Changeset e1fe7e for src/FunctionApproximation/Extractors.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/Extractors.hpp (modified) (3 diffs)

src/FunctionApproximation/Extractors.hpp

@@ -304 +304 @@
   /** Reorder arguments by increasing distance.
    *
-   * \param args arguments to reorder
+   * \param listargs list of arguments to reorder each
    * \return reordered args
    */
-  FunctionModel::arguments_t reorderArgumentsByIncreasingDistance(
-      const FunctionModel::arguments_t &args
+  FunctionModel::list_of_arguments_t reorderArgumentsByIncreasingDistance(
+      const FunctionModel::list_of_arguments_t &listargs
       );
 
@@ -318 +318 @@
    * \sa filterArgumentsByParticleTypes()
    *
+   * \param listargs list of arguments to reorder each
+   * \param _types particle type vector
+   * \return reordered args
+   */
+  FunctionModel::list_of_arguments_t reorderArgumentsByParticleTypes(
+      const FunctionModel::list_of_arguments_t &eachargs,
+      const ParticleTypes_t &_types
+      );
+
+  /** Filter arguments according to types, allowing multiples.
+   *
+   * If particle types is (0,1,2) and three arguments, each with a pair of types,
+   * are given, then the alignment will be: (0,1), (0,2), and (1,2).
+   *
    * \param args arguments to reorder
    * \param _types particle type vector
-   * \return reordered args
-   */
-  FunctionModel::arguments_t reorderArgumentsByParticleTypes(
-      const FunctionModel::arguments_t &args,
-      const ParticleTypes_t &_types
-      );
-
-  /** Filter arguments according to types.
-   *
-   * If particle types is (0,1,2) and three arguments, each with a pair of types,
-   * are given, then the alignment will be: (0,1), (0,2), and (1,2).
-   *
-   * \param args arguments to reorder
-   * \param _types particle type vector
-   * \return filtered args
-   */
-  FunctionModel::arguments_t filterArgumentsByParticleTypes(
+   * \return filtered list of args
+   */
+  FunctionModel::list_of_arguments_t filterArgumentsByParticleTypes(
       const FunctionModel::arguments_t &args,
       const ParticleTypes_t &_types
@@ -361 +361 @@
       const FunctionModel::arguments_t &secondargs);
 
+  /** Combines two argument lists by concatenation.
+   *
+   * @param firstlistargs first list of argument tuples
+   * @param secondlistargs second list of argument tuples
+   * @return concatenated lists
+   */
+  FunctionModel::list_of_arguments_t concatenateListOfArguments(
+      const FunctionModel::list_of_arguments_t &firstlistargs,
+      const FunctionModel::list_of_arguments_t &secondlistargs);
+
 }; /* namespace Extractors */