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root/OpenMD/trunk/src/brains/ForceField.cpp

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trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 1195 by cpuglis, Thu Dec 6 20:04:02 2007 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (file contents), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

#	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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 47 | Line 47
47		* @version 1.0
48		*/
49
50	+	#include <algorithm>
51		#include "UseTheForce/ForceField.hpp"
52		#include "utils/simError.h"
53	<	#include "UseTheForce/DarkSide/atype_interface.h"
54	<	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
54	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
55	<	namespace oopse {
53	>	#include "utils/Tuple.hpp"
54	>	namespace OpenMD {
55
56		ForceField::ForceField() {
57	+
58		char* tempPath;
59		tempPath = getenv("FORCE_PARAM_PATH");
60	<
60	>
61		if (tempPath == NULL) {
62		//convert a macro from compiler to a string in c++
63		STR_DEFINE(ffPath_, FRC_PATH );
#	Line 66 | Line 66 | namespace oopse {
66		}
67		}
68
69	<
70	<	ForceField::~ForceField() {
71	<	deleteAtypes();
72	<	deleteSwitch();
73	<	}
74	<
69	>	/**
70	>	* getAtomType by string
71	>	*
72	>	* finds the requested atom type in this force field using the string
73	>	* name of the atom type.
74	>	*/
75		AtomType* ForceField::getAtomType(const std::string &at) {
76		std::vector<std::string> keys;
77		keys.push_back(at);
78		return atomTypeCont_.find(keys);
79		}
80
81	+	/**
82	+	* getAtomType by ident
83	+	*
84	+	* finds the requested atom type in this force field using the
85	+	* integer ident instead of the string name of the atom type.
86	+	*/
87	+	AtomType* ForceField::getAtomType(int ident) {
88	+	std::string at = atypeIdentToName.find(ident)->second;
89	+	return getAtomType(at);
90	+	}
91	+
92		BondType* ForceField::getBondType(const std::string &at1,
93		const std::string &at2) {
94		std::vector<std::string> keys;
#	Line 89 | Line 100 | namespace oopse {
100		if (bondType) {
101		return bondType;
102		} else {
103	<	//if no exact match found, try wild card match
104	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
103	>	AtomType* atype1;
104	>	AtomType* atype2;
105	>	std::vector<std::string> at1key;
106	>	at1key.push_back(at1);
107	>	atype1 = atomTypeCont_.find(at1key);
108	>
109	>	std::vector<std::string> at2key;
110	>	at2key.push_back(at2);
111	>	atype2 = atomTypeCont_.find(at2key);
112	>
113	>	// query atom types for their chains of responsibility
114	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
115	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
116	>
117	>	std::vector<AtomType*>::iterator i;
118	>	std::vector<AtomType*>::iterator j;
119	>
120	>	int ii = 0;
121	>	int jj = 0;
122	>	int bondTypeScore;
123	>
124	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
125	>
126	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
127	>	jj = 0;
128	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
129	>
130	>	bondTypeScore = ii + jj;
131	>
132	>	std::vector<std::string> myKeys;
133	>	myKeys.push_back((*i)->getName());
134	>	myKeys.push_back((*j)->getName());
135	>
136	>	BondType* bondType = bondTypeCont_.find(myKeys);
137	>	if (bondType) {
138	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
139	>	}
140	>	jj++;
141	>	}
142	>	ii++;
143	>	}
144	>
145	>
146	>	if (foundBonds.size() > 0) {
147	>	// sort the foundBonds by the score:
148	>	std::sort(foundBonds.begin(), foundBonds.end());
149	>
150	>	int bestScore = foundBonds[0].first;
151	>	std::vector<std::string> theKeys = foundBonds[0].second;
152	>
153	>	BondType* bestType = bondTypeCont_.find(theKeys);
154	>
155	>	return bestType;
156	>	} else {
157	>	//if no exact match found, try wild card match
158	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
159	>	}
160		}
161		}
162	<
162	>
163		BendType* ForceField::getBendType(const std::string &at1,
164		const std::string &at2,
165		const std::string &at3) {
#	Line 107 | Line 173 | namespace oopse {
173		if (bendType) {
174		return bendType;
175		} else {
176	<	//if no exact match found, try wild card match
177	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
176	>
177	>	AtomType* atype1;
178	>	AtomType* atype2;
179	>	AtomType* atype3;
180	>	std::vector<std::string> at1key;
181	>	at1key.push_back(at1);
