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(Memory::ignore(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)
|
---|
478 | * function_prefactor(
|
---|
479 | params[beta],
|
---|
480 | zeta)
|
---|
481 | * (-1.) * temp / (1.+temp*zeta);
|
---|
482 | double factor = function_derivative_h(r_ij);
|
---|
483 | result += tempres*factor;
|
---|
484 | if (result != result)
|
---|
485 | ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor);
|
---|
486 | break;
|
---|
487 | }
|
---|
488 | default:
|
---|
489 | ASSERT(0, "ManyBodyPotential_Tersoff::parameter_derivative() - derivative to unknown parameter desired.");
|
---|
490 | break;
|
---|
491 | }
|
---|
492 | if (result != result)
|
---|
493 | ELOG(1, "result is NaN.");
|
---|
494 | }
|
---|
495 | }
|
---|
496 | return results_t(1,-result);
|
---|
497 | }
|
---|
498 |
|
---|
499 | ManyBodyPotential_Tersoff::result_t
|
---|
500 | ManyBodyPotential_Tersoff::function_derivative_c(
|
---|
501 | const argument_t &r_ij
|
---|
502 | ) const
|
---|
503 | {
|
---|
504 | double result = 0.;
|
---|
505 | std::vector<arguments_t> triples = triplefunction(r_ij, S);
|
---|
506 | for (std::vector<arguments_t>::const_iterator iter = triples.begin();
|
---|
507 | iter != triples.end(); ++iter) {
|
---|
508 | ASSERT( iter->size() == 2,
|
---|
509 | "ManyBodyPotential_Tersoff::function_derivative_c() - the triples result must contain exactly two distances.");
|
---|
510 | const argument_t &r_ik = (*iter)[0];
|
---|
511 | const argument_t &r_jk = (*iter)[1];
|
---|
512 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance);
|
---|
513 | const double cutoff = function_cutoff(r_ik.distance);
|
---|
514 | result += (cutoff == 0.) ?
|
---|
515 | 0. : cutoff * omega * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * (
|
---|
516 | params[c]/Helpers::pow(params[d],2)
|
---|
517 | - params[c] / ( Helpers::pow(params[d],2) + Helpers::pow(tempangle,2) )
|
---|
518 | );
|
---|
519 | }
|
---|
520 | return result;
|
---|
521 | }
|
---|
522 |
|
---|
523 | ManyBodyPotential_Tersoff::result_t
|
---|
524 | ManyBodyPotential_Tersoff::function_derivative_d(
|
---|
525 | const argument_t &r_ij
|
---|
526 | ) const
|
---|
527 | {
|
---|
528 | double result = 0.;
|
---|
529 | std::vector<arguments_t> triples = triplefunction(r_ij, S);
|
---|
530 | for (std::vector<arguments_t>::const_iterator iter = triples.begin();
|
---|
531 | iter != triples.end(); ++iter) {
|
---|
532 | ASSERT( iter->size() == 2,
|
---|
533 | "ManyBodyPotential_Tersoff::function_derivative_d() - the triples result must contain exactly two distances.");
|
---|
534 | const argument_t &r_ik = (*iter)[0];
|
---|
535 | const argument_t &r_jk = (*iter)[1];
|
---|
536 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance);
|
---|
537 | const double cutoff = function_cutoff(r_ik.distance);
|
---|
538 | result += (cutoff == 0.) ?
|
---|
539 | 0. : cutoff * omega * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * (
|
---|
540 | - Helpers::pow(params[c],2)/Helpers::pow(params[d],3)
|
---|
541 | + Helpers::pow(params[c],2) * params[d]
|
---|
542 | / Helpers::pow(Helpers::pow(params[d],2) + Helpers::pow(tempangle,2),2)
|
---|
543 | );
|
---|
544 | }
|
---|
545 | return result;
|
---|
546 | }
|
---|
547 |
|
---|
548 | ManyBodyPotential_Tersoff::result_t
|
---|
549 | ManyBodyPotential_Tersoff::function_derivative_h(
|
---|
550 | const argument_t &r_ij
|
---|
551 | ) const
|
---|
552 | {
|
---|
553 | double result = 0.;
|
---|
554 | std::vector<arguments_t> triples = triplefunction(r_ij, S);
|
---|
555 | for (std::vector<arguments_t>::const_iterator iter = triples.begin();
|
---|
556 | iter != triples.end(); ++iter) {
|
---|
557 | ASSERT( iter->size() == 2,
|
---|
558 | "ManyBodyPotential_Tersoff::function_derivative_h() - the triples result must contain exactly two distances.");
|
---|
559 | const argument_t &r_ik = (*iter)[0];
|
---|
560 | const argument_t &r_jk = (*iter)[1];
|
---|
561 | const double tempangle = params[h] - function_theta(r_ij.distance, r_ik.distance, r_jk.distance);
|
---|
562 | const double cutoff = function_cutoff(r_ik.distance);
|
---|
563 | result += (cutoff == 0.) ?
