source: src/World.hpp@ f71baf

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Last change on this file since f71baf was f71baf, checked in by Frederik Heber <heber@…>, 14 years ago

Made BondGraph an instance of World, removed from config.

  • Property mode set to 100644
File size: 13.6 KB
Line 
1/*
2 * World.hpp
3 *
4 * Created on: Feb 3, 2010
5 * Author: crueger
6 */
7
8#ifndef WORLD_HPP_
9#define WORLD_HPP_
10
11/*********************************************** includes ***********************************/
12
13#include <string>
14#include <map>
15#include <vector>
16#include <set>
17#include <boost/thread.hpp>
18#include <boost/shared_ptr.hpp>
19
20#include "types.hpp"
21#include "Actions/ActionTraits.hpp"
22#include "Descriptors/SelectiveIterator.hpp"
23#include "CodePatterns/Observer.hpp"
24#include "CodePatterns/Cacheable.hpp"
25#include "CodePatterns/Singleton.hpp"
26#include "CodePatterns/ObservedContainer.hpp"
27#include "CodePatterns/Range.hpp"
28#include "AtomSet.hpp"
29
30// include config.h
31#ifdef HAVE_CONFIG_H
32#include <config.h>
33#endif
34
35// forward declarations
36class atom;
37class AtomDescriptor;
38class AtomDescriptor_impl;
39template<typename T> class AtomsCalculation;
40class BondGraph;
41class Box;
42class config;
43class ManipulateAtomsProcess;
44class RealSpaceMatrix;
45class molecule;
46class MoleculeDescriptor;
47class MoleculeDescriptor_impl;
48class MoleculeListClass;
49class periodentafel;
50class ThermoStatContainer;
51
52
53/****************************************** forward declarations *****************************/
54
55/********************************************** Class World *******************************/
56
57class World : public Singleton<World>, public Observable
58{
59
60// Make access to constructor and destructor possible from inside the singleton
61friend class Singleton<World>;
62
63// necessary for coupling with descriptors
64friend class AtomDescriptor_impl;
65friend class AtomDescriptor;
66friend class MoleculeDescriptor_impl;
67friend class MoleculeDescriptor;
68// coupling with descriptors over selection
69friend class AtomSelectionDescriptor_impl;
70friend class MoleculeSelectionDescriptor_impl;
71
72// Actions, calculations etc associated with the World
73friend class ManipulateAtomsProcess;
74template<typename> friend class AtomsCalculation;
75public:
76 // some typedefs for the CONSTRUCT_... macros (no "," allows in a single parameter name)
77 typedef std::map<atomId_t,atom*> AtomSTLSet;
78 typedef std::map<moleculeId_t,molecule*> MoleculeSTLSet;
79
80 // Types for Atom and Molecule structures
81 typedef ObservedContainer< AtomSTLSet > AtomSet;
82 typedef ObservedContainer< MoleculeSTLSet > MoleculeSet;
83
84 typedef ATOMSET(std::vector) AtomComposite;
85
86 /***** getter and setter *****/
87 // reference to pointer is used for legacy reason... reference will be removed latter to keep encapsulation of World object
88 /**
89 * returns the periodentafel for the world.
90 */
91 periodentafel *&getPeriode();
92
93 /** Returns the BondGraph for the World.
94 *
95 * @return reference to BondGraph
96 */
97 BondGraph *&getBondGraph();
98
99 /** Sets the World's BondGraph.
100 *
101 * @param _BG new BondGraph
102 */
103 void setBondGraph(BondGraph *_BG);
104 /**
105 * returns the configuration for the world.
106 */
107 config *&getConfig();
108
109 /**
110 * returns the first atom that matches a given descriptor.
111 * Do not rely on ordering for descriptors that match more than one atom.
112 */
113 atom* getAtom(AtomDescriptor descriptor);
114
115 /**
116 * returns a vector containing all atoms that match a given descriptor
117 */
118 AtomComposite getAllAtoms(AtomDescriptor descriptor);
119 AtomComposite getAllAtoms();
120
121 /**
122 * returns a calculation that calls a given function on all atoms matching a descriptor.
