Changeset df350c

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:

9897ee9

Parents:

caa00e9

git-author:

Frederik Heber <heber@…> (12/06/12 10:38:00)

git-committer:

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

Message:

Added reorderArgumentsByParticleTypes() to Extractors.

• this is the more proper function instead of reorderArgumentsByIncreasingDistance() as we actually need to match with those particle types of the potential receiving the arguments.
• reorderArgumentsByIncreasingDistance() was a hack only for angle potential.
• now Extractors namespace needs to know about ParticleTypes_t, so far the typedef is copied.

Location:

src/FunctionApproximation

Files:

• Extractors.cpp (modified) (1 diff)
• Extractors.hpp (modified) (2 diffs)

src/FunctionApproximation/Extractors.cpp

@@ -506 +506 @@
 }
 
+FunctionModel::arguments_t Extractors::reorderArgumentsByParticleTypes(
+    const FunctionModel::arguments_t &args,
+    const ParticleTypes_t &_types
+    )
+{
+  typedef std::list< argument_t > ListArguments_t;
+  ListArguments_t availableList(args.begin(), args.end());
+  FunctionModel::arguments_t returnargs;
+  returnargs.reserve(args.size());
+
+  // TODO: fill a lookup map such that we don't have O(M^3) scaling, if M is number
+  // of types (and we always must have M(M-1)/2 args) but O(M^2 log(M)). However, as
+  // M is very small (<=3), this is not necessary fruitful now.
+//  typedef ParticleTypes_t firsttype;
+//  typedef ParticleTypes_t secondtype;
+//  typedef std::map< firsttype, std::map< secondtype, boost::ref(args) > > ArgsLookup_t;
+//  ArgsLookup_t ArgsLookup;
+
+  // basically, we have two choose any two pairs out of types but only those
+  // where the first is less than the letter. Hence, we start the second
+  // iterator at the current position of the first one and skip the equal case.
+  for (ParticleTypes_t::const_iterator firstiter = _types.begin();
+      firstiter != _types.end();
+      ++firstiter) {
+    for (ParticleTypes_t::const_iterator seconditer = firstiter;
+        seconditer != _types.end();
+        ++seconditer) {
+      if (seconditer == firstiter)
+        continue;
+
+      // search the right one in _args (we might allow switching places of
+      // firstiter and seconditer, as distance is symmetric).
+      ListArguments_t::iterator iter = availableList.begin();
+      for (;iter != availableList.end(); ++iter) {
+        LOG(3, "DEBUG: Current args is " << *iter << ".");
+        if ((iter->types.first == *firstiter)
+              && (iter->types.second == *seconditer)) {
+          returnargs.push_back( *iter );
+          break;
+        }
+        else if ((iter->types.first == *seconditer)
+              && (iter->types.second == *firstiter)) {
+          argument_t flippedtypes(*iter);
+          std::swap( flippedtypes.indices.first, flippedtypes.indices.second );
+          std::swap( flippedtypes.types.first, flippedtypes.types.second );
+          returnargs.push_back( flippedtypes );
+          break;
+        }
+      }
+      ASSERT( iter != availableList.end(),
+          "Extractors::reorderArgumentsByParticleTypes() - could not find arguments to "
+          +toString(*firstiter)+","+toString(*seconditer)+".");
+      availableList.erase(iter);
+    }
+  }
+//  LOG(2, "DEBUG: Final list of args is " << returnargs << ".");
+
+  return returnargs;
+}

src/FunctionApproximation/Extractors.hpp

@@ -33 +33 @@
   typedef std::map< element_t, chargeiters_t > elementtargets_t;
   typedef std::vector< chargeiters_t > targets_per_combination_t;
+  //!> typedef for particle designation
+  typedef int ParticleType_t;
+  //!> typedef for a vector of particle designations
+  typedef std::vector<ParticleType_t> ParticleTypes_t;
 
   /** Namespace for some internal helper functions.
@@ -297 +301 @@
       );
 
+  /** Reorder arguments according to types.
+   *
+   * If particle types is (0,1,2) and three argumens, 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
+      );
 }; /* namespace Extractors */