Ignore:
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:
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.
Location:
src/Potentials/Specifics
Files:
5 edited

Legend:

Unmodified
Added
Removed

  • src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

    rd52819 r775dd1a  
    7979
    8080ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff(
    81     const ParticleTypes_t &_ParticleTypes,
    82     boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction
     81    const ParticleTypes_t &_ParticleTypes
    8382    ) :
    8483    SerializablePotential(_ParticleTypes),
    … …  
    9089    chi(1.),
    9190    omega(1.),
    92     triplefunction(_triplefunction)
     91    triplefunction(&Helpers::NoOp_Triplefunction)
    9392{
    9493  // have some decent defaults for parameter_derivative checking
    … …  
    122121    const double &_d,
    123122    const double &_h,
    124     const double &_offset,
    125     boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction) :
     123    const double &_offset) :
    126124  SerializablePotential(_ParticleTypes),
    127125  params(parameters_t(MAXPARAMS, 0.)),
    … …  
    132130  chi(_chi),
    133131  omega(_mu),
    134   triplefunction(_triplefunction)
     132  triplefunction(&Helpers::NoOp_Triplefunction)
    135133{
    136134//  Info info(__func__);

  • src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

    rd52819 r775dd1a  
    4747  /** Constructor for class ManyBodyPotential_Tersoff.
    4848   *
    49    * @param _triplefunction function that returns a list of triples (i.e. the
    50    *        two remaining distances) to a given pair of points (contained as
    51    *        indices within the argument)
     49   * \param _ParticleTypes particle types for this potential
    5250   */
    5351  ManyBodyPotential_Tersoff(
    54       const ParticleTypes_t &_ParticleTypes,
    55       boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction
     52      const ParticleTypes_t &_ParticleTypes
    5653      );
    5754
    … …  
    9592      const double &_d,
    9693      const double &_h,
    97       const double &_offset,
    98       boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction);
     94      const double &_offset);
    9995
    10096  /** Destructor of class ManyBodyPotential_Tersoff.
    … …  
    187183   */
    188184  FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
     185
     186  /** Sets the magic triple function that we use for getting angle distances.
     187   *
     188   * @param _triplefunction function that returns a list of triples (i.e. the
     189   *        two remaining distances) to a given pair of points (contained as
     190   *        indices within the argument)
     191   */
     192  void setTriplefunction(
     193      boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction
     194      )
     195  {
     196    triplefunction = _triplefunction;
     197  }
    189198
    190199private:
    … …  
    337346private:
    338347  //!> bound function that obtains the triples for the internal coordinationb summation.
    339   const boost::function< std::vector< arguments_t >(const argument_t &, const double)> &triplefunction;
     348  boost::function< std::vector< arguments_t >(const argument_t &, const double)> triplefunction;
    340349
    341350  //!> static definitions of the parameter name for this potential

  • src/Potentials/Specifics/SaturationPotential.cpp

    rd52819 r775dd1a  
    7070
    7171SaturationPotential::SaturationPotential(
    72     const ParticleTypes_t &_ParticleTypes,
    73     const double _saturation_cutoff,
    74     boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction) :
     72    const ParticleTypes_t &_ParticleTypes) :
    7573  SerializablePotential(_ParticleTypes),
    7674  morse(_ParticleTypes),
    7775  angle(symmetrizeTypes(_ParticleTypes)),
    78   energy_offset(0.),
    79   triplefunction(_triplefunction),
    80   saturation_cutoff(_saturation_cutoff)
     76  energy_offset(0.)
    8177{
    8278  // have some decent defaults for parameter_derivative checking
    … …  
    9591    const double _morse_dissociation_energy,
    9692    const double _angle_spring_constant,
    97     const double _angle_equilibrium_distance,
    98     const double _saturation_cutoff,
    99     boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction) :
     93    const double _angle_equilibrium_distance) :
    10094  SerializablePotential(_ParticleTypes),
    10195  morse(_ParticleTypes),
    10296  angle(symmetrizeTypes(_ParticleTypes)),
    103   energy_offset(_all_energy_offset),
    104   triplefunction(_triplefunction),
    105   saturation_cutoff(_saturation_cutoff)
     97  energy_offset(_all_energy_offset)
    10698{
    10799  ASSERT( _ParticleTypes.size() == (size_t)2,