123 * the calculation is not called at this point and can be used as an action, i.e. be stored in
124 * menus, be kept around for later use etc.
125 */
126 template<typename T> AtomsCalculation<T>* calcOnAtoms(boost::function<T(atom*)>,const ActionTraits &_trait,AtomDescriptor);
127 template<typename T> AtomsCalculation<T>* calcOnAtoms(boost::function<T(atom*)>,const ActionTraits &_trait);
128
129 /**
130 * get the number of atoms in the World
131 */
132 int numAtoms();
133
134 /**
135 * returns the first molecule that matches a given descriptor.
136 * Do not rely on ordering for descriptors that match more than one molecule.
137 */
138 molecule *getMolecule(MoleculeDescriptor descriptor);
139
140 /**
141 * returns a vector containing all molecules that match a given descriptor
142 */
143 std::vector<molecule*> getAllMolecules(MoleculeDescriptor descriptor);
144 std::vector<molecule*> getAllMolecules();
145
146 /**
147 * get the number of molecules in the World
148 */
149 int numMolecules();
150
151 /**
152 * get the domain size as a symmetric matrix (6 components)
153 */
154 Box& getDomain();
155
156 /**
157 * Set the domain size from a matrix object
158 *
159 * Matrix needs to be symmetric
160 */
161 void setDomain(const RealSpaceMatrix &mat);
162
163 /**
164 * set the domain size as a symmetric matrix (6 components)
165 */
166 void setDomain(double * matrix);
167
168 /**
169 * set the current time of the world.
170 *
171 * @param _step time step to set to
172 */
173 void setTime(const unsigned int _step);
174
175 /**
176 * get the default name
177 */
178 std::string getDefaultName();
179
180 /**
181 * set the default name
182 */
183 void setDefaultName(std::string name);
184
185 /**
186 * get pointer to World's ThermoStatContainer
187 */
188 ThermoStatContainer * getThermostats();
189
190 /*
191 * get the ExitFlag
192 */
193 int getExitFlag();
194
195 /*
196 * set the ExitFlag
197 */
198 void setExitFlag(int flag);
199
200 /***** Methods to work with the World *****/
201
202 /**
203 * create a new molecule. This method should be used whenever any kind of molecule is needed. Assigns a unique
204 * ID to the molecule and stores it in the World for later retrieval. Do not create molecules directly.
205 */
206 molecule *createMolecule();
207
208 void destroyMolecule(molecule*);
209 void destroyMolecule(moleculeId_t);
210
211 /**
212 * Create a new atom. This method should be used whenever any atom is needed. Assigns a unique ID and stores
213 * the atom in the World. If the atom is not destroyed it will automatically be destroyed when the world ends.
214 */
215 atom *createAtom();
216
217 /**
218 * Registers a Atom unknown to world. Needed in some rare cases, e.g. when cloning atoms, or in some unittests.
219 * Do not re-register Atoms already known to the world since this will cause double-frees.
220 */
221 int registerAtom(atom*);
222
223 /**
224 * Delete some atom and erase it from the world. Use this whenever you need to destroy any atom. Do not call delete on
225 * atom directly since this will leave the pointer inside the world.
226 */
227 void destroyAtom(atom*);
228
229 /**
230 * Delete some atom and erase it from the world. Use this whenever you need to destroy any atom. Do not call delete on
231 * atom directly since this will leave the pointer inside the world.
232 */
233 void destroyAtom(atomId_t);
234
235 /**
236 * used when changing an atom Id.
237 * Unless you are calling this method from inside an atom don't fiddle with the third parameter.
238 *
239 * Return value indicates wether the change could be done or not.
240 */
241 bool changeAtomId(atomId_t oldId, atomId_t newId, atom* target=0);
242
243 /**
244 * used when changing an molecule Id.
