1 | /*
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2 | * Project: MoleCuilder
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3 | * Description: creates and alters molecular systems
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4 | * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
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5 | * 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 | * World.cpp
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10 | *
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11 | * Created on: Feb 3, 2010
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12 | * Author: crueger
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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 "World.hpp"
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23 |
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24 | #include <functional>
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25 |
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26 | #include "Actions/ActionTrait.hpp"
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27 | #include "Actions/ManipulateAtomsProcess.hpp"
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28 | #include "Atom/atom.hpp"
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29 | #include "Atom/AtomObserver.hpp"
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30 | #include "Box.hpp"
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31 | #include "CodePatterns/Assert.hpp"
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32 | #include "config.hpp"
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33 | #include "Descriptors/AtomDescriptor.hpp"
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34 | #include "Descriptors/AtomDescriptor_impl.hpp"
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35 | #include "Descriptors/AtomSelectionDescriptor.hpp"
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36 | #include "Descriptors/MoleculeDescriptor.hpp"
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37 | #include "Descriptors/MoleculeDescriptor_impl.hpp"
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38 | #include "Descriptors/MoleculeSelectionDescriptor.hpp"
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39 | #include "Descriptors/SelectiveIterator_impl.hpp"
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40 | #include "Element/periodentafel.hpp"
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41 | #include "Graph/BondGraph.hpp"
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42 | #include "Graph/DepthFirstSearchAnalysis.hpp"
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43 | #include "Helpers/defs.hpp"
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44 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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45 | #include "LinkedCell/LinkedCell_Controller.hpp"
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46 | #include "LinkedCell/PointCloudAdaptor.hpp"
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47 | #include "molecule.hpp"
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48 | #include "MoleculeListClass.hpp"
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49 | #include "Thermostats/ThermoStatContainer.hpp"
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50 | #include "WorldTime.hpp"
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51 |
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52 | #include "IdPool_impl.hpp"
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53 |
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54 | #include "CodePatterns/IteratorAdaptors.hpp"
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55 | #include "CodePatterns/Singleton_impl.hpp"
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56 | #include "CodePatterns/Observer/Channels.hpp"
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57 | #include "CodePatterns/Observer/ObservedContainer_impl.hpp"
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58 |
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59 | using namespace MoleCuilder;
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60 |
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61 | /******************************* Notifications ************************/
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62 |
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63 |
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64 | atom* World::_lastchangedatom = NULL;
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65 | molecule* World::_lastchangedmol = NULL;
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66 |
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67 | /******************************* getter and setter ************************/
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68 | periodentafel *&World::getPeriode()
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69 | {
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70 | return periode;
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71 | }
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72 |
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73 | BondGraph *&World::getBondGraph()
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74 | {
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75 | return BG;
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76 | }
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77 |
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78 | void World::setBondGraph(BondGraph *_BG){
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79 | delete (BG);
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80 | BG = _BG;
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81 | }
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82 |
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83 | config *&World::getConfig(){
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84 | return configuration;
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85 | }
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86 |
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87 | // Atoms
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88 |
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89 | atom* World::getAtom(AtomDescriptor descriptor){
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90 | return descriptor.find();
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91 | }
