1 | /*
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2 | * molecule_geometry.cpp
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3 | *
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4 | * Created on: Oct 5, 2009
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5 | * Author: heber
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6 | */
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7 |
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8 | #include "Helpers/MemDebug.hpp"
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9 |
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10 | #include "atom.hpp"
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11 | #include "bond.hpp"
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12 | #include "config.hpp"
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13 | #include "element.hpp"
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14 | #include "helpers.hpp"
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15 | #include "leastsquaremin.hpp"
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16 | #include "log.hpp"
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17 | #include "memoryallocator.hpp"
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18 | #include "molecule.hpp"
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19 | #include "World.hpp"
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20 | #include "Plane.hpp"
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21 | #include <boost/foreach.hpp>
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22 |
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23 |
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24 | /************************************* Functions for class molecule *********************************/
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25 |
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26 |
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27 | /** Centers the molecule in the box whose lengths are defined by vector \a *BoxLengths.
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28 | * \param *out output stream for debugging
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29 | */
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30 | bool molecule::CenterInBox()
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31 | {
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32 | bool status = true;
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33 | const Vector *Center = DetermineCenterOfAll();
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34 | const Vector *CenterBox = DetermineCenterOfBox();
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35 | double * const cell_size = World::getInstance().getDomain();
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36 | double *M = ReturnFullMatrixforSymmetric(cell_size);
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37 | double *Minv = InverseMatrix(M);
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38 |
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39 | // go through all atoms
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40 | ActOnAllVectors( &Vector::SubtractVector, *Center);
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41 | ActOnAllVectors( &Vector::SubtractVector, *CenterBox);
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42 | ActOnAllVectors( &Vector::WrapPeriodically, (const double *)M, (const double *)Minv);
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43 |
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44 | delete[](M);
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45 | delete[](Minv);
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46 | delete(Center);
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47 | return status;
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48 | };
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49 |
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50 |
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51 | /** Bounds the molecule in the box whose lengths are defined by vector \a *BoxLengths.
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52 | * \param *out output stream for debugging
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53 | */
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54 | bool molecule::BoundInBox()
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55 | {
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56 | bool status = true;
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57 | double * const cell_size = World::getInstance().getDomain();
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58 | double *M = ReturnFullMatrixforSymmetric(cell_size);
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59 | double *Minv = InverseMatrix(M);
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60 |
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61 | // go through all atoms
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62 | ActOnAllVectors( &Vector::WrapPeriodically, (const double *)M, (const double *)Minv);
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63 |
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64 | delete[](M);
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65 | delete[](Minv);
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66 | return status;
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67 | };
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68 |
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69 | /** Centers the edge of the atoms at (0,0,0).
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70 | * \param *out output stream for debugging
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71 | * \param *max coordinates of other edge, specifying box dimensions.
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72 | */
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73 | void molecule::CenterEdge(Vector *max)
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74 | {
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75 | Vector *min = new Vector;
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76 |
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77 | // Log() << Verbose(3) << "Begin of CenterEdge." << endl;
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78 | molecule::const_iterator iter = begin(); // start at first in list
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79 | if (iter != end()) { //list not empty?
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80 | for (int i=NDIM;i--;) {
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81 | max->at(i) = (*iter)->x[i];
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82 | min->at(i) = (*iter)->x[i];
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83 | }
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84 | for (; iter != end(); ++iter) {// continue with second if present
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85 | //(*iter)->Output(1,1,out);
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86 | for (int i=NDIM;i--;) {
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87 | max->at(i) = (max->at(i) < (*iter)->x[i]) ? (*iter)->x[i] : max->at(i);
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88 | min->at(i) = (min->at(i) > (*iter)->x[i]) ? (*iter)->x[i] : min->at(i);
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89 | }
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90 | }
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91 | // Log() << Verbose(4) << "Maximum is ";
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92 | // max->Output(out);
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93 | // Log() << Verbose(0) << ", Minimum is ";
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94 | // min->Output(out);
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95 | // Log() << Verbose(0) << endl;
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96 | min->Scale(-1.);
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97 | (*max) += (*min);
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98 | Translate(min);
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99 | Center.Zero();
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100 | }
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101 | delete(min);
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102 | // Log() << Verbose(3) << "End of CenterEdge." << endl;
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103 | };
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104 |
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105 | /** Centers the center of the atoms at (0,0,0).