245 * Unless you are calling this method from inside an moleucle don't fiddle with the third parameter.
246 *
247 * Return value indicates wether the change could be done or not.
248 */
249 bool changeMoleculeId(moleculeId_t oldId, moleculeId_t newId, molecule* target=0);
250
251 /**
252 * Produces a process that calls a function on all Atoms matching a given descriptor. The process is not
253 * called at this time, so it can be passed around, stored inside menuItems etc.
254 */
255 ManipulateAtomsProcess* manipulateAtoms(boost::function<void(atom*)>,std::string,AtomDescriptor);
256 ManipulateAtomsProcess* manipulateAtoms(boost::function<void(atom*)>,std::string);
257
258 /****
259 * Iterators to use internal data structures
260 * All these iterators are observed to track changes.
261 * There is a corresponding protected section with unobserved iterators,
262 * which can be used internally when the extra speed is needed
263 */
264
265 typedef SelectiveIterator<atom*,AtomSet,AtomDescriptor> AtomIterator;
266
267 /**
268 * returns an iterator over all Atoms matching a given descriptor.
269 * This iterator is observed, so don't keep it around unnecessary to
270 * avoid unintended blocking.
271 */
272 AtomIterator getAtomIter(AtomDescriptor descr);
273 AtomIterator getAtomIter();
274
275 AtomIterator atomEnd();
276
277 typedef SelectiveIterator<molecule*,MoleculeSet,MoleculeDescriptor> MoleculeIterator;
278
279 /**
280 * returns an iterator over all Molecules matching a given descriptor.
281 * This iterator is observed, so don't keep it around unnecessary to
282 * avoid unintended blocking.
283 */
284 MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
285 MoleculeIterator getMoleculeIter();
286
287 MoleculeIterator moleculeEnd();
288
289 /******** Selections of molecules and Atoms *************/
290 void clearAtomSelection();
291 void selectAtom(const atom*);
292 void selectAtom(const atomId_t);
293 void selectAllAtoms(AtomDescriptor);
294 void selectAtomsOfMolecule(const molecule*);
295 void selectAtomsOfMolecule(const moleculeId_t);
296 void unselectAtom(const atom*);
297 void unselectAtom(const atomId_t);
298 void unselectAllAtoms(AtomDescriptor);
299 void unselectAtomsOfMolecule(const molecule*);
300 void unselectAtomsOfMolecule(const moleculeId_t);
301 size_t countSelectedAtoms() const;
302 bool isSelected(const atom *_atom) const;
303 const std::vector<atom *> getSelectedAtoms() const;
304
305 void clearMoleculeSelection();
306 void selectMolecule(const molecule*);
307 void selectMolecule(const moleculeId_t);
308 void selectAllMolecules(MoleculeDescriptor);
309 void selectMoleculeOfAtom(const atom*);
310 void selectMoleculeOfAtom(const atomId_t);
311 void unselectMolecule(const molecule*);
312 void unselectMolecule(const moleculeId_t);
313 void unselectAllMolecules(MoleculeDescriptor);
314 void unselectMoleculeOfAtom(const atom*);
315 void unselectMoleculeOfAtom(const atomId_t);
316 size_t countSelectedMolecules() const;
317 bool isSelected(const molecule *_mol) const;
318 const std::vector<molecule *> getSelectedMolecules() const;
319
320 /******************** Iterators to selections *****************/
321 typedef AtomSet::iterator AtomSelectionIterator;
322 AtomSelectionIterator beginAtomSelection();
323 AtomSelectionIterator endAtomSelection();
324
325 typedef MoleculeSet::iterator MoleculeSelectionIterator;
326 MoleculeSelectionIterator beginMoleculeSelection();
327 MoleculeSelectionIterator endMoleculeSelection();
328
329protected:
330 /****
331 * Iterators to use internal data structures
332 * All these iterators are unobserved for speed reasons.