  • src/Potentials/Specifics/SaturationPotential.hpp

    rd52819 r775dd1a  
    5050public:
    5151  SaturationPotential(
    52       const ParticleTypes_t &_ParticleTypes,
    53       const double _saturation_cutoff,
    54       boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction
     52      const ParticleTypes_t &_ParticleTypes
    5553      );
    5654  SaturationPotential(
    … …  
    6159      const double _morse_dissociation_energy,
    6260      const double _angle_spring_constant,
    63       const double _angle_equilibrium_distance,
     61      const double _angle_equilibrium_distance
     62      );
     63  virtual ~SaturationPotential() {}
     64
     65  /** Setter for parameters as required by FunctionModel interface.
     66   *
     67   * \param _params given set of parameters
     68   */
     69  void setParameters(const parameters_t &_params);
     70
     71  /** Getter for parameters as required by FunctionModel interface.
     72   *
     73   * \return set of parameters
     74   */
     75  parameters_t getParameters() const;
     76
     77  /** Sets the parameter randomly within the sensible range of each parameter.
     78   *
     79   * \param data container with training data for guesstimating range
     80   */
     81  void setParametersToRandomInitialValues(const TrainingData &data);
     82
     83  /** Getter for the number of parameters of this model function.
     84   *
     85   * \return number of parameters
     86   */
     87  size_t getParameterDimension() const
     88  { return MAXPARAMS; }
     89
     90  /** Sets the magic triple function that we use for getting angle distances.
     91   *
     92   * \param _saturation_cutoff cutoff for the triplefunction
     93   * @param _triplefunction function that returns a list of triples (i.e. the
     94   *        two remaining distances) to a given pair of points (contained as
     95   *        indices within the argument)
     96   */
     97  void setTriplefunction(
    6498      const double _saturation_cutoff,
    6599      boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction
    66       );
    67   virtual ~SaturationPotential() {}
    68 
    69   /** Setter for parameters as required by FunctionModel interface.
    70    *
    71    * \param _params given set of parameters
    72    */
    73   void setParameters(const parameters_t &_params);
    74 
    75   /** Getter for parameters as required by FunctionModel interface.
    76    *
    77    * \return set of parameters
    78    */
    79   parameters_t getParameters() const;
    80 
    81   /** Sets the parameter randomly within the sensible range of each parameter.
    82    *
    83    * \param data container with training data for guesstimating range
    84    */
    85   void setParametersToRandomInitialValues(const TrainingData &data);
    86 
    87   /** Getter for the number of parameters of this model function.
    88    *
    89    * \return number of parameters
    90    */
    91   size_t getParameterDimension() const
    92   { return MAXPARAMS; }
     100      )
     101  {
     102    saturation_cutoff = _saturation_cutoff;
     103    triplefunction = _triplefunction;
     104  }
    93105
    94106  /** Evaluates the harmonic potential function for the given arguments.
    … …  
    196208
    197209  //!> bound function that obtains the triples for the internal coordinationb summation.
    198   const boost::function< std::vector< arguments_t >(const argument_t &, const double)> &triplefunction;
    199   const double saturation_cutoff;
     210  boost::function< std::vector< arguments_t >(const argument_t &, const double)> triplefunction;
     211  double saturation_cutoff;
    200212
    201213  //!> static definitions of the parameter name for this potential

  • src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp

    rd52819 r775dd1a  
    281281        (0)(1)
    282282      ;
    283   ManyBodyPotential_Tersoff tersoff(types, fct);
     283  ManyBodyPotential_Tersoff tersoff(types);
     284  tersoff.setTriplefunction(fct);
    284285  tersoff.setParameters(params);
    285286  const_cast<double &>(tersoff.R) = 1.8;
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