| 1 | /*
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| 2 | * Project: MoleCuilder
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| 3 | * Description: creates and alters molecular systems
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| 4 | * Copyright (C) 2012 University of Bonn. All rights reserved.
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| 5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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| 6 | * Please see the COPYING file or "Copyright notice" in builder.cpp for details.
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| 7 | *
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| 8 | *
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| 9 | * This file is part of MoleCuilder.
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| 10 | *
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| 11 | * MoleCuilder is free software: you can redistribute it and/or modify
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| 12 | * it under the terms of the GNU General Public License as published by
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| 13 | * the Free Software Foundation, either version 2 of the License, or
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| 14 | * (at your option) any later version.
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| 15 | *
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| 16 | * MoleCuilder is distributed in the hope that it will be useful,
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| 17 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 18 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 19 | * GNU General Public License for more details.
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| 20 | *
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| 21 | * You should have received a copy of the GNU General Public License
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| 22 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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| 23 | */
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| 24 |
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| 25 | /*
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| 26 | * ManyBodyPotential_Tersoff.cpp
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| 27 | *
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| 28 | * Created on: Sep 26, 2012
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| 29 | * Author: heber
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| 30 | */
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| 31 |
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| 32 |
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| 33 | // include config.h
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| 34 | #ifdef HAVE_CONFIG_H
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| 35 | #include <config.h>
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| 36 | #endif
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| 37 |
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| 38 | #include "CodePatterns/MemDebug.hpp"
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| 39 |
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| 40 | #include "ManyBodyPotential_Tersoff.hpp"
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| 41 |
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| 42 | #include <boost/assign/list_of.hpp> // for 'map_list_of()'
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| 43 | #include <boost/bind.hpp>
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| 44 | #include <cmath>
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| 45 | #include <string>
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| 46 |
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| 47 | #include "CodePatterns/Assert.hpp"
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| 48 | //#include "CodePatterns/Info.hpp"
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| 49 | #include "CodePatterns/Log.hpp"
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| 50 |
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| 51 | #include "FunctionApproximation/Extractors.hpp"
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| 52 | #include "FunctionApproximation/TrainingData.hpp"
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| 53 | #include "Potentials/helpers.hpp"
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| 54 | #include "Potentials/InternalCoordinates/OneBody_Constant.hpp"
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| 55 | #include "Potentials/ParticleTypeCheckers.hpp"
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| 56 | #include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
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| 57 | #include "RandomNumbers/RandomNumberGenerator.hpp"
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| 58 |
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| 59 | class Fragment;
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| 60 |
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| 61 | // static definitions
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| 62 | const ManyBodyPotential_Tersoff::ParameterNames_t
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| 63 | ManyBodyPotential_Tersoff::ParameterNames =
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| 64 | boost::assign::list_of<std::string>
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| 65 | ("A")
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| 66 | ("B")
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| 67 | ("lambda")
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| 68 | ("mu")
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| 69 | ("beta")
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| 70 | ("n")
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| 71 | ("c")
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| 72 | ("d")
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| 73 | ("h")
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| 74 | // ("R")
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| 75 | // ("S")
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| 76 | // ("lambda3")
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| 77 | // ("alpha")
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| 78 | // ("chi")
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| 79 | // ("omega")
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| 80 | ;
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| 81 | const std::string ManyBodyPotential_Tersoff::potential_token("tersoff");
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| 82 | Coordinator::ptr ManyBodyPotential_Tersoff::coordinator(new OneBody_Constant());
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| 83 |
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| 84 | ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff() :
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| 85 | EmpiricalPotential(),
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| 86 | params(parameters_t(MAXPARAMS, 0.)),
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| 87 | R(3.2),
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| 88 | S(3.5),
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| 89 | lambda3(0.),
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| 90 | alpha(0.),
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| 91 | chi(1.),
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| 92 | omega(1.),
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| 93 | triplefunction(&Helpers::NoOp_Triplefunction)
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| 94 | {}
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| 95 |
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| 96 | ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff(
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| 97 | const ParticleTypes_t &_ParticleTypes
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| 98 | ) :
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| 99 | EmpiricalPotential(_ParticleTypes),
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| 100 | params(parameters_t(MAXPARAMS, 0.)),
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| 101 | R(3.2),
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| 102 | S(3.5),
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| 103 | lambda3(0.),