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106 | * \param *out output stream for debugging
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107 | * \param *center return vector for translation vector
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108 | */
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109 | void molecule::CenterOrigin()
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110 | {
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111 | int Num = 0;
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112 | molecule::const_iterator iter = begin(); // start at first in list
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113 |
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114 | Center.Zero();
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115 |
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116 | if (iter != end()) { //list not empty?
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117 | for (; iter != end(); ++iter) { // continue with second if present
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118 | Num++;
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119 | Center += (*iter)->x;
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120 | }
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121 | Center.Scale(-1./Num); // divide through total number (and sign for direction)
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122 | Translate(&Center);
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123 | Center.Zero();
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124 | }
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125 | };
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126 |
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127 | /** Returns vector pointing to center of all atoms.
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128 | * \return pointer to center of all vector
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129 | */
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130 | Vector * molecule::DetermineCenterOfAll() const
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131 | {
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132 | molecule::const_iterator iter = begin(); // start at first in list
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133 | Vector *a = new Vector();
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134 | double Num = 0;
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135 |
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136 | a->Zero();
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137 |
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138 | if (iter != end()) { //list not empty?
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139 | for (; iter != end(); ++iter) { // continue with second if present
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140 | Num++;
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141 | (*a) += (*iter)->x;
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142 | }
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143 | a->Scale(1./Num); // divide through total mass (and sign for direction)
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144 | }
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145 | return a;
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146 | };
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147 |
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148 | /** Returns vector pointing to center of the domain.
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149 | * \return pointer to center of the domain
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150 | */
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151 | Vector * molecule::DetermineCenterOfBox() const
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152 | {
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153 | Vector *a = new Vector(0.5,0.5,0.5);
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154 |
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155 | const double *cell_size = World::getInstance().getDomain();
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156 | double *M = ReturnFullMatrixforSymmetric(cell_size);
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157 | a->MatrixMultiplication(M);
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158 | delete[](M);
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159 |
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160 | return a;
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161 | };
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162 |
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163 | /** Returns vector pointing to center of gravity.
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164 | * \param *out output stream for debugging
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165 | * \return pointer to center of gravity vector
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166 | */
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167 | Vector * molecule::DetermineCenterOfGravity()
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168 | {
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169 | molecule::const_iterator iter = begin(); // start at first in list
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170 | Vector *a = new Vector();
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171 | Vector tmp;
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172 | double Num = 0;
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173 |
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174 | a->Zero();
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175 |
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176 | if (iter != end()) { //list not empty?
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177 | for (; iter != end(); ++iter) { // continue with second if present
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178 | Num += (*iter)->type->mass;
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179 | tmp = (*iter)->type->mass * (*iter)->x;
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180 | (*a) += tmp;
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181 | }
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182 | a->Scale(1./Num); // divide through total mass (and sign for direction)
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183 | }
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184 | // Log() << Verbose(1) << "Resulting center of gravity: ";
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185 | // a->Output(out);
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186 | // Log() << Verbose(0) << endl;
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187 | return a;
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188 | };
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189 |
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190 | /** Centers the center of gravity of the atoms at (0,0,0).
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191 | * \param *out output stream for debugging
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192 | * \param *center return vector for translation vector
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193 | */
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194 | void molecule::CenterPeriodic()
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195 | {
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196 | DeterminePeriodicCenter(Center);
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197 | };
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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::CenterAtVector(Vector *newcenter)
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205 | {
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206 | Center = *newcenter;
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207 | };
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208 |
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209 |
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210 | /** Scales all atoms by \a *factor.
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211 | * \param *factor pointer to scaling factor
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212 | *
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213 | * TODO: Is this realy what is meant, i.e.
