Changeset 05f437 for src/LevMartester.cpp

Timestamp:

Feb 27, 2013, 12:39:15 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:

d76ce74

Parents:

e36ba2

git-author:

Frederik Heber <heber@…> (11/30/12 16:46:30)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:39:15)

Message:

LevMartester now contains three generalized fits to Angle, Morse, and Saturation potential.

File:

• src/LevMartester.cpp (modified) (7 diffs)

src/LevMartester.cpp

@@ -221 +221 @@
 
       // Afterwards we go through all of this type and gather the distance and the energy value
-      Fragment::charges_t h2o;
-      h2o += 8,1,1;
-      TrainingData AngleData(
-          boost::bind(&Extractors::gatherDistancesFromFragment,
-              boost::bind(&Fragment::getPositions, _1),
-              boost::bind(&Fragment::getCharges, _1),
-              boost::cref(h2o),
-              _2)
-          );
-      AngleData(homologies.getHomologousGraphs(graph));
-      LOG(1, "INFO: I gathered the following training data: " << AngleData);
-      // NOTICE that distance are in bohrradi as they come from MPQC!
-
-      // now perform the function approximation by optimizing the model function
-      FunctionModel::parameters_t params(PairPotential_Angle::MAXPARAMS, 0.);
-      params[PairPotential_Angle::energy_offset] =
-          AngleData.getTrainingOutputAverage()[0];// -1.;
-      params[PairPotential_Angle::spring_constant] = 2e+0*rand()/(double)RAND_MAX - 1.;// 1.;
-      params[PairPotential_Angle::equilibrium_distance] = 1e+0*rand()/(double)RAND_MAX;// 0.2;
       PairPotential_Angle::ParticleTypes_t types =
             boost::assign::list_of<PairPotential_Angle::ParticleType_t>
@@ -245 +226 @@
           ;
       PairPotential_Angle angle(types);
-      LOG(0, "INFO: Initial parameters are " << params << ".");
-      angle.setParameters(params);
+      Fragment::charges_t h2o;
+      h2o += 8,1,1;
+      TrainingData AngleData(angle.getFragmentSpecificExtractor(h2o));
+      AngleData(homologies.getHomologousGraphs(graph));
+      LOG(1, "INFO: I gathered the following training data: " << AngleData);
+      // NOTICE that distance are in bohrradi as they come from MPQC!
+
+      // now perform the function approximation by optimizing the model function
       FunctionModel &model = angle;
       FunctionApproximation approximator(AngleData, model);
       if (model.isBoxConstraint() && approximator.checkParameterDerivatives()) {
         // we set parameters here because we want to test with default ones
-        angle.setParameters(params);
+        srand((unsigned)time(0)); // seed with current time
+        model.setParametersToRandomInitialValues(AngleData);
+        LOG(0, "INFO: Initial parameters are " << angle.getParameters() << ".");
         approximator(FunctionApproximation::ParameterDerivative);
       } else {
@@ -275 +264 @@
       Fragment::charges_t h2o;
       h2o += 8,1;
-      TrainingData MorseData(
-          boost::bind(&Extractors::gatherDistancesFromFragment,
-              boost::bind(&Fragment::getPositions, _1),
-              boost::bind(&Fragment::getCharges, _1),
-              boost::cref(h2o),
-              _2)
-          );
-      MorseData(homologies.getHomologousGraphs(graph));
-      LOG(1, "INFO: I gathered the following training data: " << MorseData);
-      // NOTICE that distance are in bohrradi as they come from MPQC!
-
-      // now perform the function approximation by optimizing the model function
       PairPotential_Morse::ParticleTypes_t types =
             boost::assign::list_of<PairPotential_Morse::ParticleType_t>
@@ -292 +269 @@
           ;
       PairPotential_Morse morse(types);
+      TrainingData MorseData(morse.getFragmentSpecificExtractor(h2o));
+      MorseData(homologies.getHomologousGraphs(graph));
+      LOG(1, "INFO: I gathered the following training data: " << MorseData);
+      // NOTICE that distance are in bohrradi as they come from MPQC!
+
+      // now perform the function approximation by optimizing the model function
       FunctionModel &model = morse;
-      FunctionApproximation approximator(MorseData, model);
-      FunctionModel::triplefunction_t triplefunction =
