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 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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6 | */
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7 |
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8 | /*
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9 | * LinkedCell_Controller.cpp
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10 | *
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11 | * Created on: Nov 15, 2011
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12 | * Author: heber
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13 | */
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14 |
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15 | // include config.h
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16 | #ifdef HAVE_CONFIG_H
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17 | #include <config.h>
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18 | #endif
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19 |
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20 | #include "CodePatterns/MemDebug.hpp"
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21 |
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22 | #include <set>
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23 |
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24 | #include "Box.hpp"
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25 | #include "CodePatterns/Assert.hpp"
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26 | #include "CodePatterns/Log.hpp"
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27 | #include "CodePatterns/Observer/Notification.hpp"
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28 | #include "CodePatterns/Range.hpp"
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29 | #include "LinkedCell_Controller.hpp"
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30 | #include "LinkedCell_Model.hpp"
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31 | #include "LinkedCell_View.hpp"
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32 | #include "LinkedCell_View_ModelWrapper.hpp"
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33 | #include "IPointCloud.hpp"
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34 | #include "WorldTime.hpp"
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35 |
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36 |
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37 | using namespace LinkedCell;
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38 |
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39 | double LinkedCell_Controller::lower_threshold = 1.;
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40 | double LinkedCell_Controller::upper_threshold = 20.;
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41 |
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42 | /** Constructor of class LinkedCell_Controller.
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43 | *
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44 | */
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45 | LinkedCell_Controller::LinkedCell_Controller(const Box &_domain) :
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46 | Observer("LinkedCell_Controller"),
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47 | domain(_domain)
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48 | {
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49 | // sign on to specific notifications
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50 | domain.signOn(this, Box::MatrixChanged);
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51 | WorldTime::getInstance().signOn(this, WorldTime::TimeChanged);
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52 |
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53 | /// Check that upper_threshold fits within half the box.
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54 | Vector diagonal(1.,1.,1.);
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55 | diagonal.Scale(upper_threshold);
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56 | Vector diagonal_transformed = domain.getMinv() * diagonal;
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57 | double max_factor = 1.;
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58 | for (size_t i=0; i<NDIM; ++i)
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59 | if (diagonal_transformed.at(i) > 1./max_factor)
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60 | max_factor = 1./diagonal_transformed.at(i);
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61 | upper_threshold *= max_factor;
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62 |
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63 | /// Check that lower_threshold is still lower, if not set to half times upper_threshold.
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64 | if (lower_threshold > upper_threshold)
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65 | lower_threshold = 0.5*upper_threshold;
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66 | }
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67 |
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68 | /** Destructor of class LinkedCell_Controller.
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69 | *
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70 | * Here, we free all LinkedCell_Model instances again.
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71 | *
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72 | */
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73 | LinkedCell_Controller::~LinkedCell_Controller()
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74 | {
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75 | // sign off
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76 | domain.signOff(this, Box::MatrixChanged);
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77 | WorldTime::getInstance().signOff(this, WorldTime::TimeChanged);
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78 |
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79 | /// we free all LinkedCell_Model instances again.
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80 | for(MapEdgelengthModel::iterator iter = ModelsMap.begin();
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81 | !ModelsMap.empty(); iter = ModelsMap.begin()) {
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82 | delete iter->second;
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83 | ModelsMap.erase(iter);
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84 | }
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85 | }
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86 |
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87 | /** Internal function to obtain the range within which an model is suitable.
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88 | *
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89 | * \note We use statics lower_threshold and upper_threshold as min and max
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90 | * boundaries.
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91 | *
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92 | * @param distance desired egde length
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93 | * @return range within which model edge length is acceptable
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94 | */
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95 | const range<double> LinkedCell_Controller::getHeuristicRange(const double distance) const
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96 | {
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97 | const double lower = 0.5*distance < lower_threshold ? lower_threshold : 0.5*distance;
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98 | const double upper = 2.*distance > upper_threshold ? upper_threshold : 2.*distance;
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99 | range<double> HeuristicInterval(lower, upper);
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100 | return HeuristicInterval;
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101 | }
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102 |
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103 | /** Internal function to decide whether a suitable model is present or not.