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| 104 | alpha(0.),
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| 105 | chi(1.),
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| 106 | omega(1.),
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| 107 | triplefunction(&Helpers::NoOp_Triplefunction)
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| 108 | {
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| 109 | // have some decent defaults for parameter_derivative checking
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| 110 | params[A] = 3000.;
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| 111 | params[B] = 300.;
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| 112 | params[lambda] = 5.;
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| 113 | params[mu] = 3.;
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| 114 | params[beta] = 2.;
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| 115 | params[n] = 1.;
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| 116 | params[c] = 0.01;
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| 117 | params[d] = 1.;
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| 118 | params[h] = 0.01;
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| 119 | }
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| 120 |
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| 121 | ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff(
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| 122 | const ParticleTypes_t &_ParticleTypes,
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| 123 | const double &_R,
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| 124 | const double &_S,
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| 125 | const double &_A,
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| 126 | const double &_B,
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| 127 | const double &_lambda,
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| 128 | const double &_mu,
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| 129 | const double &_lambda3,
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| 130 | const double &_alpha,
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| 131 | const double &_beta,
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| 132 | const double &_chi,
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| 133 | const double &_omega,
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| 134 | const double &_n,
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| 135 | const double &_c,
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| 136 | const double &_d,
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| 137 | const double &_h) :
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| 138 | EmpiricalPotential(_ParticleTypes),
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| 139 | params(parameters_t(MAXPARAMS, 0.)),
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| 140 | R(_R),
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| 141 | S(_S),
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| 142 | lambda3(_lambda3),
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| 143 | alpha(_alpha),
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| 144 | chi(_chi),
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| 145 | omega(_mu),
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| 146 | triplefunction(&Helpers::NoOp_Triplefunction)
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| 147 | {
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| 148 | // Info info(__func__);
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| 149 | // R = _R;
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| 150 | // S = _S;
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| 151 | params[A] = _A;
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| 152 | params[B] = _B;
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| 153 | params[lambda] = _lambda;
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| 154 | params[mu] = _mu;
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| 155 | // lambda3 = _lambda3;
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| 156 | // alpha = _alpha;
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| 157 | params[beta] = _beta;
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| 158 | // chi = _chi;
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| 159 | // omega = _omega;
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| 160 | params[n] = _n;
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| 161 | params[c] = _c;
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| 162 | params[d] = _d;
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| 163 | params[h] = _h;
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| 164 | }
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| 165 |
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| 166 | void ManyBodyPotential_Tersoff::setParameters(const parameters_t &_params)
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| 167 | {
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| 168 | const size_t paramsDim = _params.size();
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| 169 | ASSERT( paramsDim <= getParameterDimension(),
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| 170 | "ManyBodyPotential_Tersoff::setParameters() - we need not more than "
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| 171 | +toString(getParameterDimension())+" parameters.");
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| 172 | for (size_t i=0; i< paramsDim; ++i)
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| 173 | params[i] = _params[i];
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| 174 |
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| 175 | #ifndef NDEBUG
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| 176 | parameters_t check_params(getParameters());
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| 177 | check_params.resize(paramsDim); // truncate to same size
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| 178 | ASSERT( check_params == _params,
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| 179 | "ManyBodyPotential_Tersoff::setParameters() - failed, mismatch in to be set "
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| 180 | +toString(_params)+" and set "+toString(check_params)+" params.");
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| 181 | #endif
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| 182 | }
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| 183 |
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| 184 | ManyBodyPotential_Tersoff::results_t
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| 185 | ManyBodyPotential_Tersoff::operator()(
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| 186 | const list_of_arguments_t &listarguments
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| 187 | ) const
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| 188 | {
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| 189 | // Info info(__func__);
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| 190 | result_t result = 0.;
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| 191 | for(list_of_arguments_t::const_iterator iter = listarguments.begin();
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| 192 | iter != listarguments.end(); ++iter) {
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| 193 | const arguments_t &arguments = *iter;
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| 194 | for(arguments_t::const_iterator argiter = arguments.begin();
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| 195 | argiter != arguments.end();
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| 196 | ++argiter) {
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| 197 | const argument_t &r_ij = *argiter;
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| 198 | ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
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| 199 | arguments_t(1, r_ij), getParticleTypes()),
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| 200 | "ManyBodyPotential_Tersoff::operator() - types don't match with ones in arguments.");
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| 201 |
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| 202 | const double cutoff = function_cutoff(r_ij.distance);
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| 203 | const double temp = (cutoff == 0.) ?
