[5d1611] | 1 | /*
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| 2 | * World.cpp
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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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[112b09] | 8 | #include "Helpers/MemDebug.hpp"
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| 9 |
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[5d1611] | 10 | #include "World.hpp"
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| 11 |
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[d346b6] | 12 | #include "atom.hpp"
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[8e1f7af] | 13 | #include "config.hpp"
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[354859] | 14 | #include "molecule.hpp"
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| 15 | #include "periodentafel.hpp"
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[43dad6] | 16 | #include "ThermoStatContainer.hpp"
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[fc1b24] | 17 | #include "Descriptors/AtomDescriptor.hpp"
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[865a945] | 18 | #include "Descriptors/AtomDescriptor_impl.hpp"
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[1c51c8] | 19 | #include "Descriptors/MoleculeDescriptor.hpp"
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| 20 | #include "Descriptors/MoleculeDescriptor_impl.hpp"
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[6e97e5] | 21 | #include "Descriptors/SelectiveIterator_impl.hpp"
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[7c4e29] | 22 | #include "Actions/ManipulateAtomsProcess.hpp"
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[6d574a] | 23 | #include "Helpers/Assert.hpp"
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[d346b6] | 24 |
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[23b547] | 25 | #include "Patterns/Singleton_impl.hpp"
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| 26 |
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[d346b6] | 27 | using namespace std;
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[4d9c01] | 28 |
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[5d1611] | 29 | /******************************* getter and setter ************************/
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[354859] | 30 | periodentafel *&World::getPeriode(){
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[5d1611] | 31 | return periode;
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| 32 | }
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| 33 |
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[8e1f7af] | 34 | config *&World::getConfig(){
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| 35 | return configuration;
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| 36 | }
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| 37 |
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[1c51c8] | 38 | // Atoms
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| 39 |
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[7a1ce5] | 40 | atom* World::getAtom(AtomDescriptor descriptor){
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[fc1b24] | 41 | return descriptor.find();
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| 42 | }
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| 43 |
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[7a1ce5] | 44 | vector<atom*> World::getAllAtoms(AtomDescriptor descriptor){
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[fc1b24] | 45 | return descriptor.findAll();
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| 46 | }
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| 47 |
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[0e2a47] | 48 | vector<atom*> World::getAllAtoms(){
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| 49 | return getAllAtoms(AllAtoms());
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| 50 | }
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| 51 |
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[354859] | 52 | int World::numAtoms(){
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| 53 | return atoms.size();
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| 54 | }
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| 55 |
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[1c51c8] | 56 | // Molecules
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| 57 |
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| 58 | molecule *World::getMolecule(MoleculeDescriptor descriptor){
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| 59 | return descriptor.find();
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| 60 | }
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| 61 |
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| 62 | std::vector<molecule*> World::getAllMolecules(MoleculeDescriptor descriptor){
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| 63 | return descriptor.findAll();
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| 64 | }
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| 65 |
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[97ebf8] | 66 | std::vector<molecule*> World::getAllMolecules(){
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| 67 | return getAllMolecules(AllMolecules());
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| 68 | }
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| 69 |
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[354859] | 70 | int World::numMolecules(){
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| 71 | return molecules_deprecated->ListOfMolecules.size();
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| 72 | }
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| 73 |
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[5f612ee] | 74 | // system
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| 75 |
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| 76 | double * World::getDomain() {
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| 77 | return cell_size;
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| 78 | }
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| 79 |
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| 80 | void World::setDomain(double * matrix)
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| 81 | {
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[b9c847] | 82 | OBSERVE;
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| 83 | cell_size[0] = matrix[0];
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| 84 | cell_size[1] = matrix[1];
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| 85 | cell_size[2] = matrix[2];
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| 86 | cell_size[3] = matrix[3];
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| 87 | cell_size[4] = matrix[4];
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| 88 | cell_size[5] = matrix[5];
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[5f612ee] | 89 | }
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| 90 |
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[387b36] | 91 | std::string World::getDefaultName() {
