1 | /*
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2 | * Project: MoleCuilder
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3 | * Description: creates and alters molecular systems
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4 | * Copyright (C) 2012 University of Bonn. All rights reserved.
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5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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6 | *
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7 | *
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8 | * This file is part of MoleCuilder.
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9 | *
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10 | * MoleCuilder is free software: you can redistribute it and/or modify
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11 | * it under the terms of the GNU General Public License as published by
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12 | * the Free Software Foundation, either version 2 of the License, or
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13 | * (at your option) any later version.
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14 | *
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15 | * MoleCuilder is distributed in the hope that it will be useful,
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16 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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17 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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18 | * GNU General Public License for more details.
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19 | *
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20 | * You should have received a copy of the GNU General Public License
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21 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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22 | */
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23 |
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24 | /*
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25 | * LinkedCell_Controller.cpp
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26 | *
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27 | * Created on: Nov 15, 2011
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28 | * Author: heber
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29 | */
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30 |
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31 | // include config.h
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32 | #ifdef HAVE_CONFIG_H
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33 | #include <config.h>
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34 | #endif
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35 |
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36 | //#include "CodePatterns/MemDebug.hpp"
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37 |
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38 | #include <set>
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39 |
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40 | #include "Box.hpp"
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41 | #include "CodePatterns/Assert.hpp"
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42 | #include "CodePatterns/Log.hpp"
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43 | #include "CodePatterns/Observer/Notification.hpp"
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44 | #include "CodePatterns/Range.hpp"
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45 | #include "LinkedCell_Controller.hpp"
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46 | #include "LinkedCell_Model.hpp"
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47 | #include "LinkedCell_View.hpp"
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48 | #include "LinkedCell_View_ModelWrapper.hpp"
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49 | #include "IPointCloud.hpp"
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50 | #include "WorldTime.hpp"
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51 |
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52 |
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53 | using namespace LinkedCell;
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54 |
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55 | double LinkedCell_Controller::lower_threshold = 1.;
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56 | double LinkedCell_Controller::upper_threshold = 20.;
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57 |
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58 | /** Constructor of class LinkedCell_Controller.
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59 | *
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60 | */
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61 | LinkedCell_Controller::LinkedCell_Controller(const Box &_domain) :
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62 | Observer("LinkedCell_Controller"),
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63 | domain(_domain)
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64 | {
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65 | // sign on to specific notifications
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66 | domain.signOn(this, Box::MatrixChanged);
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67 | WorldTime::getInstance().signOn(this, WorldTime::TimeChanged);
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68 |
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69 | /// Check that upper_threshold fits within half the box.
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70 | Vector diagonal(1.,1.,1.);
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71 | diagonal.Scale(upper_threshold);
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72 | Vector diagonal_transformed = domain.getMinv() * diagonal;
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73 | double max_factor = 1.;
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74 | for (size_t i=0; i<NDIM; ++i)
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75 | if (diagonal_transformed.at(i) > 1./max_factor)
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76 | max_factor = 1./diagonal_transformed.at(i);
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77 | upper_threshold *= max_factor;
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78 |
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79 | /// Check that lower_threshold is still lower, if not set to half times upper_threshold.
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80 | if (lower_threshold > upper_threshold)
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81 | lower_threshold = 0.5*upper_threshold;
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82 | }
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83 |
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84 | /** Destructor of class LinkedCell_Controller.
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85 | *
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86 | * Here, we free all LinkedCell_Model instances again.
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87 | *
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88 | */
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89 | LinkedCell_Controller::~LinkedCell_Controller()
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90 | {
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91 | // sign off
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92 | domain.signOff(this, Box::MatrixChanged);
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93 | WorldTime::getInstance().signOff(this, WorldTime::TimeChanged);
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94 |
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95 | /// we free all LinkedCell_Model instances again.
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96 | for(MapEdgelengthModel::iterator iter = ModelsMap.begin();
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97 | !ModelsMap.empty(); iter = ModelsMap.begin()) {
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98 | delete iter->second;
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99 | ModelsMap.erase(iter);
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100 | }
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101 | }
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102 |
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103 | /** Internal function to obtain the range within which an model is suitable.
