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) 2010-2012 University of Bonn. All rights reserved.
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5 | *
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6 | *
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7 | * This file is part of MoleCuilder.
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8 | *
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9 | * MoleCuilder is free software: you can redistribute it and/or modify
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10 | * it under the terms of the GNU General Public License as published by
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11 | * the Free Software Foundation, either version 2 of the License, or
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12 | * (at your option) any later version.
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13 | *
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14 | * MoleCuilder is distributed in the hope that it will be useful,
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15 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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16 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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17 | * GNU General Public License for more details.
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18 | *
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19 | * You should have received a copy of the GNU General Public License
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20 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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21 | */
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22 |
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23 | /*
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24 | * molecule_geometry.cpp
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25 | *
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26 | * Created on: Oct 5, 2009
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27 | * Author: heber
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28 | */
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29 |
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30 | // include config.h
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31 | #ifdef HAVE_CONFIG_H
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32 | #include <config.h>
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33 | #endif
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34 |
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35 | //#include "CodePatterns/MemDebug.hpp"
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36 |
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37 | #include "Atom/atom.hpp"
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38 | #include "Bond/bond.hpp"
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39 | #include "Box.hpp"
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40 | #include "CodePatterns/Log.hpp"
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41 | #include "CodePatterns/Verbose.hpp"
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42 | #include "config.hpp"
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43 | #include "Element/element.hpp"
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44 | #include "Graph/BondGraph.hpp"
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45 | #include "LinearAlgebra/leastsquaremin.hpp"
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46 | #include "LinearAlgebra/Line.hpp"
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47 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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48 | #include "LinearAlgebra/Plane.hpp"
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49 | #include "molecule.hpp"
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50 | #include "World.hpp"
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51 |
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52 | #include <boost/foreach.hpp>
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53 |
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54 | #include <gsl/gsl_eigen.h>
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55 | #include <gsl/gsl_multimin.h>
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56 |
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57 |
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58 | /************************************* Functions for class molecule *********************************/
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59 |
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60 | /** Returns vector pointing to center of the domain.
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61 | * \return pointer to center of the domain
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62 | */
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63 | #ifdef HAVE_INLINE
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64 | inline
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65 | #else
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66 | static
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67 | #endif
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68 | const Vector DetermineCenterOfBox()
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69 | {
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70 | Vector a(0.5,0.5,0.5);
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71 | const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
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72 | a *= M;
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73 | return a;
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74 | }
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75 |
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76 | /** Centers the molecule in the box whose lengths are defined by vector \a *BoxLengths.
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77 | * \param *out output stream for debugging
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78 | */
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79 | bool molecule::CenterInBox()
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80 | {
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81 | bool status = true;
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82 | const Vector Center = DetermineCenterOfAll();
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83 | const Vector CenterBox = DetermineCenterOfBox();
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84 | Box &domain = World::getInstance().getDomain();
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85 |
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86 | // go through all atoms
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87 | Translate(CenterBox - Center);
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88 | getAtomSet().transformNodes(boost::bind(&Box::enforceBoundaryConditions,domain,_1));
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89 |
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90 | return status;
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91 | }
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92 |
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93 |
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94 | /** Bounds the molecule in the box whose lengths are defined by vector \a *BoxLengths.
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95 | * \param *out output stream for debugging
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96 | */
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97 | bool molecule::BoundInBox()
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98 | {
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99 | bool status = true;
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100 | Box &domain = World::getInstance().getDomain();
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101 |
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102 | // go through all atoms
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103 | getAtomSet().transformNodes(boost::bind(&Box::enforceBoundaryConditions,domain,_1));
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104 |
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105 | return status;
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106 | }
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107 |
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108 | /** Centers the edge of the atoms at (0,0,0).
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109 | */
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110 | void molecule::CenterEdge()
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111 | {
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112 | const_iterator iter = const_cast<const molecule &>(*this).begin();
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113 | if (iter != const_cast<const molecule &>(*this).end()) { //list not empty?
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114 | Vector min = (*begin())->getPosition();
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115 | for (;iter != const_cast<const molecule &>(*this).end(); ++iter) { // continue with second if present
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116 | const Vector ¤tPos = (*iter)->getPosition();
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117 | for (size_t i=0;i<NDIM;++i)
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118 | if (min[i] > currentPos[i])
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119 | min[i] = currentPos[i];
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120 | }
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121 | Translate(-1.*min);
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122 | }
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123 | }
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124 |
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125 | /** Centers the center of the atoms at (0,0,0).