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92 |
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93 | World::AtomComposite World::getAllAtoms(AtomDescriptor descriptor){
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94 | return descriptor.findAll();
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95 | }
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96 |
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97 | World::AtomComposite World::getAllAtoms(){
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98 | return getAllAtoms(AllAtoms());
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99 | }
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100 |
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101 | int World::numAtoms(){
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102 | return atoms.size();
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103 | }
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104 |
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105 | // Molecules
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106 |
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107 | molecule *World::getMolecule(MoleculeDescriptor descriptor){
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108 | return descriptor.find();
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109 | }
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110 |
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111 | std::vector<molecule*> World::getAllMolecules(MoleculeDescriptor descriptor){
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112 | return descriptor.findAll();
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113 | }
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114 |
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115 | std::vector<molecule*> World::getAllMolecules(){
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116 | return getAllMolecules(AllMolecules());
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117 | }
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118 |
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119 | int World::numMolecules(){
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120 | return molecules_deprecated->ListOfMolecules.size();
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121 | }
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122 |
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123 | // system
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124 |
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125 | Box& World::getDomain() {
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126 | return *cell_size;
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127 | }
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128 |
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129 | void World::setDomain(const RealSpaceMatrix &mat){
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130 | OBSERVE;
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131 | *cell_size = mat;
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132 | }
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133 |
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134 | void World::setDomain(double * matrix)
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135 | {
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136 | OBSERVE;
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137 | RealSpaceMatrix M = ReturnFullMatrixforSymmetric(matrix);
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138 | cell_size->setM(M);
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139 | }
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140 |
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141 | LinkedCell::LinkedCell_View World::getLinkedCell(const double distance)
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142 | {
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143 | // we have to grope past the ObservedContainer mechanism and transmorph the map
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144 | // into a traversable list for the adaptor
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145 | PointCloudAdaptor< AtomSet::set_t, MapValueIterator<AtomSet::set_t::iterator> > atomset(
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146 | &(atoms.getContent()),
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147 | std::string("WorldsAtoms"));
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148 | return LCcontroller->getView(distance, atomset);
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149 | }
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150 |
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151 | void World::setTime(const unsigned int _step)
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152 | {
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153 | if (_step != WorldTime::getTime()) {
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154 | // set new time
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155 | WorldTime::getInstance().setTime(_step);
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156 | // TODO: removed when BondGraph creates the adjacency
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157 | // 1. remove all of World's molecules
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158 | for (MoleculeIterator iter = getMoleculeIter();
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159 | getMoleculeIter() != moleculeEnd();
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160 | iter = getMoleculeIter()) {
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161 | getMolecules()->erase(*iter);
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162 | destroyMolecule(*iter);
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163 | }
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164 | // 2. (re-)create bondgraph
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165 | AtomComposite Set = getAllAtoms();
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166 | BG->CreateAdjacency(Set);
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167 |
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168 | // 3. scan for connected subgraphs => molecules
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169 | DepthFirstSearchAnalysis DFS;
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170 | DFS();