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104 | *
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105 | * \note We use statics lower_threshold and upper_threshold as min and max
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106 | * boundaries.
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107 | *
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108 | * @param distance desired egde length
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109 | * @return range within which model edge length is acceptable
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110 | */
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111 | const range<double> LinkedCell_Controller::getHeuristicRange(const double distance) const
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112 | {
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113 | const double lower = 0.5*distance < lower_threshold ? lower_threshold : 0.5*distance;
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114 | const double upper = 2.*distance > upper_threshold ? upper_threshold : 2.*distance;
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115 | range<double> HeuristicInterval(lower, upper);
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116 | return HeuristicInterval;
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117 | }
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118 |
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119 | static size_t checkLengthsLess(
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120 | const Vector &Lengths,
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121 | const double min_distance)
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122 | {
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123 | size_t counter=0;
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124 | for (size_t i=0;i<NDIM;++i) {
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125 | if (Lengths[i] < min_distance)
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126 | ++counter;
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127 | }
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128 | return counter;
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129 | }
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130 |
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131 | /** Given some given \a distance return it such that it is larger equal than some minimum
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132 | * sensible value with respect to the current domain.
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133 | *
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134 | * The sensible minimum distance \f$\Delta\f$ is computed as follows:
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135 | * \f$ \frac {l_1} \Delta \frac {l_2} \Delta \frac {l_3} \Delta \leq M \f$, where M is the
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136 | * maximum number of linked cells. Where some additional thought must be given
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137 | * to rounding issues. Hence, we calculate \f$ (\frac {l_i} d)^{\frac 1 d}+.5\f$,
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138 | * where d is the assumed dimensionality of the domain: d=3 for cubic, d=2 for
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139 | * a planar, d=1 for a bar-like system.
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140 | *
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141 | * \param distance distance compared with minimum value
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142 | * \return minimum sensible value or \a distance if larger
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143 | */
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144 | double LinkedCell_Controller::getMinimumSensibleLength(double distance) const
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145 | {
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146 | // first check the box with respect to the given distance
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147 | // as we must not generate more than 10^3 cells per axis due to
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148 | // memory constraints
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149 | const RealSpaceMatrix &M = domain.getM();
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150 | RealSpaceMatrix UnitMatrix;
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151 | UnitMatrix.setIdentity();
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152 | UnitMatrix *= M;
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153 | Vector Lengths = UnitMatrix.transformToEigenbasis();
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154 | double max_length = 0.;
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155 | double volume = 1.;
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156 | double min_distance = lower_threshold;
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157 | for (size_t dim=NDIM; dim>0; --dim) {
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158 | const double fraction = pow(MAX_LINKEDCELLNODES+1., 1./(double)dim);
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159 | for (size_t i=0;i<NDIM;++i) {
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160 | max_length = std::max(Lengths[i], max_length);
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161 | // the length dropping out for dimensionality less than 3 must appear
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162 | // just as factor of 1 not less.
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163 | if (Lengths[i] < min_distance)
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164 | volume *= pow(min_distance, 1./(double)dim)+.5;
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165 | else
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166 | volume *= pow(Lengths[i], 1./(double)dim)+.5; //.5 for rounding issues
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167 | }
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168 | min_distance = volume/fraction;
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169 | // assuming a (cubic-like) 3d system
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170 | if (checkLengthsLess(Lengths, min_distance) == 0)
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171 | break;
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172 | }
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173 | if (distance < min_distance) {
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174 | LOG(1, "INFO: Setting LC distance from given " << distance
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175 | << " to " << min_distance << " due to box size.");
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176 | distance = min_distance;
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177 | }
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178 | return distance;
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179 | }
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180 |
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181 | /** Internal function to decide whether a suitable model is present or not.
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182 | *
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183 | * Here, the heuristic for deciding whether a new linked cell structure has to
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184 | * be constructed or not is implemented. The current heuristic is as follows:
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185 | * -# the best model should have at least half the desired length (such
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186 | * that most we have to look two neighbor shells wide and not one).
