| [610c11] | 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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| [acc9b1] | 5 | * Copyright (C)  2013 Frederik Heber. All rights reserved. | 
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| [610c11] | 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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| [ed2551] | 42 | #include <boost/assign/list_of.hpp> // for 'map_list_of()' | 
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| [610c11] | 43 | #include <boost/bind.hpp> | 
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|  | 44 | #include <cmath> | 
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| [ed2551] | 45 | #include <string> | 
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| [610c11] | 46 |  | 
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|  | 47 | #include "CodePatterns/Assert.hpp" | 
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| [ffc368] | 48 | //#include "CodePatterns/Info.hpp" | 
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| [f904d5] | 49 | #include "CodePatterns/Log.hpp" | 
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| [610c11] | 50 |  | 
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| [7b019a] | 51 | #include "FunctionApproximation/Extractors.hpp" | 
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| [d52819] | 52 | #include "FunctionApproximation/TrainingData.hpp" | 
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| [610c11] | 53 | #include "Potentials/helpers.hpp" | 
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| [94453f1] | 54 | #include "Potentials/InternalCoordinates/OneBody_Constant.hpp" | 
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| [b760bc3] | 55 | #include "Potentials/ParticleTypeCheckers.hpp" | 
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| [0932c2] | 56 | #include "RandomNumbers/RandomNumberGeneratorFactory.hpp" | 
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|  | 57 | #include "RandomNumbers/RandomNumberGenerator.hpp" | 
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| [610c11] | 58 |  | 
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| [7b019a] | 59 | class Fragment; | 
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|  | 60 |  | 
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| [ed2551] | 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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| [94453f1] | 82 | Coordinator::ptr ManyBodyPotential_Tersoff::coordinator(new OneBody_Constant()); | 
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| [ed2551] | 83 |  | 
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| [713888] | 84 | ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff() : | 
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|  | 85 | EmpiricalPotential(), | 
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| [a82d33] | 86 | params(parameters_t(MAXPARAMS, 0.)), | 
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| [713888] | 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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| [e7579e] | 96 | ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff( | 
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| [775dd1a] | 97 | const ParticleTypes_t &_ParticleTypes | 
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| [e7579e] | 98 | ) : | 
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| [fdd23a] | 99 | EmpiricalPotential(_ParticleTypes), | 
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| [e7579e] | 100 | params(parameters_t(MAXPARAMS, 0.)), | 
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| [752dc7] | 101 | R(3.2), | 
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|  | 102 | S(3.5), | 
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| [990a62] | 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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| [775dd1a] | 107 | triplefunction(&Helpers::NoOp_Triplefunction) | 
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| [dbf8c8] | 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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| [e7579e] | 120 |  | 
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|  | 121 | ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff( | 
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| [ed2551] | 122 | const ParticleTypes_t &_ParticleTypes, | 
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| [ffc368] | 123 | const double &_R, | 
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|  | 124 | const double &_S, | 
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| [e7579e] | 125 | const double &_A, | 
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|  | 126 | const double &_B, | 
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| [ffc368] | 127 | const double &_lambda, | 
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|  | 128 | const double &_mu, | 
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| [e7579e] | 129 | const double &_lambda3, | 
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|  | 130 | const double &_alpha, | 
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|  | 131 | const double &_beta, | 
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| [ffc368] | 132 | const double &_chi, | 
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|  | 133 | const double &_omega, | 
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| [e7579e] | 134 | const double &_n, | 
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|  | 135 | const double &_c, | 
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|  | 136 | const double &_d, | 
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| [b15ae7] | 137 | const double &_h) : | 
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| [fdd23a] | 138 | EmpiricalPotential(_ParticleTypes), | 
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| [e7579e] | 139 | params(parameters_t(MAXPARAMS, 0.)), | 