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171 | DFS.UpdateMoleculeStructure();
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172 | }
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173 | }
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174 |
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175 | std::string World::getDefaultName() {
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176 | return defaultName;
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177 | }
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178 |
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179 | void World::setDefaultName(std::string name)
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180 | {
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181 | OBSERVE;
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182 | defaultName = name;
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183 | };
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184 |
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185 | class ThermoStatContainer * World::getThermostats()
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186 | {
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187 | return Thermostats;
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188 | }
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189 |
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190 |
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191 | int World::getExitFlag() {
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192 | return ExitFlag;
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193 | }
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194 |
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195 | void World::setExitFlag(int flag) {
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196 | if (ExitFlag < flag)
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197 | ExitFlag = flag;
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198 | }
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199 |
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200 | /******************** Methods to change World state *********************/
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201 |
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202 | molecule* World::createMolecule(){
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203 | OBSERVE;
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204 | molecule *mol = NULL;
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205 | mol = NewMolecule();
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206 | moleculeId_t id = moleculeIdPool.getNextId();
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207 | ASSERT(!molecules.count(id),"proposed id did not specify an unused ID");
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208 | mol->setId(id);
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209 | // store the molecule by ID
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210 | molecules[mol->getId()] = mol;
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211 | mol->signOn(this);
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212 | _lastchangedmol = mol;
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213 | NOTIFY(MoleculeInserted);
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214 | return mol;
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215 | }
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216 |
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217 | void World::destroyMolecule(molecule* mol){
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218 | OBSERVE;
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219 | ASSERT(mol,"Molecule that was meant to be destroyed did not exist");
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220 | destroyMolecule(mol->getId());
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221 | }
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222 |
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223 | void World::destroyMolecule(moleculeId_t id){
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224 | molecule *mol = molecules[id];
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225 | ASSERT(mol,"Molecule id that was meant to be destroyed did not exist");
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226 | // give notice about immediate removal
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227 | {
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228 | OBSERVE;
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229 | _lastchangedmol = mol;
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230 | NOTIFY(MoleculeRemoved);
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231 | }
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232 | DeleteMolecule(mol);
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233 | if (isMoleculeSelected(id))
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234 | selectedMolecules.erase(id);
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235 | molecules.erase(id);
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236 | moleculeIdPool.releaseId(id);
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237 | }
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238 |
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239 | atom *World::createAtom(){
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240 | OBSERVE;
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241 | atomId_t id = atomIdPool.getNextId();
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242 | ASSERT(!atoms.count(id),"proposed id did not specify an unused ID");
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243 | atom *res = NewAtom(id);
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244 | res->setWorld(this);
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245 | // sign on to global atom change tracker
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246 | AtomObserver::getInstance().AtomInserted(res);
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247 | // store the atom by ID
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248 | atoms[res->getId()] = res;
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249 | _lastchangedatom = res;
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250 | NOTIFY(AtomInserted);
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251 | return res;
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252 | }
