Changeset 775dd1a for src/Potentials/Specifics/SaturationPotential.hpp

Timestamp:

Feb 27, 2013, 12:39:03 PM (13 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

0dad5f

Parents:

d52819

git-author:

Frederik Heber <heber@…> (11/30/12 16:44:24)

git-committer:

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

Message:

Triplefunction for Saturation and Tersoff potential have to be given extra.

• this avoids a loop with TrainingData and getFragmentSpecificExtractor.

File:

• src/Potentials/Specifics/SaturationPotential.hpp (modified) (3 diffs)

src/Potentials/Specifics/SaturationPotential.hpp

@@ -50 +50 @@
 public:
   SaturationPotential(
-      const ParticleTypes_t &_ParticleTypes,
-      const double _saturation_cutoff,
-      boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction
+      const ParticleTypes_t &_ParticleTypes
       );
   SaturationPotential(
@@ -61 +59 @@
       const double _morse_dissociation_energy,
       const double _angle_spring_constant,
-      const double _angle_equilibrium_distance,
+      const double _angle_equilibrium_distance
+      );
+  virtual ~SaturationPotential() {}
+
+  /** Setter for parameters as required by FunctionModel interface.
+   *
+   * \param _params given set of parameters
+   */
+  void setParameters(const parameters_t &_params);
+
+  /** Getter for parameters as required by FunctionModel interface.
+   *
+   * \return set of parameters
+   */
+  parameters_t getParameters() const;
+
+  /** Sets the parameter randomly within the sensible range of each parameter.
+   *
+   * \param data container with training data for guesstimating range
+   */
+  void setParametersToRandomInitialValues(const TrainingData &data);
+
+  /** Getter for the number of parameters of this model function.
+   *
+   * \return number of parameters
+   */
+  size_t getParameterDimension() const
+  { return MAXPARAMS; }
+
+  /** Sets the magic triple function that we use for getting angle distances.
+   *
+   * \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
-      );
-  virtual ~SaturationPotential() {}
-
-  /** Setter for parameters as required by FunctionModel interface.
-   *
-   * \param _params given set of parameters
-   */
-  void setParameters(const parameters_t &_params);
-
-  /** Getter for parameters as required by FunctionModel interface.
-   *
-   * \return set of parameters
-   */
-  parameters_t getParameters() const;
-
-  /** Sets the parameter randomly within the sensible range of each parameter.
-   *
-   * \param data container with training data for guesstimating range
-   */
-  void setParametersToRandomInitialValues(const TrainingData &data);
-
-  /** Getter for the number of parameters of this model function.
-   *
-   * \return number of parameters
-   */
-  size_t getParameterDimension() const
-  { return MAXPARAMS; }
+      )
+  {
+    saturation_cutoff = _saturation_cutoff;
+    triplefunction = _triplefunction;
+  }
 
   /** Evaluates the harmonic potential function for the given arguments.
@@ -196 +208 @@
 
   //!> bound function that obtains the triples for the internal coordinationb summation.
-  const boost::function< std::vector< arguments_t >(const argument_t &, const double)> &triplefunction;
-  const double saturation_cutoff;
+  boost::function< std::vector< arguments_t >(const argument_t &, const double)> triplefunction;
+  double saturation_cutoff;
 
   //!> static definitions of the parameter name for this potential