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126 | * \param *out output stream for debugging
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127 | * \param *center return vector for translation vector
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128 | */
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129 | void molecule::CenterOrigin()
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130 | {
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131 | int Num = 0;
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132 | const_iterator iter = const_cast<const molecule &>(*this).begin(); // start at first in list
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133 | Vector Center;
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134 |
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135 | Center.Zero();
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136 | if (iter != const_cast<const molecule &>(*this).end()) { //list not empty?
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137 | for (; iter != const_cast<const molecule &>(*this).end(); ++iter) { // continue with second if present
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138 | Num++;
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139 | Center += (*iter)->getPosition();
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140 | }
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141 | Center.Scale(-1./(double)Num); // divide through total number (and sign for direction)
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142 | Translate(Center);
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143 | }
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144 | }
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145 |
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146 | /** Returns vector pointing to center of all atoms.
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147 | * \return pointer to center of all vector
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148 | */
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149 | const Vector molecule::DetermineCenterOfAll() const
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150 | {
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151 | const_iterator iter = begin(); // start at first in list
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152 | Vector a;
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153 | double Num = 0;
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154 |
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155 | a.Zero();
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156 |
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157 | if (iter != end()) { //list not empty?
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158 | for (; iter != end(); ++iter) { // continue with second if present
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159 | Num++;
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160 | a += (*iter)->getPosition();
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161 | }
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162 | a.Scale(1./(double)Num); // divide through total mass (and sign for direction)
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163 | }
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164 | return a;
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165 | }
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166 |
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167 |
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168 | /** Returns vector pointing to center of gravity.
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169 | * \param *out output stream for debugging
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170 | * \return pointer to center of gravity vector
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171 | */
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172 | const Vector molecule::DetermineCenterOfGravity() const
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173 | {
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174 | const_iterator iter = begin(); // start at first in list
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175 | Vector a;
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176 | Vector tmp;
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177 | double Num = 0;
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178 |
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179 | a.Zero();
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180 |
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181 | if (iter != end()) { //list not empty?
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182 | for (; iter != end(); ++iter) { // continue with second if present
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183 | Num += (*iter)->getType()->getMass();
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184 | tmp = (*iter)->getType()->getMass() * (*iter)->getPosition();
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185 | a += tmp;
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186 | }
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187 | a.Scale(1./Num); // divide through total mass
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188 | }
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189 | LOG(1, "INFO: Resulting center of gravity: " << a << ".");
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190 | return a;
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191 | }
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192 |
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193 | /** Centers the center of gravity of the atoms at (0,0,0).
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194 | * \param *out output stream for debugging
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195 | * \param *center return vector for translation vector
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196 | */
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197 | void molecule::CenterPeriodic()
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198 | {
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199 | Vector NewCenter;
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200 | DeterminePeriodicCenter(NewCenter);
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201 | Translate(-1.*NewCenter);
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202 | }
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203 |
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204 |
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205 | /** Centers the center of gravity of the atoms at (0,0,0).
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206 | * \param *out output stream for debugging
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207 | * \param *center return vector for translation vector
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208 | */
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209 | void molecule::CenterAtVector(const Vector &newcenter)
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210 | {
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211 | Translate(-1.*newcenter);
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212 | }
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213 |
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214 | /** Calculate the inertia tensor of a the molecule.