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214 | * x=(x[0]*factor[0],x[1]*factor[1],x[2]*factor[2]) (current impl)
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215 | * or rather
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216 | * x=(**factor) * x (as suggested by comment)
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217 | */
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218 | void molecule::Scale(const double ** const factor)
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219 | {
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220 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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221 | for (int j=0;j<MDSteps;j++)
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222 | (*iter)->Trajectory.R.at(j).ScaleAll(*factor);
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223 | (*iter)->x.ScaleAll(*factor);
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224 | }
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225 | };
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226 |
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227 | /** Translate all atoms by given vector.
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228 | * \param trans[] translation vector.
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229 | */
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230 | void molecule::Translate(const Vector *trans)
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231 | {
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232 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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233 | for (int j=0;j<MDSteps;j++)
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234 | (*iter)->Trajectory.R.at(j) += (*trans);
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235 | (*iter)->x += (*trans);
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236 | }
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237 | };
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238 |
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239 | /** Translate the molecule periodically in the box.
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240 | * \param trans[] translation vector.
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241 | * TODO treatment of trajetories missing
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242 | */
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243 | void molecule::TranslatePeriodically(const Vector *trans)
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244 | {
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245 | double * const cell_size = World::getInstance().getDomain();
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246 | double *M = ReturnFullMatrixforSymmetric(cell_size);
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247 | double *Minv = InverseMatrix(M);
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248 |
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249 | // go through all atoms
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250 | ActOnAllVectors( &Vector::AddVector, *trans);
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251 | ActOnAllVectors( &Vector::WrapPeriodically, (const double *)M, (const double *)Minv);
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252 |
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253 | delete[](M);
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254 | delete[](Minv);
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255 | };
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256 |
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257 |
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258 | /** Mirrors all atoms against a given plane.
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259 | * \param n[] normal vector of mirror plane.
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260 | */
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261 | void molecule::Mirror(const Vector *n)
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262 | {
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263 | OBSERVE;
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264 | Plane p(*n,0);
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265 | BOOST_FOREACH( atom* iter, atoms ){
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266 | (*iter->node) = p.mirrorVector(*iter->node);
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267 | }
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268 | };
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269 |
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270 | /** Determines center of molecule (yet not considering atom masses).
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271 | * \param center reference to return vector
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272 | */
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273 | void molecule::DeterminePeriodicCenter(Vector ¢er)
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274 | {
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275 | double * const cell_size = World::getInstance().getDomain();
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276 | double *matrix = ReturnFullMatrixforSymmetric(cell_size);
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277 | double *inversematrix = InverseMatrix(matrix);
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278 | double tmp;
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279 | bool flag;
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280 | Vector Testvector, Translationvector;
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281 |
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282 | do {
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283 | Center.Zero();
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284 | flag = true;
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285 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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286 | #ifdef ADDHYDROGEN
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287 | if ((*iter)->type->Z != 1) {
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288 | #endif
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289 | Testvector = (*iter)->x;
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290 | Testvector.MatrixMultiplication(inversematrix);
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291 | Translationvector.Zero();
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292 | for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
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293 | if ((*iter)->nr < (*Runner)->GetOtherAtom((*iter))->nr) // otherwise we shift one to, the other fro and gain nothing
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294 | for (int j=0;j<NDIM;j++) {
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295 | tmp = (*iter)->x[j] - (*Runner)->GetOtherAtom(*iter)->x[j];
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296 | if ((fabs(tmp)) > BondDistance) {
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297 | flag = false;
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298 | DoLog(0) && (Log() << Verbose(0) << "Hit: atom " << (*iter)->getName() << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl);
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299 | if (tmp > 0)
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300 | Translationvector[j] -= 1.;
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301 | else
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302 | Translationvector[j] += 1.;
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303 | }
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304 | }
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305 | }
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306 | Testvector += Translationvector;
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307 | Testvector.MatrixMultiplication(matrix);
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308 | Center += Testvector;
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309 | Log() << Verbose(1) << "vector is: " << Testvector << endl;
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310 | #ifdef ADDHYDROGEN
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311 | // now also change all hydrogens
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312 | for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
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313 | if ((*Runner)->GetOtherAtom((*iter))->type->Z == 1) {
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314 | Testvector = (*Runner)->GetOtherAtom((*iter))->x;
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315 | Testvector.MatrixMultiplication(inversematrix);
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316 | Testvector += Translationvector;
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317 | Testvector.MatrixMultiplication(matrix);
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318 | Center += Testvector;
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319 | Log() << Verbose(1) << "Hydrogen vector is: " << Testvector << endl;
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320 | }
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321 | }
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322 | }
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323 | #endif
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324 | }
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325 | } while (!flag);
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326 | delete[](matrix);
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327 | delete[](inversematrix);
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328 |
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329 | Center.Scale(1./static_cast<double>(getAtomCount()));
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330 | };
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331 |
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332 | /** Transforms/Rotates the given molecule into its principal axis system.