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253 |
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254 |
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255 | int World::registerAtom(atom *atom){
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256 | OBSERVE;
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257 | atomId_t id = atomIdPool.getNextId();
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258 | atom->setId(id);
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259 | atom->setWorld(this);
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260 | atoms[atom->getId()] = atom;
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261 | return atom->getId();
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262 | }
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263 |
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264 | void World::destroyAtom(atom* atom){
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265 | int id = atom->getId();
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266 | destroyAtom(id);
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267 | }
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268 |
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269 | void World::destroyAtom(atomId_t id) {
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270 | atom *atom = atoms[id];
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271 | ASSERT(atom,"Atom ID that was meant to be destroyed did not exist");
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272 | // give notice about immediate removal
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273 | {
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274 | OBSERVE;
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275 | _lastchangedatom = atom;
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276 | NOTIFY(AtomRemoved);
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277 | }
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278 | DeleteAtom(atom);
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279 | if (isAtomSelected(id))
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280 | selectedAtoms.erase(id);
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281 | atoms.erase(id);
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282 | atomIdPool.releaseId(id);
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283 | }
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284 |
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285 | bool World::changeAtomId(atomId_t oldId, atomId_t newId, atom* target){
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286 | OBSERVE;
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287 | // in case this call did not originate from inside the atom, we redirect it,
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288 | // to also let it know that it has changed
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289 | if(!target){
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290 | target = atoms[oldId];
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291 | ASSERT(target,"Atom with that ID not found");
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292 | return target->changeId(newId);
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293 | }
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294 | else{
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295 | if(atomIdPool.reserveId(newId)){
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296 | atoms.erase(oldId);
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297 | atoms.insert(pair<atomId_t,atom*>(newId,target));
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298 | return true;
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299 | }
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300 | else{
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301 | return false;
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302 | }
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303 | }
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304 | }
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305 |
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306 | bool World::changeMoleculeId(moleculeId_t oldId, moleculeId_t newId, molecule* target){
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307 | OBSERVE;
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308 | // in case this call did not originate from inside the atom, we redirect it,
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309 | // to also let it know that it has changed
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310 | if(!target){
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311 | target = molecules[oldId];
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312 | ASSERT(target,"Molecule with that ID not found");
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313 | return target->changeId(newId);
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314 | }
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315 | else{
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316 | if(moleculeIdPool.reserveId(newId)){
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317 | molecules.erase(oldId);
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318 | molecules.insert(pair<moleculeId_t,molecule*>(newId,target));
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319 | return true;
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320 | }
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321 | else{
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322 | return false;
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323 | }
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324 | }
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325 | }
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326 |
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327 | ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name,AtomDescriptor descr){
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328 | ActionTrait manipulateTrait(name);
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329 | return new ManipulateAtomsProcess(op, descr,manipulateTrait,false);
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330 | }
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331 |
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332 | ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name){