|
---|
564 | 0. : cutoff * omega * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3)) * (
|
---|
565 | ( Helpers::pow(params[c],2)*tempangle )
|
---|
566 | / Helpers::pow(Helpers::pow(params[d],2) + Helpers::pow(tempangle,2),2)
|
---|
567 | );
|
---|
568 | }
|
---|
569 | return result;
|
---|
570 | }
|
---|
571 |
|
---|
572 | ManyBodyPotential_Tersoff::result_t
|
---|
573 | ManyBodyPotential_Tersoff::function_cutoff(
|
---|
574 | const double &distance
|
---|
575 | ) const
|
---|
576 | {
|
---|
577 | // Info info(__func__);
|
---|
578 | double result = 0.;
|
---|
579 | if (distance < R)
|
---|
580 | result = 1.;
|
---|
581 | else if (distance > S)
|
---|
582 | result = 0.;
|
---|
583 | else {
|
---|
584 | result = (0.5 + 0.5 * cos( M_PI * (distance - R)/(S-R)));
|
---|
585 | }
|
---|
586 | // LOG(2, "DEBUG: function_cutoff(" << distance << ") = " << result);
|
---|
587 | return result;
|
---|
588 | }
|
---|
589 |
|
---|
590 | ManyBodyPotential_Tersoff::result_t
|
---|
591 | ManyBodyPotential_Tersoff::function_prefactor(
|
---|
592 | const double &alpha,
|
---|
593 | const double &eta
|
---|
594 | ) const
|
---|
595 | {
|
---|
596 | // Info info(__func__);
|
---|
597 | const double result = chi * pow(
|
---|
598 | (1. + pow(alpha * eta, params[n])),
|
---|
599 | -1./(2.*params[n]));
|
---|
600 | // LOG(2, "DEBUG: function_prefactor(" << alpha << "," << eta << ") = " << result);
|
---|
601 | return result;
|
---|
602 | }
|
---|
603 |
|
---|
604 | ManyBodyPotential_Tersoff::result_t
|
---|
605 | ManyBodyPotential_Tersoff::function_smoother(
|
---|
606 | const double &prefactor,
|
---|
607 | const double &lambda,
|
---|
608 | const double &distance
|
---|
609 | ) const
|
---|
610 | {
|
---|
611 | // Info info(__func__);
|
---|
612 | const double result = prefactor * exp(-lambda * distance);
|
---|
613 | // LOG(2, "DEBUG: function_smoother(" << prefactor << "," << lambda << "," << distance << ") = " << result);
|
---|
614 | return result;
|
---|
615 | }
|
---|
616 |
|
---|
617 | ManyBodyPotential_Tersoff::result_t
|
---|
618 | ManyBodyPotential_Tersoff::function_eta(
|
---|
619 | const argument_t &r_ij
|
---|
620 | ) const
|
---|
621 | {
|
---|
622 | // Info info(__func__);
|
---|
623 | result_t result = 0.;
|
---|
624 |
|
---|
625 | // get all triples within the cutoff
|
---|
626 | std::vector<arguments_t> triples = triplefunction(r_ij, S);
|
---|
627 | for (std::vector<arguments_t>::const_iterator iter = triples.begin();
|
---|
628 | iter != triples.end(); ++iter) {
|
---|
629 | ASSERT( iter->size() == 2,
|
---|
630 | "ManyBodyPotential_Tersoff::function_zeta() - the triples result must contain of exactly two distances.");
|
---|
631 | const argument_t &r_ik = (*iter)[0];
|
---|
632 | result += function_cutoff(r_ik.distance)
|
---|
633 | * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3));
|
---|
634 | }
|
---|
635 |
|
---|
636 | // LOG(2, "DEBUG: function_eta(" << r_ij.distance << ") = " << result);
|
---|
637 | return result;
|
---|
638 | }
|
---|
639 |
|
---|
640 | ManyBodyPotential_Tersoff::result_t
|
---|
641 | ManyBodyPotential_Tersoff::function_zeta(
|
---|
642 | const argument_t &r_ij
|
---|
643 | ) const
|
---|
644 | {
|
---|
645 | // Info info(__func__);
|
---|
646 | result_t result = 0.;
|
---|
647 |
|
---|
648 | // get all triples within the cutoff
|
---|
649 | std::vector<arguments_t> triples = triplefunction(r_ij, S);
|
---|
650 | for (std::vector<arguments_t>::const_iterator iter = triples.begin();
|
---|
651 | iter != triples.end(); ++iter) {
|
---|
652 | ASSERT( iter->size() == 2,
|
---|
653 | "ManyBodyPotential_Tersoff::function_zeta() - the triples result must contain exactly two distances.");
|
---|
654 | const argument_t &r_ik = (*iter)[0];
|
---|
655 | const argument_t &r_jk = (*iter)[1];
