[610c11] | 1 | /*
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| 2 | * ManyBodyPotential_Tersoff.hpp
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| 3 | *
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| 4 | * Created on: Sep 26, 2012
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| 5 | * Author: heber
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| 6 | */
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| 7 |
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| 8 | #ifndef MANYBODYPOTENTIAL_TERSOFF_HPP_
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| 9 | #define MANYBODYPOTENTIAL_TERSOFF_HPP_
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| 10 |
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| 11 | // include config.h
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| 12 | #ifdef HAVE_CONFIG_H
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| 13 | #include <config.h>
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| 14 | #endif
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| 15 |
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| 16 | #include <boost/function.hpp>
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| 17 | #include <cmath>
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[d03292] | 18 | #include <limits>
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[610c11] | 19 |
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[4f82f8] | 20 | #include "Potentials/EmpiricalPotential.hpp"
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| 21 |
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[713888] | 22 | class PotentialFactory;
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[d52819] | 23 | class TrainingData;
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| 24 |
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[610c11] | 25 | /** This class is the implementation of the Tersoff potential function.
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| 26 | *
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| 27 | * \note The arguments_t argument list is here in the following order:
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[dd966f] | 28 | * -# first \f$ r_{ij} \f$,
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| 29 | * -# then all \f$ r_{ik} \f$ that are within the cutoff, i.e. \f$ r_{ik} < R + D\f$
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[610c11] | 30 | *
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| 31 | */
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[ed2551] | 32 | class ManyBodyPotential_Tersoff :
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[fdd23a] | 33 | public EmpiricalPotential
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[610c11] | 34 | {
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[ffc368] | 35 | //!> grant unit test access to internal parts
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| 36 | friend class ManyBodyPotential_TersoffTest;
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[713888] | 37 | //!> grant PotentialFactory access to default cstor
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| 38 | friend class PotentialFactory;
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[3ccea3] | 39 | // some repeated typedefs to avoid ambiguities
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| 40 | typedef FunctionModel::arguments_t arguments_t;
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| 41 | typedef FunctionModel::result_t result_t;
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| 42 | typedef FunctionModel::results_t results_t;
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| 43 | typedef EmpiricalPotential::derivative_components_t derivative_components_t;
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[e7579e] | 44 | typedef FunctionModel::parameters_t parameters_t;
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[713888] | 45 | private:
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| 46 | /** Private default constructor.
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| 47 | *
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| 48 | * This prevents creation of potential without set ParticleTypes_t.
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| 49 | *
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| 50 | */
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| 51 | ManyBodyPotential_Tersoff();
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| 52 |
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[610c11] | 53 | public:
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| 54 | /** Constructor for class ManyBodyPotential_Tersoff.
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| 55 | *
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[775dd1a] | 56 | * \param _ParticleTypes particle types for this potential
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[610c11] | 57 | */
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| 58 | ManyBodyPotential_Tersoff(
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[775dd1a] | 59 | const ParticleTypes_t &_ParticleTypes
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[e7579e] | 60 | );
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| 61 |
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| 62 | /** Constructor for class ManyBodyPotential_Tersoff.
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| 63 | *
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[ffc368] | 64 | * @param _R offset for cutoff
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| 65 | * @param _S halfwidth for cutoff relative to \a _R
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[e7579e] | 66 | * @param A
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| 67 | * @param B
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[ffc368] | 68 | * @param lambda
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| 69 | * @param mu
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[e7579e] | 70 | * @param lambda3
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| 71 | * @param alpha
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| 72 | * @param beta
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[ffc368] | 73 | * @param chi
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| 74 | * @param omega
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[e7579e] | 75 | * @param n
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| 76 | * @param c
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| 77 | * @param d
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| 78 | * @param h
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| 79 | * @param _triplefunction function that returns a list of triples (i.e. the
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| 80 | * two remaining distances) to a given pair of points (contained as
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| 81 | * indices within the argument)
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| 82 | */
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| 83 | ManyBodyPotential_Tersoff(
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[ed2551] | 84 | const ParticleTypes_t &_ParticleTypes,
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[ffc368] | 85 | const double &_R,
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| 86 | const double &_S,
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| 87 | const double &_A,
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| 88 | const double &_B,
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| 89 | const double &_lambda,
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| 90 | const double &_mu,
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| 91 | const double &_lambda3,
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| 92 | const double &_alpha,
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| 93 | const double &_beta,
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| 94 | const double &_chi,
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| 95 | const double &_omega,
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| 96 | const double &_n,
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| 97 | const double &_c,
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| 98 | const double &_d,
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[b15ae7] | 99 | const double &_h);
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[e7579e] | 100 |
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[610c11] | 101 | /** Destructor of class ManyBodyPotential_Tersoff.
