Changeset e36ba2 for src

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:

05f437

Parents:

0dad5f

git-author:

Frederik Heber <heber@…> (12/07/12 15:13:34)

git-committer:

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

Message:

FunctionModel extended by triplefunction setter, does nothing by default.

• SaturationPotential's setTriplefunction() removed.
• Tersoff's setTriplefunction now truely sets the function.
• LevMartester always sets a triple function whether the potential uses it or not.

Location:

src

Files:

• FunctionApproximation/FunctionModel.hpp (modified) (2 diffs)
• LevMartester.cpp (modified) (4 diffs)
• Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) (1 diff)
• Potentials/Specifics/SaturationPotential.hpp (modified) (1 diff)

src/FunctionApproximation/FunctionModel.hpp

@@ -47 +47 @@
   //!> typedef for a vector of particle tyoes
   typedef std::vector< double > charges_t;
+  //!> typedef for the magic triple function that gets the other two distances for a given argument
+  typedef boost::function< std::vector<arguments_t>(const argument_t &, const double)> triplefunction_t;
 
 public:
@@ -75 +77 @@
    */
   virtual size_t getParameterDimension() const=0;
+
+  /** Sets the magic triple function that we use for getting angle distances.
+   *
+   * @param _triplefunction function that returns a list of triples (i.e. the
+   *        two remaining distances) to a given pair of points (contained as
+   *        indices within the argument)
+   */
+  virtual void setTriplefunction(triplefunction_t &_triplefunction)
+  {}
 
   /** Evaluates the function with the given \a arguments and the current set of

src/LevMartester.cpp

@@ -287 +287 @@
 
       // now perform the function approximation by optimizing the model function
-      FunctionModel::parameters_t params(PairPotential_Morse::MAXPARAMS, 0.);
-      params[PairPotential_Morse::dissociation_energy] = 1e+0*rand()/(double)RAND_MAX;// 0.5;
-      params[PairPotential_Morse::energy_offset] =
-          MorseData.getTrainingOutputAverage()[0];// -1.;
-      params[PairPotential_Morse::spring_constant] = 1e+0*rand()/(double)RAND_MAX;// 1.;
-      params[PairPotential_Morse::equilibrium_distance] =  3e+0*rand()/(double)RAND_MAX;//2.9;
       PairPotential_Morse::ParticleTypes_t types =
             boost::assign::list_of<PairPotential_Morse::ParticleType_t>
@@ -298 +292 @@
           ;
       PairPotential_Morse morse(types);
-      LOG(0, "INFO: Initial parameters are " << params << ".");
-      morse.setParameters(params);
       FunctionModel &model = morse;
-      FunctionApproximation approximator(MorseData, model); // we only give CC distance, hence 1 input dim
+      FunctionApproximation approximator(MorseData, model);
+      FunctionModel::triplefunction_t triplefunction =
+          boost::bind(&getTripleFromArgument, boost::cref(MorseData.getTrainingInputs()), _1, _2);
       if (model.isBoxConstraint() && approximator.checkParameterDerivatives()) {
         // we set parameters here because we want to test with default ones
-        morse.setParameters(params);
+        srand((unsigned)time(0)); // seed with current time
+        model.setParametersToRandomInitialValues(MorseData);
+        model.setTriplefunction(triplefunction);
+        LOG(0, "INFO: Initial parameters are " << model.getParameters() << ".");
         approximator(FunctionApproximation::ParameterDerivative);
       } else {
@@ -344 +341 @@
       boost::function< std::vector<FunctionModel::arguments_t>(const argument_t &, const double)> triplefunction =
           boost::bind(&getTripleFromArgument, boost::cref(TersoffData.getTrainingInputs()), _1, _2);
-      srand((unsigned)time(0)); // seed with current time
-      params[SaturationPotential::all_energy_offset] =
-          TersoffData.getTrainingOutputAverage()[0]; //1e+1*rand()/(double)RAND_MAX;//3.487900e+00;
-      params[SaturationPotential::morse_spring_constant] =
-        //  morseparams[PairPotential_Morse::spring_constant]; //
-        1e+1*rand()/(double)RAND_MAX;//1.393600e+03;
-      params[SaturationPotential::morse_equilibrium_distance] =
-       //   morseparams[PairPotential_Morse::equilibrium_distance]; //
-        3e+0*rand()/(double)RAND_MAX;//3.467000e+02;
-      params[SaturationPotential::morse_dissociation_energy] =
-       //   morseparams[PairPotential_Morse::dissociation_energy]; //
-        1e+0*rand()/(double)RAND_MAX;//3.487900e+00;
-      params[SaturationPotential::angle_spring_constant] =
-       //   angleparams[PairPotential_Angle::spring_constant]; //
-        1e+1*rand()/(double)RAND_MAX;//3.487900e+00;
-      params[SaturationPotential::angle_equilibrium_distance] =
-       //   angleparams[PairPotential_Angle::equilibrium_distance]; //
-        2e+0*rand()/(double)RAND_MAX - 1.;//3.487900e+00;
-      LOG(0, "INFO: Initial parameters are " << params << ".");
       SaturationPotential::ParticleTypes_t types =
             boost::assign::list_of<SaturationPotential::ParticleType_t>
@@ -369 +347 @@
 
       SaturationPotential saturation(types);
-      // saturation has internal triplefunction now
-//      saturation.setTriplefunction(2.5, triplefunction);
       FunctionModel &model = saturation;
       FunctionApproximation approximator(TersoffData, model); // CH4 has 5 atoms, hence 5*4/2 distances
       if (model.isBoxConstraint() && approximator.checkParameterDerivatives()) {
         // we set parameters here because we want to test with default ones
-        saturation.setParameters(params);
+        srand((unsigned)time(0)); // seed with current time
+        model.setParametersToRandomInitialValues(TersoffData);
+        model.setTriplefunction(triplefunction);
         approximator(FunctionApproximation::ParameterDerivative);
       } else {

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -190 +190 @@
    *        indices within the argument)
    */
-  void setTriplefunction(
-      boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction
-      )
-  {
-    triplefunction = _triplefunction;
-  }
+  void setTriplefunction(triplefunction_t &_triplefunction)
+  { triplefunction = _triplefunction;  }
 
 private:

src/Potentials/Specifics/SaturationPotential.hpp

@@ -88 +88 @@
   { return MAXPARAMS; }
 
-  /** Sets the magic triple function that we use for getting angle distances.
-   *
-   * \note does nothing as we have an internal triplefunction
-   *
-   * \param _saturation_cutoff cutoff for the triplefunction
-   * @param _triplefunction function that returns a list of triples (i.e. the
-   *        two remaining distances) to a given pair of points (contained as
-   *        indices within the argument)
-   */
-  void setTriplefunction(
-      const double _saturation_cutoff,
-      boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction
-      )
-  {
-  }
-
   /** Evaluates the harmonic potential function for the given arguments.
    *