source: src/World.hpp@ 02ce36

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Last change on this file since 02ce36 was 02ce36, checked in by Frederik Heber <heber@…>, 13 years ago

We now require CodePatterns 1.2.0.

  • this is due to the updated Observer structure and multi_array MemDebug bugfix.
  • Property mode set to 100644
File size: 15.1 KB
RevLine 
[5d1611]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
[3e4fb6]11// include config.h
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
[b34306]16/*********************************************** includes ***********************************/
17
[7c4e29]18#include <string>
[d346b6]19#include <map>
[fc1b24]20#include <vector>
[354859]21#include <set>
[7c4e29]22#include <boost/thread.hpp>
[865a945]23#include <boost/shared_ptr.hpp>
[5d1611]24
[3139b2]25#include "Actions/ActionTrait.hpp"
[6f0841]26#include "Atom/AtomSet.hpp"
[6e97e5]27#include "Descriptors/SelectiveIterator.hpp"
[02ce36]28#include "CodePatterns/Observer/Observable.hpp"
29#include "CodePatterns/Observer/Observer.hpp"
[ad011c]30#include "CodePatterns/Cacheable.hpp"
31#include "CodePatterns/Singleton.hpp"
[02ce36]32#include "CodePatterns/Observer/ObservedContainer.hpp"
[ad011c]33#include "CodePatterns/Range.hpp"
[3e4fb6]34#include "IdPool.hpp"
35#include "types.hpp"
[5d1611]36
37// forward declarations
[4d9c01]38class atom;
[fc1b24]39class AtomDescriptor;
[7a1ce5]40class AtomDescriptor_impl;
[f71baf]41class BondGraph;
[84c494]42class Box;
[43dad6]43class config;
[cca9ef]44class RealSpaceMatrix;
[43dad6]45class molecule;
[1c51c8]46class MoleculeDescriptor;
47class MoleculeDescriptor_impl;
[43dad6]48class MoleculeListClass;
49class periodentafel;
50class ThermoStatContainer;
[5d1611]51
[ce7fdc]52namespace MoleCuilder {
53 class ManipulateAtomsProcess;
54 template<typename T> class AtomsCalculation;
55}
[fa0b18]56
[b34306]57/****************************************** forward declarations *****************************/
[23b547]58
[b34306]59/********************************************** Class World *******************************/
[23b547]60
[7188b1]61namespace detail {
62 template <class T> const T* lastChanged()
63 {
64 ASSERT(0, "detail::lastChanged() - only specializations may be used.");
65 return NULL;
66 }
67}
68
[23b547]69class World : public Singleton<World>, public Observable
[5d1611]70{
[23b547]71
72// Make access to constructor and destructor possible from inside the singleton
73friend class Singleton<World>;
74
[b54ac8]75// necessary for coupling with descriptors
[7a1ce5]76friend class AtomDescriptor_impl;
[865a945]77friend class AtomDescriptor;
[1c51c8]78friend class MoleculeDescriptor_impl;
79friend class MoleculeDescriptor;
[41aa39]80// coupling with descriptors over selection
81friend class AtomSelectionDescriptor_impl;
[cf0ca1]82friend class MoleculeSelectionDescriptor_impl;
[865a945]83
[b54ac8]84// Actions, calculations etc associated with the World
[ce7fdc]85friend class MoleCuilder::ManipulateAtomsProcess;
86template<typename> friend class MoleCuilder::AtomsCalculation;
[5d1611]87public:
[5f1d5b8]88 // some typedefs for the CONSTRUCT_... macros (no "," allows in a single parameter name)
89 typedef std::map<atomId_t,atom*> AtomSTLSet;
90 typedef std::map<moleculeId_t,molecule*> MoleculeSTLSet;
[23b547]91
92 // Types for Atom and Molecule structures
[5f1d5b8]93 typedef ObservedContainer< AtomSTLSet > AtomSet;
94 typedef ObservedContainer< MoleculeSTLSet > MoleculeSet;
[5d1611]95
[4d72e4]96 typedef ATOMSET(std::vector) AtomComposite;
97
[7188b1]98 /******* Notifications *******/
99
100 //!> enumeration of present notification types
101 enum NotificationType {
102 AtomInserted,
103 AtomRemoved,
104 AtomChanged,
105 MoleculeInserted,
106 MoleculeRemoved,
107 MoleculeChanged,
108 NotificationType_MAX
109 };
110
111 //>! access to last changed element (atom or molecule)
112 template <class T> const T* lastChanged() const
113 { return detail::lastChanged<T>(); }
114
115 /***** getter and setter *****/
[354859]116 // reference to pointer is used for legacy reason... reference will be removed latter to keep encapsulation of World object
[02ee15]117 /**
118 * returns the periodentafel for the world.
