 };
 

src/FunctionApproximation/TrainingData.hpp ¶

@@ -19 +19 @@
 #include "Fragmentation/Homology/HomologyContainer.hpp"
 #include "FunctionApproximation/FunctionApproximation.hpp"
-
-class Fragment;
+#include "FunctionApproximation/FunctionModel.hpp"
 
 /** This class encapsulates the training data for a given potential function
@@ -39 +38 @@
   //!> Training tuple output vector pair
   typedef FunctionApproximation::outputs_t OutputVector_t;
-  //!> Typedef for a function containing how to extract required information from a Fragment.
-  typedef boost::function< FunctionModel::arguments_t (const Fragment &, const size_t)> extractor_t;
   //!> Typedef for a table with columns of all distances and the energy
   typedef std::vector< std::vector<double> > DistanceEnergyTable_t;
@@ -48 +45 @@
    *
    */
-  explicit TrainingData(const extractor_t &_extractor) :
+  explicit TrainingData(const FunctionModel::extractor_t &_extractor) :
       extractor(_extractor)
   {}
@@ -118 +115 @@
   OutputVector_t EnergyVector;
   //!> function to be used for training input data extraction from a fragment
-  const extractor_t extractor;
+  const FunctionModel::extractor_t extractor;
 };