Changeset e1fe7e for src/FunctionApproximation/FunctionModel.hpp

Timestamp:

Jun 27, 2014, 9:32:55 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:

550f2a

Parents:

16227a

git-author:

Frederik Heber <heber@…> (02/27/14 20:15:41)

git-committer:

Frederik Heber <heber@…> (06/27/14 21:32:55)

Message:

FunctionModel now uses list_of_arguments to split sequence of subsets of distances.

• this fixes ambiguities with the set of distances: Imagine the distances within a water molecule as OH (A) and HH (B). We then may have a sequence of argument_t as AABAAB. And with the current implementation of CompoundPotential::splitUpArgumentsByModels() we would always choose the latter (and more complex) model. Hence, we make two calls to TriplePotential_Angle, instead of calls twice to PairPotential_Harmonic for A, one to PairPotential_Harmonic for B, and once to TriplePotential_Angle for AAB.
• now, we new list looks like A,A,B,AAB where each tuple of distances can be uniquely associated with a specific potential.
• changed signatures of EmpiricalPotential::operator(), ::derivative(), ::parameter_derivative(). This involved changing all of the current specific potentials and CompoundPotential.
• TrainingData must discern between the InputVector_t (just all distances) and the FilteredInputVector_t (tuples of subsets of distances).
• FunctionApproximation now has list_of_arguments_t as parameter to evaluate() and evaluate_derivative().
• DOCU: docu change in TrainingData.

File:

• src/FunctionApproximation/FunctionModel.hpp (modified) (5 diffs)

src/FunctionApproximation/FunctionModel.hpp ¶

@@ -15 +15 @@
 
 #include <boost/function.hpp>
+#include <list>
 #include <vector>
 
@@ -58 +59 @@
   //!> typedef for the whole set of parameters of the function
   typedef std::vector<parameter_t> parameters_t;
-  //!> typedef for the argument vector as input to the function
+  //!> typedef for the argument vector as input to the function (subset of distances)
   typedef std::vector<argument_t> arguments_t;
+  //!> typedef for a list of argument vectors as input to the function (list of subsets)
+  typedef std::list<arguments_t> list_of_arguments_t;
   //!> typedef for a single result degree of freedom
   typedef double result_t;
@@ -65 +68 @@
   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 boost::function< list_of_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 boost::function< list_of_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;
@@ -114 +117 @@
    * \return result of the function
    */
-  virtual results_t operator()(const arguments_t &arguments) const=0;
+  virtual results_t operator()(const list_of_arguments_t &arguments) const=0;
 
   /** Evaluates the derivative of the function with the given \a arguments
@@ -124 +127 @@
    *         input
    */
-  virtual results_t parameter_derivative(const arguments_t &arguments, const size_t index) const=0;
+  virtual results_t parameter_derivative(const list_of_arguments_t &arguments, const size_t index) const=0;
 
   /** States whether lower and upper boundaries should be used to constraint