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333 | return manipulateAtoms(op,name,AllAtoms());
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334 | }
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335 |
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336 | /********************* Internal Change methods for double Callback and Observer mechanism ********/
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337 |
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338 | void World::doManipulate(ManipulateAtomsProcess *proc){
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339 | proc->signOn(this);
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340 | {
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341 | OBSERVE;
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342 | proc->doManipulate(this);
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343 | }
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344 | proc->signOff(this);
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345 | }
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346 | /******************************* Iterators ********************************/
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347 |
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348 | // external parts with observers
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349 |
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350 | CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet,AtomDescriptor);
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351 |
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352 | World::AtomIterator
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353 | World::getAtomIter(AtomDescriptor descr){
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354 | return AtomIterator(descr,atoms);
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355 | }
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356 |
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357 | World::AtomIterator
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358 | World::getAtomIter(){
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359 | return AtomIterator(AllAtoms(),atoms);
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360 | }
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361 |
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362 | World::AtomIterator
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363 | World::atomEnd(){
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364 | return AtomIterator(AllAtoms(),atoms,atoms.end());
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365 | }
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366 |
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367 | CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet,MoleculeDescriptor);
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368 |
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369 | World::MoleculeIterator
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370 | World::getMoleculeIter(MoleculeDescriptor descr){
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371 | return MoleculeIterator(descr,molecules);
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372 | }
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373 |
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374 | World::MoleculeIterator
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375 | World::getMoleculeIter(){
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376 | return MoleculeIterator(AllMolecules(),molecules);
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377 | }
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378 |
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379 | World::MoleculeIterator
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380 | World::moleculeEnd(){
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381 | return MoleculeIterator(AllMolecules(),molecules,molecules.end());
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382 | }
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383 |
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384 | // Internal parts, without observers
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385 |
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386 | // Build the AtomIterator from template
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387 | CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet::set_t,AtomDescriptor);
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388 |
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389 |
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390 | World::internal_AtomIterator
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391 | World::getAtomIter_internal(AtomDescriptor descr){
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392 | return internal_AtomIterator(descr,atoms.getContent());
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393 | }
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394 |
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395 | World::internal_AtomIterator
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396 | World::atomEnd_internal(){
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397 | return internal_AtomIterator(AllAtoms(),atoms.getContent(),atoms.end_internal());
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398 | }
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399 |
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400 | // build the MoleculeIterator from template
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401 | CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet::set_t,MoleculeDescriptor);
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402 |
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403 | World::internal_MoleculeIterator World::getMoleculeIter_internal(MoleculeDescriptor descr){
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404 | return internal_MoleculeIterator(descr,molecules.getContent());
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405 | }
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406 |
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407 | World::internal_MoleculeIterator World::moleculeEnd_internal(){
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408 | return internal_MoleculeIterator(AllMolecules(),molecules.getContent(),molecules.end_internal());
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409 | }