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| 102 | *
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| 103 | */
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| 104 | virtual ~ManyBodyPotential_Tersoff() {}
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| 105 |
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| 106 | /** Evaluates the Tersoff potential for the given arguments.
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| 107 | *
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| 108 | * @param arguments single distance
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| 109 | * @return value of the potential function
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| 110 | */
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[4f82f8] | 111 | results_t operator()(const arguments_t &arguments) const;
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[610c11] | 112 |
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| 113 | /** Evaluates the derivative of the Tersoff potential with respect to the
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| 114 | * input variables.
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| 115 | *
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| 116 | * @param arguments single distance
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| 117 | * @return vector with components of the derivative
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| 118 | */
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| 119 | derivative_components_t derivative(const arguments_t &arguments) const;
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| 120 |
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[3ccea3] | 121 | /** Evaluates the derivative of the function with the given \a arguments
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| 122 | * with respect to a specific parameter indicated by \a index.
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| 123 | *
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| 124 | * \param arguments set of arguments as input variables to the function
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| 125 | * \param index derivative of which parameter
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| 126 | * \return result vector containing the derivative with respect to the given
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| 127 | * input
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| 128 | */
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[e7579e] | 129 | results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
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| 130 |
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[94453f1] | 131 | /** Returns the functor that converts argument_s into the
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| 132 | * internal coordinate described by this potential function.
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| 133 | *
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| 134 | * \return coordinator functor
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| 135 | */
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| 136 | Coordinator::ptr getCoordinator() const
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| 137 | { return coordinator; }
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| 138 |
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[6efcae] | 139 | /** Return the token name of this specific potential.
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[67cd3a] | 140 | *
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[6efcae] | 141 | * \return token name of the potential
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[67cd3a] | 142 | */
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[ed2551] | 143 | const std::string& getToken() const
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| 144 | { return potential_token; }
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| 145 |
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| 146 | /** Returns a vector of parameter names.
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| 147 | *
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| 148 | * This is required from the specific implementation
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| 149 | *
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| 150 | * \return vector of strings containing parameter names
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| 151 | */
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| 152 | const ParameterNames_t& getParameterNames() const
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| 153 | { return ParameterNames; }
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[67cd3a] | 154 |
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[d03292] | 155 | /** States whether lower and upper boundaries should be used to constraint
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| 156 | * the parameter search for this function model.
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| 157 | *
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| 158 | * \return true - constraints should be used, false - else
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| 159 | */
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| 160 | bool isBoxConstraint() const {
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| 161 | return true;
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| 162 | }
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| 163 |
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| 164 | /** Returns a vector which are the lower boundaries for each parameter_t
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| 165 | * of this FunctionModel.
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| 166 | *
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| 167 | * \return vector of parameter_t resembling lowest allowed values
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| 168 | */
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| 169 | parameters_t getLowerBoxConstraints() const {
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| 170 | parameters_t lowerbound(getParameterDimension(), -std::numeric_limits<double>::max());
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| 171 | // lowerbound[R] = 0.;
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| 172 | // lowerbound[S] = 0.;
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| 173 | // lowerbound[lambda3] = 0.;
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| 174 | // lowerbound[alpha] = 0.;
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| 175 | lowerbound[beta] = std::numeric_limits<double>::min();
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| 176 | lowerbound[n] = std::numeric_limits<double>::min();
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| 177 | lowerbound[c] = std::numeric_limits<double>::min();
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| 178 | lowerbound[d] = std::numeric_limits<double>::min();
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| 179 | return lowerbound;
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| 180 | }
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| 181 |
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| 182 | /** Returns a vector which are the upper boundaries for each parameter_t
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| 183 | * of this FunctionModel.