182	>	atype1 = atomTypeCont_.find(at1key);
183	>
184	>	std::vector<std::string> at2key;
185	>	at2key.push_back(at2);
186	>	atype2 = atomTypeCont_.find(at2key);
187	>
188	>	std::vector<std::string> at3key;
189	>	at3key.push_back(at3);
190	>	atype3 = atomTypeCont_.find(at3key);
191	>
192	>	// query atom types for their chains of responsibility
193	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
194	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
195	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
196	>
197	>	std::vector<AtomType*>::iterator i;
198	>	std::vector<AtomType*>::iterator j;
199	>	std::vector<AtomType*>::iterator k;
200	>
201	>	int ii = 0;
202	>	int jj = 0;
203	>	int kk = 0;
204	>	int IKscore;
205	>
206	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
207	>
208	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
209	>	ii = 0;
210	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
211	>	kk = 0;
212	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
213	>
214	>	IKscore = ii + kk;
215	>
216	>	std::vector<std::string> myKeys;
217	>	myKeys.push_back((*i)->getName());
218	>	myKeys.push_back((*j)->getName());
219	>	myKeys.push_back((*k)->getName());
220	>
221	>	BendType* bendType = bendTypeCont_.find(myKeys);
222	>	if (bendType) {
223	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
224	>	}
225	>	kk++;
226	>	}
227	>	ii++;
228	>	}
229	>	jj++;
230	>	}
231	>
232	>	if (foundBends.size() > 0) {
233	>	std::sort(foundBends.begin(), foundBends.end());
234	>	int jscore = foundBends[0].first;
235	>	int ikscore = foundBends[0].second;
236	>	std::vector<std::string> theKeys = foundBends[0].third;
237	>
238	>	BendType* bestType = bendTypeCont_.find(theKeys);
239	>	return bestType;
240	>	} else {
241	>	//if no exact match found, try wild card match
242	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
243	>	}
244		}
245		}
246
#	Line 122 | Line 254 | namespace oopse {
254		keys.push_back(at3);
255		keys.push_back(at4);
256
257	+
258	+	//try exact match first
259		TorsionType* torsionType = torsionTypeCont_.find(keys);
260		if (torsionType) {
261		return torsionType;
262		} else {
263	<	//if no exact match found, try wild card match
264	<	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
265	<	}
266	<
267	<	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
263	>
264	>	AtomType* atype1;
265	>	AtomType* atype2;
266	>	AtomType* atype3;
267	>	AtomType* atype4;
268	>	std::vector<std::string> at1key;
269	>	at1key.push_back(at1);
270	>	atype1 = atomTypeCont_.find(at1key);
271	>
272	>	std::vector<std::string> at2key;
273	>	at2key.push_back(at2);
274	>	atype2 = atomTypeCont_.find(at2key);
275	>
276	>	std::vector<std::string> at3key;
277	>	at3key.push_back(at3);
278	>	atype3 = atomTypeCont_.find(at3key);
279	>
280	>	std::vector<std::string> at4key;
281	>	at4key.push_back(at4);
282	>	atype4 = atomTypeCont_.find(at4key);
283	>
284	>	// query atom types for their chains of responsibility
285	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
286	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
287	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
288	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
289	>
290	>	std::vector<AtomType*>::iterator i;
291	>	std::vector<AtomType*>::iterator j;
292	>	std::vector<AtomType*>::iterator k;
293	>	std::vector<AtomType*>::iterator l;
294	>
295	>	int ii = 0;
296	>	int jj = 0;
297	>	int kk = 0;
298	>	int ll = 0;
299	>	int ILscore;
300	>	int JKscore;
301	>
302	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
303	>
304	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
305	>	kk = 0;
306	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
307	>	ii = 0;
308	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
309	>	ll = 0;
310	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
311	>
312	>	ILscore = ii + ll;
313	>	JKscore = jj + kk;
314	>
315	>	std::vector<std::string> myKeys;
316	>	myKeys.push_back((*i)->getName());
317	>	myKeys.push_back((*j)->getName());
318	>	myKeys.push_back((*k)->getName());
319	>	myKeys.push_back((*l)->getName());
320	>
321	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
322	>	if (torsionType) {
323	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
324	>	}
325	>	ll++;
326	>	}
327	>	ii++;
328	>	}
329	>	kk++;
330	>	}
331	>	jj++;
332	>	}
333	>
334	>	if (foundTorsions.size() > 0) {
335	>	std::sort(foundTorsions.begin(), foundTorsions.end());