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410 |
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411 | /************************** Selection of Atoms and molecules ******************/
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412 |
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413 | // Atoms
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414 |
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415 | void World::clearAtomSelection(){
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416 | OBSERVE;
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417 | NOTIFY(SelectionChanged);
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418 | selectedAtoms.clear();
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419 | }
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420 |
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421 | void World::invertAtomSelection(){
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422 | // get all atoms not selected
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423 | AtomComposite invertedSelection(getAllAtoms());
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424 | bool (World::*predicate)(const atom*) const = &World::isSelected; // needed for type resolution of overloaded function
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425 | AtomComposite::iterator iter =
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426 | std::remove_if(invertedSelection.begin(), invertedSelection.end(),
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427 | std::bind1st(std::mem_fun(predicate), this));
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428 | invertedSelection.erase(iter, invertedSelection.end());
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429 | // apply new selection
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430 | selectedAtoms.clear();
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431 | void (World::*selector)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
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432 | std::for_each(invertedSelection.begin(),invertedSelection.end(),
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433 | std::bind1st(std::mem_fun(selector),this)); // func is select... see above
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434 | }
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435 |
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436 | void World::selectAtom(const atom *_atom){
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437 | OBSERVE;
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438 | NOTIFY(SelectionChanged);
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439 | // atom * is unchanged in this function, but we do store entity as changeable
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440 | ASSERT(_atom,"Invalid pointer in selection of atom");
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441 | selectedAtoms[_atom->getId()]=const_cast<atom *>(_atom);
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442 | }
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443 |
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444 | void World::selectAtom(const atomId_t id){
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445 | OBSERVE;
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446 | NOTIFY(SelectionChanged);
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447 | ASSERT(atoms.count(id),"Atom Id selected that was not in the world");
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448 | selectedAtoms[id]=atoms[id];
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449 | }
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450 |
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451 | void World::selectAllAtoms(AtomDescriptor descr){
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452 | OBSERVE;
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453 | NOTIFY(SelectionChanged);
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454 | internal_AtomIterator begin = getAtomIter_internal(descr);
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455 | internal_AtomIterator end = atomEnd_internal();
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456 | void (World::*func)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
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457 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
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458 | }
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459 |
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460 | void World::selectAtomsOfMolecule(const molecule *_mol){
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461 | OBSERVE;
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462 | NOTIFY(SelectionChanged);
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463 | ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
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464 | // need to make it const to get the fast iterators
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465 | const molecule *mol = _mol;
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466 | void (World::*func)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
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467 | for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is select... see above
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468 | }
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469 |
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470 | void World::selectAtomsOfMolecule(const moleculeId_t id){
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471 | OBSERVE;
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472 | NOTIFY(SelectionChanged);
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473 | ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
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474 | selectAtomsOfMolecule(molecules[id]);
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475 | }
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476 |
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477 | void World::unselectAtom(const atom *_atom){
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478 | OBSERVE;
|
---|
479 | NOTIFY(SelectionChanged);
|
---|
480 | ASSERT(_atom,"Invalid pointer in unselection of atom");
|
---|
481 | unselectAtom(_atom->getId());
|
---|
482 | }
|
---|
483 |
|