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[5f612ee] | 92 | return defaultName;
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| 93 | }
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| 94 |
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[387b36] | 95 | void World::setDefaultName(std::string name)
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[5f612ee] | 96 | {
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[387b36] | 97 | defaultName = name;
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[5f612ee] | 98 | };
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| 99 |
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[43dad6] | 100 | class ThermoStatContainer * World::getThermostats()
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| 101 | {
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| 102 | return Thermostats;
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| 103 | }
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| 104 |
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| 105 |
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[e4b5de] | 106 | int World::getExitFlag() {
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| 107 | return ExitFlag;
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| 108 | }
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| 109 |
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| 110 | void World::setExitFlag(int flag) {
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| 111 | if (ExitFlag < flag)
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| 112 | ExitFlag = flag;
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| 113 | }
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[5f612ee] | 114 |
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[afb47f] | 115 | /******************** Methods to change World state *********************/
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| 116 |
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[354859] | 117 | molecule* World::createMolecule(){
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| 118 | OBSERVE;
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| 119 | molecule *mol = NULL;
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[cbc5fb] | 120 | mol = NewMolecule();
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[6d574a] | 121 | ASSERT(!molecules.count(currMoleculeId),"currMoleculeId did not specify an unused ID");
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[cbc5fb] | 122 | mol->setId(currMoleculeId++);
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[244d26] | 123 | // store the molecule by ID
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[cbc5fb] | 124 | molecules[mol->getId()] = mol;
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[354859] | 125 | mol->signOn(this);
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| 126 | return mol;
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| 127 | }
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| 128 |
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[cbc5fb] | 129 | void World::destroyMolecule(molecule* mol){
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| 130 | OBSERVE;
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| 131 | destroyMolecule(mol->getId());
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| 132 | }
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| 133 |
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| 134 | void World::destroyMolecule(moleculeId_t id){
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| 135 | OBSERVE;
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| 136 | molecule *mol = molecules[id];
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[6d574a] | 137 | ASSERT(mol,"Molecule id that was meant to be destroyed did not exist");
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[cbc5fb] | 138 | DeleteMolecule(mol);
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| 139 | molecules.erase(id);
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| 140 | }
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| 141 |
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[5f612ee] | 142 | double *World::cell_size = NULL;
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[7c4e29] | 143 |
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[46d958] | 144 | atom *World::createAtom(){
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| 145 | OBSERVE;
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[88d586] | 146 | atomId_t id = getNextAtomId();
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| 147 | atom *res = NewAtom(id);
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[46d958] | 148 | res->setWorld(this);
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[244d26] | 149 | // store the atom by ID
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[46d958] | 150 | atoms[res->getId()] = res;
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| 151 | return res;
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| 152 | }
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| 153 |
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[5f612ee] | 154 |
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[46d958] | 155 | int World::registerAtom(atom *atom){
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| 156 | OBSERVE;
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[88d586] | 157 | atomId_t id = getNextAtomId();
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| 158 | atom->setId(id);
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[46d958] | 159 | atom->setWorld(this);
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| 160 | atoms[atom->getId()] = atom;
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| 161 | return atom->getId();
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| 162 | }
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| 163 |
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| 164 | void World::destroyAtom(atom* atom){
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| 165 | OBSERVE;
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| 166 | int id = atom->getId();
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| 167 | destroyAtom(id);
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| 168 | }
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| 169 |
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[cbc5fb] | 170 | void World::destroyAtom(atomId_t id) {
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[46d958] | 171 | OBSERVE;
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| 172 | atom *atom = atoms[id];
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[6d574a] | 173 | ASSERT(atom,"Atom ID that was meant to be destroyed did not exist");
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[46d958] | 174 | DeleteAtom(atom);
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| 175 | atoms.erase(id);
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[88d586] | 176 | releaseAtomId(id);
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| 177 | }
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| 178 |
