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root/OpenMD/branches/development/src/visitors/AtomVisitor.cpp

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trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 992 by chrisfen, Wed Jun 21 18:28:27 2006 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <cstring>
#	Line 44 | Line 45
45		#include "primitives/DirectionalAtom.hpp"
46		#include "primitives/RigidBody.hpp"
47
48	<	namespace oopse {
48	>	namespace OpenMD {
49		void BaseAtomVisitor::visit(RigidBody *rb) {
50		//vector<Atom*> myAtoms;
51		//vector<Atom*>::iterator atomIter;
#	Line 73 | Line 74 | namespace oopse {
74		return data == NULL ? false : true;
75		}
76
77	<	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
78	<	std::set<std::string>::iterator strIter;
78	<	strIter = ssdAtomType.find(atomType);
79	<	return strIter != ssdAtomType.end() ? true : false;
80	<	}
81	<
82	<	void SSDAtomVisitor::visit(DirectionalAtom *datom) {
83	<	std::vector<AtomInfo*>atoms;
84	<
85	<	//we need to convert SSD into 4 differnet atoms
86	<	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
87	<	//of the water with a dipole moment
88	<	Vector3d h1(0.0, -0.75695, 0.5206);
89	<	Vector3d h2(0.0, 0.75695, 0.5206);
90	<	Vector3d ox(0.0, 0.0, -0.0654);
91	<	Vector3d u(0, 0, 1);
92	<	RotMat3x3d   rotMatrix;
93	<	RotMat3x3d   rotTrans;
94	<	AtomInfo *   atomInfo;
95	<	Vector3d     pos;
96	<	Vector3d     newVec;
97	<	Quat4d       q;
98	<	AtomData *   atomData;
99	<	GenericData *data;
100	<	bool         haveAtomData;
101	<
102	<	//if atom is not SSD atom, just skip it
103	<	if (!isSSDAtom(datom->getType()))
104	<	return;
105	<
106	<	data = datom->getPropertyByName("ATOMDATA");
107	<
108	<	if (data != NULL) {
109	<	atomData = dynamic_cast<AtomData *>(data);
110	<
111	<	if (atomData == NULL) {
112	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
113	<	atomData = new AtomData;
114	<	haveAtomData = false;
115	<	} else
116	<	haveAtomData = true;
117	<	} else {
118	<	atomData = new AtomData;
119	<	haveAtomData = false;
120	<	}
121	<
122	<	pos = datom->getPos();
123	<	q = datom->getQ();
124	<	rotMatrix = datom->getA();
125	<
126	<	// We need A^T to convert from body-fixed to space-fixed:
127	<	//transposeMat3(rotMatrix, rotTrans);
128	<	rotTrans = rotMatrix.transpose();
129	<
130	<	//center of mass of the water molecule
131	<	//matVecMul3(rotTrans, u, newVec);
132	<	newVec = rotTrans * u;
133	<
134	<	atomInfo = new AtomInfo;
135	<	atomInfo->atomTypeName = "X";
136	<	atomInfo->pos[0] = pos[0];
137	<	atomInfo->pos[1] = pos[1];
138	<	atomInfo->pos[2] = pos[2];
139	<	atomInfo->dipole[0] = newVec[0];
140	<	atomInfo->dipole[1] = newVec[1];
141	<	atomInfo->dipole[2] = newVec[2];
142	<
143	<	atomData->addAtomInfo(atomInfo);
144	<
145	<	//oxygen
146	<	//matVecMul3(rotTrans, ox, newVec);
147	<	newVec = rotTrans * ox;
148	<
149	<	atomInfo = new AtomInfo;
150	<	atomInfo->atomTypeName = "O";
151	<	atomInfo->pos[0] = pos[0] + newVec[0];
152	<	atomInfo->pos[1] = pos[1] + newVec[1];
153	<	atomInfo->pos[2] = pos[2] + newVec[2];
154	<	atomInfo->dipole[0] = 0.0;
155	<	atomInfo->dipole[1] = 0.0;
156	<	atomInfo->dipole[2] = 0.0;
157	<	atomData->addAtomInfo(atomInfo);
158	<
159	<	//hydrogen1