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333 | * \param *out output stream for debugging
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334 | * \param DoRotate whether to rotate (true) or only to determine the PAS.
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335 | * TODO treatment of trajetories missing
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336 | */
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337 | void molecule::PrincipalAxisSystem(bool DoRotate)
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338 | {
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339 | double InertiaTensor[NDIM*NDIM];
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340 | Vector *CenterOfGravity = DetermineCenterOfGravity();
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341 |
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342 | CenterPeriodic();
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343 |
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344 | // reset inertia tensor
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345 | for(int i=0;i<NDIM*NDIM;i++)
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346 | InertiaTensor[i] = 0.;
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347 |
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348 | // sum up inertia tensor
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349 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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350 | Vector x = (*iter)->x;
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351 | //x.SubtractVector(CenterOfGravity);
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352 | InertiaTensor[0] += (*iter)->type->mass*(x[1]*x[1] + x[2]*x[2]);
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353 | InertiaTensor[1] += (*iter)->type->mass*(-x[0]*x[1]);
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354 | InertiaTensor[2] += (*iter)->type->mass*(-x[0]*x[2]);
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355 | InertiaTensor[3] += (*iter)->type->mass*(-x[1]*x[0]);
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356 | InertiaTensor[4] += (*iter)->type->mass*(x[0]*x[0] + x[2]*x[2]);
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357 | InertiaTensor[5] += (*iter)->type->mass*(-x[1]*x[2]);
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358 | InertiaTensor[6] += (*iter)->type->mass*(-x[2]*x[0]);
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359 | InertiaTensor[7] += (*iter)->type->mass*(-x[2]*x[1]);
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360 | InertiaTensor[8] += (*iter)->type->mass*(x[0]*x[0] + x[1]*x[1]);
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361 | }
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362 | // print InertiaTensor for debugging
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363 | DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << endl);
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364 | for(int i=0;i<NDIM;i++) {
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365 | for(int j=0;j<NDIM;j++)
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366 | DoLog(0) && (Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ");
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367 | DoLog(0) && (Log() << Verbose(0) << endl);
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368 | }
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369 | DoLog(0) && (Log() << Verbose(0) << endl);
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370 |
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371 | // diagonalize to determine principal axis system
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372 | gsl_eigen_symmv_workspace *T = gsl_eigen_symmv_alloc(NDIM);
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373 | gsl_matrix_view m = gsl_matrix_view_array(InertiaTensor, NDIM, NDIM);
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374 | gsl_vector *eval = gsl_vector_alloc(NDIM);
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375 | gsl_matrix *evec = gsl_matrix_alloc(NDIM, NDIM);
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376 | gsl_eigen_symmv(&m.matrix, eval, evec, T);
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377 | gsl_eigen_symmv_free(T);
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378 | gsl_eigen_symmv_sort(eval, evec, GSL_EIGEN_SORT_ABS_DESC);
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379 |
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380 | for(int i=0;i<NDIM;i++) {
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381 | DoLog(1) && (Log() << Verbose(1) << "eigenvalue = " << gsl_vector_get(eval, i));
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382 | DoLog(0) && (Log() << Verbose(0) << ", eigenvector = (" << evec->data[i * evec->tda + 0] << "," << evec->data[i * evec->tda + 1] << "," << evec->data[i * evec->tda + 2] << ")" << endl);
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383 | }
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384 |
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385 | // check whether we rotate or not
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386 | if (DoRotate) {
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387 | DoLog(1) && (Log() << Verbose(1) << "Transforming molecule into PAS ... ");
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388 | // the eigenvectors specify the transformation matrix
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389 | ActOnAllVectors( &Vector::MatrixMultiplication, (const double *) evec->data );
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390 | DoLog(0) && (Log() << Verbose(0) << "done." << endl);
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391 |
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392 | // summing anew for debugging (resulting matrix has to be diagonal!)
