Changeset e7579e


Ignore:
Timestamp:
Dec 19, 2012, 3:25:53 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:
ffc368
Parents:
76cbd0
git-author:
Frederik Heber <heber@…> (10/04/12 11:34:36)
git-committer:
Frederik Heber <heber@…> (12/19/12 15:25:53)
Message:

Changed ManyBodyPotential_Tersoff to also have parameters_t instead of single member variable definitions.

  • added enum to give each entry in params a meaning.
  • modified setter and getter for parameters accordingly.
  • default constructor is now private, as we always need the triplefunction.
  • changed other constructors accordingly.
Location:
src/Potentials/Specifics
Files:
2 edited

Legend:

Unmodified
Added
Removed

  • src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

    r76cbd0 re7579e  
    4646#include "Potentials/helpers.hpp"
    4747
     48ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff(
     49    boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction
     50    ) :
     51    params(parameters_t(MAXPARAMS, 0.)),
     52    triplefunction(_triplefunction)
     53{}
     54
     55ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff(
     56    const double &_cutoff_offset,
     57    const double &_cutoff_halfwidth,
     58    const double &_A,
     59    const double &_B,
     60    const double &_lambda1,
     61    const double &_lambda2,
     62    const double &_lambda3,
     63    const double &_alpha,
     64    const double &_beta,
     65    const double &_n,
     66    const double &_c,
     67    const double &_d,
     68    const double &_h,
     69    boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction) :
     70  params(parameters_t(MAXPARAMS, 0.)),
     71  triplefunction(_triplefunction)
     72{
     73  params[cutoff_offset] = _cutoff_offset;
     74  params[cutoff_halfwidth] = _cutoff_halfwidth;
     75  params[A] = _A;
     76  params[B] = _B;
     77  params[lambda1] = _lambda1;
     78  params[lambda2] = _lambda2;
     79  params[lambda3] = _lambda3;
     80  params[alpha] = _alpha;
     81  params[beta] = _beta;
     82  params[n] = _n;
     83  params[c] = _c;
     84  params[d] = _d;
     85  params[h] = _h;
     86}
     87
    4888ManyBodyPotential_Tersoff::results_t
    4989ManyBodyPotential_Tersoff::operator()(
    … …  
    5595  const double result = (cutoff == 0.) ? 0. : cutoff * (
    5696      function_prefactor(
    57           manybodyparameter_alpha,
     97          alpha,
    5898          boost::bind(&ManyBodyPotential_Tersoff::function_eta,
    5999              boost::cref(*this),
    … …  
    61101      * function_smoother(
    62102          distance,
    63           manybodyparameter_A,
    64           manybodyparameter_lambda1)
     103          A,
     104          lambda1)
    65105      +
    66106      function_prefactor(
    67           manybodyparameter_beta,
     107          beta,
    68108          boost::bind(&ManyBodyPotential_Tersoff::function_zeta,
    69109              boost::cref(*this),
    … …  
    71111      * function_smoother(
    72112          distance,
    73           -manybodyparameter_B,
    74           manybodyparameter_lambda2)
     113          -B,
     114          lambda2)
    75115  );
    76116  return std::vector<result_t>(1, result);
    … …  
    99139{
    100140  return pow(
    101       (1. + Helpers::pow(alpha * etafunction(), manybodyparameter_n)),
    102       -1./(2.*manybodyparameter_n));
     141      (1. + Helpers::pow(alpha * etafunction(), n)),
     142      -1./(2.*n));
    103143}
    104144
    … …  
    118158    const argument_t &r_ik = (*iter)[0];
    119159    result += function_cutoff(r_ik.distance)
    120         * exp( Helpers::pow(manybodyparameter_lambda3 * (r_ij.distance - r_ik.distance) ,3));
     160        * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3));
    121161  }
    122162
    … …  
    142182        function_cutoff(r_ik.distance)
    143183        * function_angle(r_ij.distance, r_ik.distance, r_jk.distance)
    144         * exp( Helpers::pow(manybodyparameter_lambda3 * (r_ij.distance - r_ik.distance) ,3));
     184        * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3));
    145185  }
    146186
    … …  
    159199  const double result =
    160200      1.
    161       + (Helpers::pow(manybodyparameter_c, 2)/Helpers::pow(manybodyparameter_d, 2))
    162       - Helpers::pow(manybodyparameter_c, 2)/(Helpers::pow(manybodyparameter_d, 2) +
    163           Helpers::pow(manybodyparameter_h - cos(angle/divisor),2));
     201      + (Helpers::pow(c, 2)/Helpers::pow(d, 2))
     202      - Helpers::pow(c, 2)/(Helpers::pow(d, 2) +
     203          Helpers::pow(h - cos(angle/divisor),2));
    164204  return result;
    165205}