333 * There is a corresponding public section to these methods,
334 * which produce observed iterators.*/
335
336 // Atoms
337 typedef SelectiveIterator<atom*,AtomSet::set_t,AtomDescriptor> internal_AtomIterator;
338
339 /**
340 * returns an iterator over all Atoms matching a given descriptor.
341 * used for internal purposes, like AtomProcesses and AtomCalculations.
342 */
343 internal_AtomIterator getAtomIter_internal(AtomDescriptor descr);
344
345 /**
346 * returns an iterator to the end of the AtomSet. Due to overloading this iterator
347 * can be compared to iterators produced by getAtomIter (see the mis-matching types).
348 * Thus it can be used to detect when such an iterator is at the end of the list.
349 * used for internal purposes, like AtomProcesses and AtomCalculations.
350 */
351 internal_AtomIterator atomEnd_internal();
352
353 // Molecules
354 typedef SelectiveIterator<molecule*,MoleculeSet::set_t,MoleculeDescriptor> internal_MoleculeIterator;
355
356
357 /**
358 * returns an iterator over all Molecules matching a given descriptor.
359 * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
360 */
361 internal_MoleculeIterator getMoleculeIter_internal(MoleculeDescriptor descr);
362
363 /**
364 * returns an iterator to the end of the MoleculeSet. Due to overloading this iterator
365 * can be compared to iterators produced by getMoleculeIter (see the mis-matching types).
366 * Thus it can be used to detect when such an iterator is at the end of the list.
367 * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
368 */
369 internal_MoleculeIterator moleculeEnd_internal();
370
371
372 /******* Internal manipulation routines for double callback and Observer mechanism ******/
373 void doManipulate(ManipulateAtomsProcess *);
374
375private:
376
377 atomId_t getNextAtomId();
378 void releaseAtomId(atomId_t);
379 bool reserveAtomId(atomId_t);
380 void defragAtomIdPool();
381
382 moleculeId_t getNextMoleculeId();
383 void releaseMoleculeId(moleculeId_t);
384 bool reserveMoleculeId(moleculeId_t);
385 void defragMoleculeIdPool();
386
387 BondGraph *BG;
388 periodentafel *periode;
389 config *configuration;
390 Box *cell_size;
391 std::string defaultName;
392 class ThermoStatContainer *Thermostats;
393 int ExitFlag;
394private:
395
396 AtomSet atoms;
397 AtomSet selectedAtoms;
398 typedef std::set<range<atomId_t> > atomIdPool_t;
399 /**
400 * stores the pool for all available AtomIds below currAtomId
401 *
402 * The pool contains ranges of free ids in the form [bottom,top).
403 */
404 atomIdPool_t atomIdPool;
405 atomId_t currAtomId; //!< stores the next available Id for atoms
406 size_t lastAtomPoolSize; //!< size of the pool after last defrag, to skip some defrags
407 unsigned int numAtomDefragSkips;
408
409 MoleculeSet molecules;
410 MoleculeSet selectedMolecules;
411 typedef std::set<range<atomId_t> > moleculeIdPool_t;
412 /**
413 * stores the pool for all available AtomIds below currAtomId
414 *
415 * The pool contains ranges of free ids in the form [bottom,top).
416 */
417 moleculeIdPool_t moleculeIdPool;
418 moleculeId_t currMoleculeId;
419 size_t lastMoleculePoolSize; //!< size of the pool after last defrag, to skip some defrags
420 unsigned int numMoleculeDefragSkips;
421private:
422 /**
423 * private constructor to ensure creation of the world using
424 * the singleton pattern.
425 */
426 World();
427
428 /**
429 * private destructor to ensure destruction of the world using the
430 * singleton pattern.
431 */
432 virtual ~World();
433
434 /*****
435 * some legacy stuff that is include for now but will be removed later
436 *****/
437public:
438 MoleculeListClass *&getMolecules();
439
440private:
441 MoleculeListClass *molecules_deprecated;
442};
443
444#endif /* WORLD_HPP_ */
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