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187 | * -# the best model should have at most twice the desired length but
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188 | * no less than 1 angstroem.
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189 | *
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190 | * \note Dealing out a pointer is here (hopefully) safe because the function is
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191 | * internal and we - inside this class - know what we are doing.
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192 | *
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193 | * @param distance edge length of the requested linked cell structure
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194 | * @return NULL - there is no fitting LinkedCell_Model, else - pointer to instance
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195 | */
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196 | const LinkedCell_Model *LinkedCell_Controller::getBestModel(double distance) const
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197 | {
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198 | /// Bound distance to be within [lower_threshold, upper_threshold).
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199 | /// Note that we need to stay away from upper boundary a bit,
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200 | /// otherwise the distance will end up outside of the interval.
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201 | if (distance < lower_threshold)
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202 | distance = lower_threshold;
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203 | if (distance > upper_threshold)
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204 | distance = upper_threshold - std::numeric_limits<double>::round_error();
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205 |
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206 | /// Look for all models within [0.5 distance, 2. distance).
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207 | MapEdgelengthModel::const_iterator bestmatch = ModelsMap.end();
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208 | if (!ModelsMap.empty()) {
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209 | for(MapEdgelengthModel::const_iterator iter = ModelsMap.begin();
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210 | iter != ModelsMap.end(); ++iter) {
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211 | // check that we are truely within range
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212 | range<double> HeuristicInterval(getHeuristicRange(iter->first));
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213 | if (HeuristicInterval.isInRange(distance)) {
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214 | // if it's the first match or a closer one, pick
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215 | if ((bestmatch == ModelsMap.end())
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216 | || (fabs(bestmatch->first - distance) > fabs(iter->first - distance)))
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217 | bestmatch = iter;
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218 | }
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219 | }
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220 | }
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221 |
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222 | /// Return best match or NULL if none found.
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223 | if (bestmatch != ModelsMap.end())
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224 | return bestmatch->second;
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225 | else
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226 | return NULL;
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227 | }
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228 |
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229 | /** Internal function to insert a new model and check for valid insertion.
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230 | *
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231 | * @param distance edge length of new model
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232 | * @param instance pointer to model
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233 | */
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234 | void LinkedCell_Controller::insertNewModel(const double edgelength, const LinkedCell_Model* instance)
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235 | {
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236 | std::pair< MapEdgelengthModel::iterator, bool> inserter =
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237 | ModelsMap.insert( std::make_pair(edgelength, instance) );
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238 | ASSERT(inserter.second,
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239 | "LinkedCell_Controller::getView() - LinkedCell_Model instance with distance "
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240 | +toString(edgelength)+" already present.");
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241 | }
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242 |
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243 | /** Returns the a suitable LinkedCell_Model contained in a LinkedCell_View
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244 | * for the requested \a distance.
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245 | *
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246 | * \sa getBestModel()
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247 | *
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248 | * @param distance edge length of the requested linked cell structure
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249 | * @param set of initial points to insert when new model is created (not always), should be World's
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250 | * @return LinkedCell_View wrapping the best LinkedCell_Model
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251 | */
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252 | LinkedCell_View LinkedCell_Controller::getView(const double distance, IPointCloud &set)
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253 | {
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254 | // distance should be a given minimum length dependent on domain at least
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255 | const double ConstraintDistance = getMinimumSensibleLength(distance);
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256 |
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257 | /// Look for best instance.
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258 | const LinkedCell_Model * const LCModel_best = getBestModel(ConstraintDistance);
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259 |
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260 | /// Construct new instance if none found,
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261 | if (LCModel_best == NULL) {
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262 | LinkedCell_Model * const LCModel_new = new LinkedCell_Model(ConstraintDistance, domain);
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263 | LCModel_new->insertPointCloud(set);
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264 | insertNewModel(ConstraintDistance, LCModel_new);
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265 | LinkedCell_View view(*LCModel_new);
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266 | return view;
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267 | } else {
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268 | /// else construct interface and return.