119 */
[354859]120 periodentafel *&getPeriode();
[02ee15]121
[f71baf]122 /** Returns the BondGraph for the World.
123 *
124 * @return reference to BondGraph
125 */
126 BondGraph *&getBondGraph();
127
128 /** Sets the World's BondGraph.
129 *
130 * @param _BG new BondGraph
131 */
132 void setBondGraph(BondGraph *_BG);
[8e1f7af]133 /**
134 * returns the configuration for the world.
135 */
136 config *&getConfig();
137
[7188b1]138 /** Returns a notification_ptr for a specific type.
139 *
140 * @param type request type
141 * @return reference to instance
142 */
143 Notification_ptr getNotification(enum NotificationType type) const;
144
[02ee15]145 /**
146 * returns the first atom that matches a given descriptor.
147 * Do not rely on ordering for descriptors that match more than one atom.
148 */
[7a1ce5]149 atom* getAtom(AtomDescriptor descriptor);
[02ee15]150
151 /**
152 * returns a vector containing all atoms that match a given descriptor
153 */
[4d72e4]154 AtomComposite getAllAtoms(AtomDescriptor descriptor);
155 AtomComposite getAllAtoms();
[b54ac8]156
[02ee15]157 /**
158 * returns a calculation that calls a given function on all atoms matching a descriptor.
159 * the calculation is not called at this point and can be used as an action, i.e. be stored in
160 * menus, be kept around for later use etc.
161 */
[3139b2]162 template<typename T> MoleCuilder::AtomsCalculation<T>* calcOnAtoms(boost::function<T(atom*)>,const MoleCuilder::ActionTrait &_trait,AtomDescriptor);
163 template<typename T> MoleCuilder::AtomsCalculation<T>* calcOnAtoms(boost::function<T(atom*)>,const MoleCuilder::ActionTrait &_trait);
[b54ac8]164
[02ee15]165 /**
166 * get the number of atoms in the World
167 */
[354859]168 int numAtoms();
[02ee15]169
[1c51c8]170 /**
171 * returns the first molecule that matches a given descriptor.
172 * Do not rely on ordering for descriptors that match more than one molecule.
173 */
174 molecule *getMolecule(MoleculeDescriptor descriptor);
175
176 /**
177 * returns a vector containing all molecules that match a given descriptor
178 */
179 std::vector<molecule*> getAllMolecules(MoleculeDescriptor descriptor);
[97ebf8]180 std::vector<molecule*> getAllMolecules();
[1c51c8]181
[02ee15]182 /**
183 * get the number of molecules in the World
184 */
[354859]185 int numMolecules();
186
[5f612ee]187 /**
188 * get the domain size as a symmetric matrix (6 components)
189 */
[84c494]190 Box& getDomain();
191
192 /**
193 * Set the domain size from a matrix object
194 *
195 * Matrix needs to be symmetric
196 */
[cca9ef]197 void setDomain(const RealSpaceMatrix &mat);
[5f612ee]198
199 /**
200 * set the domain size as a symmetric matrix (6 components)
201 */
202 void setDomain(double * matrix);
203
[d297a3]204 /**
205 * set the current time of the world.
