1 | /*
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2 | * World.hpp
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3 | *
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4 | * Created on: Feb 3, 2010
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5 | * Author: crueger
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6 | */
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7 |
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8 | #ifndef WORLD_HPP_
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9 | #define WORLD_HPP_
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10 |
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11 | /*********************************************** includes ***********************************/
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12 |
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13 | #include <string>
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14 | #include <map>
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15 | #include <vector>
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16 | #include <set>
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17 | #include <boost/thread.hpp>
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18 | #include <boost/shared_ptr.hpp>
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19 |
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20 | #include "types.hpp"
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21 | #include "Actions/ActionTraits.hpp"
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22 | #include "Descriptors/SelectiveIterator.hpp"
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23 | #include "CodePatterns/Observer.hpp"
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24 | #include "CodePatterns/Cacheable.hpp"
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25 | #include "CodePatterns/Singleton.hpp"
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26 | #include "CodePatterns/ObservedContainer.hpp"
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27 | #include "CodePatterns/Range.hpp"
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28 | #include "AtomSet.hpp"
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29 |
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30 | // include config.h
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31 | #ifdef HAVE_CONFIG_H
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32 | #include <config.h>
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33 | #endif
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34 |
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35 | // forward declarations
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36 | class atom;
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37 | class AtomDescriptor;
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38 | class AtomDescriptor_impl;
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39 | template<typename T> class AtomsCalculation;
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40 | class Box;
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41 | class config;
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42 | class ManipulateAtomsProcess;
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43 | class RealSpaceMatrix;
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44 | class molecule;
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45 | class MoleculeDescriptor;
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46 | class MoleculeDescriptor_impl;
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47 | class MoleculeListClass;
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48 | class periodentafel;
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49 | class ThermoStatContainer;
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50 |
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51 |
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52 | /****************************************** forward declarations *****************************/
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53 |
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54 | /********************************************** Class World *******************************/
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55 |
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56 | class World : public Singleton<World>, public Observable
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57 | {
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58 |
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59 | // Make access to constructor and destructor possible from inside the singleton
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60 | friend class Singleton<World>;
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61 |
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62 | // necessary for coupling with descriptors
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63 | friend class AtomDescriptor_impl;
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64 | friend class AtomDescriptor;
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65 | friend class MoleculeDescriptor_impl;
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66 | friend class MoleculeDescriptor;
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67 | // coupling with descriptors over selection
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68 | friend class AtomSelectionDescriptor_impl;
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69 | friend class MoleculeSelectionDescriptor_impl;
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70 |
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71 | // Actions, calculations etc associated with the World
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72 | friend class ManipulateAtomsProcess;
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73 | template<typename> friend class AtomsCalculation;
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74 | public:
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75 | // some typedefs for the CONSTRUCT_... macros (no "," allows in a single parameter name)
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76 | typedef std::map<atomId_t,atom*> AtomSTLSet;
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77 | typedef std::map<moleculeId_t,molecule*> MoleculeSTLSet;
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78 |
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79 | // Types for Atom and Molecule structures
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80 | typedef ObservedContainer< AtomSTLSet > AtomSet;
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81 | typedef ObservedContainer< MoleculeSTLSet > MoleculeSet;
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82 |
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83 | typedef ATOMSET(std::vector) AtomComposite;
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84 |
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85 | /***** getter and setter *****/
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86 | // reference to pointer is used for legacy reason... reference will be removed latter to keep encapsulation of World object
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87 | /**
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88 | * returns the periodentafel for the world.
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89 | */
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90 | periodentafel *&getPeriode();
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91 |
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92 | /**
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93 | * returns the configuration for the world.
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94 | */
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95 | config *&getConfig();
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96 |
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97 | /**
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98 | * returns the first atom that matches a given descriptor.
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99 | * Do not rely on ordering for descriptors that match more than one atom.
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100 | */
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101 | atom* getAtom(AtomDescriptor descriptor);
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102 |
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103 | /**
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104 | * returns a vector containing all atoms that match a given descriptor
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105 | */
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106 | AtomComposite getAllAtoms(AtomDescriptor descriptor);
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107 | AtomComposite getAllAtoms();
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108 |
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109 | /**
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110 | * returns a calculation that calls a given function on all atoms matching a descriptor.
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111 | * the calculation is not called at this point and can be used as an action, i.e. be stored in
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112 | * menus, be kept around for later use etc.