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| 204 | 0. :
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| 205 | cutoff * (
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| 206 | function_prefactor(
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| 207 | alpha,
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| 208 | function_eta(r_ij))
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| 209 | * function_smoother(
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| 210 | params[A],
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| 211 | params[lambda],
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| 212 | r_ij.distance)
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| 213 | +
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| 214 | function_prefactor(
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| 215 | params[beta],
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| 216 | function_zeta(r_ij))
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| 217 | * function_smoother(
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| 218 | -params[B],
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| 219 | params[mu],
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| 220 | r_ij.distance)
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| 221 | );
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| 222 | result += temp;
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| 223 | }
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| 224 | }
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| 225 | // LOG(2, "DEBUG: operator()(" << r_ij.distance << ") = " << result);
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| 226 | return results_t(1, result);
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| 227 | }
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| 228 |
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| 229 | ManyBodyPotential_Tersoff::derivative_components_t
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| 230 | ManyBodyPotential_Tersoff::derivative(
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| 231 | const list_of_arguments_t &listarguments
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| 232 | ) const
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| 233 | {
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| 234 | // Info info(__func__);
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| 235 | return derivative_components_t();
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| 236 | }
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| 237 |
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| 238 | ManyBodyPotential_Tersoff::results_t
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| 239 | ManyBodyPotential_Tersoff::parameter_derivative(
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| 240 | const list_of_arguments_t &listarguments,
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| 241 | const size_t index
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| 242 | ) const
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| 243 | {
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| 244 | // Info info(__func__);
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| 245 | // ASSERT( arguments.size() == 1,
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| 246 | // "ManyBodyPotential_Tersoff::parameter_derivative() - requires exactly one argument.");
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| 247 |
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| 248 | result_t result = 0.;
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| 249 | for(list_of_arguments_t::const_iterator iter = listarguments.begin();
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| 250 | iter != listarguments.end(); ++iter) {
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| 251 | const arguments_t &arguments = *iter;
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| 252 | for(arguments_t::const_iterator argiter = arguments.begin();
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| 253 | argiter != arguments.end();
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| 254 | ++argiter) {
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| 255 | const argument_t &r_ij = *argiter;
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| 256 | ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
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| 257 | arguments_t(1, r_ij), getParticleTypes()),
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| 258 | "ManyBodyPotential_Tersoff::operator() - types don't match with ones in arguments.");
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| 259 |
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| 260 | switch (index) {
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| 261 | // case R:
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| 262 | // {
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| 263 | // result += 0.;
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| 264 | // break;
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| 265 | // }
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| 266 | // case S:
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| 267 | // {
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| 268 | // result += 0.;
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| 269 | // break;
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| 270 | // }
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| 271 | case A:
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| 272 | {
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| 273 | const double cutoff = function_cutoff(r_ij.distance);
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| 274 | result += (cutoff == 0.) ?
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| 275 | 0. :
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| 276 | cutoff *
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| 277 | function_prefactor(
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| 278 | alpha,
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| 279 | function_eta(r_ij))
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| 280 | * function_smoother(
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| 281 | 1.,
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| 282 | params[lambda],
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| 283 | r_ij.distance);
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| 284 | // cutoff * function_prefactor(
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| 285 | // alpha,
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| 286 | // function_eta(r_ij))
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| 287 | // * function_smoother(
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| 288 | // 1.,
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| 289 | // params[mu],
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| 290 | // r_ij.distance);
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| 291 | break;
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| 292 | }
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| 293 | case B:
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| 294 | {
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| 295 | const double cutoff = function_cutoff(r_ij.distance);
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| 296 | result += (cutoff == 0.) ?
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| 297 | 0. :
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| 298 | cutoff * function_prefactor(
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| 299 | params[beta],
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| 300 | function_zeta(r_ij))
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| 301 | * function_smoother(
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| 302 | -1.,
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| 303 | params[mu],
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| 304 | r_ij.distance);
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| 305 | // cutoff * function_prefactor(
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| 306 | // beta,
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| 307 | // function_zeta(r_ij))
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| 308 | // * function_smoother(
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| 309 | // -params[B],
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| 310 | // params[mu],
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| 311 | // r_ij.distance)/params[B];
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| 312 | break;
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| 313 | }
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| 314 | case lambda:
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| 315 | {
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| 316 | const double cutoff = function_cutoff(r_ij.distance);
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| 317 | result += (cutoff == 0.) ?
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| 318 | 0. :
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| 319 | -r_ij.distance * cutoff *
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| 320 | function_prefactor(
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| 321 | alpha,
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| 322 | function_eta(r_ij))
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| 323 | * function_smoother(
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| 324 | params[A],
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| 325 | params[lambda],
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| 326 | r_ij.distance);
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| 327 | break;
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| 328 | }
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| 329 | case mu:
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| 330 | {
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| 331 | const double cutoff = function_cutoff(r_ij.distance);
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| 332 | result += (cutoff == 0.) ?