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| 184 | *
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| 185 | * \return vector of parameter_t resembling highest allowed values
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| 186 | */
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| 187 | parameters_t getUpperBoxConstraints() const {
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| 188 | return parameters_t(getParameterDimension(), std::numeric_limits<double>::max());
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| 189 | }
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| 190 |
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[7b019a] | 191 | /** Returns a bound function to be used with TrainingData, extracting distances
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| 192 | * from a Fragment.
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| 193 | *
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| 194 | * \return bound function extracting distances from a fragment
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| 195 | */
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[f0025d] | 196 | FunctionModel::extractor_t getSpecificExtractor() const;
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[7b019a] | 197 |
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[0f5d38] | 198 | /** Returns a bound function to be used with TrainingData, extracting distances
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| 199 | * from a Fragment.
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| 200 | *
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| 201 | * \return bound function extracting distances from a fragment
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| 202 | */
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| 203 | FunctionModel::filter_t getSpecificFilter() const;
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| 204 |
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| 205 | /** Returns the number of arguments the underlying function requires.
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| 206 | *
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| 207 | * \return number of arguments of the function
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| 208 | */
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| 209 | size_t getSpecificArgumentCount() const
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| 210 | { return 1; }
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| 211 |
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[775dd1a] | 212 | /** Sets the magic triple function that we use for getting angle distances.
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| 213 | *
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| 214 | * @param _triplefunction function that returns a list of triples (i.e. the
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| 215 | * two remaining distances) to a given pair of points (contained as
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| 216 | * indices within the argument)
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| 217 | */
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[e36ba2] | 218 | void setTriplefunction(triplefunction_t &_triplefunction)
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| 219 | { triplefunction = _triplefunction; }
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[775dd1a] | 220 |
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[610c11] | 221 | private:
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| 222 | /** This function represents the cutoff \f$ f_C \f$.
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| 223 | *
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| 224 | * @param distance variable of the function
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| 225 | * @return a value in [0,1].
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| 226 | */
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| 227 | result_t function_cutoff(
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| 228 | const double &distance
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| 229 | ) const;
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| 230 | /** This function has the exponential feature from the Morse potential.
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| 231 | *
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| 232 | * @param prefactor prefactor parameter to exp function
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| 233 | * @param lambda scale parameter of exp function's argument
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[ffc368] | 234 | * @param distance variable of the function
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[610c11] | 235 | * @return
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| 236 | */
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| 237 | result_t function_smoother(
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| 238 | const double &prefactor,
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[ffc368] | 239 | const double &lambda,
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| 240 | const double &distance
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| 241 | ) const;
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[610c11] | 242 |
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| 243 | /** This function represents \f$ (1 + \alpha^n \eta^n)^{-1/2n} \f$.