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| [752dc7] | 140 | R(_R), | 
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|  | 141 | S(_S), | 
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| [990a62] | 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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| [775dd1a] | 146 | triplefunction(&Helpers::NoOp_Triplefunction) | 
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| [e7579e] | 147 | { | 
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| [ffc368] | 148 | //  Info info(__func__); | 
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| [752dc7] | 149 | //  R = _R; | 
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|  | 150 | //  S = _S; | 
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| [e7579e] | 151 | params[A] = _A; | 
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|  | 152 | params[B] = _B; | 
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| [ffc368] | 153 | params[lambda] = _lambda; | 
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|  | 154 | params[mu] = _mu; | 
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| [990a62] | 155 | //  lambda3 = _lambda3; | 
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|  | 156 | //  alpha = _alpha; | 
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| [e7579e] | 157 | params[beta] = _beta; | 
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| [990a62] | 158 | //  chi = _chi; | 
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|  | 159 | //  omega = _omega; | 
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| [e7579e] | 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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| [086070] | 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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| [4f82f8] | 184 | ManyBodyPotential_Tersoff::results_t | 
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| [610c11] | 185 | ManyBodyPotential_Tersoff::operator()( | 
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|  | 186 | const arguments_t &arguments | 
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|  | 187 | ) const | 
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|  | 188 | { | 
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| [ffc368] | 189 | //  Info info(__func__); | 
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| [2e9486] | 190 | double result = 0.; | 
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|  | 191 | for(arguments_t::const_iterator argiter = arguments.begin(); | 
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|  | 192 | argiter != arguments.end(); | 
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|  | 193 | ++argiter) { | 
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|  | 194 | const argument_t &r_ij = *argiter; | 
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| [b760bc3] | 195 | ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes( | 
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|  | 196 | arguments_t(1, r_ij), getParticleTypes()), | 
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|  | 197 | "ManyBodyPotential_Tersoff::operator() - types don't match with ones in arguments."); | 
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|  | 198 |  | 
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| [2e9486] | 199 | const double cutoff = function_cutoff(r_ij.distance); | 
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|  | 200 | const double temp = (cutoff == 0.) ? | 
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|  | 201 | 0. : | 
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|  | 202 | cutoff * ( | 
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|  | 203 | function_prefactor( | 
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|  | 204 | alpha, | 
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|  | 205 | function_eta(r_ij)) | 
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|  | 206 | * function_smoother( | 
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|  | 207 | params[A], | 
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|  | 208 | params[lambda], | 
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|  | 209 | r_ij.distance) | 
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|  | 210 | + | 
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|  | 211 | function_prefactor( | 
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|  | 212 | params[beta], | 
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|  | 213 | function_zeta(r_ij)) | 
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|  | 214 | * function_smoother( | 
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|  | 215 | -params[B], | 
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|  | 216 | params[mu], | 
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|  | 217 | r_ij.distance) | 
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|  | 218 | ); | 
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|  | 219 | result += temp; | 
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|  | 220 | } | 
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| [ffc368] | 221 | //  LOG(2, "DEBUG: operator()(" << r_ij.distance << ") = " << result); | 
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| [b15ae7] | 222 | return std::vector<result_t>(1, result); | 
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| [610c11] | 223 | } | 
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|  | 224 |  | 
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| [ffc368] | 225 | ManyBodyPotential_Tersoff::derivative_components_t | 
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|  | 226 | ManyBodyPotential_Tersoff::derivative( | 
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|  | 227 | const arguments_t &arguments | 
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|  | 228 | ) const | 
