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) 2010 University of Bonn. All rights reserved.
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5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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6 | */
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7 |
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8 | /*
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9 | * molecule_geometry.cpp
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10 | *
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11 | * Created on: Oct 5, 2009
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12 | * Author: heber
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13 | */
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14 |
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15 | // include config.h
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16 | #ifdef HAVE_CONFIG_H
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17 | #include <config.h>
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18 | #endif
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19 |
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20 | #include "Helpers/MemDebug.hpp"
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21 |
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22 | #include "Helpers/helpers.hpp"
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23 | #include "Helpers/Log.hpp"
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24 | #include "Helpers/Verbose.hpp"
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25 | #include "LinearAlgebra/Line.hpp"
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26 | #include "LinearAlgebra/Matrix.hpp"
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27 | #include "LinearAlgebra/Plane.hpp"
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28 |
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29 | #include "atom.hpp"
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30 | #include "bond.hpp"
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31 | #include "config.hpp"
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32 | #include "element.hpp"
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33 | #include "leastsquaremin.hpp"
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34 | #include "molecule.hpp"
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35 | #include "World.hpp"
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36 |
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37 | #include "Box.hpp"
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38 |
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39 | #include <boost/foreach.hpp>
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40 |
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41 | #include <gsl/gsl_eigen.h>
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42 | #include <gsl/gsl_multimin.h>
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43 |
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44 |
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45 | /************************************* Functions for class molecule *********************************/
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46 |
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47 |
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48 | /** Centers the molecule in the box whose lengths are defined by vector \a *BoxLengths.
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49 | * \param *out output stream for debugging
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50 | */
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51 | bool molecule::CenterInBox()
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52 | {
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53 | bool status = true;
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54 | const Vector *Center = DetermineCenterOfAll();
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55 | const Vector *CenterBox = DetermineCenterOfBox();
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56 | Box &domain = World::getInstance().getDomain();
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57 |
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58 | // go through all atoms
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59 | BOOST_FOREACH(atom* iter, atoms){
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60 | *iter -= *Center;
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61 | *iter -= *CenterBox;
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62 | }
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63 | atoms.transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
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64 |
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65 | delete(Center);
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66 | delete(CenterBox);
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67 | return status;
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68 | };
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69 |
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70 |
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71 | /** Bounds the molecule in the box whose lengths are defined by vector \a *BoxLengths.
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72 | * \param *out output stream for debugging
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73 | */
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74 | bool molecule::BoundInBox()
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75 | {
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76 | bool status = true;
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77 | Box &domain = World::getInstance().getDomain();
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78 |
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79 | // go through all atoms
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80 | atoms.transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
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81 |
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82 | return status;
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83 | };
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84 |
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85 | /** Centers the edge of the atoms at (0,0,0).
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86 | * \param *out output stream for debugging
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87 | * \param *max coordinates of other edge, specifying box dimensions.
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88 | */
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89 | void molecule::CenterEdge(Vector *max)
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90 | {
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91 | Vector *min = new Vector;
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92 |
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93 | // Log() << Verbose(3) << "Begin of CenterEdge." << endl;
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94 | molecule::const_iterator iter = begin(); // start at first in list
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95 | if (iter != end()) { //list not empty?
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96 | for (int i=NDIM;i--;) {
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97 | max->at(i) = (*iter)->at(i);
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98 | min->at(i) = (*iter)->at(i);
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99 | }
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100 | for (; iter != end(); ++iter) {// continue with second if present
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101 | //(*iter)->Output(1,1,out);
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102 | for (int i=NDIM;i--;) {
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103 | max->at(i) = (max->at(i) < (*iter)->at(i)) ? (*iter)->at(i) : max->at(i);
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104 | min->at(i) = (min->at(i) > (*iter)->at(i)) ? (*iter)->at(i) : min->at(i);
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105 | }
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106 | }
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107 | // Log() << Verbose(4) << "Maximum is ";
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108 | // max->Output(out);
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109 | // Log() << Verbose(0) << ", Minimum is ";
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110 | // min->Output(out);
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111 | // Log() << Verbose(0) << endl;
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112 | min->Scale(-1.);
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113 | (*max) += (*min);
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114 | Translate(min);
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115 | }
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116 | delete(min);
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117 | // Log() << Verbose(3) << "End of CenterEdge." << endl;
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118 | };
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119 |
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120 | /** Centers the center of the atoms at (0,0,0).
