| 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], | 
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| 432 | params[mu], | 
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| 433 | r_ij.distance) | 
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| 434 | * function_prefactor( | 
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| 435 | params[beta], | 
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| 436 | zeta) | 
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| 437 | * (-1.) * temp / (1.+temp*zeta); | 
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| 438 | double factor = function_derivative_c(r_ij); | 
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| 439 | result += tempres*factor; | 
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| 440 | if (result != result) | 
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| 441 | ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor); | 
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| 442 | break; | 
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| 443 | } | 
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| 444 | case d: | 
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| 445 | { | 
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| 446 | const double zeta = function_zeta(r_ij); | 
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| 447 | const double temp = | 
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| 448 | pow(zeta, params[n]-1.) * pow(params[beta],params[n]); | 
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| 449 | const double cutoff = function_cutoff(r_ij.distance); | 
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| 450 | const double tempres = (cutoff == 0.) ? | 
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| 451 | 0. : cutoff * | 
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| 452 | function_smoother( | 
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| 453 | -params[B], | 
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| 454 | params[mu], | 
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| 455 | r_ij.distance) | 
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| 456 | * function_prefactor( | 
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| 457 | params[beta], | 
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| 458 | zeta) | 
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| 459 | * (-1.) * temp / (1.+temp*zeta); | 
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| 460 | double factor = function_derivative_d(r_ij); | 
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| 461 | result += tempres*factor; | 
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| 462 | if (result != result) | 
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| 463 | ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor); | 
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| 464 | break; | 
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| 465 | } | 
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| 466 | case h: | 
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| 467 | { | 
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| 468 | const double zeta = function_zeta(r_ij); | 
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| 469 | const double temp = | 
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| 470 | pow(zeta, params[n]-1.) * pow(params[beta],params[n]); | 
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| 471 | const double cutoff = function_cutoff(r_ij.distance); | 
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| 472 | const double tempres = (cutoff == 0.) ? | 
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| 473 | 0. : cutoff * | 
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| 474 | function_smoother( | 
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| 475 | -params[B], | 
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| 476 | params[mu], | 
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| 477 | r_ij.distance) | 
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| 478 | * function_prefactor( | 
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| 479 | params[beta], | 
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| 480 | zeta) | 
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| 481 | * (-1.) * temp / (1.+temp*zeta); | 
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| 482 | double factor = function_derivative_h(r_ij); | 
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| 483 | result += tempres*factor; | 
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| 484 | if (result != result) | 
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| 485 | ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor); | 
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| 486 | break; | 
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| 487 | } | 
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| 488 | default: | 
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| 489 | ASSERT(0, "ManyBodyPotential_Tersoff::parameter_derivative() - derivative to unknown parameter desired."); | 
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| 490 | break; | 
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| 491 | } | 
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| 492 | if (result != result) | 
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| 493 | ELOG(1, "result is NaN."); | 
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| 494 | } | 
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| 495 | } | 
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| 496 | return results_t(1,-result); | 
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| 497 | } | 
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| 498 |  | 
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| 499 | ManyBodyPotential_Tersoff::result_t | 
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| 500 | ManyBodyPotential_Tersoff::function_derivative_c( | 
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| 501 | const argument_t &r_ij | 
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| 502 | ) const | 
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| 503 | { | 
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| 504 | double result = 0.; | 
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| 505 | std::vector<arguments_t> triples = triplefunction(r_ij, S); | 
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| 506 | for (std::vector<arguments_t>::const_iterator iter = triples.begin(); | 
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| 507 | iter != triples.end(); ++iter) { | 
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| 508 | ASSERT( iter->size() == 2, | 
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| 509 | "ManyBodyPotential_Tersoff::function_derivative_c() - the triples result must contain exactly two distances."); | 
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| 510 | const argument_t &r_ik = (*iter)[0]; | 
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| 511 | const argument_t &r_jk = (*iter)[1]; | 
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| 512 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance); | 
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| 513 | const double cutoff = function_cutoff(r_ik.distance); | 
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| 514 | result += (cutoff == 0.) ? | 
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| 515 | 0. : cutoff * omega * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * ( | 
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| 516 | params[c]/Helpers::pow(params[d],2) | 
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| 517 | - params[c] / ( Helpers::pow(params[d],2) + Helpers::pow(tempangle,2) ) | 
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| 518 | ); | 
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| 519 | } | 
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| 520 | return result; | 
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| 521 | } | 
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| 522 |  | 
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| 523 | ManyBodyPotential_Tersoff::result_t | 
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| 524 | ManyBodyPotential_Tersoff::function_derivative_d( | 
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| 525 | const argument_t &r_ij | 
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| 526 | ) const | 
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| 527 | { | 
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| 528 | double result = 0.; | 
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| 529 | std::vector<arguments_t> triples = triplefunction(r_ij, S); | 
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| 530 | for (std::vector<arguments_t>::const_iterator iter = triples.begin(); | 
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| 531 | iter != triples.end(); ++iter) { | 
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| 532 | ASSERT( iter->size() == 2, | 
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| 533 | "ManyBodyPotential_Tersoff::function_derivative_d() - the triples result must contain exactly two distances."); | 
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| 534 | const argument_t &r_ik = (*iter)[0]; | 
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| 535 | const argument_t &r_jk = (*iter)[1]; | 
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| 536 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance); | 
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| 537 | const double cutoff = function_cutoff(r_ik.distance); | 