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215 | *
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216 | * @return inertia tensor
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217 | */
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218 | RealSpaceMatrix molecule::getInertiaTensor() const
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219 | {
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220 | RealSpaceMatrix InertiaTensor;
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221 | const Vector CenterOfGravity = DetermineCenterOfGravity();
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222 |
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223 | // reset inertia tensor
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224 | InertiaTensor.setZero();
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225 |
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226 | // sum up inertia tensor
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227 | for (const_iterator iter = begin(); iter != end(); ++iter) {
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228 | Vector x = (*iter)->getPosition();
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229 | x -= CenterOfGravity;
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230 | const double mass = (*iter)->getType()->getMass();
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231 | InertiaTensor.at(0,0) += mass*(x[1]*x[1] + x[2]*x[2]);
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232 | InertiaTensor.at(0,1) += mass*(-x[0]*x[1]);
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233 | InertiaTensor.at(0,2) += mass*(-x[0]*x[2]);
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234 | InertiaTensor.at(1,0) += mass*(-x[1]*x[0]);
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235 | InertiaTensor.at(1,1) += mass*(x[0]*x[0] + x[2]*x[2]);
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236 | InertiaTensor.at(1,2) += mass*(-x[1]*x[2]);
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237 | InertiaTensor.at(2,0) += mass*(-x[2]*x[0]);
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238 | InertiaTensor.at(2,1) += mass*(-x[2]*x[1]);
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239 | InertiaTensor.at(2,2) += mass*(x[0]*x[0] + x[1]*x[1]);
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240 | }
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241 | // print InertiaTensor
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242 | LOG(1, "INFO: The inertia tensor of molecule " << getName() << " is:" << InertiaTensor);
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243 |
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244 | return InertiaTensor;
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245 | }
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246 |
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247 | /** Rotates the molecule in such a way that biggest principal axis corresponds
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248 | * to given \a Axis.
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249 | *
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250 | * @param Axis Axis to align with biggest principal axis
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251 | */
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252 | void molecule::RotateToPrincipalAxisSystem(const Vector &Axis)
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253 | {
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254 | const Vector CenterOfGravity = DetermineCenterOfGravity();
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255 | RealSpaceMatrix InertiaTensor = getInertiaTensor();
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256 |
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257 | // diagonalize to determine principal axis system
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258 | Vector Eigenvalues = InertiaTensor.transformToEigenbasis();
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259 |
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260 | for(int i=0;i<NDIM;i++)
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261 | LOG(0, "eigenvalue = " << Eigenvalues[i] << ", eigenvector = " << InertiaTensor.column(i));
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262 |
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263 | LOG(0, "STATUS: Transforming to PAS ... ");
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264 |
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265 | // obtain first column, eigenvector to biggest eigenvalue
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266 | const Vector BiggestEigenvector(InertiaTensor.column(Eigenvalues.SmallestComponent()));
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267 | Vector DesiredAxis(Axis.getNormalized());
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268 |
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269 | // Creation Line that is the rotation axis
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270 | DesiredAxis.VectorProduct(BiggestEigenvector);
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271 | Line RotationAxis(Vector(0.,0.,0.), DesiredAxis);
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272 |
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273 | // determine angle
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274 | const double alpha = BiggestEigenvector.Angle(Axis);
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275 |
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276 | LOG(1, "INFO: Rotation angle is " << alpha);
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277 |
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278 | // and rotate
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279 | for (iterator iter = begin(); iter != end(); ++iter) {
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280 | *(*iter) -= CenterOfGravity;
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281 | (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), alpha));
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282 | *(*iter) += CenterOfGravity;
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283 | }
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284 | LOG(0, "STATUS: done.");
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285 | }
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286 |
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287 | /** Scales all atoms by \a *factor.
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288 | * \param *factor pointer to scaling factor
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289 | *
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290 | * TODO: Is this realy what is meant, i.e.
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291 | * x=(x[0]*factor[0],x[1]*factor[1],x[2]*factor[2]) (current impl)
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292 | * or rather
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293 | * x=(**factor) * x (as suggested by comment)
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294 | */
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295 | void molecule::Scale(const double *factor)
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296 | {
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297 | for (iterator iter = begin(); iter != end(); ++iter)
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298 | for (size_t j=0;j<(*iter)->getTrajectorySize();j++)
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299 | if ((*iter)->isStepPresent(j)) {
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300 | Vector temp = (*iter)->getPositionAtStep(j);
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301 | temp.ScaleAll(factor);
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302 | (*iter)->setPositionAtStep(j,temp);
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303 | }
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304 | };
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305 |
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306 | /** Translate all atoms by given vector.
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307 | * \param trans[] translation vector.
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308 | */
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309 | void molecule::Translate(const Vector &trans)
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310 | {
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311 | for (iterator iter = begin(); iter != end(); ++iter)
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312 | for (size_t j=0;j<(*iter)->getTrajectorySize();j++)
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313 | if ((*iter)->isStepPresent(j))
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314 | (*iter)->setPositionAtStep(j, (*iter)->getPositionAtStep(j) + (trans));
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315 | };
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316 |
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317 | /** Translate the molecule periodically in the box.
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318 | * \param trans[] translation vector.
