Changeset 1ba8a1 for src/FunctionApproximation

Timestamp:

Jun 27, 2014, 9:32:29 PM (11 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:

4e009d

Parents:

1b1fa5

git-author:

Frederik Heber <heber@…> (02/27/14 19:07:56)

git-committer:

Frederik Heber <heber@…> (06/27/14 21:32:29)

Message:

DOCU: Extended documentation on FunctionApproximation and potential fitting.

Location:

src/FunctionApproximation

Files:

• Extractors.hpp (modified) (1 diff)
• FunctionApproximation.hpp (modified) (1 diff)

src/FunctionApproximation/Extractors.hpp

@@ -22 +22 @@
 
 /** Namespace containing all simple extractor functions.
+ *
+ * Extractor functions extract distances from a given fragment matching with
+ * a given set of particle types (i.e. elements, e.h. H2O).
+ * Filter functions extract a subset of distances from a given set of distances
+ * to be used with a specific model.
+ *
+ * To this end, each FunctionModel has both a filter and an extractor function.
+ *
+ * The functions in this namespace act as helpers or basic building blocks in
+ * constructing such filters and extractors.
  *
  */

src/FunctionApproximation/FunctionApproximation.hpp

@@ -40 +40 @@
  * <a href="http://www.ics.forth.gr/~lourakis/levmar/index.html">LevMar</a>
  * package.
+ *
+ * \section FunctionApproximation-details Details on the inner workings.
+ *
+ *  FunctionApproximation::operator() is the main function that performs the
+ *  non-linear regression. It consists of the following steps:
+ *  -# hand given (initial) parameters over to model.
+ *  -# convert output vector to format suitable to levmar
+ *  -# allocate memory for levmar to work in
+ *  -# depending on whether the model is constrained or not and whether we
+ *   have a derivative, we make use of various levmar functions with prepared
+ *   parameters.
+ *  -# memory is free'd and some final infos is given.
+ *
+ *  levmar needs to evaluate the model. To this end, FunctionApproximation has
+ *  two functions whose signatures is such as to match with the one required
+ *  by the levmar package. Hence,
+ *  -# FunctionApproximation::LevMarCallback()
+ *  -# FunctionApproximation::LevMarDerivativeCallback()
+ *  are used as callbacks by levmar only.
+ *  These hand over the current set of parameters to the model, then both bind
+ *  FunctionApproximation::evaluate() and
+ *  FunctionApproximation::evaluateDerivative(), respectively, and execute
+ *  FunctionModel::operator() or FunctionModel::parameter_derivative(),
+ *  respectively.
  *
  */