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104 | *
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105 | * Here, the heuristic for deciding whether a new linked cell structure has to
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106 | * be constructed or not is implemented. The current heuristic is as follows:
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107 | * -# the best model should have at least half the desired length (such
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108 | * that most we have to look two neighbor shells wide and not one).
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109 | * -# the best model should have at most twice the desired length but
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110 | * no less than 1 angstroem.
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111 | *
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112 | * \note Dealing out a pointer is here (hopefully) safe because the function is
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113 | * internal and we - inside this class - know what we are doing.
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114 | *
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115 | * @param distance edge length of the requested linked cell structure
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116 | * @return NULL - there is no fitting LinkedCell_Model, else - pointer to instance
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117 | */
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118 | const LinkedCell_Model *LinkedCell_Controller::getBestModel(double distance) const
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119 | {
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120 | /// Bound distance to be within [lower_threshold, upper_threshold).
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121 | /// Note that we need to stay away from upper boundary a bit,
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122 | /// otherwise the distance will end up outside of the interval.
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123 | if (distance < lower_threshold)
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124 | distance = lower_threshold;
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125 | if (distance > upper_threshold)
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126 | distance = upper_threshold - std::numeric_limits<double>::round_error();
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127 |
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128 | /// Look for all models within [0.5 distance, 2. distance).
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129 | MapEdgelengthModel::const_iterator bestmatch = ModelsMap.end();
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130 | if (!ModelsMap.empty()) {
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131 | for(MapEdgelengthModel::const_iterator iter = ModelsMap.begin();
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132 | iter != ModelsMap.end(); ++iter) {
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133 | // check that we are truely within range
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134 | range<double> HeuristicInterval(getHeuristicRange(iter->first));
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135 | if (HeuristicInterval.isInRange(distance)) {
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136 | // if it's the first match or a closer one, pick
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137 | if ((bestmatch == ModelsMap.end())
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138 | || (fabs(bestmatch->first - distance) > fabs(iter->first - distance)))
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139 | bestmatch = iter;
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140 | }
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141 | }
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142 | }
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143 |
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144 | /// Return best match or NULL if none found.
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145 | if (bestmatch != ModelsMap.end())
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146 | return bestmatch->second;
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147 | else
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148 | return NULL;
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149 | }
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150 |
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151 | /** Internal function to insert a new model and check for valid insertion.
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152 | *
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153 | * @param distance edge length of new model
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154 | * @param instance pointer to model
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155 | */
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156 | void LinkedCell_Controller::insertNewModel(const double edgelength, const LinkedCell_Model* instance)
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157 | {
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158 | std::pair< MapEdgelengthModel::iterator, bool> inserter =
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159 | ModelsMap.insert( std::make_pair(edgelength, instance) );
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160 | ASSERT(inserter.second,
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161 | "LinkedCell_Controller::getView() - LinkedCell_Model instance with distance "
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162 | +toString(edgelength)+" already present.");
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163 | }
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164 |
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165 | /** Returns the a suitable LinkedCell_Model contained in a LinkedCell_View
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166 | * for the requested \a distance.
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167 | *
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168 | * \sa getBestModel()
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169 | *
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170 | * @param distance edge length of the requested linked cell structure
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171 | * @param set of initial points to insert when new model is created (not always), should be World's
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172 | * @return LinkedCell_View wrapping the best LinkedCell_Model
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173 | */
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174 | LinkedCell_View LinkedCell_Controller::getView(const double distance, IPointCloud &set)
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175 | {
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176 | /// Look for best instance.
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177 | const LinkedCell_Model * const LCModel_best = getBestModel(distance);
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178 |
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179 | /// Construct new instance if none found,
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180 | if (LCModel_best == NULL) {
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181 | LinkedCell_Model * const LCModel_new = new LinkedCell_Model(distance, domain);
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182 | LCModel_new->insertPointCloud(set);
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183 | insertNewModel(distance, LCModel_new);
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184 | LinkedCell_View view(*LCModel_new);
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185 | return view;
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186 | } else {
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187 | /// else construct interface and return.