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113 | */
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114 | template<typename T> AtomsCalculation<T>* calcOnAtoms(boost::function<T(atom*)>,const ActionTraits &_trait,AtomDescriptor);
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115 | template<typename T> AtomsCalculation<T>* calcOnAtoms(boost::function<T(atom*)>,const ActionTraits &_trait);
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116 |
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117 | /**
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118 | * get the number of atoms in the World
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119 | */
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120 | int numAtoms();
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121 |
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122 | /**
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123 | * returns the first molecule that matches a given descriptor.
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124 | * Do not rely on ordering for descriptors that match more than one molecule.
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125 | */
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126 | molecule *getMolecule(MoleculeDescriptor descriptor);
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127 |
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128 | /**
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129 | * returns a vector containing all molecules that match a given descriptor
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130 | */
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131 | std::vector<molecule*> getAllMolecules(MoleculeDescriptor descriptor);
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132 | std::vector<molecule*> getAllMolecules();
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133 |
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134 | /**
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135 | * get the number of molecules in the World
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136 | */
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137 | int numMolecules();
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138 |
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139 | /**
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140 | * get the domain size as a symmetric matrix (6 components)
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141 | */
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142 | Box& getDomain();
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143 |
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144 | /**
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145 | * Set the domain size from a matrix object
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146 | *
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147 | * Matrix needs to be symmetric
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148 | */
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149 | void setDomain(const RealSpaceMatrix &mat);
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150 |
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151 | /**
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152 | * set the domain size as a symmetric matrix (6 components)
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153 | */
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154 | void setDomain(double * matrix);
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155 |
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156 | /**
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157 | * get the default name
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158 | */
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159 | std::string getDefaultName();
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160 |
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161 | /**
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162 | * set the default name
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163 | */
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164 | void setDefaultName(std::string name);
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165 |
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166 | /**
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167 | * get pointer to World's ThermoStatContainer
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168 | */
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169 | ThermoStatContainer * getThermostats();
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170 |
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171 | /*
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172 | * get the ExitFlag
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173 | */
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174 | int getExitFlag();
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175 |
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176 | /*
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177 | * set the ExitFlag
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178 | */
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179 | void setExitFlag(int flag);
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180 |
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181 | /***** Methods to work with the World *****/
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182 |
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183 | /**
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184 | * create a new molecule. This method should be used whenever any kind of molecule is needed. Assigns a unique
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185 | * ID to the molecule and stores it in the World for later retrieval. Do not create molecules directly.
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186 | */
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187 | molecule *createMolecule();
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188 |
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189 | void destroyMolecule(molecule*);
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190 | void destroyMolecule(moleculeId_t);
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191 |
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192 | /**
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193 | * Create a new atom. This method should be used whenever any atom is needed. Assigns a unique ID and stores
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194 | * the atom in the World. If the atom is not destroyed it will automatically be destroyed when the world ends.
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195 | */
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196 | atom *createAtom();
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197 |
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198 | /**
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199 | * Registers a Atom unknown to world. Needed in some rare cases, e.g. when cloning atoms, or in some unittests.
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200 | * Do not re-register Atoms already known to the world since this will cause double-frees.
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201 | */
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202 | int registerAtom(atom*);
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203 |
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204 | /**
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205 | * Delete some atom and erase it from the world. Use this whenever you need to destroy any atom. Do not call delete on
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206 | * atom directly since this will leave the pointer inside the world.
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207 | */
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208 | void destroyAtom(atom*);
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209 |
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210 | /**
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211 | * Delete some atom and erase it from the world. Use this whenever you need to destroy any atom. Do not call delete on
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212 | * atom directly since this will leave the pointer inside the world.
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213 | */
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214 | void destroyAtom(atomId_t);
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215 |
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216 | /**
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217 | * used when changing an atom Id.
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218 | * Unless you are calling this method from inside an atom don't fiddle with the third parameter.
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219 | *
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220 | * Return value indicates wether the change could be done or not.
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221 | */
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222 | bool changeAtomId(atomId_t oldId, atomId_t newId, atom* target=0);
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223 |
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224 | /**
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225 | * used when changing an molecule Id.
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226 | * Unless you are calling this method from inside an moleucle don't fiddle with the third parameter.
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227 | *
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228 | * Return value indicates wether the change could be done or not.