336	>	int jkscore = foundTorsions[0].first;
337	>	int ilscore = foundTorsions[0].second;
338	>	std::vector<std::string> theKeys = foundTorsions[0].third;
339	>
340	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
341	>	return bestType;
342	>	} else {
343	>	//if no exact match found, try wild card match
344	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
345	>	}
346	>	}
347		}
348
349	+	InversionType* ForceField::getInversionType(const std::string &at1,
350	+	const std::string &at2,
351	+	const std::string &at3,
352	+	const std::string &at4) {
353	+	std::vector<std::string> keys;
354	+	keys.push_back(at1);
355	+	keys.push_back(at2);
356	+	keys.push_back(at3);
357	+	keys.push_back(at4);
358	+
359	+	//try exact match first
360	+	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
361	+	if (inversionType) {
362	+	return inversionType;
363	+	} else {
364	+
365	+	AtomType* atype1;
366	+	AtomType* atype2;
367	+	AtomType* atype3;
368	+	AtomType* atype4;
369	+	std::vector<std::string> at1key;
370	+	at1key.push_back(at1);
371	+	atype1 = atomTypeCont_.find(at1key);
372	+
373	+	std::vector<std::string> at2key;
374	+	at2key.push_back(at2);
375	+	atype2 = atomTypeCont_.find(at2key);
376	+
377	+	std::vector<std::string> at3key;
378	+	at3key.push_back(at3);
379	+	atype3 = atomTypeCont_.find(at3key);
380	+
381	+	std::vector<std::string> at4key;
382	+	at4key.push_back(at4);
383	+	atype4 = atomTypeCont_.find(at4key);
384	+
385	+	// query atom types for their chains of responsibility
386	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
387	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
388	+	std::vector<AtomType*> at3Chain = atype3->allYourBase();
389	+	std::vector<AtomType*> at4Chain = atype4->allYourBase();
390	+
391	+	std::vector<AtomType*>::iterator i;
392	+	std::vector<AtomType*>::iterator j;
393	+	std::vector<AtomType*>::iterator k;
394	+	std::vector<AtomType*>::iterator l;
395	+
396	+	int ii = 0;
397	+	int jj = 0;
398	+	int kk = 0;
399	+	int ll = 0;
400	+	int Iscore;
401	+	int JKLscore;
402	+
403	+	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
404	+
405	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
406	+	kk = 0;
407	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
408	+	ii = 0;
409	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
410	+	ll = 0;
411	+	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
412	+
413	+	Iscore = ii;
414	+	JKLscore = jj + kk + ll;
415	+
416	+	std::vector<std::string> myKeys;
417	+	myKeys.push_back((*i)->getName());
418	+	myKeys.push_back((*j)->getName());
419	+	myKeys.push_back((*k)->getName());
420	+	myKeys.push_back((*l)->getName());
421	+
422	+	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
423	+	if (inversionType) {
424	+	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
425	+	}
426	+	ll++;
427	+	}
428	+	ii++;
429	+	}
430	+	kk++;
431	+	}
432	+	jj++;
433	+	}
434	+
435	+	if (foundInversions.size() > 0) {
436	+	std::sort(foundInversions.begin(), foundInversions.end());
437	+	int iscore = foundInversions[0].first;
438	+	int jklscore = foundInversions[0].second;
439	+	std::vector<std::string> theKeys = foundInversions[0].third;
440	+
441	+	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
442	+	return bestType;
443	+	} else {
444	+	//if no exact match found, try wild card match
445	+	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
446	+	}
447	+	}
448	+	}
449	+
450		NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
451	+
452		std::vector<std::string> keys;
453		keys.push_back(at1);
454		keys.push_back(at2);
#	Line 143 | Line 458 | namespace oopse {
458		if (nbiType) {
459		return nbiType;
460		} else {
461	<	//if no exact match found, try wild card match
462	<	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
463	<	}
461	>	AtomType* atype1;
462	>	AtomType* atype2;
463	>	std::vector<std::string> at1key;
464	>	at1key.push_back(at1);
465	>	atype1 = atomTypeCont_.find(at1key);
466	>
467	>	std::vector<std::string> at2key;
468	>	at2key.push_back(at2);
469	>	atype2 = atomTypeCont_.find(at2key);
470	>
471	>	// query atom types for their chains of responsibility
472	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
473	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
474	>
475	>	std::vector<AtomType*>::iterator i;
476	>	std::vector<AtomType*>::iterator j;
477	>
478	>	int ii = 0;
479	>	int jj = 0;