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393 | // reset inertia tensor
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394 | for(int i=0;i<NDIM*NDIM;i++)
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395 | InertiaTensor[i] = 0.;
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396 |
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397 | // sum up inertia tensor
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398 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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399 | Vector x = (*iter)->x;
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400 | InertiaTensor[0] += (*iter)->type->mass*(x[1]*x[1] + x[2]*x[2]);
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401 | InertiaTensor[1] += (*iter)->type->mass*(-x[0]*x[1]);
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402 | InertiaTensor[2] += (*iter)->type->mass*(-x[0]*x[2]);
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403 | InertiaTensor[3] += (*iter)->type->mass*(-x[1]*x[0]);
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404 | InertiaTensor[4] += (*iter)->type->mass*(x[0]*x[0] + x[2]*x[2]);
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405 | InertiaTensor[5] += (*iter)->type->mass*(-x[1]*x[2]);
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406 | InertiaTensor[6] += (*iter)->type->mass*(-x[2]*x[0]);
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407 | InertiaTensor[7] += (*iter)->type->mass*(-x[2]*x[1]);
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408 | InertiaTensor[8] += (*iter)->type->mass*(x[0]*x[0] + x[1]*x[1]);
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409 | }
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410 | // print InertiaTensor for debugging
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411 | DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << endl);
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412 | for(int i=0;i<NDIM;i++) {
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413 | for(int j=0;j<NDIM;j++)
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414 | DoLog(0) && (Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ");
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415 | DoLog(0) && (Log() << Verbose(0) << endl);
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416 | }
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417 | DoLog(0) && (Log() << Verbose(0) << endl);
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418 | }
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419 |
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420 | // free everything
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421 | delete(CenterOfGravity);
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422 | gsl_vector_free(eval);
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423 | gsl_matrix_free(evec);
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424 | };
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425 |
|
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426 |
|
---|
427 | /** Align all atoms in such a manner that given vector \a *n is along z axis.
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428 | * \param n[] alignment vector.