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319 | * TODO treatment of trajectories missing
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320 | */
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321 | void molecule::TranslatePeriodically(const Vector &trans)
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322 | {
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323 | Translate(trans);
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324 | Box &domain = World::getInstance().getDomain();
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325 | getAtomSet().transformNodes(boost::bind(&Box::enforceBoundaryConditions,domain,_1));
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326 | };
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327 |
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328 |
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329 | /** Mirrors all atoms against a given plane.
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330 | * \param n[] normal vector of mirror plane.
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331 | */
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332 | void molecule::Mirror(const Vector &n)
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333 | {
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334 | Plane p(n,0);
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335 | getAtomSet().transformNodes(boost::bind(&Plane::mirrorVector,p,_1));
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336 | };
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337 |
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338 | /** Determines center of molecule (yet not considering atom masses).
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339 | * \param center reference to return vector
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340 | * \param treatment whether to treat hydrogen special or not
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341 | */
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342 | void molecule::DeterminePeriodicCenter(Vector ¢er, const enum HydrogenTreatment treatment)
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343 | {
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344 | const RealSpaceMatrix &matrix = World::getInstance().getDomain().getM();
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345 | const RealSpaceMatrix &inversematrix = World::getInstance().getDomain().getM();
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346 | double tmp;
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347 | bool flag;
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348 | Vector Testvector, Translationvector;
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349 | Vector Center;
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350 | const BondGraph * const BG = World::getInstance().getBondGraph();
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351 |
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352 | do {
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353 | Center.Zero();
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354 | flag = true;
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355 | for (const_iterator iter = const_cast<const molecule &>(*this).begin();
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356 | iter != const_cast<const molecule &>(*this).end();
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357 | ++iter) {
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358 | if ((treatment == IncludeHydrogen) || ((*iter)->getType()->getAtomicNumber() != 1)) {
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359 | Testvector = inversematrix * (*iter)->getPosition();
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360 | Translationvector.Zero();
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361 | const BondList& ListOfBonds = (*iter)->getListOfBonds();
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362 | for (BondList::const_iterator Runner = ListOfBonds.begin();
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363 | Runner != ListOfBonds.end();
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364 | ++Runner) {
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365 | if ((*iter)->getNr() < (*Runner)->GetOtherAtom((*iter))->getNr()) // otherwise we shift one to, the other fro and gain nothing
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366 | for (int j=0;j<NDIM;j++) {
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367 | tmp = (*iter)->at(j) - (*Runner)->GetOtherAtom(*iter)->at(j);
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368 | const range<double> MinMaxBondDistance(
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369 | BG->getMinMaxDistance((*iter), (*Runner)->GetOtherAtom(*iter)));
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370 | if (fabs(tmp) > MinMaxBondDistance.last) { // check against Min is not useful for components
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371 | flag = false;
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372 | LOG(0, "Hit: atom " << (*iter)->getName() << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << ".");
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373 | if (tmp > 0)
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374 | Translationvector[j] -= 1.;
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375 | else
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376 | Translationvector[j] += 1.;
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377 | }
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378 | }
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379 | }
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380 | Testvector += Translationvector;
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381 | Testvector *= matrix;
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382 | Center += Testvector;
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383 | LOG(1, "vector is: " << Testvector);
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384 | if (treatment == ExcludeHydrogen) {
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385 | // now also change all hydrogens
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386 | for (BondList::const_iterator Runner = ListOfBonds.begin();
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387 | Runner != ListOfBonds.end();
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388 | ++Runner) {
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389 | if ((*Runner)->GetOtherAtom((*iter))->getType()->getAtomicNumber() == 1) {
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390 | Testvector = inversematrix * (*Runner)->GetOtherAtom((*iter))->getPosition();
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391 | Testvector += Translationvector;
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392 | Testvector *= matrix;
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393 | Center += Testvector;
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394 | LOG(1, "Hydrogen vector is: " << Testvector);
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395 | }
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396 | }
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397 | }
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398 | }
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399 | }
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400 | } while (!flag);
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401 |
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402 | Center.Scale(1./static_cast<double>(getAtomCount()));
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403 | CenterAtVector(Center);
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404 | };
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405 |
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406 | /** Align all atoms in such a manner that given vector \a *n is along z axis.
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407 | * \param n[] alignment vector.