-          boost::bind(&getTripleFromArgument, boost::cref(MorseData.getTrainingInputs()), _1, _2);
+      FunctionApproximation approximator(MorseData, model); // we only give CC distance, hence 1 input dim
       if (model.isBoxConstraint() && approximator.checkParameterDerivatives()) {
         // we set parameters here because we want to test with default ones
         srand((unsigned)time(0)); // seed with current time
         model.setParametersToRandomInitialValues(MorseData);
-        model.setTriplefunction(triplefunction);
-        LOG(0, "INFO: Initial parameters are " << model.getParameters() << ".");
+        LOG(0, "INFO: Initial parameters are " << morse.getParameters() << ".");
         approximator(FunctionApproximation::ParameterDerivative);
       } else {
@@ -325 +305 @@
       Fragment::charges_t h2o;
       h2o += 8,1,1;
-      TrainingData TersoffData(
-          boost::bind(&Extractors::gatherDistancesFromFragment,
-              boost::bind(&Fragment::getPositions, _1),
-              boost::bind(&Fragment::getCharges, _1),
-              boost::cref(h2o),
-              _2)
-          );
-//          TrainingData::extractor_t(&Extractors::gatherAllSymmetricDistances) // gather first carbon pair
-//          );
-      TersoffData( homologies.getHomologousGraphs(graph) );
-      LOG(1, "INFO: I gathered the following training data: " << TersoffData);
-      // NOTICE that distance are in bohrradi as they come from MPQC!
-
-      // now perform the function approximation by optimizing the model function
-      boost::function< std::vector<FunctionModel::arguments_t>(const argument_t &, const double)> triplefunction =
-          boost::bind(&getTripleFromArgument, boost::cref(TersoffData.getTrainingInputs()), _1, _2);
       SaturationPotential::ParticleTypes_t types =
             boost::assign::list_of<SaturationPotential::ParticleType_t>
             (8)(1)
           ;
-
       SaturationPotential saturation(types);
+      TrainingData TersoffData(saturation.getFragmentSpecificExtractor(h2o));
+      boost::function< std::vector<FunctionModel::arguments_t>(const argument_t &, const double)> triplefunction =
+          boost::bind(&getTripleFromArgument, boost::cref(TersoffData.getTrainingInputs()), _1, _2);
+      saturation.setTriplefunction(triplefunction);
+
+      TersoffData( homologies.getHomologousGraphs(graph) );
+      LOG(1, "INFO: I gathered the following training data: " << TersoffData);
+      // NOTICE that distance are in bohrradi as they come from MPQC!
+
+      // now perform the function approximation by optimizing the model function
       FunctionModel &model = saturation;
       FunctionApproximation approximator(TersoffData, model); // CH4 has 5 atoms, hence 5*4/2 distances
@@ -353 +326 @@
         srand((unsigned)time(0)); // seed with current time
         model.setParametersToRandomInitialValues(TersoffData);
-        model.setTriplefunction(triplefunction);
         approximator(FunctionApproximation::ParameterDerivative);
       } else {
@@ -362 +334 @@
       LOG(0, "RESULT: " << saturation << ".");
 
-  //    std::cout << "\tsaturationparticle:";
-  //    std::cout << "\tparticle_type=C,";
-  //    std::cout << "\tA=" << params[SaturationPotential::A] << ",";
-  //    std::cout << "\tB=" << params[SaturationPotential::B] << ",";
-  //    std::cout << "\tlambda=" << params[SaturationPotential::lambda] << ",";
-  //    std::cout << "\tmu=" << params[SaturationPotential::mu] << ",";
-  //    std::cout << "\tbeta=" << params[SaturationPotential::beta] << ",";
-  //    std::cout << "\tn=" << params[SaturationPotential::n] << ",";
-  //    std::cout << "\tc=" << params[SaturationPotential::c] << ",";
-  //    std::cout << "\td=" << params[SaturationPotential::d] << ",";
-  //    std::cout << "\th=" << params[SaturationPotential::h] << ",";
-  ////    std::cout << "\toffset=" << params[SaturationPotential::offset] << ",";
-  //    std::cout << "\tR=" << saturation.R << ",";
-  //    std::cout << "\tS=" << saturation.S << ";";
-  //    std::cout << std::endl;
-
       // check L2 and Lmax error against training set
       LOG(1, "INFO: L2sum = " << TersoffData.getL2Error(model)