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| 333 | 0. :
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| 334 | -r_ij.distance * cutoff *(
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| 335 | function_prefactor(
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| 336 | params[beta],
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| 337 | function_zeta(r_ij))
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| 338 | * function_smoother(
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| 339 | -params[B],
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| 340 | params[mu],
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| 341 | r_ij.distance)
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| 342 | );
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| 343 | break;
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| 344 | }
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| 345 | // case lambda3:
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| 346 | // {
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| 347 | // result += 0.;
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| 348 | // break;
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| 349 | // }
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| 350 | // case alpha:
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| 351 | // {
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| 352 | // const double temp =
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| 353 | // pow(alpha*function_eta(r_ij), params[n]);
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| 354 | // const double cutoff = function_cutoff(r_ij.distance);
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| 355 | // result += (cutoff == 0.) || (alpha == 0. )?
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| 356 | // 0. :
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| 357 | // function_smoother(
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| 358 | // params[A],
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| 359 | // params[lambda],
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| 360 | // r_ij.distance)
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| 361 | // * (-.5) * alpha * (temp/alpha)
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| 362 | // / (1. + temp)
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| 363 | // ;
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| 364 | // break;
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| 365 | // }
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| 366 | // case chi:
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| 367 | // {
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| 368 | // result += 0.;
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| 369 | // break;
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| 370 | // }
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| 371 | // case omega:
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| 372 | // {
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| 373 | // result += 0.;
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| 374 | // break;
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| 375 | // }
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| 376 | case beta:
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| 377 | {
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| 378 | const double temp =
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| 379 | pow(params[beta]*function_zeta(r_ij), params[n]);
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| 380 | const double cutoff = function_cutoff(r_ij.distance);
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| 381 | result += (cutoff == 0.) || (params[beta] == 0. )?
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| 382 | 0. : cutoff *
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| 383 | function_smoother(
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| 384 | -params[B],
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| 385 | params[mu],
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| 386 | r_ij.distance)
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| 387 | * (-.5)
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| 388 | * function_prefactor(
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| 389 | params[beta],
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| 390 | function_zeta(r_ij))
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| 391 | * (temp/params[beta])
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| 392 | / (1. + temp)
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| 393 | ;
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| 394 | break;
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| 395 | }
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| 396 | case n:
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| 397 | {
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| 398 | const double zeta = function_zeta(r_ij);
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| 399 | const double temp = pow( params[beta]*zeta , params[n]);
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| 400 | const double cutoff = function_cutoff(r_ij.distance);
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| 401 | const double tempres = ((cutoff == 0.) || (zeta == 0.)) ? // zeta must be caught if zero due to log
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| 402 | 0. : .5 * cutoff *
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| 403 | function_smoother(
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| 404 | -params[B],
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| 405 | params[mu],
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| 406 | r_ij.distance)
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| 407 | * function_prefactor(
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| 408 | params[beta],
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| 409 | function_zeta(r_ij))
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| 410 | * ( log(1.+temp)/(params[n]*params[n]) - temp
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| 411 | * (log(function_zeta(r_ij)) + log(params[beta]))
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| 412 | /(params[n]*(1.+temp)))
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| 413 | ;
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| 414 | // if (tempres != tempres)
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| 415 | // LOG(2, "DEBUG: tempres is NaN.");
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| 416 | // LOG(2, "DEBUG: Adding " << tempres << " for p.d. w.r.t n, temp=" << temp << ", cutoff=" << cutoff);
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| 417 | result += tempres;
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| 418 | break;
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| 419 | }
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| 420 | case c:
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| 421 | {
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| 422 | const double zeta = function_zeta(r_ij);
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| 423 | if (zeta == 0.)
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| 424 | break;
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| 425 | const double temp =
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| 426 | pow(zeta, params[n]-1.) * pow(params[beta],params[n]);
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| 427 | const double cutoff = function_cutoff(r_ij.distance);
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| 428 | const double tempres = (cutoff == 0.) ?
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| 429 | 0. : cutoff *
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| 430 | function_smoother(
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| 431 | -params[B],
|
|---|
| 432 | params[mu],
|
|---|
| 433 | r_ij.distance)
|
|---|
| 434 | * function_prefactor(
|
|---|
| 435 | params[beta],
|
|---|
| 436 | zeta)
|
|---|
| 437 | * (-1.) * temp / (1.+temp*zeta);
|
|---|
| 438 | double factor = function_derivative_c(r_ij);
|
|---|
| 439 | result += tempres*factor;
|
|---|
| 440 | if (result != result)
|
|---|
| 441 | ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor);
|
|---|
| 442 | break;
|
|---|
| 443 | }
|
|---|
| 444 | case d:
|
|---|
| 445 | {
|
|---|
| 446 | const double zeta = function_zeta(r_ij);
|
|---|
| 447 | const double temp =
|
|---|
| 448 | pow(zeta, params[n]-1.) * pow(params[beta],params[n]);
|
|---|
| 449 | const double cutoff = function_cutoff(r_ij.distance);
|
|---|
| 450 | const double tempres = (cutoff == 0.) ?