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269 | LinkedCell_View view(*LCModel_best);
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270 | return view;
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271 | }
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272 | }
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273 |
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274 | /** Internal function to re-create all present and used models for the new Box.
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275 | *
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276 | * This is necessary in the following cases:
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277 | * -# the Box is changed
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278 | * -# we step on to a different time step, i.e. all atomic positions change
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279 | *
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280 | * The main problem are the views currently in use.
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281 | *
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282 | * We make use of LinkedCell:LinkedCell_View::RAIIMap as there all present are
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283 | * listed. We go through the list, create a map with old model ref as keys to
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284 | * just newly created ones, and finally go again through each view and exchange
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285 | * the model against the new ones via a simple map lookup.
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286 | *
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287 | */
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288 | void LinkedCell_Controller::updateModels()
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289 | {
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290 | LOG(1, "INFO: Updating all models.");
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291 |
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292 | typedef std::map<const LinkedCell_Model *, LinkedCell_Model *> ModelLookup;
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293 | ModelLookup models;
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294 |
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295 | // set up map, for now with NULL pointers
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296 | for (LinkedCell_View::ModelInstanceMap::const_iterator iter = LinkedCell_View::RAIIMap.begin();
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297 | iter != LinkedCell_View::RAIIMap.end(); ++iter) {
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298 | #ifndef NDEBUG
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299 | std::pair< ModelLookup::iterator, bool > inserter =
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300 | #endif
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301 | models.insert( std::pair<const LinkedCell_Model *, LinkedCell_Model *>( (*iter)->LC->getModel(), NULL) );
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302 | LOG(2, "INFO: Added " << (*iter)->LC->getModel() << " to list of models to replace.");
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303 | ASSERT( inserter.second,
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304 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - failed to insert old model "
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305 | +toString( (*iter)->LC->getModel() )+",NULL into models, is already present");
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306 | }
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307 |
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308 | // invert MapEdgelengthModel
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309 | LOG(2, "INFO: ModelsMap is " << ModelsMap << ".");
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310 | typedef std::map<const LinkedCell_Model*, double > MapEdgelengthModel_inverted;
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311 | MapEdgelengthModel_inverted ModelsMap_inverted;
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312 | for (MapEdgelengthModel::const_iterator iter = ModelsMap.begin();
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313 | iter != ModelsMap.end(); ++iter) {
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314 | #ifndef NDEBUG
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315 | MapEdgelengthModel_inverted::const_iterator assertiter = ModelsMap_inverted.find(iter->second);
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316 | ASSERT( assertiter == ModelsMap_inverted.end(),
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317 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - ModelsMap is not invertible, value "
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318 | +toString(iter->second)+" is already present.");
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319 | #endif
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320 | ModelsMap_inverted.insert( std::make_pair(iter->second, iter->first) );
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321 | }
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322 | LOG(2, "INFO: Inverted ModelsMap is " << ModelsMap_inverted << ".");
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323 |
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324 | // go through map and re-create models
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325 | for (ModelLookup::iterator iter = models.begin(); iter != models.end(); ++iter) {
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326 | // delete old model
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327 | const LinkedCell_Model * const oldref = iter->first;
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328 | #ifndef NDEBUG
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329 | MapEdgelengthModel_inverted::const_iterator assertiter = ModelsMap_inverted.find(oldref);
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330 | ASSERT( assertiter != ModelsMap_inverted.end(),
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331 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - ModelsMap_inverted does not contain old model "
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332 | +toString(oldref)+".");
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333 | #endif
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334 | const double distance = ModelsMap_inverted[oldref];
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335 | // create new one, afterwards erase old model (this is for unit test to get different memory addresses)
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336 | LinkedCell_Model * const newref = new LinkedCell_Model(distance, domain);
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337 | MapEdgelengthModel::iterator oldmodeliter = ModelsMap.find(distance);
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338 | delete oldmodeliter->second;
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339 | ModelsMap.erase(oldmodeliter);
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340 | LOG(2, "INFO: oldref is " << oldref << ", newref is " << newref << ".");
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341 | iter->second = newref;
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342 | // replace in ModelsMap
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343 | #ifndef NDEBUG
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344 | std::pair< MapEdgelengthModel::iterator, bool > inserter =
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345 | #endif
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346 | ModelsMap.insert( std::make_pair(distance, newref) );