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| 538 | result += (cutoff == 0.) ? | 
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| 539 | 0. : cutoff * omega  * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * ( | 
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| 540 | - Helpers::pow(params[c],2)/Helpers::pow(params[d],3) | 
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| 541 | + Helpers::pow(params[c],2) * params[d] | 
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| 542 | / Helpers::pow(Helpers::pow(params[d],2) + Helpers::pow(tempangle,2),2) | 
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| 543 | ); | 
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| 544 | } | 
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| 545 | return result; | 
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| 546 | } | 
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| 547 |  | 
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| 548 | ManyBodyPotential_Tersoff::result_t | 
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| 549 | ManyBodyPotential_Tersoff::function_derivative_h( | 
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| 550 | const argument_t &r_ij | 
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| 551 | ) const | 
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| 552 | { | 
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| 553 | double result = 0.; | 
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| 554 | std::vector<arguments_t> triples = triplefunction(r_ij, S); | 
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| 555 | for (std::vector<arguments_t>::const_iterator iter = triples.begin(); | 
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| 556 | iter != triples.end(); ++iter) { | 
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| 557 | ASSERT( iter->size() == 2, | 
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| 558 | "ManyBodyPotential_Tersoff::function_derivative_h() - the triples result must contain exactly two distances."); | 
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| 559 | const argument_t &r_ik = (*iter)[0]; | 
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| 560 | const argument_t &r_jk = (*iter)[1]; | 
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| 561 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance); | 
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| 562 | const double cutoff = function_cutoff(r_ik.distance); | 
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| 563 | result += (cutoff == 0.) ? | 
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| 564 | 0. : cutoff * omega  * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * ( | 
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| 565 | ( Helpers::pow(params[c],2)*tempangle ) | 
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| 566 | / Helpers::pow(Helpers::pow(params[d],2) + Helpers::pow(tempangle,2),2) | 
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| 567 | ); | 
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| 568 | } | 
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| 569 | return result; | 
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| 570 | } | 
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| 571 |  | 
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| 572 | ManyBodyPotential_Tersoff::result_t | 
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| 573 | ManyBodyPotential_Tersoff::function_cutoff( | 
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| 574 | const double &distance | 
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| 575 | ) const | 
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| 576 | { | 
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| 577 | //  Info info(__func__); | 
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| 578 | double result = 0.; | 
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| 579 | if (distance < R) | 
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| 580 | result = 1.; | 
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| 581 | else if (distance > S) | 
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| 582 | result = 0.; | 
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| 583 | else { | 
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| 584 | result = (0.5 + 0.5 * cos( M_PI * (distance - R)/(S-R))); | 
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| 585 | } | 
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| 586 | //  LOG(2, "DEBUG: function_cutoff(" << distance << ") = " << result); | 
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| 587 | return result; | 
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| 588 | } | 
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| 589 |  | 
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| 590 | ManyBodyPotential_Tersoff::result_t | 
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| 591 | ManyBodyPotential_Tersoff::function_prefactor( | 
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| 592 | const double &alpha, | 
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| 593 | const double &eta | 
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| 594 | ) const | 
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| 595 | { | 
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| 596 | //  Info info(__func__); | 
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| 597 | const double result = chi * pow( | 
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| 598 | (1. + pow(alpha * eta, params[n])), | 
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| 599 | -1./(2.*params[n])); | 
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| 600 | //  LOG(2, "DEBUG: function_prefactor(" << alpha << "," << eta << ") = " << result); | 
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| 601 | return result; | 
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| 602 | } | 
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| 603 |  | 
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| 604 | ManyBodyPotential_Tersoff::result_t | 
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| 605 | ManyBodyPotential_Tersoff::function_smoother( | 
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| 606 | const double &prefactor, | 
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| 607 | const double &lambda, | 
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| 608 | const double &distance | 
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| 609 | ) const | 
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| 610 | { | 
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| 611 | //  Info info(__func__); | 
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| 612 | const double result = prefactor * exp(-lambda * distance); | 
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| 613 | //  LOG(2, "DEBUG: function_smoother(" << prefactor << "," << lambda << "," << distance << ") = " << result); | 
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| 614 | return result; | 
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| 615 | } | 
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| 616 |  | 
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| 617 | ManyBodyPotential_Tersoff::result_t | 
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| 618 | ManyBodyPotential_Tersoff::function_eta( | 
|---|
| 619 | const argument_t &r_ij | 
|---|
| 620 | ) const | 
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| 621 | { | 
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| 622 | //  Info info(__func__); | 
|---|
| 623 | result_t result = 0.; | 
|---|
| 624 |  | 
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| 625 | // get all triples within the cutoff | 
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| 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]; | 
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| 632 | result += function_cutoff(r_ik.distance) | 
|---|
| 633 | * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)); | 
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| 634 | } | 
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| 635 |  | 
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| 636 | //  LOG(2, "DEBUG: function_eta(" << r_ij.distance << ") = " << result); | 
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| 637 | return result; | 
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| 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); | 
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| 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]; | 
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| 655 | const argument_t &r_jk = (*iter)[1]; | 
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| 656 | result += | 
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| 657 | function_cutoff(r_ik.distance) | 
|---|
| 658 | * omega | 
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| 659 | * function_angle(r_ij.distance, r_ik.distance, r_jk.distance) | 
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| 660 | * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)); | 
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| 661 | } | 
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| 662 |  | 
|---|
| 663 | //  LOG(2, "DEBUG: function_zeta(" << r_ij.distance << ") = " << result); | 
|---|
| 664 | return result; | 
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| 665 | } | 
|---|
| 666 |  | 
|---|
| 667 | ManyBodyPotential_Tersoff::result_t | 
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| 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 |  | 
|---|