|
|---|
| 451 | 0. : cutoff *
|
|---|
| 452 | function_smoother(
|
|---|
| 453 | -params[B],
|
|---|
| 454 | params[mu],
|
|---|
| 455 | r_ij.distance)
|
|---|
| 456 | * function_prefactor(
|
|---|
| 457 | params[beta],
|
|---|
| 458 | zeta)
|
|---|
| 459 | * (-1.) * temp / (1.+temp*zeta);
|
|---|
| 460 | double factor = function_derivative_d(r_ij);
|
|---|
| 461 | result += tempres*factor;
|
|---|
| 462 | if (result != result)
|
|---|
| 463 | ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor);
|
|---|
| 464 | break;
|
|---|
| 465 | }
|
|---|
| 466 | case h:
|
|---|
| 467 | {
|
|---|
| 468 | const double zeta = function_zeta(r_ij);
|
|---|
| 469 | const double temp =
|
|---|
| 470 | pow(zeta, params[n]-1.) * pow(params[beta],params[n]);
|
|---|
| 471 | const double cutoff = function_cutoff(r_ij.distance);
|
|---|
| 472 | const double tempres = (cutoff == 0.) ?
|
|---|
| 473 | 0. : cutoff *
|
|---|
| 474 | function_smoother(
|
|---|
| 475 | -params[B],
|
|---|
| 476 | params[mu],
|
|---|
| 477 | r_ij.distance)
|
|---|
| 478 | * function_prefactor(
|
|---|
| 479 | params[beta],
|
|---|
| 480 | zeta)
|
|---|
| 481 | * (-1.) * temp / (1.+temp*zeta);
|
|---|
| 482 | double factor = function_derivative_h(r_ij);
|
|---|
| 483 | result += tempres*factor;
|
|---|
| 484 | if (result != result)
|
|---|
| 485 | ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor);
|
|---|
| 486 | break;
|
|---|
| 487 | }
|
|---|
| 488 | default:
|
|---|
| 489 | ASSERT(0, "ManyBodyPotential_Tersoff::parameter_derivative() - derivative to unknown parameter desired.");
|
|---|
| 490 | break;
|
|---|
| 491 | }
|
|---|
| 492 | if (result != result)
|
|---|
| 493 | ELOG(1, "result is NaN.");
|
|---|
| 494 | }
|
|---|
| 495 | }
|
|---|
| 496 | return results_t(1,-result);
|
|---|
| 497 | }
|
|---|
| 498 |
|
|---|
| 499 | ManyBodyPotential_Tersoff::result_t
|
|---|
| 500 | ManyBodyPotential_Tersoff::function_derivative_c(
|
|---|
| 501 | const argument_t &r_ij
|
|---|
| 502 | ) const
|
|---|
| 503 | {
|
|---|
| 504 | double result = 0.;
|
|---|
| 505 | std::vector<arguments_t> triples = triplefunction(r_ij, S);
|
|---|
| 506 | for (std::vector<arguments_t>::const_iterator iter = triples.begin();
|
|---|
| 507 | iter != triples.end(); ++iter) {
|
|---|
| 508 | ASSERT( iter->size() == 2,
|
|---|
| 509 | "ManyBodyPotential_Tersoff::function_derivative_c() - the triples result must contain exactly two distances.");
|
|---|
| 510 | const argument_t &r_ik = (*iter)[0];
|
|---|
| 511 | const argument_t &r_jk = (*iter)[1];
|
|---|
| 512 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance);
|
|---|
| 513 | const double cutoff = function_cutoff(r_ik.distance);
|
|---|
| 514 | result += (cutoff == 0.) ?
