Changeset d8821e for src/Actions/PotentialAction/FitPotentialAction.cpp

Timestamp:

Jul 14, 2014, 11:16:23 AM (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:

2a03b0

Parents:

c73e35 (diff), a61dbb (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable

Conflicts:

src/Actions/ActionQueue.cpp
src/Actions/FragmentationAction/FragmentationAction.cpp
src/Actions/PotentialAction/FitParticleChargesAction.cpp

• in ActionQueue taking over both changes.
• FragmentationAction added Status message where we don't complain for not having HAVE_JOBMARKET anymore. Removed.
• FitParticleChargesAction had charge averaging and error message in case of no present fragments overlapping.

File:

• src/Actions/PotentialAction/FitPotentialAction.cpp (modified) (5 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
@@ -158 +164 @@
     } 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()
@@ -240 +242 @@
       size_t counter=1;
       if (DoLog(3)) {
-        const FunctionModel::arguments_t &inputs = data.getTrainingInputs()[0];
+        const FunctionModel::arguments_t &inputs = data.getAllArguments()[0];
         for (FunctionModel::arguments_t::const_iterator iter = inputs.begin();
             iter != inputs.end(); ++iter) {
@@ -265 +267 @@
     }
 
+    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);
@@ -304 +308 @@
 
     // create a map of each fragment with error.
-    typedef std::multimap< double, size_t > WorseFragmentMap_t;
-    WorseFragmentMap_t WorseFragmentMap;
     HomologyContainer::range_t fragmentrange = homologies.getHomologousGraphs(graph);
-    // fragments make it into the container in reversed order, hence count from top down
-    size_t index= std::distance(fragmentrange.first, fragmentrange.second)-1;
-    for (HomologyContainer::const_iterator iter = fragmentrange.first;
-        iter != fragmentrange.second;
-        ++iter) {
-      const Fragment& fragment = iter->second.fragment;
-      const double &energy = iter->second.energy;
-
-      // create arguments from the fragment
-      FunctionModel::extractor_t extractor = model->getSpecificExtractor();
-      FunctionModel::arguments_t args = extractor(fragment, 1);
-
-      // calculate value from potential
-      const double fitvalue = (*model)(args)[0];
-
-      // insert difference into map
-      const double error = fabs(energy - fitvalue);
-      WorseFragmentMap.insert( std::make_pair( error, index-- ) );
-
-      {
-        // give only the distances in the debugging text
-        std::stringstream streamargs;
-        BOOST_FOREACH (argument_t arg, args) {
-          streamargs << " " << arg.distance*AtomicLengthToAngstroem;
-        }
-        LOG(2, "DEBUG: frag.#" << index+1 << "'s error is |" << energy << " - " << fitvalue
-            << "| = " << error << " for args " << streamargs.str() << ".");
-      }
-    }
+    TrainingData::L2ErrorConfigurationIndexMap_t WorseFragmentMap =
+        data.getWorstFragmentMap(*model, fragmentrange);
     LOG(0, "RESULT: WorstFragmentMap " << WorseFragmentMap << ".");