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root/OpenMD/branches/development/src/primitives/Molecule.hpp

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trunk/src/primitives/Molecule.hpp (file contents), Revision 305 by tim, Mon Feb 7 22:39:19 2005 UTC vs.
branches/development/src/primitives/Molecule.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 58 | Line 59
59		#include "primitives/Bond.hpp"
60		#include "primitives/Bend.hpp"
61		#include "primitives/Torsion.hpp"
62	+	#include "primitives/Inversion.hpp"
63		#include "primitives/CutoffGroup.hpp"
64	+	#include "utils/PropertyMap.hpp"
65
66	<	namespace oopse{
66	>	namespace OpenMD{
67
68	<	class Constraint;
68	>	class Constraint;
69
70	<	/**
71	<	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
72	<	* @brief
73	<	*/
74	<	class Molecule {
75	<	public:
70	>	/**
71	>	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
72	>	* @brief
73	>	*/
74	>	class Molecule {
75	>	public:
76
77	<	typedef std::vector<Atom*>::iterator AtomIterator;
78	<	typedef std::vector<Bond*>::iterator BondIterator;
79	<	typedef std::vector<Bend*>::iterator BendIterator;
80	<	typedef std::vector<Torsion*>::iterator TorsionIterator;
81	<	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
82	<	typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
83	<	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
84	<	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
85	<	typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
86	<
77	>	typedef std::vector<Atom*>::iterator AtomIterator;
78	>	typedef std::vector<Bond*>::iterator BondIterator;
79	>	typedef std::vector<Bend*>::iterator BendIterator;
80	>	typedef std::vector<Torsion*>::iterator TorsionIterator;
81	>	typedef std::vector<Inversion*>::iterator InversionIterator;
82	>	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
83	>	typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
84	>	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
85	>	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
86	>	typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
87	>
88	>
89	>	Molecule(int stampId, int globalIndex, const std::string& molName);
90	>	virtual ~Molecule();
91
92	<	Molecule(int stampId, int globalIndex, const std::string& molName);
93	<	virtual ~Molecule();
92	>	/**
93	>	* Returns the global index of this molecule.
94	>	* @return  the global index of this molecule
95	>	*/
96	>	int getGlobalIndex() {
97	>	return globalIndex_;
98	>	}
99	>
100	>	/**
101	>	* Returns the stamp id of this molecule
102	>	* @note Ideally, every molecule should keep a pointer of its
103	>	* molecule stamp instead of its stamp id. However, the pointer
104	>	* will become invalid, if the molecule migrate to other
105	>	* processor.
106	>	*/
107	>	int getStampId() {
108	>	return stampId_;
109	>	}
110	>
111	>	/** Returns the name of the molecule */
112	>	std::string getType() {
113	>	return moleculeName_;
114	>	}
115	>
116	>	/**
117	>	* Sets the global index of this molecule.
118	>	* @param new global index to be set
119	>	*/
120	>	void setGlobalIndex(int index) {
121	>	globalIndex_ = index;
122	>	}
123	>
124	>
125	>	/** add an atom into this molecule */
126	>	void addAtom(Atom* atom);
127	>
128	>	/** add a bond into this molecule */
129	>	void addBond(Bond* bond);
130	>
131	>	/** add a bend into this molecule */
132	>	void addBend(Bend* bend);
133	>
134	>	/** add a torsion into this molecule*/
135	>	void addTorsion(Torsion* torsion);
136
137	<	/**
138	<	* Returns the global index of this molecule.