---|
484 | void World::unselectAtom(const atomId_t id){
|
---|
485 | OBSERVE;
|
---|
486 | NOTIFY(SelectionChanged);
|
---|
487 | ASSERT(atoms.count(id),"Atom Id unselected that was not in the world");
|
---|
488 | selectedAtoms.erase(id);
|
---|
489 | }
|
---|
490 |
|
---|
491 | void World::unselectAllAtoms(AtomDescriptor descr){
|
---|
492 | OBSERVE;
|
---|
493 | NOTIFY(SelectionChanged);
|
---|
494 | internal_AtomIterator begin = getAtomIter_internal(descr);
|
---|
495 | internal_AtomIterator end = atomEnd_internal();
|
---|
496 | void (World::*func)(const atom*) = &World::unselectAtom; // needed for type resolution of overloaded function
|
---|
497 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is unselect... see above
|
---|
498 | }
|
---|
499 |
|
---|
500 | void World::unselectAtomsOfMolecule(const molecule *_mol){
|
---|
501 | OBSERVE;
|
---|
502 | NOTIFY(SelectionChanged);
|
---|
503 | ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
|
---|
504 | // need to make it const to get the fast iterators
|
---|
505 | const molecule *mol = _mol;
|
---|
506 | void (World::*func)(const atom*) = &World::unselectAtom; // needed for type resolution of overloaded function
|
---|
507 | for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is unselect... see above
|
---|
508 | }
|
---|
509 |
|
---|
510 | void World::unselectAtomsOfMolecule(const moleculeId_t id){
|
---|
511 | OBSERVE;
|
---|
512 | NOTIFY(SelectionChanged);
|
---|
513 | ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
|
---|
514 | unselectAtomsOfMolecule(molecules[id]);
|
---|
515 | }
|
---|
516 |
|
---|
517 | size_t World::countSelectedAtoms() const {
|
---|
518 | size_t count = 0;
|
---|
519 | for (AtomSet::const_iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter)
|
---|
520 | count++;
|
---|
521 | return count;
|
---|
522 | }
|
---|
523 |
|
---|
524 | bool World::isSelected(const atom *_atom) const {
|
---|
525 | return isAtomSelected(_atom->getId());
|
---|
526 | }
|
---|
527 |
|
---|
528 | bool World::isAtomSelected(const atomId_t no) const {
|
---|
529 | return selectedAtoms.find(no) != selectedAtoms.end();
|
---|
530 | }
|
---|
531 |
|
---|
532 | const std::vector<atom *> World::getSelectedAtoms() const {
|
---|
533 | std::vector<atom *> returnAtoms;
|
---|
534 | returnAtoms.resize(countSelectedAtoms());
|
---|
535 | int count = 0;
|
---|
536 | for (AtomSet::const_iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter)
|
---|
537 | returnAtoms[count++] = iter->second;
|
---|
538 | return returnAtoms;
|
---|
539 | }
|
---|
540 |
|
---|
541 |
|
---|
542 | // Molecules
|
---|
543 |
|
---|
544 | void World::clearMoleculeSelection(){
|
---|
545 | OBSERVE;
|
---|
546 | NOTIFY(SelectionChanged);
|
---|
547 | selectedMolecules.clear();
|
---|
548 | }
|
---|
549 |
|
---|
550 | void World::invertMoleculeSelection(){
|
---|
551 | // get all molecules not selected
|
---|
552 | typedef std::vector<molecule *> MoleculeVector_t;
|
---|
553 | MoleculeVector_t invertedSelection(getAllMolecules());
|
---|
554 | bool (World::*predicate)(const molecule*) const = &World::isSelected; // needed for type resolution of overloaded function
|
---|
555 | MoleculeVector_t::iterator iter =
|
---|
556 | std::remove_if(invertedSelection.begin(), invertedSelection.end(),
|
---|
557 | std::bind1st(std::mem_fun(predicate), this));
|
---|
558 | invertedSelection.erase(iter, invertedSelection.end());
|
---|
559 | // apply new selection
|
---|
560 | selectedMolecules.clear();
|
---|
561 | void (World::*selector)(const molecule*) = &World::selectMolecule; // needed for type resolution of overloaded function
|
---|
562 | std::for_each(invertedSelection.begin(),invertedSelection.end(),
|
---|
563 | std::bind1st(std::mem_fun(selector),this)); // func is select... see above
|
---|
564 | }
|
---|
565 |
|
---|
566 | void World::selectMolecule(const molecule *_mol){
|
---|
567 | OBSERVE;
|
---|
568 | NOTIFY(SelectionChanged);
|
---|
569 | // molecule * is unchanged in this function, but we do store entity as changeable
|
---|
570 | ASSERT(_mol,"Invalid pointer to molecule in selection");
|
---|
571 | selectedMolecules[_mol->getId()]=const_cast<molecule *>(_mol);
|
---|
572 | }
|
---|
573 |
|
---|
574 | void World::selectMolecule(const moleculeId_t id){
|
---|
575 | OBSERVE;
|
---|
576 | NOTIFY(SelectionChanged);
|
---|
577 | ASSERT(molecules.count(id),"Molecule Id selected that was not in the world");
|
---|
578 | selectedMolecules[id]=molecules[id];
|
---|
579 | }
|
---|
580 |
|
---|
581 | void World::selectAllMolecules(MoleculeDescriptor descr){
|
---|
582 | OBSERVE;
|
---|
583 | NOTIFY(SelectionChanged);
|
---|
584 | internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
|
---|
585 | internal_MoleculeIterator end = moleculeEnd_internal();
|
---|
586 | void (World::*func)(const molecule*) = &World::selectMolecule; // needed for type resolution of overloaded function
|
---|
587 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
|
---|
588 | }
|
---|
589 |
|
---|
590 | void World::selectMoleculeOfAtom(const atom *_atom){
|
---|
591 | OBSERVE;
|
---|
592 | NOTIFY(SelectionChanged);
|
---|
593 | ASSERT(_atom,"Invalid atom pointer in selection of MoleculeOfAtom");
|
---|
594 | molecule *mol=_atom->getMolecule();
|
---|
595 | // the atom might not be part of a molecule
|
---|
596 | if(mol){
|
---|
597 | selectMolecule(mol);
|
---|
598 | }
|
---|
599 | }
|
---|
600 |
|
---|
601 | void World::selectMoleculeOfAtom(const atomId_t id){
|
---|
602 | OBSERVE;
|
---|
603 | NOTIFY(SelectionChanged);
|
---|
604 | ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
|
---|
605 | selectMoleculeOfAtom(atoms[id]);
|
---|
606 | }
|
---|
607 |
|
---|
608 | void World::unselectMolecule(const molecule *_mol){
|
---|
609 | OBSERVE;
|
---|
610 | NOTIFY(SelectionChanged);
|
---|
611 | ASSERT(_mol,"invalid pointer in unselection of molecule");
|
---|
612 | unselectMolecule(_mol->getId());
|
---|
613 | }
|
---|
614 |
|
---|
615 | void World::unselectMolecule(const moleculeId_t id){
|
---|
616 | OBSERVE;
|
---|
617 | NOTIFY(SelectionChanged);
|
---|
618 | ASSERT(molecules.count(id),"No such molecule with ID in unselection");
|
---|
619 | selectedMolecules.erase(id);
|
---|
620 | }
|
---|
621 |
|
---|
622 | void World::unselectAllMolecules(MoleculeDescriptor descr){
|
---|
623 | OBSERVE;
|
---|
624 | NOTIFY(SelectionChanged);
|
---|
625 | internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
|
---|
626 | internal_MoleculeIterator end = moleculeEnd_internal();
|
---|
