Changeset caa00e9 for src/FunctionApproximation/Extractors.hpp

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:

df350c

Parents:

dbf8c8

git-author:

Frederik Heber <heber@…> (12/06/12 10:35:37)

git-committer:

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

Message:

Added gatherAllDistancesFromFragment() to Extractors.

• gatherDistancesFromFragment() did only get the first matching distance, but e.g. for SaturationPotential we need to get all from (8,1,1) for types (8,1).
• this involved three helper functions initially similar in spirit, but we get all combinations via a simple recursion with pickLastElementAsTarget().

File:

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

src/FunctionApproximation/Extractors.hpp

@@ -14 +14 @@
 #endif
 
+#include <boost/function.hpp>
+
 #include "Fragmentation/SetValues/Fragment.hpp"
 #include "FunctionApproximation/FunctionModel.hpp"
@@ -30 +32 @@
   typedef std::map< element_t, count_t> elementcounts_t;
   typedef std::map< element_t, chargeiters_t > elementtargets_t;
+  typedef std::vector< chargeiters_t > targets_per_combination_t;
 
   /** Namespace for some internal helper functions.
@@ -117 +120 @@
         const Fragment::charges_t& charges,
         const Fragment::charges_t elements
+        );
+
+    /** Brings all charges together in a map.
+     *
+     * @param charges charges as possible keys and their iterators as values in the map
+     * @param elements list of charges to pick as keys
+     * @return map of key and a vector of charge iterators
+     */
+    elementtargets_t convertChargesToTargetMap(
+        const Fragment::charges_t& charges,
+        Fragment::charges_t elements
+        );
+
+    /** Brings combinatorially together desired list of \a charges and \a targets.
+     *
+     * @param charges list of desired charges
+     * @param elementtargets map of available targets per element
+     * @return vector of chargeiters with all unique combinations
+     */
+    targets_per_combination_t
+    CombineChargesAndTargets(
+        const Fragment::charges_t& charges,
+        const elementtargets_t& elementtargets
+        );
+
+    /** Recursive function to pick the next target.
+     *
+     * This is used by \sa CombineChargesAndTargets()
+     *
+     * @param charges set of charges, reduced by one per recursion
+     * @param elementtargets targets, map of targets to pick from
+     * @param currenttargets current set of targets, "global" through recursion
+     * @param addFunction bound function to add a set when complete
+     */
+    void pickLastElementAsTarget(
+        Fragment::charges_t elements,
+        elementtargets_t elementtargets,
+        chargeiters_t& currenttargets,
+        boost::function<void (const chargeiters_t &currenttargets)> &addFunction
+        );
+
+    /** Converts a list of chargeiters to a list of respective arguments.
+     *
+     * @param positions positions from fragment
+     * @param charges charges associated to each element in \a positions
+     * @param combinations vector of chargeiters
+     * \param globalid refers to the index within the global set of configurations
+     * @return list of arguments
+     */
+    FunctionModel::arguments_t
+    convertTargetsToArguments(
+        const Fragment::positions_t& positions,
+        const Fragment::charges_t& charges,
+        const targets_per_combination_t combinations,
+        const size_t globalid
         );
   }
@@ -199 +257 @@
    * \param charges all nuclei charges
    * \param elements tuple of desired elements
+   * \param globalid refers to the index within the global set of configurations
    * \return vector of arguments_t containing those matched with elements
    */
@@ -208 +267 @@
       );
 
+  /** Gather all combinations of charges as distance arguments from the fragment.
+   *
+   * E.g. we have a water fragment, i.e. (8,1,1) and we we want elements (8,1),
+   * then two arguments are returned, first to second and first to third.
+   *
+   * With \sa gatherDistancesFromFragment() only the first distance would be
+   * returned.
+   *
+   * @param positions positions in fragment
+   * @param charges charges in fragment
+   * @param elements list of desired elements
+   * @param globalid some global id to discern training data tuples
+   * @return list of arguments with distances
+   */
+  FunctionModel::arguments_t gatherAllDistancesFromFragment(
+      const Fragment::positions_t& positions,
+      const Fragment::charges_t& charges,
+      const Fragment::charges_t elements,
+      const size_t globalid
+      );
+
   /** Reorder arguments by increasing distance.
    *