139	<	* @return  the global index of this molecule
140	<	*/
141	<	int getGlobalIndex() {
142	<	return globalIndex_;
143	<	}
137	>	/** add an improper torsion into this molecule*/
138	>	void addInversion(Inversion* inversion);
139	>
140	>	/** add a rigidbody into this molecule */
141	>	void addRigidBody(RigidBody *rb);
142	>
143	>	/** add a cutoff group into this molecule */
144	>	void addCutoffGroup(CutoffGroup* cp);
145	>
146	>	void addConstraintPair(ConstraintPair* consPair);
147	>
148	>	void addConstraintElem(ConstraintElem* consElem);
149	>
150	>	/** */
151	>	void complete();
152	>
153	>	/** Returns the total number of atoms in this molecule */
154	>	unsigned int getNAtoms() {
155	>	return atoms_.size();
156	>	}
157	>
158	>	/** Returns the total number of bonds in this molecule */
159	>	unsigned int getNBonds(){
160	>	return bonds_.size();
161	>	}
162	>
163	>	/** Returns the total number of bends in this molecule */
164	>	unsigned int getNBends() {
165	>	return bends_.size();
166	>	}
167	>
168	>	/** Returns the total number of torsions in this molecule */
169	>	unsigned int getNTorsions() {
170	>	return torsions_.size();
171	>	}
172
173	<	/**
174	<	* Returns the stamp id of this molecule
175	<	* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
176	<	* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
177	<	*/
178	<	int getStampId() {
179	<	return stampId_;
180	<	}
173	>	/** Returns the total number of improper torsions in this molecule */
174	>	unsigned int getNInversions() {
175	>	return inversions_.size();
176	>	}
177	>
178	>	/** Returns the total number of rigid bodies in this molecule */
179	>	unsigned int getNRigidBodies() {
180	>	return rigidBodies_.size();
181	>	}
182	>
183	>	/** Returns the total number of integrable objects in this molecule */
184	>	unsigned int getNIntegrableObjects() {
185	>	return integrableObjects_.size();
186	>	}
187	>
188	>	/** Returns the total number of cutoff groups in this molecule */
189	>	unsigned int getNCutoffGroups() {
190	>	return cutoffGroups_.size();
191	>	}
192	>
193	>	/** Returns the total number of constraints in this molecule */
194	>	unsigned int getNConstraintPairs() {
195	>	return constraintPairs_.size();
196	>	}
197	>
198	>	Atom* getAtomAt(unsigned int i) {
199	>	assert(i < atoms_.size());
200	>	return atoms_[i];
201	>	}
202	>
203	>	RigidBody* getRigidBodyAt(unsigned int i) {
204	>	assert(i < rigidBodies_.size());
205	>	return rigidBodies_[i];
206	>	}
207	>
208	>	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
209	>	i = atoms_.begin();
210	>	return (i == atoms_.end()) ? NULL : *i;
211	>	}
212	>
213	>	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
214	>	++i;
215	>	return (i == atoms_.end()) ? NULL : *i;
216	>	}
217	>
218	>	Bond* beginBond(std::vector<Bond*>::iterator& i) {
219	>	i = bonds_.begin();
220	>	return (i == bonds_.end()) ? NULL : *i;
221	>	}
222	>
223	>	Bond* nextBond(std::vector<Bond*>::iterator& i) {
224	>	++i;
225	>	return (i == bonds_.end()) ? NULL : *i;
226	>
227	>	}
228	>
229	>	Bend* beginBend(std::vector<Bend*>::iterator& i) {
230	>	i = bends_.begin();
231	>	return (i == bends_.end()) ? NULL : *i;
232	>	}
233	>
234	>	Bend* nextBend(std::vector<Bend*>::iterator& i) {
235	>	++i;
236	>	return (i == bends_.end()) ? NULL : *i;
237	>	}
238	>
239	>	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
240	>	i = torsions_.begin();
241	>	return (i == torsions_.end()) ? NULL : *i;
242	>	}
243	>
244	>	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
245	>	++i;
246	>	return (i == torsions_.end()) ? NULL : *i;
247	>	}
248
249	<	/** Returns the name of the molecule */
250	<	std::string getType() {
251	<	return moleculeName_;
252	<	}
253	<
254	<	/**
255	<	* Sets the global index of this molecule.
256	<	* @param new global index to be set
257	<	*/
258	<	void setGlobalIndex(int index) {
259	<	globalIndex_ = index;
260	<	}
249	>	Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
250	>	i = inversions_.begin();
251	>	return (i == inversions_.end()) ? NULL : *i;
252	>	}
253	>
254	>	Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
255	>	++i;
256	>	return (i == inversions_.end()) ? NULL : *i;
257	>	}
258	>
259	>	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
260	>	i = rigidBodies_.begin();
261	>	return (i == rigidBodies_.end()) ? NULL : *i;
262	>	}
263	>
264	>	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
265	>	++i;
266	>	return (i == rigidBodies_.end()) ? NULL : *i;
267	>	}
268	>
269	>	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
270	>	i = integrableObjects_.begin();
271	>	return (i == integrableObjects_.end()) ? NULL : *i;
272	>	}
273	>
274	>	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
275	>	++i;
276	>	return (i == integrableObjects_.end()) ? NULL : *i;