|
---|
656 | result +=
|
---|
657 | function_cutoff(r_ik.distance)
|
---|
658 | * omega
|
---|
659 | * function_angle(r_ij.distance, r_ik.distance, r_jk.distance)
|
---|
660 | * exp( Helpers::pow(lambda3 * (r_ij.distance - r_ik.distance) ,3));
|
---|
661 | }
|
---|
662 |
|
---|
663 | // LOG(2, "DEBUG: function_zeta(" << r_ij.distance << ") = " << result);
|
---|
664 | return result;
|
---|
665 | }
|
---|
666 |
|
---|
667 | ManyBodyPotential_Tersoff::result_t
|
---|
668 | ManyBodyPotential_Tersoff::function_theta(
|
---|
669 | const double &r_ij,
|
---|
670 | const double &r_ik,
|
---|
671 | const double &r_jk
|
---|
672 | ) const
|
---|
673 | {
|
---|
674 | const double angle = Helpers::pow(r_ij,2) + Helpers::pow(r_ik,2) - Helpers::pow(r_jk,2);
|
---|
675 | const double divisor = 2.* r_ij * r_ik;
|
---|
676 | if (divisor != 0.) {
|
---|
677 | LOG(2, "DEBUG: cos(theta)= " << angle/divisor);
|
---|
678 | return angle/divisor;
|
---|
679 | } else
|
---|
680 | return 0.;
|
---|
681 | }
|
---|
682 |
|
---|
683 | ManyBodyPotential_Tersoff::result_t
|
---|
684 | ManyBodyPotential_Tersoff::function_angle(
|
---|
685 | const double &r_ij,
|
---|
686 | const double &r_ik,
|
---|
687 | const double &r_jk
|
---|
688 | ) const
|
---|
689 | {
|
---|
690 | // Info info(__func__);
|
---|
691 | const double result =
|
---|
692 | 1.
|
---|
693 | + (Helpers::pow(params[c]/params[d], 2))
|
---|
694 | - Helpers::pow(params[c], 2)/(Helpers::pow(params[d], 2) +
|
---|
695 | Helpers::pow(params[h] - function_theta(r_ij, r_ik, r_jk),2));
|
---|
696 |
|
---|
697 | // LOG(2, "DEBUG: function_angle(" << r_ij << "," << r_ik << "," << r_jk << ") = " << result);
|
---|
698 | return result;
|
---|
699 | }
|
---|
700 |
|
---|
701 | FunctionModel::filter_t ManyBodyPotential_Tersoff::getSpecificFilter() const
|
---|
702 | {
|
---|
703 | FunctionModel::filter_t returnfunction =
|
---|
704 | boost::bind(&Extractors::filterArgumentsByParticleTypes,
|
---|
705 | _1,
|
---|
706 | getParticleTypes());
|
---|
707 | return returnfunction;
|
---|
708 | }
|
---|
709 |
|
---|
710 | void
|
---|
711 | ManyBodyPotential_Tersoff::setParametersToRandomInitialValues(
|
---|
712 | const TrainingData &data)
|
---|
713 | {
|
---|
714 | RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
|
---|
715 | const double rng_min = random.min();
|
---|
716 | const double rng_max = random.max();
|
---|
717 | // params[ManyBodyPotential_Tersoff::R] = 1./AtomicLengthToAngstroem;
|
---|
718 | // params[ManyBodyPotential_Tersoff::S] = 2./AtomicLengthToAngstroem;
|
---|
719 | params[ManyBodyPotential_Tersoff::A] = 1e+4*(random()/(rng_max-rng_min));//1.393600e+03;
|
---|
720 | params[ManyBodyPotential_Tersoff::B] = 1e+4*(random()/(rng_max-rng_min));//3.467000e+02;
|
---|
721 | params[ManyBodyPotential_Tersoff::lambda] = 1e+1*(random()/(rng_max-rng_min));//3.487900e+00;
|
---|
722 | params[ManyBodyPotential_Tersoff::mu] = 1e+1*(random()/(rng_max-rng_min));//2.211900e+00;
|
---|
723 | // params[ManyBodyPotential_Tersoff::lambda3] = 0.;
|
---|
724 | // params[ManyBodyPotential_Tersoff::alpha] = 0.;
|
---|
725 | params[ManyBodyPotential_Tersoff::beta] = 1e-1*(random()/(rng_max-rng_min));//1.572400e-07;
|
---|
726 | // params[ManyBodyPotential_Tersoff::chi] = 1.;
|
---|
727 | // params[ManyBodyPotential_Tersoff::omega] = 1.;
|
---|
728 | params[ManyBodyPotential_Tersoff::n] = 1e+1*(random()/(rng_max-rng_min));//7.275100e-01;
|
---|
729 | params[ManyBodyPotential_Tersoff::c] = 1e+1*(random()/(rng_max-rng_min));//3.804900e+04;
|
---|
730 | params[ManyBodyPotential_Tersoff::d] = 1e+1*(random()/(rng_max-rng_min));//4.384000e+00;
|
---|
731 | params[ManyBodyPotential_Tersoff::h] = 1e+1*(random()/(rng_max-rng_min));//-5.705800e-01;
|
---|
732 | }
|
---|
733 |
|
---|