160	<	//matVecMul3(rotTrans, h1, newVec);
161	<	newVec = rotTrans * h1;
162	<	atomInfo = new AtomInfo;
163	<	atomInfo->atomTypeName = "H";
164	<	atomInfo->pos[0] = pos[0] + newVec[0];
165	<	atomInfo->pos[1] = pos[1] + newVec[1];
166	<	atomInfo->pos[2] = pos[2] + newVec[2];
167	<	atomInfo->dipole[0] = 0.0;
168	<	atomInfo->dipole[1] = 0.0;
169	<	atomInfo->dipole[2] = 0.0;
170	<	atomData->addAtomInfo(atomInfo);
171	<
172	<	//hydrogen2
173	<	//matVecMul3(rotTrans, h2, newVec);
174	<	newVec = rotTrans * h2;
175	<	atomInfo = new AtomInfo;
176	<	atomInfo->atomTypeName = "H";
177	<	atomInfo->pos[0] = pos[0] + newVec[0];
178	<	atomInfo->pos[1] = pos[1] + newVec[1];
179	<	atomInfo->pos[2] = pos[2] + newVec[2];
180	<	atomInfo->dipole[0] = 0.0;
181	<	atomInfo->dipole[1] = 0.0;
182	<	atomInfo->dipole[2] = 0.0;
183	<	atomData->addAtomInfo(atomInfo);
184	<
185	<	//add atom data into atom's property
186	<
187	<	if (!haveAtomData) {
188	<	atomData->setID("ATOMDATA");
189	<	datom->addProperty(atomData);
190	<	}
191	<
192	<	setVisited(datom);
193	<	}
194	<
195	<	const std::string SSDAtomVisitor::toString() {
196	<	char   buffer[65535];
197	<	std::string result;
198	<
199	<	sprintf(buffer,
200	<	"------------------------------------------------------------------\n");
201	<	result += buffer;
202	<
203	<	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204	<	result += buffer;
205	<
206	<	sprintf(buffer,
207	<	"Visitor Description: Convert SSD into 4 different atoms\n");
208	<	result += buffer;
209	<
210	<	sprintf(buffer,
211	<	"------------------------------------------------------------------\n");
212	<	result += buffer;
213	<
214	<	return result;
215	<	}
216	<
217	<	bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
218	<	std::set<std::string>::iterator strIter;
219	<	strIter = linearAtomType.find(atomType);
220	<
221	<	return strIter != linearAtomType.end() ? true : false;
222	<	}
223	<
224	<	void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
225	<	linearAtomType.insert(atomType);
226	<	}
227	<
228	<	void LinearAtomVisitor::visit(DirectionalAtom* datom){
229	<	std::vector<AtomInfo*> atoms;
230	<	//we need to convert linear into 4 different atoms
231	<	Vector3d c1(0.0, 0.0, -1.8);
232	<	Vector3d c2(0.0, 0.0, -0.6);
233	<	Vector3d c3(0.0, 0.0,  0.6);
234	<	Vector3d c4(0.0, 0.0,  1.8);
235	<	RotMat3x3d rotMatrix;
236	<	RotMat3x3d rotTrans;
237	<	AtomInfo* atomInfo;
238	<	Vector3d pos;
239	<	Vector3d newVec;
240	<	Quat4d q;
241	<	AtomData* atomData;
242	<	GenericData* data;
243	<	bool haveAtomData;
244	<	AtomType* atomType;
245	<	//if atom is not SSD atom, just skip it
246	<	if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
247	<	return;
248	<
249	<	//setup GayBerne type in fortran side
250	<	data = datom->getAtomType()->getPropertyByName("GayBerne");
251	<	if (data != NULL) {
252	<	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
253	<
254	<	if (gayBerneData != NULL) {
255	<	GayBerneParam gayBerneParam = gayBerneData->getData();
256	<
257	<	// double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
258	<	double halfLen = gayBerneParam.GB_l/2.0;
259	<	c1[2] = -halfLen;
260	<	c2[2] = -halfLen /2;
261	<	c3[2] = halfLen/2;
262	<	c4[2] = halfLen;
263	<
264	<	}
265	<
266	<	else {
