Changeset 0f5d38 for src/FunctionApproximation

Timestamp:

Aug 9, 2013, 2:20:35 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:

51e0e3

Parents:

f0025d

git-author:

Frederik Heber <heber@…> (06/25/13 10:54:50)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:20:35)

Message:

Added getSpecificFilter() and getSpecificArgumentCount() to FunctionModel.

• implemented getSpecificArgumentCount() in all specific potentials.
• added NoOp_filterfunction to Helpers.
• enhanced Documentation on FunctionModel on new Extractor,Filter,Count system.
• rewrote CompoundPotential::getSpecificExtractor() using Helpers::returnEmptyArguments() such that first model does not have to be treated special anymore.

File:

• src/FunctionApproximation/FunctionModel.hpp (modified) (3 diffs)

src/FunctionApproximation/FunctionModel.hpp

@@ -29 +29 @@
  * as possible.
  *
+ * We always work in distances, i.e. pairs of atoms and the distance in between.
+ * As fragments do not contain these distances directly but the atomic positions
+ * (and charges) instead, we need to extract these from the fragment. For this
+ * purpose we need a bound function, termed an 'Extractor'. However, this is only
+ * required when one wants to use a FunctionModel directly on a given fragment.
+ * In FunctionApproximation we instead have TrainingData generate automatically
+ * a list of all pair-wise distances. The FunctionModel's Extractor may however
+ * create a more specific (and tighter) list of arguments, which however can
+ * then only be used with this specific FunctionModel.
+ *
+ * Furthermore, the underlying function to fit may require these distances, or
+ * arguments (termed so if paired with charges and atomic indices), to be in a
+ * certain order or does need only a subset. For this purpose we need another
+ * bound function, called a 'Filter'.
+ *
+ * As a fragment may contain multiple sets of arguments or distances that serve
+ * as valid function arguments, we need to split these sets up, such that they
+ * can be served one by one to the function. For this purpose we need a function
+ * that gives the number of arguments per set. (note that the Filter is supposed
+ * to place related arguments consecutively.
+ *
  */
 class FunctionModel
@@ -45 +66 @@
   //!> 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 function containing how to filter required distances from a full argument list.
+  typedef boost::function< arguments_t (const arguments_t &)> filter_t;
   //!> typedef for the magic triple function that gets the other two distances for a given argument
   typedef boost::function< std::vector<arguments_t>(const argument_t &, const double)> triplefunction_t;
@@ -130 +153 @@
    */
   virtual extractor_t getSpecificExtractor() const=0;
+
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \return bound function extracting distances from a fragment
+   */
+  virtual filter_t getSpecificFilter() const=0;
+
+  /** Returns the number of arguments the underlying function requires.
+   *
+   * \return number of arguments of the function
+   */
+  virtual size_t getSpecificArgumentCount() const=0;
 };