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|  | 229 | { | 
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|  | 230 | //  Info info(__func__); | 
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|  | 231 | return ManyBodyPotential_Tersoff::derivative_components_t(); | 
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|  | 232 | } | 
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|  | 233 |  | 
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|  | 234 | ManyBodyPotential_Tersoff::results_t | 
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|  | 235 | ManyBodyPotential_Tersoff::parameter_derivative( | 
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|  | 236 | const arguments_t &arguments, | 
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|  | 237 | const size_t index | 
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|  | 238 | ) const | 
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|  | 239 | { | 
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|  | 240 | //  Info info(__func__); | 
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|  | 241 | //  ASSERT( arguments.size() == 1, | 
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| [2e9486] | 242 | //      "ManyBodyPotential_Tersoff::parameter_derivative() - requires exactly one argument."); | 
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| [56c5de4] | 243 |  | 
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| [2e9486] | 244 | double result = 0.; | 
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|  | 245 | for(arguments_t::const_iterator argiter = arguments.begin(); | 
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|  | 246 | argiter != arguments.end(); | 
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|  | 247 | ++argiter) { | 
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|  | 248 | const argument_t &r_ij = *argiter; | 
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| [b760bc3] | 249 | ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes( | 
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|  | 250 | arguments_t(1, r_ij), getParticleTypes()), | 
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|  | 251 | "ManyBodyPotential_Tersoff::operator() - types don't match with ones in arguments."); | 
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| [55fe788] | 252 |  | 
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| [ffc368] | 253 | switch (index) { | 
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| [752dc7] | 254 | //    case R: | 
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|  | 255 | //    { | 
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| [2e9486] | 256 | //      result += 0.; | 
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| [752dc7] | 257 | //      break; | 
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|  | 258 | //    } | 
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|  | 259 | //    case S: | 
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|  | 260 | //    { | 
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| [2e9486] | 261 | //      result += 0.; | 
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| [752dc7] | 262 | //      break; | 
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|  | 263 | //    } | 
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| [ffc368] | 264 | case A: | 
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|  | 265 | { | 
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| [ca8d82] | 266 | const double cutoff = function_cutoff(r_ij.distance); | 
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| [2e9486] | 267 | result += (cutoff == 0.) ? | 
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| [ca8d82] | 268 | 0. : | 
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|  | 269 | cutoff * | 
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|  | 270 | function_prefactor( | 
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|  | 271 | alpha, | 
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|  | 272 | function_eta(r_ij)) | 
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|  | 273 | * function_smoother( | 
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|  | 274 | 1., | 
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|  | 275 | params[lambda], | 
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|  | 276 | r_ij.distance); | 
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|  | 277 | //          cutoff * 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[mu], | 
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|  | 283 | //              r_ij.distance); | 
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| [ffc368] | 284 | break; | 
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|  | 285 | } | 
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|  | 286 | case B: | 
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|  | 287 | { | 
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| [ca8d82] | 288 | const double cutoff = function_cutoff(r_ij.distance); | 
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| [2e9486] | 289 | result += (cutoff == 0.) ? | 
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| [ca8d82] | 290 | 0. : | 
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|  | 291 | cutoff * function_prefactor( | 
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|  | 292 | params[beta], | 
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|  | 293 | function_zeta(r_ij)) | 
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|  | 294 | * function_smoother( | 
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|  | 295 | -1., | 
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|  | 296 | params[mu], | 
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|  | 297 | r_ij.distance); | 
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|  | 298 | //          cutoff * function_prefactor( | 