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188 | LinkedCell_View view(*LCModel_best);
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189 | return view;
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190 | }
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191 | }
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192 |
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193 | /** Internal function to re-create all present and used models for the new Box.
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194 | *
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195 | * This is necessary in the following cases:
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196 | * -# the Box is changed
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197 | * -# we step on to a different time step, i.e. all atomic positions change
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198 | *
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199 | * The main problem are the views currently in use.
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200 | *
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201 | * We make use of LinkedCell:LinkedCell_View::RAIIMap as there all present are
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202 | * listed. We go through the list, create a map with old model ref as keys to
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203 | * just newly created ones, and finally go again through each view and exchange
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204 | * the model against the new ones via a simple map lookup.
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205 | *
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206 | */
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207 | void LinkedCell_Controller::updateModels()
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208 | {
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209 | LOG(1, "INFO: Updating all models.");
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210 |
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211 | typedef std::map<const LinkedCell_Model *, LinkedCell_Model *> ModelLookup;
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212 | ModelLookup models;
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213 |
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214 | // set up map, for now with NULL pointers
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215 | for (LinkedCell_View::ModelInstanceMap::const_iterator iter = LinkedCell_View::RAIIMap.begin();
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216 | iter != LinkedCell_View::RAIIMap.end(); ++iter) {
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217 | #ifndef NDEBUG
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218 | std::pair< ModelLookup::iterator, bool > inserter =
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219 | #endif
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220 | models.insert( std::pair<const LinkedCell_Model *, LinkedCell_Model *>( (*iter)->LC->getModel(), NULL) );
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221 | LOG(2, "INFO: Added " << (*iter)->LC->getModel() << " to list of models to replace.");
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222 | ASSERT( inserter.second,
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223 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - failed to insert old model "
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224 | +toString( (*iter)->LC->getModel() )+","+toString(NULL)+" into models, is already present");
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225 | }
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226 |
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227 | // invert MapEdgelengthModel
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228 | LOG(2, "INFO: ModelsMap is " << ModelsMap << ".");
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229 | typedef std::map<const LinkedCell_Model*, double > MapEdgelengthModel_inverted;
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230 | MapEdgelengthModel_inverted ModelsMap_inverted;
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231 | for (MapEdgelengthModel::const_iterator iter = ModelsMap.begin();
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232 | iter != ModelsMap.end(); ++iter) {
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233 | #ifndef NDEBUG
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234 | MapEdgelengthModel_inverted::const_iterator assertiter = ModelsMap_inverted.find(iter->second);
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235 | ASSERT( assertiter == ModelsMap_inverted.end(),
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236 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - ModelsMap is not invertible, value "
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237 | +toString(iter->second)+" is already present.");
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238 | #endif
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239 | ModelsMap_inverted.insert( std::make_pair(iter->second, iter->first) );
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240 | }
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241 | LOG(2, "INFO: Inverted ModelsMap is " << ModelsMap_inverted << ".");
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242 |
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243 | // go through map and re-create models
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244 | for (ModelLookup::iterator iter = models.begin(); iter != models.end(); ++iter) {
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245 | // delete old model
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246 | const LinkedCell_Model * const oldref = iter->first;
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247 | #ifndef NDEBUG
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248 | MapEdgelengthModel_inverted::const_iterator assertiter = ModelsMap_inverted.find(oldref);
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249 | ASSERT( assertiter != ModelsMap_inverted.end(),
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250 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - ModelsMap_inverted does not contain old model "
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251 | +toString(oldref)+".");
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252 | #endif
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253 | const double distance = ModelsMap_inverted[oldref];
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254 | // create new one, afterwards erase old model (this is for unit test to get different memory addresses)
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255 | LinkedCell_Model * const newref = new LinkedCell_Model(distance, domain);
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256 | MapEdgelengthModel::iterator oldmodeliter = ModelsMap.find(distance);
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257 | delete oldmodeliter->second;
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258 | ModelsMap.erase(oldmodeliter);
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259 | LOG(2, "INFO: oldref is " << oldref << ", newref is " << newref << ".");
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260 | iter->second = newref;
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261 | // replace in ModelsMap
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262 | #ifndef NDEBUG
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263 | std::pair< MapEdgelengthModel::iterator, bool > inserter =
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264 | #endif
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265 | ModelsMap.insert( std::make_pair(distance, newref) );