267	<	sprintf( painCave.errMsg,
268	<	"Can not cast GenericData to GayBerneParam\n");
269	<	painCave.severity = OOPSE_ERROR;
270	<	painCave.isFatal = 1;
271	<	simError();
272	<	}
273	<	}
274	<
275	<
276	<	data = datom->getPropertyByName("ATOMDATA");
277	<	if(data != NULL){
278	<	atomData = dynamic_cast<AtomData*>(data);
279	<	if(atomData == NULL){
280	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
281	<	atomData = new AtomData;
282	<	haveAtomData = false;
283	<	} else {
284	<	haveAtomData = true;
285	<	}
286	<	} else {
287	<	atomData = new AtomData;
288	<	haveAtomData = false;
289	<	}
290	<
291	<
292	<	pos = datom->getPos();
293	<	q = datom->getQ();
294	<	rotMatrix = datom->getA();
295	<
296	<	// We need A^T to convert from body-fixed to space-fixed:
297	<	rotTrans = rotMatrix.transpose();
298	<
299	<	newVec = rotTrans * c1;
300	<	atomInfo = new AtomInfo;
301	<	atomInfo->atomTypeName = "C";
302	<	atomInfo->pos[0] = pos[0] + newVec[0];
303	<	atomInfo->pos[1] = pos[1] + newVec[1];
304	<	atomInfo->pos[2] = pos[2] + newVec[2];
305	<	atomInfo->dipole[0] = 0.0;
306	<	atomInfo->dipole[1] = 0.0;
307	<	atomInfo->dipole[2] = 0.0;
308	<	atomData->addAtomInfo(atomInfo);
309	<
310	<	newVec = rotTrans * c2;
311	<	atomInfo = new AtomInfo;
312	<	atomInfo->atomTypeName = "C";
313	<	atomInfo->pos[0] = pos[0] + newVec[0];
314	<	atomInfo->pos[1] = pos[1] + newVec[1];
315	<	atomInfo->pos[2] = pos[2] + newVec[2];
316	<	atomInfo->dipole[0] = 0.0;
317	<	atomInfo->dipole[1] = 0.0;
318	<	atomInfo->dipole[2] = 0.0;
319	<	atomData->addAtomInfo(atomInfo);
320	<
321	<	newVec = rotTrans * c3;
322	<	atomInfo = new AtomInfo;
323	<	atomInfo->atomTypeName = "C";
324	<	atomInfo->pos[0] = pos[0] + newVec[0];
325	<	atomInfo->pos[1] = pos[1] + newVec[1];
326	<	atomInfo->pos[2] = pos[2] + newVec[2];
327	<	atomInfo->dipole[0] = 0.0;
328	<	atomInfo->dipole[1] = 0.0;
329	<	atomInfo->dipole[2] = 0.0;
330	<	atomData->addAtomInfo(atomInfo);
331	<
332	<	newVec = rotTrans * c4;
333	<	atomInfo = new AtomInfo;
334	<	atomInfo->atomTypeName = "C";
335	<	atomInfo->pos[0] = pos[0] + newVec[0];
336	<	atomInfo->pos[1] = pos[1] + newVec[1];
337	<	atomInfo->pos[2] = pos[2] + newVec[2];
338	<	atomInfo->dipole[0] = 0.0;
339	<	atomInfo->dipole[1] = 0.0;
340	<	atomInfo->dipole[2] = 0.0;
341	<	atomData->addAtomInfo(atomInfo);
342	<
343	<	//add atom data into atom's property
344	<
345	<	if(!haveAtomData){
346	<	atomData->setID("ATOMDATA");
347	<	datom->addProperty(atomData);
348	<	}
349	<
350	<	setVisited(datom);
351	<
352	<	}
353	<
354	<	const std::string LinearAtomVisitor::toString(){
355	<	char buffer[65535];
356	<	std::string result;
357	<
358	<	sprintf(buffer ,"------------------------------------------------------------------\n");
359	<	result += buffer;
360	<
361	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
362	<	result += buffer;
363	<
364	<	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
365	<	result += buffer;
366	<
367	<	sprintf(buffer ,"------------------------------------------------------------------\n");
368	<	result += buffer;
369	<
370	<	return result;
371	<	}
372	<
373	<	bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
374	<	std::set<std::string>::iterator strIter;
375	<	strIter = GBLipidAtomType.find(atomType);