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|  | 299 | //              beta, | 
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|  | 300 | //              function_zeta(r_ij)) | 
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|  | 301 | //          * function_smoother( | 
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|  | 302 | //              -params[B], | 
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|  | 303 | //              params[mu], | 
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|  | 304 | //              r_ij.distance)/params[B]; | 
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| [ffc368] | 305 | break; | 
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|  | 306 | } | 
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|  | 307 | case lambda: | 
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|  | 308 | { | 
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|  | 309 | const double cutoff = function_cutoff(r_ij.distance); | 
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| [2e9486] | 310 | result += (cutoff == 0.) ? | 
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| [ffc368] | 311 | 0. : | 
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| [ca8d82] | 312 | -r_ij.distance * cutoff * | 
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|  | 313 | function_prefactor( | 
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|  | 314 | alpha, | 
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|  | 315 | function_eta(r_ij)) | 
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|  | 316 | * function_smoother( | 
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|  | 317 | params[A], | 
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|  | 318 | params[lambda], | 
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|  | 319 | r_ij.distance); | 
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| [ffc368] | 320 | break; | 
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|  | 321 | } | 
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|  | 322 | case mu: | 
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|  | 323 | { | 
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|  | 324 | const double cutoff = function_cutoff(r_ij.distance); | 
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| [2e9486] | 325 | result += (cutoff == 0.) ? | 
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| [ffc368] | 326 | 0. : | 
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| [f904d5] | 327 | -r_ij.distance * cutoff *( | 
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| [ffc368] | 328 | function_prefactor( | 
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|  | 329 | params[beta], | 
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|  | 330 | function_zeta(r_ij)) | 
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|  | 331 | * function_smoother( | 
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|  | 332 | -params[B], | 
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|  | 333 | params[mu], | 
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|  | 334 | r_ij.distance) | 
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|  | 335 | ); | 
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|  | 336 | break; | 
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|  | 337 | } | 
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| [990a62] | 338 | //    case lambda3: | 
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|  | 339 | //    { | 
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| [2e9486] | 340 | //      result += 0.; | 
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| [990a62] | 341 | //      break; | 
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|  | 342 | //    } | 
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|  | 343 | //    case alpha: | 
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|  | 344 | //    { | 
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|  | 345 | //      const double temp = | 
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|  | 346 | //          pow(alpha*function_eta(r_ij), params[n]); | 
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|  | 347 | //      const double cutoff = function_cutoff(r_ij.distance); | 
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| [2e9486] | 348 | //      result += (cutoff == 0.) || (alpha == 0. )? | 
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| [990a62] | 349 | //          0. : | 
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|  | 350 | //          function_smoother( | 
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| [ca8d82] | 351 | //              params[A], | 
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| [990a62] | 352 | //              params[lambda], | 
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|  | 353 | //              r_ij.distance) | 
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|  | 354 | //          * (-.5) * alpha * (temp/alpha) | 
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|  | 355 | //          / (1. + temp) | 
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|  | 356 | //          ; | 
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|  | 357 | //      break; | 
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|  | 358 | //    } | 
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|  | 359 | //    case chi: | 
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|  | 360 | //    { | 
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| [2e9486] | 361 | //      result += 0.; | 
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| [990a62] | 362 | //      break; | 
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|  | 363 | //    } | 
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|  | 364 | //    case omega: | 
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|  | 365 | //    { | 