627 | void (World::*func)(const molecule*) = &World::unselectMolecule; // needed for type resolution of overloaded function
|
---|
628 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is unselect... see above
|
---|
629 | }
|
---|
630 |
|
---|
631 | void World::unselectMoleculeOfAtom(const atom *_atom){
|
---|
632 | OBSERVE;
|
---|
633 | NOTIFY(SelectionChanged);
|
---|
634 | ASSERT(_atom,"Invalid atom pointer in selection of MoleculeOfAtom");
|
---|
635 | molecule *mol=_atom->getMolecule();
|
---|
636 | // the atom might not be part of a molecule
|
---|
637 | if(mol){
|
---|
638 | unselectMolecule(mol);
|
---|
639 | }
|
---|
640 | }
|
---|
641 |
|
---|
642 | void World::unselectMoleculeOfAtom(const atomId_t id){
|
---|
643 | OBSERVE;
|
---|
644 | NOTIFY(SelectionChanged);
|
---|
645 | ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
|
---|
646 | unselectMoleculeOfAtom(atoms[id]);
|
---|
647 | }
|
---|
648 |
|
---|
649 | size_t World::countSelectedMolecules() const {
|
---|
650 | size_t count = 0;
|
---|
651 | for (MoleculeSet::const_iterator iter = selectedMolecules.begin(); iter != selectedMolecules.end(); ++iter)
|
---|
652 | count++;
|
---|
653 | return count;
|
---|
654 | }
|
---|
655 |
|
---|
656 | bool World::isSelected(const molecule *_mol) const {
|
---|
657 | return isMoleculeSelected(_mol->getId());
|
---|
658 | }
|
---|
659 |
|
---|
660 | bool World::isMoleculeSelected(const moleculeId_t no) const {
|
---|
661 | return selectedMolecules.find(no) != selectedMolecules.end();
|
---|
662 | }
|
---|
663 |
|
---|
664 | const std::vector<molecule *> World::getSelectedMolecules() const {
|
---|
665 | std::vector<molecule *> returnMolecules;
|
---|
666 | returnMolecules.resize(countSelectedMolecules());
|
---|
667 | int count = 0;
|
---|
668 | for (MoleculeSet::const_iterator iter = selectedMolecules.begin(); iter != selectedMolecules.end(); ++iter)
|
---|
669 | returnMolecules[count++] = iter->second;
|
---|
670 | return returnMolecules;
|
---|
671 | }
|
---|
672 |
|
---|
673 | /******************* Iterators over Selection *****************************/
|
---|
674 | World::AtomSelectionIterator World::beginAtomSelection(){
|
---|
675 | return selectedAtoms.begin();
|
---|
676 | }
|
---|
677 |
|
---|
678 | World::AtomSelectionIterator World::endAtomSelection(){
|
---|
679 | return selectedAtoms.end();
|
---|
680 | }
|
---|
681 |
|
---|
682 | World::AtomSelectionConstIterator World::beginAtomSelection() const{
|
---|
683 | return selectedAtoms.begin();
|
---|
684 | }
|
---|
685 |
|
---|
686 | World::AtomSelectionConstIterator World::endAtomSelection() const{
|
---|
687 | return selectedAtoms.end();
|
---|
688 | }
|
---|
689 |
|
---|
690 |
|
---|
691 | World::MoleculeSelectionIterator World::beginMoleculeSelection(){
|
---|
692 | return selectedMolecules.begin();
|
---|
693 | }
|
---|
694 |
|
---|
695 | World::MoleculeSelectionIterator World::endMoleculeSelection(){
|
---|
696 | return selectedMolecules.end();
|
---|
697 | }
|
---|
698 |
|
---|
699 | World::MoleculeSelectionConstIterator World::beginMoleculeSelection() const{
|
---|
700 | return selectedMolecules.begin();
|
---|
701 | }
|
---|
702 |
|
---|
703 | World::MoleculeSelectionConstIterator World::endMoleculeSelection() const{
|
---|
704 | return selectedMolecules.end();
|
---|
705 | }
|
---|
706 |
|
---|
707 | /******************************* Singleton Stuff **************************/
|
---|
708 |
|
---|
709 | World::World() :
|
---|
710 | Observable("World"),
|
---|
711 | BG(new BondGraph(true)), // assume Angstroem for the moment
|
---|
712 | periode(new periodentafel(true)),
|
---|
713 | configuration(new config),
|
---|
714 | Thermostats(new ThermoStatContainer),
|
---|
715 | ExitFlag(0),
|
---|
716 | atoms(this),
|
---|
717 | selectedAtoms(this),
|
---|
718 | atomIdPool(0, 20, 100),
|
---|
719 | molecules(this),
|
---|
720 | selectedMolecules(this),
|
---|
721 | moleculeIdPool(0, 20,100),
|
---|
722 | molecules_deprecated(new MoleculeListClass(this))
|
---|
723 | {
|
---|
724 | cell_size = new Box;
|
---|
725 | RealSpaceMatrix domain;
|
---|
726 | domain.at(0,0) = 20;
|
---|
727 | domain.at(1,1) = 20;
|
---|
728 | domain.at(2,2) = 20;
|
---|
729 | cell_size->setM(domain);
|
---|
730 | LCcontroller = new LinkedCell::LinkedCell_Controller(*cell_size);
|
---|
731 | defaultName = "none";
|
---|
732 | Channels *OurChannel = new Channels;
|
---|
733 | NotificationChannels.insert( std::make_pair( this, OurChannel) );
|
---|
734 | for (size_t type = 0; type < (size_t)NotificationType_MAX; ++type)
|
---|
735 | OurChannel->addChannel(type);
|
---|
736 | molecules_deprecated->signOn(this);
|
---|
737 | }
|
---|
738 |
|
---|
739 | World::~World()
|
---|
740 | {
|
---|
741 | molecules_deprecated->signOff(this);
|
---|
742 | delete LCcontroller;
|
---|
743 | delete cell_size;
|
---|
744 | delete molecules_deprecated;
|
---|
745 | MoleculeSet::iterator molIter;
|
---|
746 | for(molIter=molecules.begin();molIter!=molecules.end();++molIter){
|
---|
747 | DeleteMolecule((*molIter).second);
|
---|
748 | }
|
---|
749 | molecules.clear();
|
---|
750 | AtomSet::iterator atIter;
|
---|
751 | for(atIter=atoms.begin();atIter!=atoms.end();++atIter){
|
---|
752 | DeleteAtom((*atIter).second);
|
---|
753 | }
|
---|
754 | atoms.clear();
|
---|
755 |
|
---|
756 | // empty notifications
|
---|
757 | std::map<Observable *, Channels*>::iterator iter = NotificationChannels.find(this);
|
---|
758 | ASSERT(iter != NotificationChannels.end(),
|
---|
759 | "World::~World() - cannot find our Channels in NotificationChannels.");
|
---|
760 | delete iter->second;
|
---|
761 | NotificationChannels.erase(iter);
|
---|
762 |
|
---|
763 | delete BG;
|
---|
764 | delete periode;
|
---|
765 | delete configuration;
|
---|
766 | delete Thermostats;
|
---|
767 | }
|
---|
768 |
|
---|
769 | // Explicit instantiation of the singleton mechanism at this point
|
---|
770 |
|
---|
771 | // moleculeId_t und atomId_t sind gleicher Basistyp, deswegen nur einen von beiden konstruieren
|
---|
772 | CONSTRUCT_IDPOOL(atomId_t, uniqueId)
|
---|
773 | CONSTRUCT_IDPOOL(moleculeId_t, continuousId)
|
---|
774 |
|
---|
775 | CONSTRUCT_SINGLETON(World)
|
---|
776 |
|
---|
777 | CONSTRUCT_OBSERVEDCONTAINER(World::AtomSTLSet)
|
---|
778 |
|
---|
779 | CONSTRUCT_OBSERVEDCONTAINER(World::MoleculeSTLSet)
|
---|
780 |
|
---|
781 | /******************************* deprecated Legacy Stuff ***********************/
|
---|
782 |
|
---|
783 | MoleculeListClass *&World::getMolecules() {
|
---|
784 | return molecules_deprecated;
|
---|
785 | }
|
---|