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408 | */
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409 | void molecule::Align(const Vector &n)
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410 | {
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411 | double alpha, tmp;
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412 | Vector z_axis;
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413 | Vector alignment(n);
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414 | z_axis[0] = 0.;
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415 | z_axis[1] = 0.;
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416 | z_axis[2] = 1.;
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417 |
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418 | // rotate on z-x plane
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419 | LOG(0, "Begin of Aligning all atoms.");
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420 | alpha = atan(-alignment.at(0)/alignment.at(2));
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421 | LOG(1, "INFO: Z-X-angle: " << alpha << " ... ");
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422 | for (iterator iter = begin(); iter != end(); ++iter) {
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423 | tmp = (*iter)->at(0);
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424 | (*iter)->set(0, cos(alpha) * tmp + sin(alpha) * (*iter)->at(2));
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425 | (*iter)->set(2, -sin(alpha) * tmp + cos(alpha) * (*iter)->at(2));
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426 | for (int j=0;j<MDSteps;j++) {
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427 | Vector temp;
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428 | temp[0] = cos(alpha) * (*iter)->getPositionAtStep(j)[0] + sin(alpha) * (*iter)->getPositionAtStep(j)[2];
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429 | temp[2] = -sin(alpha) * (*iter)->getPositionAtStep(j)[0] + cos(alpha) * (*iter)->getPositionAtStep(j)[2];
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430 | (*iter)->setPositionAtStep(j,temp);
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431 | }
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432 | }
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433 | // rotate n vector
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434 | tmp = alignment.at(0);
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435 | alignment.at(0) = cos(alpha) * tmp + sin(alpha) * alignment.at(2);
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436 | alignment.at(2) = -sin(alpha) * tmp + cos(alpha) * alignment.at(2);
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437 | LOG(1, "alignment vector after first rotation: " << alignment);
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438 |
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439 | // rotate on z-y plane
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440 | alpha = atan(-alignment.at(1)/alignment.at(2));
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441 | LOG(1, "INFO: Z-Y-angle: " << alpha << " ... ");
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442 | for (iterator iter = begin(); iter != end(); ++iter) {
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443 | tmp = (*iter)->at(1);
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444 | (*iter)->set(1, cos(alpha) * tmp + sin(alpha) * (*iter)->at(2));
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445 | (*iter)->set(2, -sin(alpha) * tmp + cos(alpha) * (*iter)->at(2));
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446 | for (int j=0;j<MDSteps;j++) {
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447 | Vector temp;
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448 | temp[1] = cos(alpha) * (*iter)->getPositionAtStep(j)[1] + sin(alpha) * (*iter)->getPositionAtStep(j)[2];
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449 | temp[2] = -sin(alpha) * (*iter)->getPositionAtStep(j)[1] + cos(alpha) * (*iter)->getPositionAtStep(j)[2];
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450 | (*iter)->setPositionAtStep(j,temp);
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451 | }
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452 | }
|
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453 | // rotate n vector (for consistency check)
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454 | tmp = alignment.at(1);
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455 | alignment.at(1) = cos(alpha) * tmp + sin(alpha) * alignment.at(2);
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456 | alignment.at(2) = -sin(alpha) * tmp + cos(alpha) * alignment.at(2);
|
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457 |
|
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458 | LOG(1, "alignment vector after second rotation: " << alignment);
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459 | LOG(0, "End of Aligning all atoms.");
|
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460 | };
|
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461 |
|
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462 |
|
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463 | /** Calculates sum over least square distance to line hidden in \a *x.
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464 | * \param *x offset and direction vector
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465 | * \param *params pointer to lsq_params structure
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466 | * \return \f$ sum_i^N | y_i - (a + t_i b)|^2\f$
|
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467 | */
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468 | double LeastSquareDistance (const gsl_vector * x, void * params)
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469 | {
|
---|
470 | double res = 0, t;
|
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471 | Vector a,b,c,d;
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472 | struct lsq_params *par = (struct lsq_params *)params;
|
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473 |
|
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474 | // initialize vectors
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475 | a[0] = gsl_vector_get(x,0);
|
---|
476 | a[1] = gsl_vector_get(x,1);
|
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477 | a[2] = gsl_vector_get(x,2);
|
---|
478 | b[0] = gsl_vector_get(x,3);
|
---|
479 | b[1] = gsl_vector_get(x,4);
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480 | b[2] = gsl_vector_get(x,5);
|
---|
481 | // go through all atoms
|
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482 | for (molecule::const_iterator iter = par->mol->begin(); iter != par->mol->end(); ++iter) {
|
---|
483 | if ((*iter)->getType() == ((struct lsq_params *)params)->type) { // for specific type
|
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484 | c = (*iter)->getPosition() - a;
|
---|
485 | t = c.ScalarProduct(b); // get direction parameter
|
---|
486 | d = t*b; // and create vector
|
---|
487 | c -= d; // ... yielding distance vector
|
---|
488 | res += d.ScalarProduct(d); // add squared distance
|
---|
489 | }
|
---|
490 | }
|
---|
491 | return res;
|
---|
492 | };
|
---|
493 |
|
---|
494 | /** By minimizing the least square distance gains alignment vector.