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| [2e9486] | 366 | //      result += 0.; | 
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| [990a62] | 367 | //      break; | 
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|  | 368 | //    } | 
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| [ffc368] | 369 | case beta: | 
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|  | 370 | { | 
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|  | 371 | const double temp = | 
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|  | 372 | pow(params[beta]*function_zeta(r_ij), params[n]); | 
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|  | 373 | const double cutoff = function_cutoff(r_ij.distance); | 
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| [2e9486] | 374 | result += (cutoff == 0.) || (params[beta] == 0. )? | 
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| [ffc368] | 375 | 0. : cutoff * | 
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|  | 376 | function_smoother( | 
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|  | 377 | -params[B], | 
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|  | 378 | params[mu], | 
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|  | 379 | r_ij.distance) | 
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| [f904d5] | 380 | * (-.5) | 
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|  | 381 | * function_prefactor( | 
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|  | 382 | params[beta], | 
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|  | 383 | function_zeta(r_ij)) | 
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|  | 384 | * (temp/params[beta]) | 
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| [ffc368] | 385 | / (1. + temp) | 
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|  | 386 | ; | 
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|  | 387 | break; | 
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|  | 388 | } | 
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|  | 389 | case n: | 
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|  | 390 | { | 
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| [bc55c9] | 391 | const double zeta = function_zeta(r_ij); | 
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|  | 392 | const double temp = pow( params[beta]*zeta , params[n]); | 
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| [ffc368] | 393 | const double cutoff = function_cutoff(r_ij.distance); | 
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| [bc55c9] | 394 | const double tempres = ((cutoff == 0.) || (zeta == 0.)) ? // zeta must be caught if zero due to log | 
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| [f904d5] | 395 | 0. : .5 * cutoff * | 
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| [ffc368] | 396 | function_smoother( | 
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|  | 397 | -params[B], | 
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|  | 398 | params[mu], | 
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|  | 399 | r_ij.distance) | 
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| [f904d5] | 400 | * function_prefactor( | 
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|  | 401 | params[beta], | 
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|  | 402 | function_zeta(r_ij)) | 
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| [ffc368] | 403 | * ( log(1.+temp)/(params[n]*params[n]) - temp | 
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|  | 404 | * (log(function_zeta(r_ij)) + log(params[beta])) | 
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|  | 405 | /(params[n]*(1.+temp))) | 
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|  | 406 | ; | 
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| [bc55c9] | 407 | //      if (tempres != tempres) | 
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|  | 408 | //      LOG(2, "DEBUG: tempres is NaN."); | 
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|  | 409 | //      LOG(2, "DEBUG: Adding " << tempres << " for p.d. w.r.t n, temp=" << temp << ", cutoff=" << cutoff); | 
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|  | 410 | result += tempres; | 
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| [ffc368] | 411 | break; | 
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|  | 412 | } | 
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|  | 413 | case c: | 
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|  | 414 | { | 
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| [f904d5] | 415 | const double zeta = function_zeta(r_ij); | 
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| [ca8d82] | 416 | if (zeta == 0.) | 
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|  | 417 | break; | 
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| [f904d5] | 418 | const double temp = | 
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| [ca8d82] | 419 | pow(zeta, params[n]-1.) * pow(params[beta],params[n]); | 
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| [f904d5] | 420 | const double cutoff = function_cutoff(r_ij.distance); | 
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| [2e9486] | 421 | const double tempres = (cutoff == 0.) ? | 
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| [ca8d82] | 422 | 0. : cutoff * | 
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| [f904d5] | 423 | function_smoother( | 
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|  | 424 | -params[B], | 
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|  | 425 | params[mu], | 
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|  | 426 | r_ij.distance) | 
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|  | 427 | * function_prefactor( | 
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|  | 428 | params[beta], | 
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|  | 429 | zeta) | 