|
---|
429 | */
|
---|
430 | void molecule::Align(Vector *n)
|
---|
431 | {
|
---|
432 | double alpha, tmp;
|
---|
433 | Vector z_axis;
|
---|
434 | z_axis[0] = 0.;
|
---|
435 | z_axis[1] = 0.;
|
---|
436 | z_axis[2] = 1.;
|
---|
437 |
|
---|
438 | // rotate on z-x plane
|
---|
439 | DoLog(0) && (Log() << Verbose(0) << "Begin of Aligning all atoms." << endl);
|
---|
440 | alpha = atan(-n->at(0)/n->at(2));
|
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441 | DoLog(1) && (Log() << Verbose(1) << "Z-X-angle: " << alpha << " ... ");
|
---|
442 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
|
---|
443 | tmp = (*iter)->x[0];
|
---|
444 | (*iter)->x[0] = cos(alpha) * tmp + sin(alpha) * (*iter)->x[2];
|
---|
445 | (*iter)->x[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->x[2];
|
---|
446 | for (int j=0;j<MDSteps;j++) {
|
---|
447 | tmp = (*iter)->Trajectory.R.at(j)[0];
|
---|
448 | (*iter)->Trajectory.R.at(j)[0] = cos(alpha) * tmp + sin(alpha) * (*iter)->Trajectory.R.at(j)[2];
|
---|
449 | (*iter)->Trajectory.R.at(j)[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->Trajectory.R.at(j)[2];
|
---|
450 | }
|
---|
451 | }
|
---|
452 | // rotate n vector
|
---|
453 | tmp = n->at(0);
|
---|
454 | n->at(0) = cos(alpha) * tmp + sin(alpha) * n->at(2);
|
---|
455 | n->at(2) = -sin(alpha) * tmp + cos(alpha) * n->at(2);
|
---|
456 | DoLog(1) && (Log() << Verbose(1) << "alignment vector after first rotation: " << n << endl);
|
---|
457 |
|
---|
458 | // rotate on z-y plane
|
---|
459 | alpha = atan(-n->at(1)/n->at(2));
|
---|
460 | DoLog(1) && (Log() << Verbose(1) << "Z-Y-angle: " << alpha << " ... ");
|
---|
461 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
|
---|
462 | tmp = (*iter)->x[1];
|
---|
463 | (*iter)->x[1] = cos(alpha) * tmp + sin(alpha) * (*iter)->x[2];
|
---|
464 | (*iter)->x[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->x[2];
|
---|
465 | for (int j=0;j<MDSteps;j++) {
|
---|
466 | tmp = (*iter)->Trajectory.R.at(j)[1];
|
---|
467 | (*iter)->Trajectory.R.at(j)[1] = cos(alpha) * tmp + sin(alpha) * (*iter)->Trajectory.R.at(j)[2];
|
---|
468 | (*iter)->Trajectory.R.at(j)[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->Trajectory.R.at(j)[2];
|
---|
469 | }
|
---|
470 | }
|
---|
471 | // rotate n vector (for consistency check)
|
---|
472 | tmp = n->at(1);
|
---|
473 | n->at(1) = cos(alpha) * tmp + sin(alpha) * n->at(2);
|
---|
474 | n->at(2) = -sin(alpha) * tmp + cos(alpha) * n->at(2);
|
---|
475 |
|
---|
476 |
|
---|
477 | DoLog(1) && (Log() << Verbose(1) << "alignment vector after second rotation: " << n << endl);
|
---|
478 | DoLog(0) && (Log() << Verbose(0) << "End of Aligning all atoms." << endl);
|
---|
479 | };
|
---|
480 |
|
---|
481 |
|
---|
482 | /** Calculates sum over least square distance to line hidden in \a *x.
|
---|
483 | * \param *x offset and direction vector
|
---|
484 | * \param *params pointer to lsq_params structure
|
---|
485 | * \return \f$ sum_i^N | y_i - (a + t_i b)|^2\f$
|
---|
486 | */
|
---|
487 | double LeastSquareDistance (const gsl_vector * x, void * params)
|
---|
488 | {
|
---|
489 | double res = 0, t;
|
---|
490 | Vector a,b,c,d;
|
---|
491 | struct lsq_params *par = (struct lsq_params *)params;
|
---|
492 |
|
---|
493 | // initialize vectors
|
---|
494 | a[0] = gsl_vector_get(x,0);
|
---|
495 | a[1] = gsl_vector_get(x,1);
|
---|
496 | a[2] = gsl_vector_get(x,2);
|
---|
497 | b[0] = gsl_vector_get(x,3);
|
---|
498 | b[1] = gsl_vector_get(x,4);
|
---|
499 | b[2] = gsl_vector_get(x,5);
|
---|
500 | // go through all atoms
|
---|
501 | for (molecule::const_iterator iter = par->mol->begin(); iter != par->mol->end(); ++iter) {
|
---|
502 | if ((*iter)->type == ((struct lsq_params *)params)->type) { // for specific type
|
---|
503 | c = (*iter)->x - a;
|
---|
504 | t = c.ScalarProduct(b); // get direction parameter
|
---|
505 | d = t*b; // and create vector
|
---|
506 | c -= d; // ... yielding distance vector
|
---|
507 | res += d.ScalarProduct(d); // add squared distance
|
---|
508 | }
|
---|
509 | }
|
---|
510 | return res;
|
---|
511 | };
|
---|
512 |
|
---|
513 | /** By minimizing the least square distance gains alignment vector.