|
|---|
| 515 | 0. : cutoff * omega * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * (
|
|---|
| 516 | params[c]/Helpers::pow(params[d],2)
|
|---|
| 517 | - params[c] / ( Helpers::pow(params[d],2) + Helpers::pow(tempangle,2) )
|
|---|
| 518 | );
|
|---|
| 519 | }
|
|---|
| 520 | return result;
|
|---|
| 521 | }
|
|---|
| 522 |
|
|---|
| 523 | ManyBodyPotential_Tersoff::result_t
|
|---|
| 524 | ManyBodyPotential_Tersoff::function_derivative_d(
|
|---|
| 525 | const argument_t &r_ij
|
|---|
| 526 | ) const
|
|---|
| 527 | {
|
|---|
| 528 | double result = 0.;
|
|---|
| 529 | std::vector<arguments_t> triples = triplefunction(r_ij, S);
|
|---|
| 530 | for (std::vector<arguments_t>::const_iterator iter = triples.begin();
|
|---|
| 531 | iter != triples.end(); ++iter) {
|
|---|
| 532 | ASSERT( iter->size() == 2,
|
|---|
| 533 | "ManyBodyPotential_Tersoff::function_derivative_d() - the triples result must contain exactly two distances.");
|
|---|
| 534 | const argument_t &r_ik = (*iter)[0];
|
|---|
| 535 | const argument_t &r_jk = (*iter)[1];
|
|---|
| 536 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance);
|
|---|
| 537 | const double cutoff = function_cutoff(r_ik.distance);
|
|---|
| 538 | result += (cutoff == 0.) ?
|
|---|
| 539 | 0. : cutoff * omega * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * (
|
|---|
| 540 | - Helpers::pow(params[c],2)/Helpers::pow(params[d],3)
|
|---|
| 541 | + Helpers::pow(params[c],2) * params[d]
|
|---|
| 542 | / Helpers::pow(Helpers::pow(params[d],2) + Helpers::pow(tempangle,2),2)
|
|---|
| 543 | );
|
|---|
| 544 | }
|
|---|
| 545 | return result;
|
|---|
| 546 | }
|
|---|
| 547 |
|
|---|
| 548 | ManyBodyPotential_Tersoff::result_t
|
|---|
| 549 | ManyBodyPotential_Tersoff::function_derivative_h(
|
|---|
| 550 | const argument_t &r_ij
|
|---|
| 551 | ) const
|
|---|
| 552 | {
|
|---|
| 553 | double result = 0.;
|
|---|
| 554 | std::vector<arguments_t> triples = triplefunction(r_ij, S);
|
|---|
| 555 | for (std::vector<arguments_t>::const_iterator iter = triples.begin();
|
|---|
| 556 | iter != triples.end(); ++iter) {
|
|---|
| 557 | ASSERT( iter->size() == 2,
|
|---|
| 558 | "ManyBodyPotential_Tersoff::function_derivative_h() - the triples result must contain exactly two distances.");
|
|---|
| 559 | const argument_t &r_ik = (*iter)[0];
|
|---|
| 560 | const argument_t &r_jk = (*iter)[1];
|
|---|
| 561 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance);
|
|---|
| 562 | const double cutoff = function_cutoff(r_ik.distance);
|
|---|
| 563 | result += (cutoff == 0.) ?
|
|---|
| 564 | 0. : cutoff * omega * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * (
|
|---|
| 565 | ( Helpers::pow(params[c],2)*tempangle )
|
|---|
| 566 | / Helpers::pow(Helpers::pow(params[d],2) + Helpers::pow(tempangle,2),2)
|
|---|
| 567 | );
|
|---|
| 568 | }
|
|---|
| 569 | return result;
|
|---|
| 570 | }
|
|---|
| 571 |
|
|---|
| 572 | ManyBodyPotential_Tersoff::result_t
|
|---|
| 573 | ManyBodyPotential_Tersoff::function_cutoff(
|
|---|
| 574 | const double &distance
|
|---|
| 575 | ) const
|
|---|
| 576 | {
|
|---|
| 577 | // Info info(__func__);
|
|---|
| 578 | double result = 0.;
|
|---|
| 579 | if (distance < R)
|
|---|
| 580 | result = 1.;
|
|---|
| 581 | else if (distance > S)
|
|---|
| 582 | result = 0.;
|
|---|
| 583 | else {
|
|---|
| 584 | result = (0.5 + 0.5 * cos( M_PI * (distance - R)/(S-R)));
|
|---|
| 585 | }
|
|---|
| 586 | // LOG(2, "DEBUG: function_cutoff(" << distance << ") = " << result);
|
|---|
| 587 | return result;
|
|---|
| 588 | }
|
|---|
| 589 |
|
|---|
| 590 | ManyBodyPotential_Tersoff::result_t
|
|---|
| 591 | ManyBodyPotential_Tersoff::function_prefactor(
|
|---|
| 592 | const double &alpha,
|
|---|
| 593 | const double &eta
|
|---|
| 594 | ) const
|
|---|
| 595 | {
|
|---|
| 596 | // Info info(__func__);
|
|---|
| 597 | const double result = chi * pow(
|
|---|
| 598 | (1. + pow(alpha * eta, params[n])),
|
|---|
| 599 | -1./(2.*params[n]));
|
|---|
| 600 | // LOG(2, "DEBUG: function_prefactor(" << alpha << "," << eta << ") = " << result);
