Changeset 49f163 for src

Timestamp:

Feb 24, 2013, 12:58:53 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:

ac868ee

Parents:

63e786

git-author:

Frederik Heber <heber@…> (10/23/12 13:09:53)

git-committer:

Frederik Heber <heber@…> (02/24/13 12:58:53)

Message:

Added gatherAllSymmetricDistanceArguments().

• using it for generation MorseData.

Location:

src

Files:

• FunctionApproximation/Extractors.cpp (modified) (2 diffs)
• FunctionApproximation/Extractors.hpp (modified) (3 diffs)
• LevMartester.cpp (modified) (1 diff)

src/FunctionApproximation/Extractors.cpp

@@ -51 +51 @@
 
 FunctionModel::arguments_t
-Extractors::_detail::gatherAllDistanceArguments(
+Extractors::gatherAllDistanceArguments(
     const Fragment::positions_t &positions,
     const size_t globalid)
@@ -61 +61 @@
   for (;firstpositer != positions.end(); ++firstpositer) {
     Fragment::positions_t::const_iterator secondpositer = positions.begin();//firstpositer;
+    for (; secondpositer != positions.end(); ++secondpositer) {
+      if (firstpositer == secondpositer)
+        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(
+              positions.begin(), firstpositer),
+          std::distance(
+              positions.begin(), secondpositer)
+          );
+      arg.globalid = globalid;
+      result.push_back(arg);
+    }
+  }
+
+  return result;
+}
+
+FunctionModel::arguments_t
+Extractors::gatherAllSymmetricDistanceArguments(
+    const Fragment::positions_t &positions,
+    const size_t globalid)
+{
+  FunctionModel::arguments_t result;
+
+  // go through current configuration and gather all other distances
+  Fragment::positions_t::const_iterator firstpositer = positions.begin();
+  for (;firstpositer != positions.end(); ++firstpositer) {
+    Fragment::positions_t::const_iterator secondpositer = firstpositer;
     for (; secondpositer != positions.end(); ++secondpositer) {
       if (firstpositer == secondpositer)

src/FunctionApproximation/Extractors.hpp

@@ -35 +35 @@
    */
   namespace _detail {
-    /** Gather all distances from a given set of positions.
-     *
-     * \param positins vector of positions
-     * \param globalid index to associated in argument_t with
-     * \return vector of argument_ , each with a distance
-     */
-    FunctionModel::arguments_t
-    gatherAllDistanceArguments(
-        const Fragment::positions_t &positions,
-        const size_t globalid);
-
     /** Gather all positions from the same aligned vector of charges.
      *
@@ -99 +88 @@
   }
 
+  /** Gather all distances from a given set of positions.
+   *
+   * \param positions vector of positions
+   * \param globalid index to associated in argument_t with
+   * \return vector of argument_ , each with a distance
+   */
+  FunctionModel::arguments_t
+  gatherAllDistanceArguments(
+      const Fragment::positions_t &positions,
+      const size_t globalid);
+
+  /** Gather all distances from a given set of positions.
+   *
+   *  Here, we only return one of the two equal distances.
+   *
+   * \param positions vector of positions
+   * \param globalid index to associated in argument_t with
+   * \return vector of argument_ , each with a distance
+   */
+  FunctionModel::arguments_t
+  gatherAllSymmetricDistanceArguments(
+      const Fragment::positions_t &positions,
+      const size_t globalid);
+
   /** Simple extractor of all unique pair distances of a given \a fragment.
    *
@@ -110 +123 @@
       ) {
     // get distance out of Fragment
-    return _detail::gatherAllDistanceArguments(fragment.getPositions(), index);
+    return gatherAllDistanceArguments(fragment.getPositions(), index);
   }
 

src/LevMartester.cpp

@@ -364 +364 @@
     // Afterwards we go through all of this type and gather the distance and the energy value
     TrainingData MorseData(
-        boost::bind(&Extractors::_detail::gatherAllDistanceArguments,
+        boost::bind(&Extractors::gatherAllSymmetricDistanceArguments,
             boost::bind(&Extractors::gatherDistanceOfTuples,
                 _1, Fragment::charges_t(2,6.)