|
---|
514 | * \bug this is not yet working properly it seems
|
---|
515 | */
|
---|
516 | void molecule::GetAlignvector(struct lsq_params * par) const
|
---|
517 | {
|
---|
518 | int np = 6;
|
---|
519 |
|
---|
520 | const gsl_multimin_fminimizer_type *T =
|
---|
521 | gsl_multimin_fminimizer_nmsimplex;
|
---|
522 | gsl_multimin_fminimizer *s = NULL;
|
---|
523 | gsl_vector *ss;
|
---|
524 | gsl_multimin_function minex_func;
|
---|
525 |
|
---|
526 | size_t iter = 0, i;
|
---|
527 | int status;
|
---|
528 | double size;
|
---|
529 |
|
---|
530 | /* Initial vertex size vector */
|
---|
531 | ss = gsl_vector_alloc (np);
|
---|
532 |
|
---|
533 | /* Set all step sizes to 1 */
|
---|
534 | gsl_vector_set_all (ss, 1.0);
|
---|
535 |
|
---|
536 | /* Starting point */
|
---|
537 | par->x = gsl_vector_alloc (np);
|
---|
538 | par->mol = this;
|
---|
539 |
|
---|
540 | gsl_vector_set (par->x, 0, 0.0); // offset
|
---|
541 | gsl_vector_set (par->x, 1, 0.0);
|
---|
542 | gsl_vector_set (par->x, 2, 0.0);
|
---|
543 | gsl_vector_set (par->x, 3, 0.0); // direction
|
---|
544 | gsl_vector_set (par->x, 4, 0.0);
|
---|
545 | gsl_vector_set (par->x, 5, 1.0);
|
---|
546 |
|
---|
547 | /* Initialize method and iterate */
|
---|
548 | minex_func.f = &LeastSquareDistance;
|
---|
549 | minex_func.n = np;
|
---|
550 | minex_func.params = (void *)par;
|
---|
551 |
|
---|
552 | s = gsl_multimin_fminimizer_alloc (T, np);
|
---|
553 | gsl_multimin_fminimizer_set (s, &minex_func, par->x, ss);
|
---|
554 |
|
---|
555 | do
|
---|
556 | {
|
---|
557 | iter++;
|
---|
558 | status = gsl_multimin_fminimizer_iterate(s);
|
---|
559 |
|
---|
560 | if (status)
|
---|
561 | break;
|
---|
562 |
|
---|
563 | size = gsl_multimin_fminimizer_size (s);
|
---|
564 | status = gsl_multimin_test_size (size, 1e-2);
|
---|
565 |
|
---|
566 | if (status == GSL_SUCCESS)
|
---|
567 | {
|
---|
568 | printf ("converged to minimum at\n");
|
---|
569 | }
|
---|
570 |
|
---|
571 | printf ("%5d ", (int)iter);
|
---|
572 | for (i = 0; i < (size_t)np; i++)
|
---|
573 | {
|
---|
574 | printf ("%10.3e ", gsl_vector_get (s->x, i));
|
---|
575 | }
|
---|
576 | printf ("f() = %7.3f size = %.3f\n", s->fval, size);
|
---|
577 | }
|
---|
578 | while (status == GSL_CONTINUE && iter < 100);
|
---|
579 |
|
---|
580 | for (i=0;i<(size_t)np;i++)
|
---|
581 | gsl_vector_set(par->x, i, gsl_vector_get(s->x, i));
|
---|
582 | //gsl_vector_free(par->x);
|
---|
583 | gsl_vector_free(ss);
|
---|
584 | gsl_multimin_fminimizer_free (s);
|
---|
585 | };
|
---|