206 *
207 * @param _step time step to set to
208 */
209 void setTime(const unsigned int _step);
210
[5f612ee]211 /**
212 * get the default name
213 */
[387b36]214 std::string getDefaultName();
[5f612ee]215
216 /**
217 * set the default name
218 */
[387b36]219 void setDefaultName(std::string name);
[5f612ee]220
[43dad6]221 /**
222 * get pointer to World's ThermoStatContainer
223 */
224 ThermoStatContainer * getThermostats();
225
[e4b5de]226 /*
227 * get the ExitFlag
228 */
229 int getExitFlag();
230
231 /*
232 * set the ExitFlag
233 */
234 void setExitFlag(int flag);
235
[354859]236 /***** Methods to work with the World *****/
[02ee15]237
238 /**
239 * create a new molecule. This method should be used whenever any kind of molecule is needed. Assigns a unique
240 * ID to the molecule and stores it in the World for later retrieval. Do not create molecules directly.
241 */
[354859]242 molecule *createMolecule();
[02ee15]243
[cbc5fb]244 void destroyMolecule(molecule*);
245 void destroyMolecule(moleculeId_t);
246
[02ee15]247 /**
248 * Create a new atom. This method should be used whenever any atom is needed. Assigns a unique ID and stores
249 * the atom in the World. If the atom is not destroyed it will automatically be destroyed when the world ends.
250 */
[46d958]251 atom *createAtom();
[02ee15]252
253 /**
254 * Registers a Atom unknown to world. Needed in some rare cases, e.g. when cloning atoms, or in some unittests.
255 * Do not re-register Atoms already known to the world since this will cause double-frees.
256 */
[46d958]257 int registerAtom(atom*);
[02ee15]258
259 /**
260 * Delete some atom and erase it from the world. Use this whenever you need to destroy any atom. Do not call delete on
261 * atom directly since this will leave the pointer inside the world.
262 */
[46d958]263 void destroyAtom(atom*);
[02ee15]264
265 /**
266 * Delete some atom and erase it from the world. Use this whenever you need to destroy any atom. Do not call delete on
267 * atom directly since this will leave the pointer inside the world.
268 */
[cbc5fb]269 void destroyAtom(atomId_t);
[865a945]270
[88d586]271 /**
272 * used when changing an atom Id.
273 * Unless you are calling this method from inside an atom don't fiddle with the third parameter.
274 *
275 * Return value indicates wether the change could be done or not.
276 */
277 bool changeAtomId(atomId_t oldId, atomId_t newId, atom* target=0);
278
[a7a087]279 /**
280 * used when changing an molecule Id.
281 * Unless you are calling this method from inside an moleucle don't fiddle with the third parameter.
282 *
283 * Return value indicates wether the change could be done or not.
284 */
285 bool changeMoleculeId(moleculeId_t oldId, moleculeId_t newId, molecule* target=0);
286
[02ee15]287 /**
288 * Produces a process that calls a function on all Atoms matching a given descriptor. The process is not
289 * called at this time, so it can be passed around, stored inside menuItems etc.
290 */
[ce7fdc]291 MoleCuilder::ManipulateAtomsProcess* manipulateAtoms(boost::function<void(atom*)>,std::string,AtomDescriptor);
292 MoleCuilder::ManipulateAtomsProcess* manipulateAtoms(boost::function<void(atom*)>,std::string);
[7c4e29]293
[fa0b18]294 /****
295 * Iterators to use internal data structures
296 * All these iterators are observed to track changes.
297 * There is a corresponding protected section with unobserved iterators,
[90c4280]298 * which can be used internally when the extra speed is needed
[fa0b18]299 */
300
301 typedef SelectiveIterator<atom*,AtomSet,AtomDescriptor> AtomIterator;
302
303 /**
304 * returns an iterator over all Atoms matching a given descriptor.
305 * This iterator is observed, so don't keep it around unnecessary to
306 * avoid unintended blocking.
307 */
308 AtomIterator getAtomIter(AtomDescriptor descr);
309 AtomIterator getAtomIter();
310
311 AtomIterator atomEnd();
312
[e3d865]313 typedef SelectiveIterator<molecule*,MoleculeSet,MoleculeDescriptor> MoleculeIterator;
[51be2a]314
[90c4280]315 /**
316 * returns an iterator over all Molecules matching a given descriptor.