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| 244 | *
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| 245 | * @param alpha prefactor to eta function
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| 246 | * @param r_ij distance argument
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[ffc368] | 247 | * @param eta result value of eta or zeta
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[610c11] | 248 | * @return \f$ (1 + \alpha^n \eta^n)^{-1/2n} \f$
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| 249 | */
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| 250 | result_t function_prefactor(
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| 251 | const double &alpha,
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[ffc368] | 252 | const double &eta
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[610c11] | 253 | ) const;
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| 254 |
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| 255 | result_t
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| 256 | function_eta(
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| 257 | const argument_t &r_ij
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| 258 | ) const;
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| 259 |
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| 260 | result_t
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| 261 | function_zeta(
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| 262 | const argument_t &r_ij
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| 263 | ) const;
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| 264 |
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[f904d5] | 265 | result_t
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| 266 | function_theta(
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| 267 | const double &r_ij,
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| 268 | const double &r_ik,
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| 269 | const double &r_jk
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| 270 | ) const;
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| 271 |
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[610c11] | 272 | result_t
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| 273 | function_angle(
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| 274 | const double &r_ij,
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| 275 | const double &r_ik,
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| 276 | const double &r_jk
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| 277 | ) const;
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| 278 |
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[e7579e] | 279 | private:
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[ca8d82] | 280 | result_t
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| 281 | function_derivative_c(
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| 282 | const argument_t &r_ij
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| 283 | ) const;
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| 284 |
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| 285 | result_t
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| 286 | function_derivative_d(
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| 287 | const argument_t &r_ij
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| 288 | ) const;
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| 289 |
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| 290 | result_t
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| 291 | function_derivative_h(
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| 292 | const argument_t &r_ij
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| 293 | ) const;
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| 294 |
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| 295 | public:
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[e7579e] | 296 | enum parameter_enum_t {
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[752dc7] | 297 | A,
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| 298 | B,
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| 299 | lambda,
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| 300 | mu,
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| 301 | beta,
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| 302 | n,
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| 303 | c,
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| 304 | d,
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| 305 | h,
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| 306 | // R,
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| 307 | // S,
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| 308 | // lambda3,
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| 309 | // alpha,
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| 310 | // chi,
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| 311 | // omega,
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[e7579e] | 312 | MAXPARAMS
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| 313 | };
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[f48ad3] | 314 |
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| 315 | private:
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[e7579e] | 316 | //!> parameter vector with parameters as in enum parameter_enum_t
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| 317 | parameters_t params;
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| 318 |
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[752dc7] | 319 | public:
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[990a62] | 320 | // some internal parameters which are fixed
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[752dc7] | 321 | const double R;
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| 322 | const double S;
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[990a62] | 323 | const double lambda3;
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| 324 | const double alpha;
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| 325 | const double chi;
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| 326 | const double omega;
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| 327 |
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[e7579e] | 328 | public:
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| 329 | /** Setter for parameters as required by FunctionModel interface.
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| 330 | *
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| 331 | * \param _params given set of parameters
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| 332 | */
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[086070] | 333 | void setParameters(const parameters_t &_params);
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[e7579e] | 334 |
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| 335 | /** Getter for parameters as required by FunctionModel interface.
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| 336 | *
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| 337 | * \return set of parameters
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| 338 | */
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| 339 | parameters_t getParameters() const
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| 340 | {
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| 341 | return params;
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| 342 | }
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| 343 |
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[d52819] | 344 | /** Sets the parameter randomly within the sensible range of each parameter.
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| 345 | *
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| 346 | * \param data container with training data for guesstimating range
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| 347 | */
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| 348 | void setParametersToRandomInitialValues(const TrainingData &data);
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| 349 |
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[e7579e] | 350 | /** Getter for the number of parameters of this model function.
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| 351 | *
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| 352 | * \return number of parameters
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| 353 | */
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| 354 | size_t getParameterDimension() const
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| 355 | {
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| 356 | return MAXPARAMS;
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| 357 | }
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| 358 |
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[610c11] | 359 | private:
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| 360 | //!> bound function that obtains the triples for the internal coordinationb summation.
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[775dd1a] | 361 | boost::function< std::vector< arguments_t >(const argument_t &, const double)> triplefunction;
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[ed2551] | 362 |
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| 363 | //!> static definitions of the parameter name for this potential
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| 364 | static const ParameterNames_t ParameterNames;
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| 365 |
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| 366 | //!> static token of this potential type
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| 367 | static const std::string potential_token;
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[94453f1] | 368 |
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| 369 | //!> internal coordinator object for converting arguments_t
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| 370 | static Coordinator::ptr coordinator;
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[610c11] | 371 | };
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| 372 |
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| 373 |
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| 374 | #endif /* MANYBODYPOTENTIAL_TERSOFF_HPP_ */
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