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| [ca8d82] | 430 | * (-1.) * temp / (1.+temp*zeta); | 
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|  | 431 | double factor = function_derivative_c(r_ij); | 
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| [2e9486] | 432 | result += tempres*factor; | 
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| [bc55c9] | 433 | if (result != result) | 
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|  | 434 | ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor); | 
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| [ffc368] | 435 | break; | 
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|  | 436 | } | 
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|  | 437 | case d: | 
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|  | 438 | { | 
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| [f904d5] | 439 | const double zeta = function_zeta(r_ij); | 
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|  | 440 | const double temp = | 
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| [ca8d82] | 441 | pow(zeta, params[n]-1.) * pow(params[beta],params[n]); | 
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| [f904d5] | 442 | const double cutoff = function_cutoff(r_ij.distance); | 
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| [2e9486] | 443 | const double tempres = (cutoff == 0.) ? | 
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| [ca8d82] | 444 | 0. : cutoff * | 
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| [f904d5] | 445 | function_smoother( | 
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|  | 446 | -params[B], | 
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|  | 447 | params[mu], | 
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|  | 448 | r_ij.distance) | 
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|  | 449 | * function_prefactor( | 
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|  | 450 | params[beta], | 
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|  | 451 | zeta) | 
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| [ca8d82] | 452 | * (-1.) * temp / (1.+temp*zeta); | 
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|  | 453 | double factor = function_derivative_d(r_ij); | 
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| [2e9486] | 454 | result += tempres*factor; | 
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| [bc55c9] | 455 | if (result != result) | 
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|  | 456 | ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor); | 
|---|
| [ffc368] | 457 | break; | 
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|  | 458 | } | 
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|  | 459 | case h: | 
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|  | 460 | { | 
|---|
| [f904d5] | 461 | const double zeta = function_zeta(r_ij); | 
|---|
|  | 462 | const double temp = | 
|---|
| [ca8d82] | 463 | pow(zeta, params[n]-1.) * pow(params[beta],params[n]); | 
|---|
| [f904d5] | 464 | const double cutoff = function_cutoff(r_ij.distance); | 
|---|
| [2e9486] | 465 | const double tempres = (cutoff == 0.) ? | 
|---|
| [ca8d82] | 466 | 0. : cutoff * | 
|---|
| [f904d5] | 467 | function_smoother( | 
|---|
|  | 468 | -params[B], | 
|---|
|  | 469 | params[mu], | 
|---|
|  | 470 | r_ij.distance) | 
|---|
|  | 471 | * function_prefactor( | 
|---|
|  | 472 | params[beta], | 
|---|
|  | 473 | zeta) | 
|---|
| [ca8d82] | 474 | * (-1.) * temp / (1.+temp*zeta); | 
|---|
|  | 475 | double factor = function_derivative_h(r_ij); | 
|---|
| [2e9486] | 476 | result += tempres*factor; | 
|---|
| [bc55c9] | 477 | if (result != result) | 
|---|
|  | 478 | ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor); | 
|---|
| [ffc368] | 479 | break; | 
|---|
|  | 480 | } | 
|---|
|  | 481 | default: | 
|---|
| [b15ae7] | 482 | ASSERT(0, "ManyBodyPotential_Tersoff::parameter_derivative() - derivative to unknown parameter desired."); | 
|---|
| [ffc368] | 483 | break; | 
|---|
|  | 484 | } | 
|---|
| [bc55c9] | 485 | if (result != result) | 
|---|
|  | 486 | ELOG(1, "result is NaN."); | 
|---|
| [2e9486] | 487 | } | 
|---|
|  | 488 | return results_t(1,-result); | 
|---|
| [ffc368] | 489 | } | 
|---|
|  | 490 |  | 
|---|
| [ca8d82] | 491 | ManyBodyPotential_Tersoff::result_t | 
|---|
|  | 492 | ManyBodyPotential_Tersoff::function_derivative_c( | 
|---|
|  | 493 | const argument_t &r_ij | 
|---|
|  | 494 | ) const | 
|---|
|  | 495 | { | 
|---|
|  | 496 | double result = 0.; | 
|---|
|  | 497 | std::vector<arguments_t> triples = triplefunction(r_ij, S); | 
|---|
|  | 498 | for (std::vector<arguments_t>::const_iterator iter = triples.begin(); | 
|---|
|  | 499 | iter != triples.end(); ++iter) { | 
|---|
|  | 500 | ASSERT( iter->size() == 2, | 
|---|
|  | 501 | "ManyBodyPotential_Tersoff::function_derivative_c() - the triples result must contain exactly two distances."); | 
|---|
|  | 502 | const argument_t &r_ik = (*iter)[0]; | 
|---|
|  | 503 | const argument_t &r_jk = (*iter)[1]; | 
|---|
|  | 504 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance); | 
|---|
|  | 505 | const double cutoff = function_cutoff(r_ik.distance); | 
|---|
|  | 506 | result += (cutoff == 0.) ? | 
|---|
|  | 507 | 0. : cutoff * omega * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * ( | 
|---|
|  | 508 | params[c]/Helpers::pow(params[d],2) | 
|---|
|  | 509 | - params[c] / ( Helpers::pow(params[d],2) + Helpers::pow(tempangle,2) ) | 
|---|
|  | 510 | ); | 
|---|
|  | 511 | } | 
|---|
|  | 512 | return result; | 
|---|
|  | 513 | } | 
|---|
|  | 514 |  | 
|---|
|  | 515 | ManyBodyPotential_Tersoff::result_t | 
|---|
|  | 516 | ManyBodyPotential_Tersoff::function_derivative_d( | 
|---|
|  | 517 | const argument_t &r_ij | 
|---|
|  | 518 | ) const | 
|---|
|  | 519 | { | 
|---|
|  | 520 | double result = 0.; | 
|---|
|  | 521 | std::vector<arguments_t> triples = triplefunction(r_ij, S); | 
|---|