480	>	int nbiTypeScore;
481	>
482	>	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
483	>
484	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
485	>	jj = 0;
486	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
487	>
488	>	nbiTypeScore = ii + jj;
489	>
490	>	std::vector<std::string> myKeys;
491	>	myKeys.push_back((*i)->getName());
492	>	myKeys.push_back((*j)->getName());
493	>
494	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
495	>	if (nbiType) {
496	>	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
497	>	}
498	>	jj++;
499	>	}
500	>	ii++;
501	>	}
502	>
503	>
504	>	if (foundNBI.size() > 0) {
505	>	// sort the foundNBI by the score:
506	>	std::sort(foundNBI.begin(), foundNBI.end());
507	>
508	>	int bestScore = foundNBI[0].first;
509	>	std::vector<std::string> theKeys = foundNBI[0].second;
510	>
511	>	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
512	>	return bestType;
513	>	} else {
514	>	//if no exact match found, try wild card match
515	>	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
516	>	}
517	>	}
518		}
519
520		BondType* ForceField::getExactBondType(const std::string &at1,
#	Line 177 | Line 546 | namespace oopse {
546		keys.push_back(at4);
547		return torsionTypeCont_.find(keys);
548		}
549	<
549	>
550	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
551	>	const std::string &at2,
552	>	const std::string &at3,
553	>	const std::string &at4){
554	>	std::vector<std::string> keys;
555	>	keys.push_back(at1);
556	>	keys.push_back(at2);
557	>	keys.push_back(at3);
558	>	keys.push_back(at4);
559	>	return inversionTypeCont_.find(keys);
560	>	}
561	>
562		NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
563		std::vector<std::string> keys;
564		keys.push_back(at1);
565		keys.push_back(at2);
566		return nonBondedInteractionTypeCont_.find(keys);
567		}
568	+
569
188	–
570		bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
571		std::vector<std::string> keys;
572		keys.push_back(at);
573	+	atypeIdentToName[atomType->getIdent()] = at;
574		return atomTypeCont_.add(keys, atomType);
575		}
576
577	+	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
578	+	std::vector<std::string> keys;
579	+	keys.push_back(at);
580	+	atypeIdentToName[atomType->getIdent()] = at;
581	+	return atomTypeCont_.replace(keys, atomType);
582	+	}
583	+
584		bool ForceField::addBondType(const std::string &at1, const std::string &at2,
585		BondType* bondType) {
586		std::vector<std::string> keys;
#	Line 222 | Line 611 | namespace oopse {
611		return torsionTypeCont_.add(keys, torsionType);
612		}
613
614	+	bool ForceField::addInversionType(const std::string &at1,
615	+	const std::string &at2,
616	+	const std::string &at3,
617	+	const std::string &at4,
618	+	InversionType* inversionType) {
619	+	std::vector<std::string> keys;
620	+	keys.push_back(at1);
621	+	keys.push_back(at2);
622	+	keys.push_back(at3);
623	+	keys.push_back(at4);
624	+	return inversionTypeCont_.add(keys, inversionType);
625	+	}
626	+
627		bool ForceField::addNonBondedInteractionType(const std::string &at1,
628		const std::string &at2,
629		NonBondedInteractionType* nbiType) {
#	Line 250 | Line 652 | namespace oopse {
652		} else {
653		sprintf( painCave.errMsg,
654		"Can not cast GenericData to LJParam\n");
655	<	painCave.severity = OOPSE_ERROR;
655	>	painCave.severity = OPENMD_ERROR;
656		painCave.isFatal = 1;
657		simError();
658		}
659		} else {
660		sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
661	<	painCave.severity = OOPSE_ERROR;
661	>	painCave.severity = OPENMD_ERROR;
662		painCave.isFatal = 1;
663		simError();
664		}
#	Line 286 | Line 688 | namespace oopse {
688		"\tHave you tried setting the FORCE_PARAM_PATH environment "
689		"variable?\n",
690		forceFieldFilename.c_str() );
691	<	painCave.severity = OOPSE_ERROR;
691	>	painCave.severity = OPENMD_ERROR;
692		painCave.isFatal = 1;
693		simError();
694		}
#	Line 294 | Line 696 | namespace oopse {
696		return ffStream;
697		}
698
699	<	void ForceField::setFortranForceOptions(){
298	<	ForceOptions theseFortranOptions;
299	<	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
300	<	setfForceOptions(&theseFortranOptions);
301	<	}
302	<	} //end namespace oopse
699	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 1195 by cpuglis, Thu Dec 6 20:04:02 2007 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

#	Line 0 | Line 1
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