317 * This iterator is observed, so don't keep it around unnecessary to
318 * avoid unintended blocking.
319 */
[5d880e]320 MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
321 MoleculeIterator getMoleculeIter();
322
323 MoleculeIterator moleculeEnd();
324
[90c4280]325 /******** Selections of molecules and Atoms *************/
326 void clearAtomSelection();
[e4afb4]327 void selectAtom(const atom*);
328 void selectAtom(const atomId_t);
[90c4280]329 void selectAllAtoms(AtomDescriptor);
[e4afb4]330 void selectAtomsOfMolecule(const molecule*);
331 void selectAtomsOfMolecule(const moleculeId_t);
332 void unselectAtom(const atom*);
333 void unselectAtom(const atomId_t);
[61d655e]334 void unselectAllAtoms(AtomDescriptor);
[e4afb4]335 void unselectAtomsOfMolecule(const molecule*);
336 void unselectAtomsOfMolecule(const moleculeId_t);
[e472eab]337 size_t countSelectedAtoms() const;
[e4afb4]338 bool isSelected(const atom *_atom) const;
[89643d]339 bool isAtomSelected(const atomId_t no) const;
[e472eab]340 const std::vector<atom *> getSelectedAtoms() const;
[90c4280]341
342 void clearMoleculeSelection();
[e4afb4]343 void selectMolecule(const molecule*);
344 void selectMolecule(const moleculeId_t);
[e472eab]345 void selectAllMolecules(MoleculeDescriptor);
[e4afb4]346 void selectMoleculeOfAtom(const atom*);
347 void selectMoleculeOfAtom(const atomId_t);
348 void unselectMolecule(const molecule*);
349 void unselectMolecule(const moleculeId_t);
[e472eab]350 void unselectAllMolecules(MoleculeDescriptor);
[e4afb4]351 void unselectMoleculeOfAtom(const atom*);
352 void unselectMoleculeOfAtom(const atomId_t);
[e472eab]353 size_t countSelectedMolecules() const;
[e4afb4]354 bool isSelected(const molecule *_mol) const;
[89643d]355 bool isMoleculeSelected(const moleculeId_t no) const;
[e472eab]356 const std::vector<molecule *> getSelectedMolecules() const;
[90c4280]357
[3839e5]358 /******************** Iterators to selections *****************/
359 typedef AtomSet::iterator AtomSelectionIterator;
360 AtomSelectionIterator beginAtomSelection();
361 AtomSelectionIterator endAtomSelection();
[38f991]362 typedef AtomSet::const_iterator AtomSelectionConstIterator;
363 AtomSelectionConstIterator beginAtomSelection() const;
364 AtomSelectionConstIterator endAtomSelection() const;
[3839e5]365
366 typedef MoleculeSet::iterator MoleculeSelectionIterator;
367 MoleculeSelectionIterator beginMoleculeSelection();
368 MoleculeSelectionIterator endMoleculeSelection();
[38f991]369 typedef MoleculeSet::const_iterator MoleculeSelectionConstIterator;
370 MoleculeSelectionConstIterator beginMoleculeSelection() const;
371 MoleculeSelectionConstIterator endMoleculeSelection() const;
[3839e5]372
[865a945]373protected:
[fa0b18]374 /****
375 * Iterators to use internal data structures
376 * All these iterators are unobserved for speed reasons.
377 * There is a corresponding public section to these methods,
378 * which produce observed iterators.*/
[1c51c8]379
380 // Atoms
[e3d865]381 typedef SelectiveIterator<atom*,AtomSet::set_t,AtomDescriptor> internal_AtomIterator;
[865a945]382
[02ee15]383 /**
384 * returns an iterator over all Atoms matching a given descriptor.
385 * used for internal purposes, like AtomProcesses and AtomCalculations.
386 */
[fa0b18]387 internal_AtomIterator getAtomIter_internal(AtomDescriptor descr);
[02ee15]388
389 /**
[d2dbac0]390 * returns an iterator to the end of the AtomSet. Due to overloading this iterator
[02ee15]391 * can be compared to iterators produced by getAtomIter (see the mis-matching types).