376	<
377	<	return strIter != GBLipidAtomType.end() ? true : false;
378	<	}
379	<
380	<	void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
381	<	std::vector<AtomInfo*> atoms;
382	<	//we need to convert linear into 4 different atoms
383	<	Vector3d c1(0.0, 0.0, -6.25);
384	<	Vector3d c2(0.0, 0.0, -2.1);
385	<	Vector3d c3(0.0, 0.0,  2.1);
386	<	Vector3d c4(0.0, 0.0,  6.25);
387	<	RotMat3x3d rotMatrix;
388	<	RotMat3x3d rotTrans;
389	<	AtomInfo* atomInfo;
390	<	Vector3d pos;
391	<	Vector3d newVec;
392	<	Quat4d q;
393	<	AtomData* atomData;
394	<	GenericData* data;
395	<	bool haveAtomData;
396	<
397	<	//if atom is not GBlipid atom, just skip it
398	<	if(!isGBLipidAtom(datom->getType()))
399	<	return;
400	<
401	<	data = datom->getPropertyByName("ATOMDATA");
402	<	if(data != NULL){
403	<	atomData = dynamic_cast<AtomData*>(data);
404	<	if(atomData == NULL){
405	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
406	<	atomData = new AtomData;
407	<	haveAtomData = false;
408	<	} else {
409	<	haveAtomData = true;
410	<	}
411	<	} else {
412	<	atomData = new AtomData;
413	<	haveAtomData = false;
414	<	}
415	<
416	<
417	<	pos = datom->getPos();
418	<	q = datom->getQ();
419	<	rotMatrix = datom->getA();
420	<
421	<	// We need A^T to convert from body-fixed to space-fixed:
422	<	rotTrans = rotMatrix.transpose();
423	<
424	<	newVec = rotTrans * c1;
425	<	atomInfo = new AtomInfo;
426	<	atomInfo->atomTypeName = "K";
427	<	atomInfo->pos[0] = pos[0] + newVec[0];
428	<	atomInfo->pos[1] = pos[1] + newVec[1];
429	<	atomInfo->pos[2] = pos[2] + newVec[2];
430	<	atomInfo->dipole[0] = 0.0;
431	<	atomInfo->dipole[1] = 0.0;
432	<	atomInfo->dipole[2] = 0.0;
433	<	atomData->addAtomInfo(atomInfo);
434	<
435	<	newVec = rotTrans * c2;
436	<	atomInfo = new AtomInfo;
437	<	atomInfo->atomTypeName = "K";
438	<	atomInfo->pos[0] = pos[0] + newVec[0];
439	<	atomInfo->pos[1] = pos[1] + newVec[1];
440	<	atomInfo->pos[2] = pos[2] + newVec[2];
441	<	atomInfo->dipole[0] = 0.0;
442	<	atomInfo->dipole[1] = 0.0;
443	<	atomInfo->dipole[2] = 0.0;
444	<	atomData->addAtomInfo(atomInfo);
445	<
446	<	newVec = rotTrans * c3;
447	<	atomInfo = new AtomInfo;
448	<	atomInfo->atomTypeName = "K";
449	<	atomInfo->pos[0] = pos[0] + newVec[0];
450	<	atomInfo->pos[1] = pos[1] + newVec[1];
451	<	atomInfo->pos[2] = pos[2] + newVec[2];
452	<	atomInfo->dipole[0] = 0.0;
453	<	atomInfo->dipole[1] = 0.0;
454	<	atomInfo->dipole[2] = 0.0;
455	<	atomData->addAtomInfo(atomInfo);
456	<
457	<	newVec = rotTrans * c4;
458	<	atomInfo = new AtomInfo;
459	<	atomInfo->atomTypeName = "K";
460	<	atomInfo->pos[0] = pos[0] + newVec[0];
461	<	atomInfo->pos[1] = pos[1] + newVec[1];
462	<	atomInfo->pos[2] = pos[2] + newVec[2];
463	<	atomInfo->dipole[0] = 0.0;
464	<	atomInfo->dipole[1] = 0.0;
465	<	atomInfo->dipole[2] = 0.0;
466	<	atomData->addAtomInfo(atomInfo);
467	<
468	<	//add atom data into atom's property
469	<
470	<	if(!haveAtomData){
471	<	atomData->setID("ATOMDATA");
472	<	datom->addProperty(atomData);
473	<	}
474	<
475	<	setVisited(datom);
476	<
477	<	}
478	<
479	<	const std::string GBLipidAtomVisitor::toString(){
480	<	char buffer[65535];
481	<	std::string result;
482	<
483	<	sprintf(buffer ,"------------------------------------------------------------------\n");