277	>	}
278	>
279	>	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
280	>	i = cutoffGroups_.begin();
281	>	return (i == cutoffGroups_.end()) ? NULL : *i;
282	>	}
283
284	<
285	<	/** add an atom into this molecule */
286	<	void addAtom(Atom* atom);
287	<
288	<	/** add a bond into this molecule */
289	<	void addBond(Bond* bond);
290	<
291	<	/** add a bend into this molecule */
292	<	void addBend(Bend* bend);
293	<
294	<	/** add a torsion into this molecule*/
295	<	void addTorsion(Torsion* torsion);
296	<
297	<	/** add a rigidbody into this molecule */
298	<	void addRigidBody(RigidBody *rb);
299	<
300	<	/** add a cutoff group into this molecule */
301	<	void addCutoffGroup(CutoffGroup* cp);
302	<
303	<	void addConstraintPair(ConstraintPair* consPair);
284	>	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
285	>	++i;
286	>	return (i == cutoffGroups_.end()) ? NULL : *i;
287	>	}
288	>
289	>	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
290	>	i = constraintPairs_.begin();
291	>	return (i == constraintPairs_.end()) ? NULL : *i;
292	>	}
293	>
294	>	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
295	>	++i;
296	>	return (i == constraintPairs_.end()) ? NULL : *i;
297	>	}
298	>
299	>	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
300	>	i = constraintElems_.begin();
301	>	return (i == constraintElems_.end()) ? NULL : *i;
302	>	}
303	>
304	>	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
305	>	++i;
306	>	return (i == constraintElems_.end()) ? NULL : *i;
307	>	}
308
309	<	void addConstraintElem(ConstraintElem* consElem);
309	>	/**
310	>	* Returns the total potential energy of short range interaction
311	>	* of this molecule
312	>	*/
313	>	RealType getPotential();
314	>
315	>	/** get total mass of this molecule */
316	>	RealType getMass();
317	>
318	>	/** return the center of mass of this molecule */
319	>	Vector3d getCom();
320	>
321	>	/** Moves the center of this molecule */
322	>	void moveCom(const Vector3d& delta);
323	>
324	>	/** Returns the velocity of center of mass of this molecule */
325	>	Vector3d getComVel();
326
327	<	/** */
328	<	void complete();
329	<
144	<	/** Returns the total number of atoms in this molecule */
145	<	unsigned int getNAtoms() {
146	<	return atoms_.size();
147	<	}
148	<
149	<	/** Returns the total number of bonds in this molecule */
150	<	unsigned int getNBonds(){
151	<	return bonds_.size();
152	<	}
153	<
154	<	/** Returns the total number of bends in this molecule */
155	<	unsigned int getNBends() {
156	<	return bends_.size();
157	<	}
158	<
159	<	/** Returns the total number of torsions in this molecule */
160	<	unsigned int getNTorsions() {
161	<	return torsions_.size();
162	<	}
163	<
164	<	/** Returns the total number of rigid bodies in this molecule */
165	<	unsigned int getNRigidBodies() {
166	<	return rigidBodies_.size();
167	<	}
168	<
169	<	/** Returns the total number of integrable objects in this molecule */
170	<	unsigned int getNIntegrableObjects() {
171	<	return integrableObjects_.size();
172	<	}
173	<
174	<	/** Returns the total number of cutoff groups in this molecule */
175	<	unsigned int getNCutoffGroups() {
176	<	return cutoffGroups_.size();
177	<	}
178	<
179	<	/** Returns the total number of constraints in this molecule */
180	<	unsigned int getNConstraintPairs() {
181	<	return constraintPairs_.size();
182	<	}
183	<
184	<	Atom* getAtomAt(unsigned int i) {
185	<	assert(i < atoms_.size());
186	<	return atoms_[i];
187	<	}
188	<
189	<	RigidBody* getRigidBodyAt(unsigned int i) {
190	<	assert(i < rigidBodies_.size());
191	<	return rigidBodies_[i];
192	<	}
327	>	std::string getMoleculeName() {
328	>	return moleculeName_;
329	>	}
330
331	<	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
195	<	i = atoms_.begin();
196	<	return (i == atoms_.end()) ? NULL : *i;
197	<	}
331	>	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
332
333	<	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
334	<	++i;
335	<	return (i == atoms_.end()) ? NULL : *i;
336	<	}
333	>	//below functions are just forward functions
334	>	/**
335	>	* Adds property into property map
336	>	* @param genData GenericData to be added into PropertyMap
337	>	*/
338	>	void addProperty(GenericData* genData);
339
340	<	Bond* beginBond(std::vector<Bond*>::iterator& i) {
341	<	i = bonds_.begin();
342	<	return (i == bonds_.end()) ? NULL : *i;
343	<	}
340	>	/**
341	>	* Removes property from PropertyMap by name
342	>	* @param propName the name of property to be removed
343	>	*/
344	>	void removeProperty(const std::string& propName);
345
346	<	Bond* nextBond(std::vector<Bond*>::iterator& i) {
347	<	++i;
348	<	return (i == bonds_.end()) ? NULL : *i;
346	>	/**
347	>	* clear all of the properties
348	>	*/
349	>	void clearProperties();