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229 | */
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230 | bool changeMoleculeId(moleculeId_t oldId, moleculeId_t newId, molecule* target=0);
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231 |
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232 | /**
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233 | * Produces a process that calls a function on all Atoms matching a given descriptor. The process is not
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234 | * called at this time, so it can be passed around, stored inside menuItems etc.
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235 | */
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236 | ManipulateAtomsProcess* manipulateAtoms(boost::function<void(atom*)>,std::string,AtomDescriptor);
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237 | ManipulateAtomsProcess* manipulateAtoms(boost::function<void(atom*)>,std::string);
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238 |
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239 | /****
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240 | * Iterators to use internal data structures
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241 | * All these iterators are observed to track changes.
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242 | * There is a corresponding protected section with unobserved iterators,
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243 | * which can be used internally when the extra speed is needed
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244 | */
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245 |
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246 | typedef SelectiveIterator<atom*,AtomSet,AtomDescriptor> AtomIterator;
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247 |
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248 | /**
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249 | * returns an iterator over all Atoms matching a given descriptor.
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250 | * This iterator is observed, so don't keep it around unnecessary to
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251 | * avoid unintended blocking.
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252 | */
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253 | AtomIterator getAtomIter(AtomDescriptor descr);
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254 | AtomIterator getAtomIter();
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255 |
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256 | AtomIterator atomEnd();
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257 |
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258 | typedef SelectiveIterator<molecule*,MoleculeSet,MoleculeDescriptor> MoleculeIterator;
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259 |
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260 | /**
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261 | * returns an iterator over all Molecules matching a given descriptor.
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262 | * This iterator is observed, so don't keep it around unnecessary to
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263 | * avoid unintended blocking.
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264 | */
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265 | MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
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266 | MoleculeIterator getMoleculeIter();
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267 |
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268 | MoleculeIterator moleculeEnd();
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269 |
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270 | /******** Selections of molecules and Atoms *************/
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271 | void clearAtomSelection();
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272 | void selectAtom(const atom*);
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273 | void selectAtom(const atomId_t);
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274 | void selectAllAtoms(AtomDescriptor);
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275 | void selectAtomsOfMolecule(const molecule*);
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276 | void selectAtomsOfMolecule(const moleculeId_t);
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277 | void unselectAtom(const atom*);
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278 | void unselectAtom(const atomId_t);
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279 | void unselectAllAtoms(AtomDescriptor);
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280 | void unselectAtomsOfMolecule(const molecule*);
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281 | void unselectAtomsOfMolecule(const moleculeId_t);
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282 | size_t countSelectedAtoms() const;
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283 | bool isSelected(const atom *_atom) const;
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284 | const std::vector<atom *> getSelectedAtoms() const;
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285 |
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286 | void clearMoleculeSelection();
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287 | void selectMolecule(const molecule*);
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288 | void selectMolecule(const moleculeId_t);
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289 | void selectAllMolecules(MoleculeDescriptor);
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290 | void selectMoleculeOfAtom(const atom*);
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291 | void selectMoleculeOfAtom(const atomId_t);
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292 | void unselectMolecule(const molecule*);
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293 | void unselectMolecule(const moleculeId_t);
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294 | void unselectAllMolecules(MoleculeDescriptor);
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295 | void unselectMoleculeOfAtom(const atom*);
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296 | void unselectMoleculeOfAtom(const atomId_t);
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297 | size_t countSelectedMolecules() const;
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298 | bool isSelected(const molecule *_mol) const;
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299 | const std::vector<molecule *> getSelectedMolecules() const;
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300 |
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301 | /******************** Iterators to selections *****************/
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302 | typedef AtomSet::iterator AtomSelectionIterator;
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303 | AtomSelectionIterator beginAtomSelection();
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304 | AtomSelectionIterator endAtomSelection();
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305 |
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306 | typedef MoleculeSet::iterator MoleculeSelectionIterator;
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307 | MoleculeSelectionIterator beginMoleculeSelection();
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308 | MoleculeSelectionIterator endMoleculeSelection();
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309 |
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310 | protected:
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311 | /****
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312 | * Iterators to use internal data structures
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313 | * All these iterators are unobserved for speed reasons.
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314 | * There is a corresponding public section to these methods,
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315 | * which produce observed iterators.*/
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316 |
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317 | // Atoms
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318 | typedef SelectiveIterator<atom*,AtomSet::set_t,AtomDescriptor> internal_AtomIterator;
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319 |
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320 | /**
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321 | * returns an iterator over all Atoms matching a given descriptor.