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347 | ASSERT( inserter.second,
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348 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - failed to insert new model "
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349 | +toString(distance)+","+toString(newref)+" into ModelsMap, is already present");
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350 | }
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351 |
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352 | // remove all remaining active models (also those that don't have an active View on them)
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353 | for (MapEdgelengthModel::iterator iter = ModelsMap.begin();
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354 | !ModelsMap.empty();
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355 | iter = ModelsMap.begin()) {
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356 | delete iter->second;
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357 | ModelsMap.erase(iter);
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358 | }
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359 |
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360 |
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361 | // delete inverted map for safety (values are gone)
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362 | ModelsMap_inverted.clear();
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363 |
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364 | // go through views and exchange the models
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365 | for (LinkedCell_View::ModelInstanceMap::const_iterator iter = LinkedCell_View::RAIIMap.begin();
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366 | iter != LinkedCell_View::RAIIMap.end(); ++iter) {
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367 | ModelLookup::const_iterator modeliter = models.find((*iter)->LC->getModel());
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368 | ASSERT( modeliter != models.end(),
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369 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - we miss a model "
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370 | +toString((*iter)->LC->getModel())+" in ModelLookup.");
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371 | // this is ugly but the only place where we have to set ourselves over the constness of the member variable
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372 | if (modeliter != models.end()) {
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373 | LOG(2, "INFO: Setting model to " << modeliter->second << " in view " << *iter << ".");
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374 | (*iter)->LC->setModel(modeliter->second);
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375 | }
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376 | }
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377 | }
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378 |
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379 | /** Callback function for Observer mechanism.
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380 | *
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381 | * @param publisher reference to the Observable that calls
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382 | */
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383 | void LinkedCell_Controller::update(Observable *publisher)
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384 | {
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385 | ELOG(2, "LinkedCell_Model received inconclusive general update from "
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386 | << publisher << ".");
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387 | }
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388 |
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389 | /** Callback function for the Notifications mechanism.
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390 | *
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391 | * @param publisher reference to the Observable that calls
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392 | * @param notification specific notification as cause of the call
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393 | */
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394 | void LinkedCell_Controller::recieveNotification(Observable *publisher, Notification_ptr notification)
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395 | {
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396 | if (publisher == &domain) {
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397 | switch(notification->getChannelNo()) {
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398 | case Box::MatrixChanged:
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399 | LOG(1, "INFO: LinkedCell_Controller got update from Box.");
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400 | updateModels();
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401 | break;
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402 | default:
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403 | ASSERT(0,
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404 | "LinkedCell_Controller::recieveNotification() - unwanted notification from Box "
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405 | +toString(notification->getChannelNo())+" received.");
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406 | break;
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407 | }
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408 | } else if (publisher == WorldTime::getPointer()) {
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409 | switch(notification->getChannelNo()) {
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410 | case WorldTime::TimeChanged:
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411 | LOG(1, "INFO: LinkedCell_Controller got update from WorldTime.");
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412 | updateModels();
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413 | break;
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414 | default:
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415 | ASSERT(0,
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416 | "LinkedCell_Controller::recieveNotification() - unwanted notification from WorldTime "
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417 | +toString(notification->getChannelNo())+" received.");
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418 | break;
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419 | }
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420 | } else {
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421 | ELOG(1, "Notification " << notification->getChannelNo()
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422 | << " from unknown publisher " << publisher << ".");
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423 | }
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424 | }
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425 |
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426 | /** Callback function when an Observer dies.
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427 | *
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428 | * @param publisher reference to the Observable that calls
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429 | */
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430 | void LinkedCell_Controller::subjectKilled(Observable *publisher)
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431 | {}
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432 |
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