|
|---|
| 601 | return result;
|
|---|
| 602 | }
|
|---|
| 603 |
|
|---|
| 604 | ManyBodyPotential_Tersoff::result_t
|
|---|
| 605 | ManyBodyPotential_Tersoff::function_smoother(
|
|---|
| 606 | const double &prefactor,
|
|---|
| 607 | const double &lambda,
|
|---|
| 608 | const double &distance
|
|---|
| 609 | ) const
|
|---|
| 610 | {
|
|---|
| 611 | // Info info(__func__);
|
|---|
| 612 | const double result = prefactor * exp(-lambda * distance);
|
|---|
| 613 | // LOG(2, "DEBUG: function_smoother(" << prefactor << "," << lambda << "," << distance << ") = " << result);
|
|---|
| 614 | return result;
|
|---|
| 615 | }
|
|---|
| 616 |
|
|---|
| 617 | ManyBodyPotential_Tersoff::result_t
|
|---|
| 618 | ManyBodyPotential_Tersoff::function_eta(
|
|---|
| 619 | const argument_t &r_ij
|
|---|
| 620 | ) const
|
|---|
| 621 | {
|
|---|
| 622 | // Info info(__func__);
|
|---|
| 623 | result_t result = 0.;
|
|---|
| 624 |
|
|---|
| 625 | // get all triples within the cutoff
|
|---|
| 626 | std::vector<arguments_t> triples = triplefunction(r_ij, S);
|
|---|
| 627 | for (std::vector<arguments_t>::const_iterator iter = triples.begin();
|
|---|
| 628 | iter != triples.end(); ++iter) {
|
|---|
| 629 | ASSERT( iter->size() == 2,
|
|---|
| 630 | "ManyBodyPotential_Tersoff::function_zeta() - the triples result must contain of exactly two distances.");
|
|---|
| 631 | const argument_t &r_ik = (*iter)[0];
|
|---|
| 632 | result += function_cutoff(r_ik.distance)
|
|---|
| 633 | * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3));
|
|---|
| 634 | }
|
|---|
| 635 |
|
|---|
| 636 | // LOG(2, "DEBUG: function_eta(" << r_ij.distance << ") = " << result);
|
|---|
| 637 | return result;
|
|---|
| 638 | }
|
|---|
| 639 |
|
|---|
| 640 | ManyBodyPotential_Tersoff::result_t
|
|---|
| 641 | ManyBodyPotential_Tersoff::function_zeta(
|
|---|
| 642 | const argument_t &r_ij
|
|---|
| 643 | ) const
|
|---|
| 644 | {
|
|---|
| 645 | // Info info(__func__);
|
|---|
| 646 | result_t result = 0.;
|
|---|
| 647 |
|
|---|
| 648 | // get all triples within the cutoff
|
|---|
| 649 | std::vector<arguments_t> triples = triplefunction(r_ij, S);
|
|---|
| 650 | for (std::vector<arguments_t>::const_iterator iter = triples.begin();
|
|---|
| 651 | iter != triples.end(); ++iter) {
|
|---|
| 652 | ASSERT( iter->size() == 2,
|
|---|
| 653 | "ManyBodyPotential_Tersoff::function_zeta() - the triples result must contain exactly two distances.");
|
|---|
| 654 | const argument_t &r_ik = (*iter)[0];
|
|---|
| 655 | const argument_t &r_jk = (*iter)[1];
|
|---|
| 656 | result +=
|
|---|
| 657 | function_cutoff(r_ik.distance)
|
|---|
| 658 | * omega
|
|---|
| 659 | * function_angle(r_ij.distance, r_ik.distance, r_jk.distance)
|
|---|
| 660 | * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3));
|
|---|
| 661 | }
|
|---|
| 662 |
|
|---|
| 663 | // LOG(2, "DEBUG: function_zeta(" << r_ij.distance << ") = " << result);
|
|---|
| 664 | return result;
|
|---|
| 665 | }
|
|---|
| 666 |
|
|---|
| 667 | ManyBodyPotential_Tersoff::result_t
|
|---|
| 668 | ManyBodyPotential_Tersoff::function_theta(
|
|---|
| 669 | const double &r_ij,
|
|---|
| 670 | const double &r_ik,
|
|---|
| 671 | const double &r_jk
|
|---|
| 672 | ) const
|
|---|
| 673 | {
|
|---|
| 674 | const double angle = Helpers::pow(r_ij,2) + Helpers::pow(r_ik,2) - Helpers::pow(r_jk,2);
|
|---|
| 675 | const double divisor = 2.* r_ij * r_ik;
|
|---|
| 676 | if (divisor != 0.) {
|
|---|
| 677 | LOG(2, "DEBUG: cos(theta)= " << angle/divisor);
|
|---|
| 678 | return angle/divisor;
|
|---|
| 679 | } else
|
|---|
| 680 | return 0.;
|
|---|
| 681 | }
|
|---|
| 682 |
|
|---|
| 683 | ManyBodyPotential_Tersoff::result_t
|
|---|
| 684 | ManyBodyPotential_Tersoff::function_angle(
|
|---|
| 685 | const double &r_ij,
|
|---|
| 686 | const double &r_ik,
|
|---|
| 687 | const double &r_jk
|
|---|
| 688 | ) const
|
|---|
| 689 | {
|
|---|
| 690 | // Info info(__func__);
|
|---|
| 691 | const double result =
|
|---|
| 692 | 1.