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322 | * used for internal purposes, like AtomProcesses and AtomCalculations.
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323 | */
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324 | internal_AtomIterator getAtomIter_internal(AtomDescriptor descr);
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325 |
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326 | /**
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327 | * returns an iterator to the end of the AtomSet. Due to overloading this iterator
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328 | * can be compared to iterators produced by getAtomIter (see the mis-matching types).
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329 | * Thus it can be used to detect when such an iterator is at the end of the list.
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330 | * used for internal purposes, like AtomProcesses and AtomCalculations.
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331 | */
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332 | internal_AtomIterator atomEnd_internal();
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333 |
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334 | // Molecules
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335 | typedef SelectiveIterator<molecule*,MoleculeSet::set_t,MoleculeDescriptor> internal_MoleculeIterator;
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336 |
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337 |
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338 | /**
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339 | * returns an iterator over all Molecules matching a given descriptor.
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340 | * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
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341 | */
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342 | internal_MoleculeIterator getMoleculeIter_internal(MoleculeDescriptor descr);
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343 |
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344 | /**
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345 | * returns an iterator to the end of the MoleculeSet. Due to overloading this iterator
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346 | * can be compared to iterators produced by getMoleculeIter (see the mis-matching types).
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347 | * Thus it can be used to detect when such an iterator is at the end of the list.
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348 | * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
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349 | */
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350 | internal_MoleculeIterator moleculeEnd_internal();
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351 |
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352 |
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353 | /******* Internal manipulation routines for double callback and Observer mechanism ******/
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354 | void doManipulate(ManipulateAtomsProcess *);
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355 |
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356 | private:
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357 |
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358 | atomId_t getNextAtomId();
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359 | void releaseAtomId(atomId_t);
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360 | bool reserveAtomId(atomId_t);
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361 | void defragAtomIdPool();
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362 |
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363 | moleculeId_t getNextMoleculeId();
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364 | void releaseMoleculeId(moleculeId_t);
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365 | bool reserveMoleculeId(moleculeId_t);
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366 | void defragMoleculeIdPool();
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367 |
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368 | periodentafel *periode;
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369 | config *configuration;
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370 | Box *cell_size;
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371 | std::string defaultName;
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372 | class ThermoStatContainer *Thermostats;
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373 | int ExitFlag;
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374 | private:
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375 |
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376 | AtomSet atoms;
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377 | AtomSet selectedAtoms;
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378 | typedef std::set<range<atomId_t> > atomIdPool_t;
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379 | /**
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380 | * stores the pool for all available AtomIds below currAtomId
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381 | *
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382 | * The pool contains ranges of free ids in the form [bottom,top).
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383 | */
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384 | atomIdPool_t atomIdPool;
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385 | atomId_t currAtomId; //!< stores the next available Id for atoms
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386 | size_t lastAtomPoolSize; //!< size of the pool after last defrag, to skip some defrags
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387 | unsigned int numAtomDefragSkips;
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388 |
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389 | MoleculeSet molecules;
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390 | MoleculeSet selectedMolecules;
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391 | typedef std::set<range<atomId_t> > moleculeIdPool_t;
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392 | /**
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393 | * stores the pool for all available AtomIds below currAtomId
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394 | *
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395 | * The pool contains ranges of free ids in the form [bottom,top).
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396 | */
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397 | moleculeIdPool_t moleculeIdPool;
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398 | moleculeId_t currMoleculeId;
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399 | size_t lastMoleculePoolSize; //!< size of the pool after last defrag, to skip some defrags
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400 | unsigned int numMoleculeDefragSkips;
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401 | private:
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402 | /**
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403 | * private constructor to ensure creation of the world using
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404 | * the singleton pattern.
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405 | */
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406 | World();
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407 |
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408 | /**
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409 | * private destructor to ensure destruction of the world using the
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410 | * singleton pattern.
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411 | */
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412 | virtual ~World();
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413 |
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414 | /*****
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415 | * some legacy stuff that is include for now but will be removed later
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416 | *****/
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417 | public:
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418 | MoleculeListClass *&getMolecules();
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419 |
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420 | private:
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421 | MoleculeListClass *molecules_deprecated;
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422 | };
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423 |
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424 | #endif /* WORLD_HPP_ */
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