Changeset 8aa597 for src/LevMartester.cpp

Timestamp:

Feb 24, 2013, 12:58:52 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:

f68c68

Parents:

355af8

git-author:

Frederik Heber <heber@…> (10/15/12 05:17:21)

git-committer:

Frederik Heber <heber@…> (02/24/13 12:58:52)

Message:

Extracted namespace Extractors into own module.

• placed gatherAllDistanceArguments() into subspace _detail inside this namespace.

File:

• src/LevMartester.cpp (modified) (4 diffs)

src/LevMartester.cpp

@@ -62 +62 @@
 #include "Fragmentation/Homology/HomologyContainer.hpp"
 #include "Fragmentation/SetValues/Fragment.hpp"
+#include "FunctionApproximation/Extractors.hpp"
 #include "FunctionApproximation/FunctionApproximation.hpp"
 #include "FunctionApproximation/FunctionModel.hpp"
@@ -107 +108 @@
 }
 
-FunctionModel::arguments_t
-gatherAllDistanceArguments(
-    const Fragment::charges_t &charges,
-    const Fragment::positions_t &positions,
-    const size_t globalid)
-{
-  FunctionModel::arguments_t result;
-
-  // go through current configuration and gather all other distances
-  Fragment::charges_t::const_iterator firstchargeiter = charges.begin();
-  Fragment::positions_t::const_iterator firstpositer = positions.begin();
-  for (;firstchargeiter != charges.end();
-      ++firstchargeiter, ++firstpositer) {
-    Fragment::charges_t::const_iterator secondchargeiter = charges.begin();//firstchargeiter;
-    Fragment::positions_t::const_iterator secondpositer = positions.begin();//firstpositer;
-    for (;
-        secondchargeiter != charges.end();
-        ++secondchargeiter, ++secondpositer) {
-      if (firstchargeiter == secondchargeiter)
-        continue;
-      argument_t arg;
-      const Vector firsttemp((*firstpositer)[0],(*firstpositer)[1],(*firstpositer)[2]);
-      const Vector secondtemp((*secondpositer)[0],(*secondpositer)[1],(*secondpositer)[2]);
-      arg.distance = firsttemp.distance(secondtemp);
-      arg.indices = std::make_pair(
-          std::distance(
-              charges.begin(), firstchargeiter),
-          std::distance(
-              charges.begin(), secondchargeiter)
-          );
-      arg.globalid = globalid;
-      result.push_back(arg);
-    }
-    ASSERT( secondpositer == positions.end(),
-        "gatherAllDistanceArguments() - there are not as many positions as charges.");
-  }
-  ASSERT( firstpositer == positions.end(),
-      "gatherAllDistanceArguments() - there are not as many positions as charges.");
-
-  return result;
-}
 
 /** This function returns the elements of the sum over index "k" for an
@@ -238 +198 @@
     return angle/divisor;
 }
-
-/** Namespace containing all simple extractor functions.
- *
- */
-namespace Extractors {
-  /** Simple extractor of all unique pair distances of a given \a fragment.
-   *
-   * \param fragment fragment with all nuclei positions
-   * \param index index refers to the index within the global set of configurations
-   * \return vector of of argument_t containing all found distances
-   */
-  FunctionModel::arguments_t gatherAllDistances(
-      const Fragment& fragment,
-      const size_t index
-      ) {
-    // get distance out of Fragment
-    const Fragment::charges_t charges = fragment.getCharges();
-    const Fragment::positions_t positions = fragment.getPositions();
-    return gatherAllDistanceArguments(charges, positions, index);
-  }
-
-  /** Gather first distance for the two matching charges.
-   *
-   * \param fragment fragment with all nuclei positions
-   * \param index index refers to the index within the global set of configurations
-   * \param firstelement first element of pair
-   * \param secondelement second element of pair, order is reflected in indices of return argument_t
-   * \return vector of of argument_t containing all found distances
-   */
-  FunctionModel::arguments_t gatherFirstDistance(
-      const Fragment& fragment,
-      const size_t index,
-      const size_t firstelement,
-      const size_t secondelement
-      ) {
-    const Fragment::charges_t charges = fragment.getCharges();
-    const Fragment::positions_t positions = fragment.getPositions();
-    typedef Fragment::charges_t::const_iterator chargeiter_t;
-    std::vector< chargeiter_t > firstpair;
-    firstpair.reserve(2);
-    firstpair +=
-        std::find(charges.begin(), charges.end(), firstelement),
-        std::find(charges.begin(), charges.end(), secondelement);
-    if ((firstpair[0] == charges.end()) || (firstpair[1] == charges.end())) {
-      // complain if tuple not found
-      ELOG(1, "Could not find pair " << firstelement << "," << secondelement
-          << " in fragment " << fragment);
-      return FunctionModel::arguments_t();
-    }
-    // convert position_t to Vector
-    std::vector< std::pair<Vector, size_t> > DistancePair;
-    for (std::vector<chargeiter_t>::const_iterator firstpairiter = firstpair.begin();
-        firstpairiter != firstpair.end(); ++firstpairiter) {
-      Fragment::positions_t::const_iterator positer = positions.begin();
-      const size_t steps = std::distance(charges.begin(), *firstpairiter);
-      std::advance(positer, steps);
-      DistancePair.push_back(
-          std::make_pair(Vector((*positer)[0], (*positer)[1], (*positer)[2]),
-              steps));
-    }
-    // finally convert Vector pair to distance-like argument
-    argument_t arg;
-    arg.indices.first = DistancePair[0].second;
-    arg.indices.second = DistancePair[1].second;
-    arg.distance = DistancePair[0].first.distance(DistancePair[1].first);
-    arg.globalid = index;
-
-    return FunctionModel::arguments_t(1, arg);
-  }
-
-}; /* namespace Extractors */
 
 /** This class encapsulates the training data for a given potential function
@@ -633 +522 @@
       const Fragment::positions_t positions = fragment.getPositions();
       FunctionModel::arguments_t args =
-          gatherAllDistanceArguments(charges, positions, DistanceEnergyVector.first.size());
+          Extractors::_detail::gatherAllDistanceArguments(positions, DistanceEnergyVector.first.size());
       DistanceEnergyVector.first.push_back( args );
       DistanceEnergyVector.second.push_back( FunctionModel::results_t(1,energy-EnergySum) );