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121 | * \param *out output stream for debugging
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122 | * \param *center return vector for translation vector
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123 | */
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124 | void molecule::CenterOrigin()
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125 | {
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126 | int Num = 0;
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127 | molecule::const_iterator iter = begin(); // start at first in list
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128 | Vector Center;
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129 |
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130 | Center.Zero();
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131 | if (iter != end()) { //list not empty?
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132 | for (; iter != end(); ++iter) { // continue with second if present
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133 | Num++;
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134 | Center += (*iter)->getPosition();
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135 | }
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136 | Center.Scale(-1./(double)Num); // divide through total number (and sign for direction)
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137 | Translate(&Center);
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138 | }
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139 | };
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140 |
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141 | /** Returns vector pointing to center of all atoms.
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142 | * \return pointer to center of all vector
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143 | */
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144 | Vector * molecule::DetermineCenterOfAll() const
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145 | {
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146 | molecule::const_iterator iter = begin(); // start at first in list
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147 | Vector *a = new Vector();
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148 | double Num = 0;
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149 |
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150 | a->Zero();
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151 |
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152 | if (iter != end()) { //list not empty?
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153 | for (; iter != end(); ++iter) { // continue with second if present
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154 | Num++;
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155 | (*a) += (*iter)->getPosition();
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156 | }
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157 | a->Scale(1./(double)Num); // divide through total mass (and sign for direction)
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158 | }
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159 | return a;
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160 | };
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161 |
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162 | /** Returns vector pointing to center of the domain.
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163 | * \return pointer to center of the domain
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164 | */
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165 | Vector * molecule::DetermineCenterOfBox() const
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166 | {
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167 | Vector *a = new Vector(0.5,0.5,0.5);
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168 | const Matrix &M = World::getInstance().getDomain().getM();
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169 | (*a) *= M;
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170 | return a;
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171 | };
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172 |
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173 | /** Returns vector pointing to center of gravity.
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174 | * \param *out output stream for debugging
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175 | * \return pointer to center of gravity vector
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176 | */
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177 | Vector * molecule::DetermineCenterOfGravity() const
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178 | {
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179 | molecule::const_iterator iter = begin(); // start at first in list
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180 | Vector *a = new Vector();
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181 | Vector tmp;
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182 | double Num = 0;
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183 |
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184 | a->Zero();
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185 |
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186 | if (iter != end()) { //list not empty?
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187 | for (; iter != end(); ++iter) { // continue with second if present
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188 | Num += (*iter)->getType()->getMass();
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189 | tmp = (*iter)->getType()->getMass() * (*iter)->getPosition();
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190 | (*a) += tmp;
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191 | }
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192 | a->Scale(1./Num); // divide through total mass
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193 | }
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194 | // Log() << Verbose(1) << "Resulting center of gravity: ";
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195 | // a->Output(out);
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196 | // Log() << Verbose(0) << endl;
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197 | return a;
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198 | };
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199 |
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200 | /** Centers the center of gravity of the atoms at (0,0,0).
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201 | * \param *out output stream for debugging
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202 | * \param *center return vector for translation vector
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203 | */
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204 | void molecule::CenterPeriodic()
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205 | {
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206 | Vector NewCenter;
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207 | DeterminePeriodicCenter(NewCenter);
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208 | // go through all atoms
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209 | BOOST_FOREACH(atom* iter, atoms){
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210 | *iter -= NewCenter;
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211 | }
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212 | };
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213 |
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214 |
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215 | /** Centers the center of gravity of the atoms at (0,0,0).
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216 | * \param *out output stream for debugging
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217 | * \param *center return vector for translation vector
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218 | */
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219 | void molecule::CenterAtVector(Vector *newcenter)
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220 | {
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221 | // go through all atoms
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222 | BOOST_FOREACH(atom* iter, atoms){
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223 | *iter -= *newcenter;
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224 | }
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225 | };
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226 |
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227 |
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228 | /** Scales all atoms by \a *factor.