392 * Thus it can be used to detect when such an iterator is at the end of the list.
393 * used for internal purposes, like AtomProcesses and AtomCalculations.
394 */
[fa0b18]395 internal_AtomIterator atomEnd_internal();
[865a945]396
[1c51c8]397 // Molecules
[e3d865]398 typedef SelectiveIterator<molecule*,MoleculeSet::set_t,MoleculeDescriptor> internal_MoleculeIterator;
[51be2a]399
[1c51c8]400
401 /**
402 * returns an iterator over all Molecules matching a given descriptor.
403 * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
404 */
[e3d865]405 internal_MoleculeIterator getMoleculeIter_internal(MoleculeDescriptor descr);
[1c51c8]406
407 /**
408 * returns an iterator to the end of the MoleculeSet. Due to overloading this iterator
409 * can be compared to iterators produced by getMoleculeIter (see the mis-matching types).
410 * Thus it can be used to detect when such an iterator is at the end of the list.
411 * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
412 */
[e3d865]413 internal_MoleculeIterator moleculeEnd_internal();
[1c51c8]414
415
[afb47f]416 /******* Internal manipulation routines for double callback and Observer mechanism ******/
[ce7fdc]417 void doManipulate(MoleCuilder::ManipulateAtomsProcess *);
[afb47f]418
[5d1611]419private:
[88d586]420
421 atomId_t getNextAtomId();
422 void releaseAtomId(atomId_t);
423 bool reserveAtomId(atomId_t);
[127a8e]424 void defragAtomIdPool();
425
426 moleculeId_t getNextMoleculeId();
427 void releaseMoleculeId(moleculeId_t);
428 bool reserveMoleculeId(moleculeId_t);
429 void defragMoleculeIdPool();
[88d586]430
[7188b1]431 friend const atom *detail::lastChanged<atom>();
432 friend const molecule *detail::lastChanged<molecule>();
433 static atom *_lastchangedatom;
434 static molecule*_lastchangedmol;
435
[f71baf]436 BondGraph *BG;
[5d1611]437 periodentafel *periode;
[8e1f7af]438 config *configuration;
[84c494]439 Box *cell_size;
[387b36]440 std::string defaultName;
[43dad6]441 class ThermoStatContainer *Thermostats;
[e4b5de]442 int ExitFlag;
[6e97e5]443private:
[127a8e]444
[1a76a6]445 AtomSet atoms;
[90c4280]446 AtomSet selectedAtoms;
[127a8e]447 /**
448 * stores the pool for all available AtomIds below currAtomId
449 *
450 * The pool contains ranges of free ids in the form [bottom,top).
451 */
[3e4fb6]452 IdPool<atomId_t> atomIdPool;
[127a8e]453
[d2dbac0]454 MoleculeSet molecules;
[90c4280]455 MoleculeSet selectedMolecules;
[1a76a6]456 /**
457 * stores the pool for all available AtomIds below currAtomId
458 *
459 * The pool contains ranges of free ids in the form [bottom,top).
460 */
[3e4fb6]461 IdPool<moleculeId_t> moleculeIdPool;
462
[5d1611]463private:
[02ee15]464 /**
465 * private constructor to ensure creation of the world using
466 * the singleton pattern.
467 */
[5d1611]468 World();
[02ee15]469
470 /**
471 * private destructor to ensure destruction of the world using the
472 * singleton pattern.
473 */
[5d1611]474 virtual ~World();
475
476 /*****
477 * some legacy stuff that is include for now but will be removed later
478 *****/
479public:
[354859]480 MoleculeListClass *&getMolecules();
[4d9c01]481
[5d1611]482private:
[354859]483 MoleculeListClass *molecules_deprecated;
[5d1611]484};
485
[7188b1]486/** Externalized stuff as member functions cannot be specialized without
487 * specializing the class, too.
488 */
489namespace detail {
490 template <> inline const atom* lastChanged<atom>() { return World::_lastchangedatom; }
491 template <> inline const molecule* lastChanged<molecule>() { return World::_lastchangedmol; }
492}
493
494
[5d1611]495#endif /* WORLD_HPP_ */
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