Changeset 4e009d for src

Timestamp:

Jun 27, 2014, 9:32:29 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:

f4496d

Parents:

1ba8a1

git-author:

Frederik Heber <heber@…> (02/27/14 17:46:49)

git-committer:

Frederik Heber <heber@…> (06/27/14 21:32:29)

Message:

Extracted function from PotentialFitPotentialAction::performCall().

• new function getNumbersFromElements().
• also added warning when take-best-of and set-threshold have both been used.

File:

• src/Actions/PotentialAction/FitPotentialAction.cpp (modified) (3 diffs)

src/Actions/PotentialAction/FitPotentialAction.cpp

@@ -113 +113 @@
 }
 
+SerializablePotential::ParticleTypes_t getNumbersFromElements(
+    const std::vector<const element *> &fragment)
+{
+  SerializablePotential::ParticleTypes_t fragmentnumbers;
+  std::transform(fragment.begin(), fragment.end(), std::back_inserter(fragmentnumbers),
+      boost::bind(&element::getAtomicNumber, _1));
+  return fragmentnumbers;
+}
+
+
 ActionState::ptr PotentialFitPotentialAction::performCall() {
   // fragment specifies the homology fragment to use
-  SerializablePotential::ParticleTypes_t fragmentnumbers;
-  {
-    const std::vector<const element *> &fragment = params.fragment.get();
-    std::transform(fragment.begin(), fragment.end(), std::back_inserter(fragmentnumbers),
-        boost::bind(&element::getAtomicNumber, _1));
-  }
+  SerializablePotential::ParticleTypes_t fragmentnumbers =
+      getNumbersFromElements(params.fragment.get());
 
   // either charges and a potential is specified or a file
@@ -160 +166 @@
     } else {
       // charges specify the potential type
-      SerializablePotential::ParticleTypes_t chargenumbers;
-      {
-        const std::vector<const element *> &charges = params.charges.get();
-        std::transform(charges.begin(), charges.end(), std::back_inserter(chargenumbers),
-            boost::bind(&element::getAtomicNumber, _1));
-      }
+      SerializablePotential::ParticleTypes_t chargenumbers =
+          getNumbersFromElements(params.charges.get());
 
       LOG(0, "STATUS: I'm training now a " << params.potentialtype.get()
@@ -267 +269 @@
     }
 
+    if ((params.threshold.get() < 1) && (params.best_of_howmany.isSet()))
+      ELOG(2, "threshold parameter always overrules max_runs, both are specified.");
     // now perform the function approximation by optimizing the model function
     FunctionApproximation approximator(data, *model);