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| 179 | bool World::changeAtomId(atomId_t oldId, atomId_t newId, atom* target){
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| 180 | OBSERVE;
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| 181 | // in case this call did not originate from inside the atom, we redirect it,
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| 182 | // to also let it know that it has changed
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| 183 | if(!target){
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| 184 | target = atoms[oldId];
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[6d574a] | 185 | ASSERT(target,"Atom with that ID not found");
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[88d586] | 186 | return target->changeId(newId);
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| 187 | }
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| 188 | else{
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| 189 | if(reserveAtomId(newId)){
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| 190 | atoms.erase(oldId);
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| 191 | atoms.insert(pair<atomId_t,atom*>(newId,target));
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| 192 | return true;
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| 193 | }
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| 194 | else{
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| 195 | return false;
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| 196 | }
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| 197 | }
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[46d958] | 198 | }
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| 199 |
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[7c4e29] | 200 | ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name,AtomDescriptor descr){
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| 201 | return new ManipulateAtomsProcess(op, descr,name,true);
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| 202 | }
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| 203 |
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[0e2a47] | 204 | ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name){
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| 205 | return manipulateAtoms(op,name,AllAtoms());
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| 206 | }
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| 207 |
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[afb47f] | 208 | /********************* Internal Change methods for double Callback and Observer mechanism ********/
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| 209 |
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| 210 | void World::doManipulate(ManipulateAtomsProcess *proc){
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| 211 | proc->signOn(this);
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| 212 | {
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| 213 | OBSERVE;
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| 214 | proc->doManipulate(this);
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| 215 | }
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| 216 | proc->signOff(this);
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| 217 | }
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[88d586] | 218 | /******************************* IDManagement *****************************/
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| 219 |
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[57adc7] | 220 | // Atoms
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| 221 |
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[88d586] | 222 | atomId_t World::getNextAtomId(){
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| 223 | // see if we can reuse some Id
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| 224 | if(atomIdPool.empty()){
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| 225 | return currAtomId++;
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| 226 | }
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| 227 | else{
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| 228 | // we give out the first ID from the pool
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| 229 | atomId_t id = *(atomIdPool.begin());
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| 230 | atomIdPool.erase(id);
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[23b547] | 231 | return id;
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[88d586] | 232 | }
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| 233 | }
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| 234 |
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| 235 | void World::releaseAtomId(atomId_t id){
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| 236 | atomIdPool.insert(id);
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| 237 | // defragmentation of the pool
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| 238 | set<atomId_t>::reverse_iterator iter;
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| 239 | // go through all Ids in the pool that lie immediately below the border
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| 240 | while(!atomIdPool.empty() && *(atomIdPool.rbegin())==(currAtomId-1)){
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| 241 | atomIdPool.erase(--currAtomId);
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| 242 | }
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| 243 | }
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[afb47f] | 244 |
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[88d586] | 245 | bool World::reserveAtomId(atomId_t id){
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| 246 | if(id>=currAtomId ){
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| 247 | // add all ids between the new one and current border as available
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| 248 | for(atomId_t pos=currAtomId; pos<id; ++pos){
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| 249 | atomIdPool.insert(pos);
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| 250 | }
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| 251 | currAtomId=id+1;
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| 252 | return true;
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| 253 | }
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| 254 | else if(atomIdPool.count(id)){
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| 255 | atomIdPool.erase(id);
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| 256 | return true;
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| 257 | }
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| 258 | else{
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| 259 | // this ID could not be reserved
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| 260 | return false;
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| 261 | }
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| 262 | }
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[57adc7] | 263 |
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| 264 | // Molecules
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| 265 |