|  | 522 | for (std::vector<arguments_t>::const_iterator iter = triples.begin(); | 
|---|
|  | 523 | iter != triples.end(); ++iter) { | 
|---|
|  | 524 | ASSERT( iter->size() == 2, | 
|---|
|  | 525 | "ManyBodyPotential_Tersoff::function_derivative_d() - the triples result must contain exactly two distances."); | 
|---|
|  | 526 | const argument_t &r_ik = (*iter)[0]; | 
|---|
|  | 527 | const argument_t &r_jk = (*iter)[1]; | 
|---|
|  | 528 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance); | 
|---|
|  | 529 | const double cutoff = function_cutoff(r_ik.distance); | 
|---|
|  | 530 | result += (cutoff == 0.) ? | 
|---|
|  | 531 | 0. : cutoff * omega  * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * ( | 
|---|
|  | 532 | - Helpers::pow(params[c],2)/Helpers::pow(params[d],3) | 
|---|
|  | 533 | + Helpers::pow(params[c],2) * params[d] | 
|---|
|  | 534 | / Helpers::pow(Helpers::pow(params[d],2) + Helpers::pow(tempangle,2),2) | 
|---|
|  | 535 | ); | 
|---|
|  | 536 | } | 
|---|
|  | 537 | return result; | 
|---|
|  | 538 | } | 
|---|
|  | 539 |  | 
|---|
|  | 540 | ManyBodyPotential_Tersoff::result_t | 
|---|
|  | 541 | ManyBodyPotential_Tersoff::function_derivative_h( | 
|---|
|  | 542 | const argument_t &r_ij | 
|---|
|  | 543 | ) const | 
|---|
|  | 544 | { | 
|---|
|  | 545 | double result = 0.; | 
|---|
|  | 546 | std::vector<arguments_t> triples = triplefunction(r_ij, S); | 
|---|
|  | 547 | for (std::vector<arguments_t>::const_iterator iter = triples.begin(); | 
|---|
|  | 548 | iter != triples.end(); ++iter) { | 
|---|
|  | 549 | ASSERT( iter->size() == 2, | 
|---|
|  | 550 | "ManyBodyPotential_Tersoff::function_derivative_h() - the triples result must contain exactly two distances."); | 
|---|
|  | 551 | const argument_t &r_ik = (*iter)[0]; | 
|---|
|  | 552 | const argument_t &r_jk = (*iter)[1]; | 
|---|
|  | 553 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance); | 
|---|
|  | 554 | const double cutoff = function_cutoff(r_ik.distance); | 
|---|
|  | 555 | result += (cutoff == 0.) ? | 
|---|
|  | 556 | 0. : cutoff * omega  * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * ( | 
|---|
|  | 557 | ( Helpers::pow(params[c],2)*tempangle ) | 
|---|
|  | 558 | / Helpers::pow(Helpers::pow(params[d],2) + Helpers::pow(tempangle,2),2) | 
|---|
|  | 559 | ); | 
|---|
|  | 560 | } | 
|---|
|  | 561 | return result; | 
|---|
|  | 562 | } | 
|---|
|  | 563 |  | 
|---|
| [4f82f8] | 564 | ManyBodyPotential_Tersoff::result_t | 
|---|
| [610c11] | 565 | ManyBodyPotential_Tersoff::function_cutoff( | 
|---|
|  | 566 | const double &distance | 
|---|
|  | 567 | ) const | 
|---|
|  | 568 | { | 
|---|
| [ffc368] | 569 | //  Info info(__func__); | 
|---|
|  | 570 | double result = 0.; | 
|---|
| [752dc7] | 571 | if (distance < R) | 
|---|
| [ffc368] | 572 | result = 1.; | 
|---|
| [752dc7] | 573 | else if (distance > S) | 
|---|
| [ffc368] | 574 | result = 0.; | 
|---|
| [610c11] | 575 | else { | 
|---|
| [752dc7] | 576 | result = (0.5 + 0.5 * cos( M_PI * (distance - R)/(S-R))); | 
|---|
| [610c11] | 577 | } | 
|---|
| [ffc368] | 578 | //  LOG(2, "DEBUG: function_cutoff(" << distance << ") = " << result); | 
|---|
|  | 579 | return result; | 
|---|
| [610c11] | 580 | } | 
|---|
|  | 581 |  | 
|---|
| [4f82f8] | 582 | ManyBodyPotential_Tersoff::result_t | 
|---|
| [610c11] | 583 | ManyBodyPotential_Tersoff::function_prefactor( | 
|---|
|  | 584 | const double &alpha, | 
|---|
| [ffc368] | 585 | const double &eta | 
|---|
| [610c11] | 586 | ) const | 
|---|
|  | 587 | { | 
|---|
| [ffc368] | 588 | //  Info info(__func__); | 
|---|
| [990a62] | 589 | const double result = chi * pow( | 
|---|
| [ffc368] | 590 | (1. + pow(alpha * eta, params[n])), | 
|---|
|  | 591 | -1./(2.*params[n])); | 
|---|
|  | 592 | //  LOG(2, "DEBUG: function_prefactor(" << alpha << "," << eta << ") = " << result); | 
|---|
|  | 593 | return result; | 
|---|
|  | 594 | } | 
|---|
|  | 595 |  | 
|---|
|  | 596 | ManyBodyPotential_Tersoff::result_t | 
|---|
|  | 597 | ManyBodyPotential_Tersoff::function_smoother( | 
|---|
|  | 598 | const double &prefactor, | 
|---|
|  | 599 | const double &lambda, | 
|---|
|  | 600 | const double &distance | 
|---|
|  | 601 | ) const | 
|---|
|  | 602 | { | 
|---|
|  | 603 | //  Info info(__func__); | 
|---|
|  | 604 | const double result = prefactor * exp(-lambda * distance); | 
|---|
|  | 605 | //  LOG(2, "DEBUG: function_smoother(" << prefactor << "," << lambda << "," << distance << ") = " << result); | 
|---|
|  | 606 | return result; | 
|---|
| [610c11] | 607 | } | 
|---|
|  | 608 |  | 
|---|
| [4f82f8] | 609 | ManyBodyPotential_Tersoff::result_t | 
|---|
| [610c11] | 610 | ManyBodyPotential_Tersoff::function_eta( | 
|---|
|  | 611 | const argument_t &r_ij | 
|---|
|  | 612 | ) const | 
|---|
|  | 613 | { | 
|---|
| [ffc368] | 614 | //  Info info(__func__); | 
|---|
| [610c11] | 615 | result_t result = 0.; | 
|---|
|  | 616 |  | 
|---|
|  | 617 | // get all triples within the cutoff | 
|---|
| [752dc7] | 618 | std::vector<arguments_t> triples = triplefunction(r_ij, S); | 
|---|
| [610c11] | 619 | for (std::vector<arguments_t>::const_iterator iter = triples.begin(); | 
|---|
|  | 620 | iter != triples.end(); ++iter) { | 
|---|
|  | 621 | ASSERT( iter->size() == 2, | 
|---|
|  | 622 | "ManyBodyPotential_Tersoff::function_zeta() - the triples result must contain of exactly two distances."); | 
|---|
|  | 623 | const argument_t &r_ik = (*iter)[0]; | 
|---|
|  | 624 | result += function_cutoff(r_ik.distance) | 
|---|
| [990a62] | 625 | * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)); | 
|---|
| [610c11] | 626 | } | 
|---|
|  | 627 |  | 
|---|
| [ffc368] | 628 | //  LOG(2, "DEBUG: function_eta(" << r_ij.distance << ") = " << result); | 
|---|
| [610c11] | 629 | return result; | 
|---|
|  | 630 | } | 
|---|
|  | 631 |  | 
|---|
| [4f82f8] | 632 | ManyBodyPotential_Tersoff::result_t | 
|---|
| [610c11] | 633 | ManyBodyPotential_Tersoff::function_zeta( | 
|---|
|  | 634 | const argument_t &r_ij | 
