Changeset 990a62


Ignore:
Timestamp:
Dec 19, 2012, 3:25:54 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:
752dc7
Parents:
ffc368
git-author:
Frederik Heber <heber@…> (10/05/12 16:45:23)
git-committer:
Frederik Heber <heber@…> (12/19/12 15:25:54)
Message:

FIX: Tersoff parameters lambda3, alpha, chi, and omega are now fixed.

  • for this we needed to exclude them from params. This is the cleanest way as suggested in levmar FAQ Q20.
Location:
src/Potentials/Specifics
Files:
3 edited

Legend:

Unmodified
Added
Removed

  • src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

    rffc368 r990a62  
    5151    ) :
    5252    params(parameters_t(MAXPARAMS, 0.)),
     53    lambda3(0.),
     54    alpha(0.),
     55    chi(1.),
     56    omega(1.),
    5357    triplefunction(_triplefunction)
    5458{}
    … …  
    7276    boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction) :
    7377  params(parameters_t(MAXPARAMS, 0.)),
     78  lambda3(_lambda3),
     79  alpha(_alpha),
     80  chi(_chi),
     81  omega(_mu),
    7482  triplefunction(_triplefunction)
    7583{
    … …  
    8189  params[lambda] = _lambda;
    8290  params[mu] = _mu;
    83   params[lambda3] = _lambda3;
    84   params[alpha] = _alpha;
     91//  lambda3 = _lambda3;
     92//  alpha = _alpha;
    8593  params[beta] = _beta;
    86   params[chi] = _chi;
    87   params[omega] = _omega;
     94//  chi = _chi;
     95//  omega = _omega;
    8896  params[n] = _n;
    8997  params[c] = _c;
    … …  
    104112      cutoff * (
    105113          function_prefactor(
    106               params[alpha],
     114              alpha,
    107115              function_eta(r_ij))
    108116          * function_smoother(
    … …  
    174182          -r_ij.distance * cutoff * params[lambda] * (
    175183          function_prefactor(
    176               params[alpha],
     184              alpha,
    177185              function_eta(r_ij))
    178186          * function_smoother(
    … …  
    201209      break;
    202210    }
    203     case lambda3:
    204     {
    205       const double result = 0.;
    206       return results_t(1, result);
    207       break;
    208     }
    209     case alpha:
    210     {
    211       const double temp =
    212           pow(params[alpha]*function_eta(r_ij), params[n]);
    213       const double cutoff = function_cutoff(r_ij.distance);
    214       const double result = (cutoff == 0.) || (params[alpha] == 0. )?
    215           0. :
    216           function_smoother(
    217               -params[A],
    218               params[lambda],
    219               r_ij.distance)
    220           * (-.5) * params[alpha] * (temp/params[alpha])
    221           / (1. + temp)
    222           ;
    223       return results_t(1, result);
    224       break;
    225     }
     211//    case lambda3:
     212//    {
     213//      const double result = 0.;
     214//      return results_t(1, result);
     215//      break;
     216//    }
     217//    case alpha:
     218//    {
     219//      const double temp =
     220//          pow(alpha*function_eta(r_ij), params[n]);
     221//      const double cutoff = function_cutoff(r_ij.distance);
     222//      const double result = (cutoff == 0.) || (alpha == 0. )?
     223//          0. :
     224//          function_smoother(
     225//              -params[A],
     226//              params[lambda],
     227//              r_ij.distance)
     228//          * (-.5) * alpha * (temp/alpha)
     229//          / (1. + temp)
     230//          ;
     231//      return results_t(1, result);
     232//      break;
     233//    }
     234//    case chi:
     235//    {
     236//      const double result = 0.;
     237//      return results_t(1, result);
     238//      break;
     239//    }
     240//    case omega:
     241//    {
     242//      const double result = 0.;
     243//      return results_t(1, result);
     244//      break;
     245//    }
    226246    case beta:
    227247    {
    … …  
    309329{
    310330//  Info info(__func__);
    311   const double result = params[chi] * pow(
     331  const double result = chi * pow(
    312332      (1. + pow(alpha * eta, params[n])),
    313333      -1./(2.*params[n]));
    … …  
    345365    const argument_t &r_ik = (*iter)[0];
    346366    result += function_cutoff(r_ik.distance)
    347         * exp( Helpers::pow(params[lambda3] * (r_ij.distance - r_ik.distance) ,3));
     367        * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3));
    348368  }
    349369
    … …  
    370390    result +=
    371391        function_cutoff(r_ik.distance)
    372         * params[omega]
     392        * omega
    373393        * function_angle(r_ij.distance, r_ik.distance, r_jk.distance)
    374         * exp( Helpers::pow(params[lambda3] * (r_ij.distance - r_ik.distance) ,3));
     394        * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3));
    375395  }
    376396

  • src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

    rffc368 r990a62  
    186186    lambda=4,
    187187    mu=5,
    188     lambda3=6,
    189     alpha=7,
    190     beta=8,
    191     chi=9,
    192     omega=10,
    193     n=11,
    194     c=12,
    195     d=13,
    196     h=14,
     188    beta=6,
     189    n=7,
     190    c=8,
     191    d=9,
     192    h=10,
     193//    lambda3=11,
     194//    alpha=12,
     195//    chi=13,
     196//    omega=14,
    197197    MAXPARAMS
    198198  };
    199199  //!> parameter vector with parameters as in enum parameter_enum_t
    200200  parameters_t params;
     201
     202  // some internal parameters which are fixed
     203  const double lambda3;
     204  const double alpha;
     205  const double chi;
     206  const double omega;
    201207
    202208public:

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

    rffc368 r990a62  
    134134  params[ManyBodyPotential_Tersoff::lambda] = 3.487900e+00;
    135135  params[ManyBodyPotential_Tersoff::mu] = 2.211900e+00;
    136   params[ManyBodyPotential_Tersoff::lambda3] = 0.;
    137   params[ManyBodyPotential_Tersoff::alpha] = 0.;
     136//  params[ManyBodyPotential_Tersoff::lambda3] = 0.;
     137//  params[ManyBodyPotential_Tersoff::alpha] = 0.;
    138138  params[ManyBodyPotential_Tersoff::beta] = 1.572400e-07;
    139   params[ManyBodyPotential_Tersoff::chi] = 1.;
    140   params[ManyBodyPotential_Tersoff::omega] = 1.;
     139//  params[ManyBodyPotential_Tersoff::chi] = 1.;
     140//  params[ManyBodyPotential_Tersoff::omega] = 1.;
    141141  params[ManyBodyPotential_Tersoff::n] = 7.275100e-01;
    142142  params[ManyBodyPotential_Tersoff::c] = 3.804900e+04;
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