|
---|
495 | * \bug this is not yet working properly it seems
|
---|
496 | */
|
---|
497 | void molecule::GetAlignvector(struct lsq_params * par) const
|
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498 | {
|
---|
499 | int np = 6;
|
---|
500 |
|
---|
501 | const gsl_multimin_fminimizer_type *T =
|
---|
502 | gsl_multimin_fminimizer_nmsimplex;
|
---|
503 | gsl_multimin_fminimizer *s = NULL;
|
---|
504 | gsl_vector *ss;
|
---|
505 | gsl_multimin_function minex_func;
|
---|
506 |
|
---|
507 | size_t iter = 0, i;
|
---|
508 | int status;
|
---|
509 | double size;
|
---|
510 |
|
---|
511 | /* Initial vertex size vector */
|
---|
512 | ss = gsl_vector_alloc (np);
|
---|
513 |
|
---|
514 | /* Set all step sizes to 1 */
|
---|
515 | gsl_vector_set_all (ss, 1.0);
|
---|
516 |
|
---|
517 | /* Starting point */
|
---|
518 | par->x = gsl_vector_alloc (np);
|
---|
519 | par->mol = this;
|
---|
520 |
|
---|
521 | gsl_vector_set (par->x, 0, 0.0); // offset
|
---|
522 | gsl_vector_set (par->x, 1, 0.0);
|
---|
523 | gsl_vector_set (par->x, 2, 0.0);
|
---|
524 | gsl_vector_set (par->x, 3, 0.0); // direction
|
---|
525 | gsl_vector_set (par->x, 4, 0.0);
|
---|
526 | gsl_vector_set (par->x, 5, 1.0);
|
---|
527 |
|
---|
528 | /* Initialize method and iterate */
|
---|
529 | minex_func.f = &LeastSquareDistance;
|
---|
530 | minex_func.n = np;
|
---|
531 | minex_func.params = (void *)par;
|
---|
532 |
|
---|
533 | s = gsl_multimin_fminimizer_alloc (T, np);
|
---|
534 | gsl_multimin_fminimizer_set (s, &minex_func, par->x, ss);
|
---|
535 |
|
---|
536 | do
|
---|
537 | {
|
---|
538 | iter++;
|
---|
539 | status = gsl_multimin_fminimizer_iterate(s);
|
---|
540 |
|
---|
541 | if (status)
|
---|
542 | break;
|
---|
543 |
|
---|
544 | size = gsl_multimin_fminimizer_size (s);
|
---|
545 | status = gsl_multimin_test_size (size, 1e-2);
|
---|
546 |
|
---|
547 | if (status == GSL_SUCCESS)
|
---|
548 | {
|
---|
549 | printf ("converged to minimum at\n");
|
---|
550 | }
|
---|
551 |
|
---|
552 | printf ("%5d ", (int)iter);
|
---|
553 | for (i = 0; i < (size_t)np; i++)
|
---|
554 | {
|
---|
555 | printf ("%10.3e ", gsl_vector_get (s->x, i));
|
---|
556 | }
|
---|
557 | printf ("f() = %7.3f size = %.3f\n", s->fval, size);
|
---|
558 | }
|
---|
559 | while (status == GSL_CONTINUE && iter < 100);
|
---|
560 |
|
---|
561 | for (i=0;i<(size_t)np;i++)
|
---|
562 | gsl_vector_set(par->x, i, gsl_vector_get(s->x, i));
|
---|
563 | //gsl_vector_free(par->x);
|
---|
564 | gsl_vector_free(ss);
|
---|
565 | gsl_multimin_fminimizer_free (s);
|
---|
566 | };
|
---|