|
|---|
| 693 | + (Helpers::pow(params[c]/params[d], 2))
|
|---|
| 694 | - Helpers::pow(params[c], 2)/(Helpers::pow(params[d], 2) +
|
|---|
| 695 | Helpers::pow(params[h] - function_theta(r_ij, r_ik, r_jk),2));
|
|---|
| 696 |
|
|---|
| 697 | // LOG(2, "DEBUG: function_angle(" << r_ij << "," << r_ik << "," << r_jk << ") = " << result);
|
|---|
| 698 | return result;
|
|---|
| 699 | }
|
|---|
| 700 |
|
|---|
| 701 | FunctionModel::filter_t ManyBodyPotential_Tersoff::getSpecificFilter() const
|
|---|
| 702 | {
|
|---|
| 703 | FunctionModel::filter_t returnfunction =
|
|---|
| 704 | boost::bind(&Extractors::filterArgumentsByParticleTypes,
|
|---|
| 705 | _1,
|
|---|
| 706 | getParticleTypes());
|
|---|
| 707 | return returnfunction;
|
|---|
| 708 | }
|
|---|
| 709 |
|
|---|
| 710 | void
|
|---|
| 711 | ManyBodyPotential_Tersoff::setParametersToRandomInitialValues(
|
|---|
| 712 | const TrainingData &data)
|
|---|
| 713 | {
|
|---|
| 714 | RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
|
|---|
| 715 | const double rng_min = random.min();
|
|---|
| 716 | const double rng_max = random.max();
|
|---|
| 717 | // params[ManyBodyPotential_Tersoff::R] = 1./AtomicLengthToAngstroem;
|
|---|
| 718 | // params[ManyBodyPotential_Tersoff::S] = 2./AtomicLengthToAngstroem;
|
|---|
| 719 | params[ManyBodyPotential_Tersoff::A] = 1e+4*(random()/(rng_max-rng_min));//1.393600e+03;
|
|---|
| 720 | params[ManyBodyPotential_Tersoff::B] = 1e+4*(random()/(rng_max-rng_min));//3.467000e+02;
|
|---|
| 721 | params[ManyBodyPotential_Tersoff::lambda] = 1e+1*(random()/(rng_max-rng_min));//3.487900e+00;
|
|---|
| 722 | params[ManyBodyPotential_Tersoff::mu] = 1e+1*(random()/(rng_max-rng_min));//2.211900e+00;
|
|---|
| 723 | // params[ManyBodyPotential_Tersoff::lambda3] = 0.;
|
|---|
| 724 | // params[ManyBodyPotential_Tersoff::alpha] = 0.;
|
|---|
| 725 | params[ManyBodyPotential_Tersoff::beta] = 1e-1*(random()/(rng_max-rng_min));//1.572400e-07;
|
|---|
| 726 | // params[ManyBodyPotential_Tersoff::chi] = 1.;
|
|---|
| 727 | // params[ManyBodyPotential_Tersoff::omega] = 1.;
|
|---|
| 728 | params[ManyBodyPotential_Tersoff::n] = 1e+1*(random()/(rng_max-rng_min));//7.275100e-01;
|
|---|
| 729 | params[ManyBodyPotential_Tersoff::c] = 1e+1*(random()/(rng_max-rng_min));//3.804900e+04;
|
|---|
| 730 | params[ManyBodyPotential_Tersoff::d] = 1e+1*(random()/(rng_max-rng_min));//4.384000e+00;
|
|---|
| 731 | params[ManyBodyPotential_Tersoff::h] = 1e+1*(random()/(rng_max-rng_min));//-5.705800e-01;
|
|---|
| 732 | }
|
|---|
| 733 |
|
|---|