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[865a945] | 266 | /******************************* Iterators ********************************/
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| 267 |
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[6e97e5] | 268 | // Build the AtomIterator from template
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| 269 | CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet,AtomDescriptor);
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| 270 |
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[865a945] | 271 |
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| 272 | World::AtomIterator World::getAtomIter(AtomDescriptor descr){
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[6e97e5] | 273 | return AtomIterator(descr,atoms);
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[865a945] | 274 | }
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[354859] | 275 |
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[6e97e5] | 276 | World::AtomIterator World::atomEnd(){
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| 277 | return AtomIterator(AllAtoms(),atoms,atoms.end());
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[7c4e29] | 278 | }
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| 279 |
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[6e97e5] | 280 | // build the MoleculeIterator from template
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| 281 | CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet,MoleculeDescriptor);
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| 282 |
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[1c51c8] | 283 | World::MoleculeIterator World::getMoleculeIter(MoleculeDescriptor descr){
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[6e97e5] | 284 | return MoleculeIterator(descr,molecules);
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[1c51c8] | 285 | }
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| 286 |
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[6e97e5] | 287 | World::MoleculeIterator World::moleculeEnd(){
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| 288 | return MoleculeIterator(AllMolecules(),molecules,molecules.end());
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[1c51c8] | 289 | }
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| 290 |
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[5d1611] | 291 | /******************************* Singleton Stuff **************************/
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| 292 |
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[7a1ce5] | 293 | World::World() :
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[cd5047] | 294 | Observable("World"),
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[354859] | 295 | periode(new periodentafel),
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[8e1f7af] | 296 | configuration(new config),
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[43dad6] | 297 | Thermostats(new ThermoStatContainer),
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[e4b5de] | 298 | ExitFlag(0),
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[d2dbac0] | 299 | atoms(),
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[24a5e0] | 300 | currAtomId(0),
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| 301 | molecules(),
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| 302 | currMoleculeId(0),
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| 303 | molecules_deprecated(new MoleculeListClass(this))
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[7dad10] | 304 | {
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[b34306] | 305 | cell_size = new double[6];
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[fd179f] | 306 | cell_size[0] = 20.;
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| 307 | cell_size[1] = 0.;
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| 308 | cell_size[2] = 20.;
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| 309 | cell_size[3] = 0.;
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| 310 | cell_size[4] = 0.;
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| 311 | cell_size[5] = 20.;
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[387b36] | 312 | defaultName = "none";
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[7dad10] | 313 | molecules_deprecated->signOn(this);
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| 314 | }
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[5d1611] | 315 |
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| 316 | World::~World()
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[354859] | 317 | {
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[028c2e] | 318 | molecules_deprecated->signOff(this);
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[5f612ee] | 319 | delete[] cell_size;
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[46d958] | 320 | delete molecules_deprecated;
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[354859] | 321 | delete periode;
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[8e1f7af] | 322 | delete configuration;
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[43dad6] | 323 | delete Thermostats;
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[cbc5fb] | 324 | MoleculeSet::iterator molIter;
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| 325 | for(molIter=molecules.begin();molIter!=molecules.end();++molIter){
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| 326 | DeleteMolecule((*molIter).second);
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| 327 | }
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| 328 | molecules.clear();
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| 329 | AtomSet::iterator atIter;
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| 330 | for(atIter=atoms.begin();atIter!=atoms.end();++atIter){
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| 331 | DeleteAtom((*atIter).second);
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[46d958] | 332 | }
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| 333 | atoms.clear();
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[354859] | 334 | }
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[5d1611] | 335 |
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[23b547] | 336 | // Explicit instantiation of the singleton mechanism at this point
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[5d1611] | 337 |
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[23b547] | 338 | CONSTRUCT_SINGLETON(World)
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[5d1611] | 339 |
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| 340 | /******************************* deprecated Legacy Stuff ***********************/
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| 341 |
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[354859] | 342 | MoleculeListClass *&World::getMolecules() {
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| 343 | return molecules_deprecated;
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[5d1611] | 344 | }
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