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229 | * \param *factor pointer to scaling factor
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230 | *
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231 | * TODO: Is this realy what is meant, i.e.
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232 | * x=(x[0]*factor[0],x[1]*factor[1],x[2]*factor[2]) (current impl)
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233 | * or rather
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234 | * x=(**factor) * x (as suggested by comment)
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235 | */
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236 | void molecule::Scale(const double ** const factor)
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237 | {
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238 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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239 | for (int j=0;j<MDSteps;j++)
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240 | (*iter)->Trajectory.R.at(j).ScaleAll(*factor);
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241 | (*iter)->ScaleAll(*factor);
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242 | }
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243 | };
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244 |
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245 | /** Translate all atoms by given vector.
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246 | * \param trans[] translation vector.
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247 | */
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248 | void molecule::Translate(const Vector *trans)
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249 | {
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250 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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251 | for (int j=0;j<MDSteps;j++)
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252 | (*iter)->Trajectory.R.at(j) += (*trans);
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253 | *(*iter) += (*trans);
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254 | }
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255 | };
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256 |
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257 | /** Translate the molecule periodically in the box.
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258 | * \param trans[] translation vector.
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259 | * TODO treatment of trajetories missing
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260 | */
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261 | void molecule::TranslatePeriodically(const Vector *trans)
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262 | {
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263 | Box &domain = World::getInstance().getDomain();
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264 |
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265 | // go through all atoms
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266 | BOOST_FOREACH(atom* iter, atoms){
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267 | *iter += *trans;
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268 | }
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269 | atoms.transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
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270 |
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271 | };
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272 |
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273 |
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274 | /** Mirrors all atoms against a given plane.
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275 | * \param n[] normal vector of mirror plane.
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276 | */
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277 | void molecule::Mirror(const Vector *n)
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278 | {
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279 | OBSERVE;
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280 | Plane p(*n,0);
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281 | atoms.transformNodes(boost::bind(&Plane::mirrorVector,p,_1));
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282 | };
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283 |
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284 | /** Determines center of molecule (yet not considering atom masses).
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285 | * \param center reference to return vector
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286 | */
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287 | void molecule::DeterminePeriodicCenter(Vector ¢er)
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288 | {
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289 | const Matrix &matrix = World::getInstance().getDomain().getM();
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290 | const Matrix &inversematrix = World::getInstance().getDomain().getM();
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291 | double tmp;
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292 | bool flag;
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293 | Vector Testvector, Translationvector;
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294 | Vector Center;
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295 |
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296 | do {
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297 | Center.Zero();
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298 | flag = true;
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299 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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300 | #ifdef ADDHYDROGEN
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301 | if ((*iter)->getType()->getAtomicNumber() != 1) {
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302 | #endif
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303 | Testvector = inversematrix * (*iter)->getPosition();
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304 | Translationvector.Zero();
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305 | for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
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306 | if ((*iter)->nr < (*Runner)->GetOtherAtom((*iter))->nr) // otherwise we shift one to, the other fro and gain nothing
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307 | for (int j=0;j<NDIM;j++) {
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308 | tmp = (*iter)->at(j) - (*Runner)->GetOtherAtom(*iter)->at(j);
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309 | if ((fabs(tmp)) > BondDistance) {
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310 | flag = false;
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311 | DoLog(0) && (Log() << Verbose(0) << "Hit: atom " << (*iter)->getName() << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl);
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312 | if (tmp > 0)
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313 | Translationvector[j] -= 1.;
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314 | else
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315 | Translationvector[j] += 1.;
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316 | }
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317 | }
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318 | }
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319 | Testvector += Translationvector;
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320 | Testvector *= matrix;
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321 | Center += Testvector;
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322 | Log() << Verbose(1) << "vector is: " << Testvector << endl;
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323 | #ifdef ADDHYDROGEN
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324 | // now also change all hydrogens
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325 | for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
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326 | if ((*Runner)->GetOtherAtom((*iter))->getType()->getAtomicNumber() == 1) {
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327 | Testvector = inversematrix * (*Runner)->GetOtherAtom((*iter))->getPosition();
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328 | Testvector += Translationvector;
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329 | Testvector *= matrix;
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330 | Center += Testvector;
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331 | Log() << Verbose(1) << "Hydrogen vector is: " << Testvector << endl;
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332 | }
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333 | }
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334 | }
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335 | #endif
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336 | }
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337 | } while (!flag);
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338 |
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339 | Center.Scale(1./static_cast<double>(getAtomCount()));
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340 | CenterAtVector(&Center);
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341 | };
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342 |
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343 | /** Align all atoms in such a manner that given vector \a *n is along z axis.