  • src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

    r76cbd0 re7579e  
    1919#include "Potentials/EmpiricalPotential.hpp"
    2020#include "FunctionApproximation/FunctionModel.hpp"
     21
     22#include "CodePatterns/Assert.hpp"
    2123
    2224/** This class is the implementation of the Tersoff potential function.
    … …  
    3436  typedef FunctionModel::results_t results_t;
    3537  typedef EmpiricalPotential::derivative_components_t derivative_components_t;
    36 private:
    37   //!> cutoff_offset offset for cutoff parameter
    38   const double cutoff_offset;
    39   //!> cutoff_halfwidth half-width for cutoff parameter
    40   const double cutoff_halfwidth;
    41   //!> many body prefactor parameter for attractive part
    42   const double manybodyparameter_A;
    43   //!> many body prefactor parameter for attractive part
    44   const double manybodyparameter_B;
    45   //!> many body scale parameter for attractive part
    46   const double manybodyparameter_lambda1;
    47   //!> many body scale parameter for attractive part
    48   const double manybodyparameter_lambda2;
    49   //!> length scale for coordination influence
    50   const double manybodyparameter_lambda3;
    51   //!> many body parameter for attractive part
    52   const double manybodyparameter_alpha;
    53   //!> many body parameter for repulsive part
    54   const double manybodyparameter_beta;
    55   //!> many body type-dependent parameter giving the power
    56   const double manybodyparameter_n;
    57   //!> many-body type-dependent parameter in angular dependence
    58   const double manybodyparameter_c;
    59   //!> many-body type-dependent parameter in angular dependence
    60   const double manybodyparameter_d;
    61   //!> many-body type-dependent parameter in angular dependence
    62   const double manybodyparameter_h;
     38  typedef FunctionModel::parameters_t parameters_t;
    6339public:
    6440  /** Constructor for class ManyBodyPotential_Tersoff.
    … …  
    6945   */
    7046  ManyBodyPotential_Tersoff(
    71       const double _cutoff_offset,
    72       const double _cutoff_halfwidth,
    73       const double A,
    74       const double B,
    75       const double lambda1,
    76       const double lambda2,
    77       const double lambda3,
    78       const double alpha,
    79       const double beta,
    80       const double n,
    81       const double c,
    82       const double d,
    83       const double h,
    84       boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction) :
    85     cutoff_offset(_cutoff_offset),
    86     cutoff_halfwidth(_cutoff_offset),
    87     manybodyparameter_A(A),
    88     manybodyparameter_B(B),
    89     manybodyparameter_lambda1(lambda1),
    90     manybodyparameter_lambda2(lambda2),
    91     manybodyparameter_lambda3(lambda3),
    92     manybodyparameter_alpha(alpha),
    93     manybodyparameter_beta(beta),
    94     manybodyparameter_n(n),
    95     manybodyparameter_c(d),
    96     manybodyparameter_d(d),
    97     manybodyparameter_h(h),
    98     triplefunction(_triplefunction)
    99   {}
     47      boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction
     48      );
     49
     50  /** Constructor for class ManyBodyPotential_Tersoff.
     51   *
     52   * @param _cutoff_offset offset for cutoff
     53   * @param _cutoff_halfwidth halfwidth for cutoff relative to \a _cutoff_offset
     54   * @param A
     55   * @param B
     56   * @param lambda1
     57   * @param lambda2
     58   * @param lambda3
     59   * @param alpha
     60   * @param beta
     61   * @param n
     62   * @param c
     63   * @param d
     64   * @param h
     65   * @param _triplefunction function that returns a list of triples (i.e. the
     66   *        two remaining distances) to a given pair of points (contained as
     67   *        indices within the argument)
     68   */
     69  ManyBodyPotential_Tersoff(
     70      const double &_cutoff_offset,
     71      const double &_cutoff_halfwidth,
     72      const double &A,
     73      const double &B,
     74      const double &lambda1,
     75      const double &lambda2,
     76      const double &lambda3,
     77      const double &alpha,
     78      const double &beta,
     79      const double &n,
     80      const double &c,
     81      const double &d,
     82      const double &h,
     83      boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction);
     84
    10085  /** Destructor of class ManyBodyPotential_Tersoff.
    10186   *
    … …  
    126111   *         input
    127112   */
    128   virtual results_t paramter_derivative(const arguments_t &arguments, const size_t index) const=0;
     113  results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
     114
     115private:
     116  /** Prohibit private default constructor.
     117   *
     118   * We essentially need the triplefunction, hence without this function cannot
     119   * be.
     120   */
     121  ManyBodyPotential_Tersoff();
    129122
    130123private:
    … …  
    183176
    184177private:
     178  enum parameter_enum_t {
     179    cutoff_offset=0,
     180    equilibrium_distance=1,
     181    cutoff_halfwidth=2,
     182    A=3,
     183    B=4,
     184    lambda1=5,
     185    lambda2=6,
     186    lambda3=7,
     187    alpha=8,
     188    beta=9,
     189    n=10,
     190    c=11,
     191    d=12,
     192    h=13,
     193    MAXPARAMS
     194  };
     195  //!> parameter vector with parameters as in enum parameter_enum_t
     196  parameters_t params;
     197
     198public:
     199  /** Setter for parameters as required by FunctionModel interface.
     200   *
     201   * \param _params given set of parameters
     202   */
     203  void setParameters(const parameters_t &_params)
     204  {
     205    ASSERT( _params.size() == getParameterDimension(),
     206        "ManyBodyPotential_Tersoff::setParameters() - we need exactly "
     207        +toString(getParameterDimension())+" parameters.");
     208    params = _params;
     209  }
     210
     211  /** Getter for parameters as required by FunctionModel interface.
     212   *
     213   * \return set of parameters
     214   */
     215  parameters_t getParameters() const
     216  {
     217    return params;
     218  }
     219
     220  /** Getter for the number of parameters of this model function.
     221   *
     222   * \return number of parameters
     223   */
     224  size_t getParameterDimension() const
     225  {
     226    return MAXPARAMS;
     227  }
     228
     229private:
    185230  //!> bound function that obtains the triples for the internal coordinationb summation.
    186231  const boost::function< std::vector< arguments_t >(const argument_t &, const double)> &triplefunction;
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