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266 | ASSERT( inserter.second,
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267 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - failed to insert new model "
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268 | +toString(distance)+","+toString(newref)+" into ModelsMap, is already present");
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269 | }
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270 |
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271 | // remove all remaining active models (also those that don't have an active View on them)
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272 | for (MapEdgelengthModel::iterator iter = ModelsMap.begin();
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273 | !ModelsMap.empty();
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274 | iter = ModelsMap.begin()) {
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275 | delete iter->second;
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276 | ModelsMap.erase(iter);
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277 | }
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278 |
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279 |
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280 | // delete inverted map for safety (values are gone)
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281 | ModelsMap_inverted.clear();
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282 |
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283 | // go through views and exchange the models
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284 | for (LinkedCell_View::ModelInstanceMap::const_iterator iter = LinkedCell_View::RAIIMap.begin();
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285 | iter != LinkedCell_View::RAIIMap.end(); ++iter) {
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286 | ModelLookup::const_iterator modeliter = models.find((*iter)->LC->getModel());
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287 | ASSERT( modeliter != models.end(),
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288 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - we miss a model "
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289 | +toString((*iter)->LC->getModel())+" in ModelLookup.");
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290 | // this is ugly but the only place where we have to set ourselves over the constness of the member variable
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291 | if (modeliter != models.end()) {
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292 | LOG(2, "INFO: Setting model to " << modeliter->second << " in view " << *iter << ".");
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293 | (*iter)->LC->setModel(modeliter->second);
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294 | }
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295 | }
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296 | }
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297 |
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298 | /** Callback function for Observer mechanism.
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299 | *
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300 | * @param publisher reference to the Observable that calls
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301 | */
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302 | void LinkedCell_Controller::update(Observable *publisher)
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303 | {
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304 | ELOG(2, "LinkedCell_Model received inconclusive general update from "
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305 | << publisher << ".");
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306 | }
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307 |
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308 | /** Callback function for the Notifications mechanism.
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309 | *
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310 | * @param publisher reference to the Observable that calls
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311 | * @param notification specific notification as cause of the call
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312 | */
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313 | void LinkedCell_Controller::recieveNotification(Observable *publisher, Notification_ptr notification)
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314 | {
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315 | if (publisher == &domain) {
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316 | switch(notification->getChannelNo()) {
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317 | case Box::MatrixChanged:
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318 | LOG(1, "INFO: LinkedCell_Controller got update from Box.");
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319 | updateModels();
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320 | break;
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321 | default:
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322 | ASSERT(0,
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323 | "LinkedCell_Controller::recieveNotification() - unwanted notification from Box "
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324 | +toString(notification->getChannelNo())+" received.");
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325 | break;
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326 | }
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327 | } else if (publisher == WorldTime::getPointer()) {
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328 | switch(notification->getChannelNo()) {
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329 | case WorldTime::TimeChanged:
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330 | LOG(1, "INFO: LinkedCell_Controller got update from WorldTime.");
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331 | updateModels();
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332 | break;
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333 | default:
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334 | ASSERT(0,
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335 | "LinkedCell_Controller::recieveNotification() - unwanted notification from WorldTime "
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336 | +toString(notification->getChannelNo())+" received.");
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337 | break;
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338 | }
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339 | } else {
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340 | ELOG(1, "Notification " << notification->getChannelNo()
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341 | << " from unknown publisher " << publisher << ".");
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342 | }
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343 | }
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344 |
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345 | /** Callback function when an Observer dies.
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346 | *
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347 | * @param publisher reference to the Observable that calls
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348 | */
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349 | void LinkedCell_Controller::subjectKilled(Observable *publisher)
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350 | {}
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351 |
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