484	<	result += buffer;
485	<
486	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
487	<	result += buffer;
488	<
489	<	sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
490	<	result += buffer;
491	<
492	<	sprintf(buffer ,"------------------------------------------------------------------\n");
493	<	result += buffer;
494	<
495	<	return result;
496	<	}
497	<
498	<	//----------------------------------------------------------------------------//
499	<
77	>	//------------------------------------------------------------------------//
78	>
79		void DefaultAtomVisitor::visit(Atom *atom) {
80		AtomData *atomData;
81		AtomInfo *atomInfo;
82		Vector3d  pos;
83	+	Vector3d  vel;
84	+	Vector3d  frc;
85	+	Vector3d  u;
86	+	RealType  c;
87
88		if (isVisited(atom))
89		return;
90	<
90	>
91		atomInfo = new AtomInfo;
92	<
92	>
93		atomData = new AtomData;
94		atomData->setID("ATOMDATA");
95	<
95	>
96		pos = atom->getPos();
97	+	vel = atom->getVel();
98	+	frc = atom->getFrc();
99		atomInfo->atomTypeName = atom->getType();
100		atomInfo->pos[0] = pos[0];
101		atomInfo->pos[1] = pos[1];
102		atomInfo->pos[2] = pos[2];
103	<	atomInfo->dipole[0] = 0.0;
104	<	atomInfo->dipole[1] = 0.0;
105	<	atomInfo->dipole[2] = 0.0;
106	<
103	>	atomInfo->vel[0] = vel[0];
104	>	atomInfo->vel[1] = vel[1];
105	>	atomInfo->vel[2] = vel[2];
106	>	atomInfo->hasVelocity = true;
107	>	atomInfo->frc[0] = frc[0];
108	>	atomInfo->frc[1] = frc[1];
109	>	atomInfo->frc[2] = frc[2];
110	>	atomInfo->hasForce = true;
111	>	atomInfo->vec[0] = 0.0;
112	>	atomInfo->vec[1] = 0.0;
113	>	atomInfo->vec[2] = 0.0;
114	>
115		atomData->addAtomInfo(atomInfo);
116	<
116	>
117		atom->addProperty(atomData);
118	<
118	>
119		setVisited(atom);
120		}
121	<
121	>
122		void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
123		AtomData *atomData;
124		AtomInfo *atomInfo;
125		Vector3d  pos;
126	+	Vector3d  vel;
127	+	Vector3d  frc;
128		Vector3d  u;
129	+	RealType  c;
130
131		if (isVisited(datom))
132		return;
133	<
133	>
134		pos = datom->getPos();
135	+	vel = datom->getVel();
136	+	frc = datom->getFrc();
137		if (datom->getAtomType()->isGayBerne()) {
138		u = datom->getA().transpose()*V3Z;
139		} else if (datom->getAtomType()->isMultipole()) {
#	Line 549 | Line 147 | namespace oopse {
147		atomInfo->pos[0] = pos[0];
148		atomInfo->pos[1] = pos[1];
149		atomInfo->pos[2] = pos[2];
150	<	atomInfo->dipole[0] = u[0];
151	<	atomInfo->dipole[1] = u[1];
152	<	atomInfo->dipole[2] = u[2];
150	>	atomInfo->vel[0] = vel[0];
151	>	atomInfo->vel[1] = vel[1];
152	>	atomInfo->vel[2] = vel[2];
153	>	atomInfo->hasVelocity = true;
154	>	atomInfo->frc[0] = frc[0];
155	>	atomInfo->frc[1] = frc[1];
156	>	atomInfo->frc[2] = frc[2];
157	>	atomInfo->hasForce = true;
158	>	atomInfo->vec[0] = u[0];
159	>	atomInfo->vec[1] = u[1];
160	>	atomInfo->vec[2] = u[2];
161	>	atomInfo->hasVector = true;
162
163		atomData->addAtomInfo(atomInfo);
164
#	Line 581 | Line 188 | namespace oopse {
188
189		return result;
190		}
191	<	} //namespace oopse
191	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 992 by chrisfen, Wed Jun 21 18:28:27 2006 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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