|---|
|  | 635 | ) const | 
|---|
|  | 636 | { | 
|---|
| [ffc368] | 637 | //  Info info(__func__); | 
|---|
| [610c11] | 638 | result_t result = 0.; | 
|---|
|  | 639 |  | 
|---|
|  | 640 | // get all triples within the cutoff | 
|---|
| [752dc7] | 641 | std::vector<arguments_t> triples = triplefunction(r_ij, S); | 
|---|
| [610c11] | 642 | for (std::vector<arguments_t>::const_iterator iter = triples.begin(); | 
|---|
|  | 643 | iter != triples.end(); ++iter) { | 
|---|
|  | 644 | ASSERT( iter->size() == 2, | 
|---|
|  | 645 | "ManyBodyPotential_Tersoff::function_zeta() - the triples result must contain exactly two distances."); | 
|---|
|  | 646 | const argument_t &r_ik = (*iter)[0]; | 
|---|
|  | 647 | const argument_t &r_jk = (*iter)[1]; | 
|---|
|  | 648 | result += | 
|---|
|  | 649 | function_cutoff(r_ik.distance) | 
|---|
| [990a62] | 650 | * omega | 
|---|
| [610c11] | 651 | * function_angle(r_ij.distance, r_ik.distance, r_jk.distance) | 
|---|
| [990a62] | 652 | * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)); | 
|---|
| [610c11] | 653 | } | 
|---|
|  | 654 |  | 
|---|
| [ffc368] | 655 | //  LOG(2, "DEBUG: function_zeta(" << r_ij.distance << ") = " << result); | 
|---|
| [610c11] | 656 | return result; | 
|---|
|  | 657 | } | 
|---|
|  | 658 |  | 
|---|
| [4f82f8] | 659 | ManyBodyPotential_Tersoff::result_t | 
|---|
| [f904d5] | 660 | ManyBodyPotential_Tersoff::function_theta( | 
|---|
| [610c11] | 661 | const double &r_ij, | 
|---|
|  | 662 | const double &r_ik, | 
|---|
|  | 663 | const double &r_jk | 
|---|
|  | 664 | ) const | 
|---|
|  | 665 | { | 
|---|
|  | 666 | const double angle = Helpers::pow(r_ij,2) + Helpers::pow(r_ik,2) - Helpers::pow(r_jk,2); | 
|---|
| [ffc368] | 667 | const double divisor = 2.* r_ij * r_ik; | 
|---|
|  | 668 | if (divisor != 0.) { | 
|---|
| [f904d5] | 669 | LOG(2, "DEBUG: cos(theta)= " << angle/divisor); | 
|---|
|  | 670 | return angle/divisor; | 
|---|
| [ffc368] | 671 | } else | 
|---|
|  | 672 | return 0.; | 
|---|
| [610c11] | 673 | } | 
|---|
| [ffc368] | 674 |  | 
|---|
| [f904d5] | 675 | ManyBodyPotential_Tersoff::result_t | 
|---|
|  | 676 | ManyBodyPotential_Tersoff::function_angle( | 
|---|
|  | 677 | const double &r_ij, | 
|---|
|  | 678 | const double &r_ik, | 
|---|
|  | 679 | const double &r_jk | 
|---|
|  | 680 | ) const | 
|---|
|  | 681 | { | 
|---|
|  | 682 | //  Info info(__func__); | 
|---|
|  | 683 | const double result = | 
|---|
|  | 684 | 1. | 
|---|
|  | 685 | + (Helpers::pow(params[c]/params[d], 2)) | 
|---|
|  | 686 | - Helpers::pow(params[c], 2)/(Helpers::pow(params[d], 2) + | 
|---|
| [ca8d82] | 687 | Helpers::pow(params[h] - function_theta(r_ij, r_ik, r_jk),2)); | 
|---|
| [f904d5] | 688 |  | 
|---|
| [ca8d82] | 689 | //  LOG(2, "DEBUG: function_angle(" << r_ij << "," << r_ik << "," << r_jk << ") = " << result); | 
|---|
| [f904d5] | 690 | return result; | 
|---|
|  | 691 | } | 
|---|
|  | 692 |  | 
|---|
| [7b019a] | 693 | FunctionModel::extractor_t | 
|---|
| [f0025d] | 694 | ManyBodyPotential_Tersoff::getSpecificExtractor() const | 
|---|
| [7b019a] | 695 | { | 
|---|
|  | 696 | FunctionModel::extractor_t returnfunction = | 
|---|
|  | 697 | boost::bind(&Extractors::gatherAllDistances, | 
|---|
|  | 698 | boost::bind(&Fragment::getPositions, _1), | 
|---|
|  | 699 | boost::bind(&Fragment::getCharges, _1), | 
|---|
|  | 700 | _2); | 
|---|
|  | 701 | return returnfunction; | 
|---|
|  | 702 | } | 
|---|
|  | 703 |  | 
|---|
| [0f5d38] | 704 | FunctionModel::filter_t ManyBodyPotential_Tersoff::getSpecificFilter() const | 
|---|
|  | 705 | { | 
|---|
|  | 706 | FunctionModel::filter_t returnfunction = | 
|---|
| [51e0e3] | 707 | boost::bind(&Extractors::filterArgumentsByParticleTypes, | 
|---|
|  | 708 | _1, | 
|---|
|  | 709 | getParticleTypes()); | 
|---|
| [0f5d38] | 710 | return returnfunction; | 
|---|
|  | 711 | } | 
|---|
|  | 712 |  | 
|---|
| [d52819] | 713 | void | 
|---|
|  | 714 | ManyBodyPotential_Tersoff::setParametersToRandomInitialValues( | 
|---|
|  | 715 | const TrainingData &data) | 
|---|
|  | 716 | { | 
|---|
| [0932c2] | 717 | RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator(); | 
|---|
|  | 718 | const double rng_min = random.min(); | 
|---|
|  | 719 | const double rng_max = random.max(); | 
|---|
| [d52819] | 720 | //  params[ManyBodyPotential_Tersoff::R] = 1./AtomicLengthToAngstroem; | 
|---|
|  | 721 | //  params[ManyBodyPotential_Tersoff::S] = 2./AtomicLengthToAngstroem; | 
|---|
| [0932c2] | 722 | params[ManyBodyPotential_Tersoff::A] = 1e+4*(random()/(rng_max-rng_min));//1.393600e+03; | 
|---|
|  | 723 | params[ManyBodyPotential_Tersoff::B] = 1e+4*(random()/(rng_max-rng_min));//3.467000e+02; | 
|---|
|  | 724 | params[ManyBodyPotential_Tersoff::lambda] = 1e+1*(random()/(rng_max-rng_min));//3.487900e+00; | 
|---|
|  | 725 | params[ManyBodyPotential_Tersoff::mu] = 1e+1*(random()/(rng_max-rng_min));//2.211900e+00; | 
|---|
| [d52819] | 726 | //  params[ManyBodyPotential_Tersoff::lambda3] = 0.; | 
|---|
|  | 727 | //  params[ManyBodyPotential_Tersoff::alpha] = 0.; | 
|---|
| [0932c2] | 728 | params[ManyBodyPotential_Tersoff::beta] = 1e-1*(random()/(rng_max-rng_min));//1.572400e-07; | 
|---|
| [d52819] | 729 | //  params[ManyBodyPotential_Tersoff::chi] = 1.; | 
|---|
|  | 730 | //  params[ManyBodyPotential_Tersoff::omega] = 1.; | 
|---|
| [0932c2] | 731 | params[ManyBodyPotential_Tersoff::n] = 1e+1*(random()/(rng_max-rng_min));//7.275100e-01; | 
|---|
|  | 732 | params[ManyBodyPotential_Tersoff::c] = 1e+1*(random()/(rng_max-rng_min));//3.804900e+04; | 
|---|
|  | 733 | params[ManyBodyPotential_Tersoff::d] = 1e+1*(random()/(rng_max-rng_min));//4.384000e+00; | 
|---|
|  | 734 | params[ManyBodyPotential_Tersoff::h] = 1e+1*(random()/(rng_max-rng_min));//-5.705800e-01; | 
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| [d52819] | 735 | } | 
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|  | 736 |  | 
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