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344 | * \param n[] alignment vector.
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345 | */
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346 | void molecule::Align(Vector *n)
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347 | {
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348 | double alpha, tmp;
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349 | Vector z_axis;
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350 | z_axis[0] = 0.;
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351 | z_axis[1] = 0.;
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352 | z_axis[2] = 1.;
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353 |
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354 | // rotate on z-x plane
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355 | DoLog(0) && (Log() << Verbose(0) << "Begin of Aligning all atoms." << endl);
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356 | alpha = atan(-n->at(0)/n->at(2));
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357 | DoLog(1) && (Log() << Verbose(1) << "Z-X-angle: " << alpha << " ... ");
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358 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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359 | tmp = (*iter)->at(0);
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360 | (*iter)->set(0, cos(alpha) * tmp + sin(alpha) * (*iter)->at(2));
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361 | (*iter)->set(2, -sin(alpha) * tmp + cos(alpha) * (*iter)->at(2));
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362 | for (int j=0;j<MDSteps;j++) {
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363 | tmp = (*iter)->Trajectory.R.at(j)[0];
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364 | (*iter)->Trajectory.R.at(j)[0] = cos(alpha) * tmp + sin(alpha) * (*iter)->Trajectory.R.at(j)[2];
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365 | (*iter)->Trajectory.R.at(j)[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->Trajectory.R.at(j)[2];
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366 | }
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367 | }
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368 | // rotate n vector
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369 | tmp = n->at(0);
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370 | n->at(0) = cos(alpha) * tmp + sin(alpha) * n->at(2);
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371 | n->at(2) = -sin(alpha) * tmp + cos(alpha) * n->at(2);
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372 | DoLog(1) && (Log() << Verbose(1) << "alignment vector after first rotation: " << n << endl);
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373 |
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374 | // rotate on z-y plane
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375 | alpha = atan(-n->at(1)/n->at(2));
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376 | DoLog(1) && (Log() << Verbose(1) << "Z-Y-angle: " << alpha << " ... ");
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377 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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378 | tmp = (*iter)->at(1);
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379 | (*iter)->set(1, cos(alpha) * tmp + sin(alpha) * (*iter)->at(2));
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380 | (*iter)->set(2, -sin(alpha) * tmp + cos(alpha) * (*iter)->at(2));
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381 | for (int j=0;j<MDSteps;j++) {
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382 | tmp = (*iter)->Trajectory.R.at(j)[1];
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383 | (*iter)->Trajectory.R.at(j)[1] = cos(alpha) * tmp + sin(alpha) * (*iter)->Trajectory.R.at(j)[2];
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384 | (*iter)->Trajectory.R.at(j)[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->Trajectory.R.at(j)[2];
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385 | }
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386 | }
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387 | // rotate n vector (for consistency check)
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388 | tmp = n->at(1);
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389 | n->at(1) = cos(alpha) * tmp + sin(alpha) * n->at(2);
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390 | n->at(2) = -sin(alpha) * tmp + cos(alpha) * n->at(2);
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391 |
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392 |
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393 | DoLog(1) && (Log() << Verbose(1) << "alignment vector after second rotation: " << n << endl);
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394 | DoLog(0) && (Log() << Verbose(0) << "End of Aligning all atoms." << endl);
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395 | };
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396 |
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397 |
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398 | /** Calculates sum over least square distance to line hidden in \a *x.