350
351	<	}
351	>	/**
352	>	* Returns all names of properties
353	>	* @return all names of properties
354	>	*/
355	>	std::vector<std::string> getPropertyNames();
356
357	<	Bend* beginBend(std::vector<Bend*>::iterator& i) {
358	<	i = bends_.begin();
359	<	return (i == bends_.end()) ? NULL : *i;
360	<	}
357	>	/**
358	>	* Returns all of the properties in PropertyMap
359	>	* @return all of the properties in PropertyMap
360	>	*/
361	>	std::vector<GenericData*> getProperties();
362
363	<	Bend* nextBend(std::vector<Bend*>::iterator& i) {
364	<	++i;
365	<	return (i == bends_.end()) ? NULL : *i;
366	<	}
363	>	/**
364	>	* Returns property
365	>	* @param propName name of property
366	>	* @return a pointer point to property with propName. If no property named propName
367	>	* exists, return NULL
368	>	*/
369	>	GenericData* getPropertyByName(const std::string& propName);
370	>
371	>	private:
372	>
373	>	int globalIndex_;
374	>
375	>	std::vector<Atom*> atoms_;
376	>	std::vector<Bond*> bonds_;
377	>	std::vector<Bend*> bends_;
378	>	std::vector<Torsion*> torsions_;
379	>	std::vector<Inversion*> inversions_;
380	>	std::vector<RigidBody*> rigidBodies_;
381	>	std::vector<StuntDouble*> integrableObjects_;
382	>	std::vector<CutoffGroup*> cutoffGroups_;
383	>	std::vector<ConstraintPair*> constraintPairs_;
384	>	std::vector<ConstraintElem*> constraintElems_;
385	>	int stampId_;
386	>	std::string moleculeName_;
387	>	PropertyMap properties_;
388
389	<	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
226	<	i = torsions_.begin();
227	<	return (i == torsions_.end()) ? NULL : *i;
228	<	}
389	>	};
390
391	<	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
231	<	++i;
232	<	return (i == torsions_.end()) ? NULL : *i;
233	<	}
234	<
235	<	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
236	<	i = rigidBodies_.begin();
237	<	return (i == rigidBodies_.end()) ? NULL : *i;
238	<	}
239	<
240	<	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
241	<	++i;
242	<	return (i == rigidBodies_.end()) ? NULL : *i;
243	<	}
244	<
245	<	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
246	<	i = integrableObjects_.begin();
247	<	return (i == integrableObjects_.end()) ? NULL : *i;
248	<	}
249	<
250	<	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
251	<	++i;
252	<	return (i == integrableObjects_.end()) ? NULL : *i;
253	<	}
254	<
255	<	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
256	<	i = cutoffGroups_.begin();
257	<	return (i == cutoffGroups_.end()) ? NULL : *i;
258	<	}
259	<
260	<	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
261	<	++i;
262	<	return (i == cutoffGroups_.end()) ? NULL : *i;
263	<	}
264	<
265	<	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
266	<	i = constraintPairs_.begin();
267	<	return (i == constraintPairs_.end()) ? NULL : *i;
268	<	}
269	<
270	<	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
271	<	++i;
272	<	return (i == constraintPairs_.end()) ? NULL : *i;
273	<	}
274	<
275	<	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
276	<	i = constraintElems_.begin();
277	<	return (i == constraintElems_.end()) ? NULL : *i;
278	<	}
279	<
280	<	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
281	<	++i;
282	<	return (i == constraintElems_.end()) ? NULL : *i;
283	<	}
284	<
285	<	/** return the total potential energy of short range interaction of this molecule */
286	<	double getPotential();
287	<
288	<	/** get total mass of this molecule */
289	<	double getMass();
290	<
291	<	/** return the center of mass of this molecule */
292	<	Vector3d getCom();
293	<
294	<	/** Moves the center of this molecule */
295	<	void moveCom(const Vector3d& delta);
296	<
297	<	/** Returns the velocity of center of mass of this molecule */
298	<	Vector3d getComVel();
299	<
300	<	std::string getMoleculeName() {
301	<	return moleculeName_;
302	<	}
303	<
304	<	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
305	<
306	<	private:
307	<
308	<	int globalIndex_;
309	<
310	<	std::vector<Atom*> atoms_;
311	<	std::vector<Bond*> bonds_;
312	<	std::vector<Bend*> bends_;
313	<	std::vector<Torsion*> torsions_;
314	<	std::vector<RigidBody*> rigidBodies_;
315	<	std::vector<StuntDouble*> integrableObjects_;
316	<	std::vector<CutoffGroup*> cutoffGroups_;
317	<	std::vector<ConstraintPair*> constraintPairs_;
318	<	std::vector<ConstraintElem*> constraintElems_;
319	<	int stampId_;
320	<	std::string moleculeName_;
321	<	};
322	<
323	<	} //namespace oopse
391	>	} //namespace OpenMD
392		#endif //

Comparing:
trunk/src/primitives/Molecule.hpp (property svn:keywords), Revision 305 by tim, Mon Feb 7 22:39:19 2005 UTC vs.
branches/development/src/primitives/Molecule.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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