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399 | * \param *x offset and direction vector
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400 | * \param *params pointer to lsq_params structure
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401 | * \return \f$ sum_i^N | y_i - (a + t_i b)|^2\f$
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402 | */
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403 | double LeastSquareDistance (const gsl_vector * x, void * params)
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404 | {
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405 | double res = 0, t;
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406 | Vector a,b,c,d;
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407 | struct lsq_params *par = (struct lsq_params *)params;
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408 |
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409 | // initialize vectors
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410 | a[0] = gsl_vector_get(x,0);
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411 | a[1] = gsl_vector_get(x,1);
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412 | a[2] = gsl_vector_get(x,2);
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413 | b[0] = gsl_vector_get(x,3);
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414 | b[1] = gsl_vector_get(x,4);
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415 | b[2] = gsl_vector_get(x,5);
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416 | // go through all atoms
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417 | for (molecule::const_iterator iter = par->mol->begin(); iter != par->mol->end(); ++iter) {
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418 | if ((*iter)->getType() == ((struct lsq_params *)params)->type) { // for specific type
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419 | c = (*iter)->getPosition() - a;
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420 | t = c.ScalarProduct(b); // get direction parameter
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421 | d = t*b; // and create vector
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422 | c -= d; // ... yielding distance vector
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423 | res += d.ScalarProduct(d); // add squared distance
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424 | }
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425 | }
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426 | return res;
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427 | };
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428 |
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429 | /** By minimizing the least square distance gains alignment vector.
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430 | * \bug this is not yet working properly it seems
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431 | */
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432 | void molecule::GetAlignvector(struct lsq_params * par) const
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433 | {
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434 | int np = 6;
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435 |
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436 | const gsl_multimin_fminimizer_type *T =
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437 | gsl_multimin_fminimizer_nmsimplex;
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438 | gsl_multimin_fminimizer *s = NULL;
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439 | gsl_vector *ss;
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440 | gsl_multimin_function minex_func;
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441 |
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442 | size_t iter = 0, i;
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443 | int status;
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444 | double size;
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445 |
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446 | /* Initial vertex size vector */
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447 | ss = gsl_vector_alloc (np);
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448 |
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449 | /* Set all step sizes to 1 */
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450 | gsl_vector_set_all (ss, 1.0);
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451 |
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452 | /* Starting point */
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453 | par->x = gsl_vector_alloc (np);
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454 | par->mol = this;
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455 |
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456 | gsl_vector_set (par->x, 0, 0.0); // offset
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457 | gsl_vector_set (par->x, 1, 0.0);
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458 | gsl_vector_set (par->x, 2, 0.0);
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459 | gsl_vector_set (par->x, 3, 0.0); // direction
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460 | gsl_vector_set (par->x, 4, 0.0);
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461 | gsl_vector_set (par->x, 5, 1.0);
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462 |
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463 | /* Initialize method and iterate */
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464 | minex_func.f = &LeastSquareDistance;
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465 | minex_func.n = np;
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466 | minex_func.params = (void *)par;
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467 |
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468 | s = gsl_multimin_fminimizer_alloc (T, np);
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469 | gsl_multimin_fminimizer_set (s, &minex_func, par->x, ss);
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470 |
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471 | do
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472 | {
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473 | iter++;
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474 | status = gsl_multimin_fminimizer_iterate(s);
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475 |
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476 | if (status)
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477 | break;
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478 |
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479 | size = gsl_multimin_fminimizer_size (s);
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480 | status = gsl_multimin_test_size (size, 1e-2);
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481 |
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482 | if (status == GSL_SUCCESS)
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483 | {
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484 | printf ("converged to minimum at\n");
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485 | }
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486 |
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487 | printf ("%5d ", (int)iter);
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488 | for (i = 0; i < (size_t)np; i++)
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489 | {
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490 | printf ("%10.3e ", gsl_vector_get (s->x, i));
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491 | }
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492 | printf ("f() = %7.3f size = %.3f\n", s->fval, size);
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493 | }
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494 | while (status == GSL_CONTINUE && iter < 100);
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495 |
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496 | for (i=0;i<(size_t)np;i++)
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497 | gsl_vector_set(par->x, i, gsl_vector_get(s->x, i));
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498 | //gsl_vector_free(par->x);
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499 | gsl_vector_free(ss);
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500 | gsl_multimin_fminimizer_free (s);
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501 | };
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