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root/OpenMD/branches/heatflux/src/brains/ForceManager.cpp

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/heatflux/src/brains/ForceManager.cpp (file contents), Revision 1682 by chuckv, Tue Feb 28 23:11:22 2012 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	<
41	>
42		/**
43		* @file ForceManager.cpp
44		* @author tlin
#	Line 50 | Line 50
50		#include "brains/ForceManager.hpp"
51		#include "primitives/Molecule.hpp"
52		#include "UseTheForce/doForces_interface.h"
53	<	#define __C
53	>	#define __OPENMD_C
54		#include "UseTheForce/DarkSide/fInteractionMap.h"
55		#include "utils/simError.h"
56	+	#include "primitives/Bond.hpp"
57		#include "primitives/Bend.hpp"
58	<	#include "primitives/Bend.hpp"
59	<	namespace oopse {
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60	>	namespace OpenMD {
61
62	<	/*
61	<	struct BendOrderStruct {
62	<	Bend* bend;
63	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
62	>	void ForceManager::calcForces() {
63
70	–	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
71	–	return b1.dataSet.deltaV < b2.dataSet.deltaV;
72	–	}
73	–
74	–	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
75	–	return t1.dataSet.deltaV < t2.dataSet.deltaV;
76	–	}
77	–	*/
78	–	void ForceManager::calcForces(bool needPotential, bool needStress) {
79	–
64		if (!info_->isFortranInitialized()) {
65		info_->update();
66		}
67
68		preCalculation();
69	<
69	>
70		calcShortRangeInteraction();
71
72	<	calcLongRangeInteraction(needPotential, needStress);
72	>	calcLongRangeInteraction();
73
74		postCalculation();
75
92	–	/*
93	–	std::vector<BendOrderStruct> bendOrderStruct;
94	–	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
95	–	BendOrderStruct tmp;
96	–	tmp.bend= const_cast<Bend*>(i->first);
97	–	tmp.dataSet = i->second;
98	–	bendOrderStruct.push_back(tmp);
99	–	}
100	–
101	–	std::vector<TorsionOrderStruct> torsionOrderStruct;
102	–	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
103	–	TorsionOrderStruct tmp;
104	–	tmp.torsion = const_cast<Torsion*>(j->first);
105	–	tmp.dataSet = j->second;
106	–	torsionOrderStruct.push_back(tmp);
107	–	}
108	–
109	–	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
110	–	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
111	–	std::cout << "bend" << std::endl;
112	–	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
113	–	Bend* bend = k->bend;
114	–	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
115	–	std::cout << "deltaV=" << k->dataSet.deltaV << ",p_theta=" << k->dataSet.prev.angle <<",p_pot=" << k->dataSet.prev.potential<< ",c_theta=" << k->dataSet.curr.angle << ", c_pot = " << k->dataSet.curr.potential <<std::endl;
116	–	}
117	–	std::cout << "torsio" << std::endl;
118	–	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
119	–	Torsion* torsion = l->torsion;
120	–	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
121	–	std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
122	–	}
123	–	*/
76		}
77
78		void ForceManager::preCalculation() {
#	Line 130 | Line 82 | namespace oopse {
82		Atom* atom;
83		Molecule::RigidBodyIterator rbIter;
84		RigidBody* rb;
85	<
85	>
86		// forces are zeroed here, before any are accumulated.
87		// NOTE: do not rezero the forces in Fortran.
88	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
88	>
89	>	for (mol = info_->beginMolecule(mi); mol != NULL;
90	>	mol = info_->nextMolecule(mi)) {
91		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
92	<	atom->zeroForcesAndTorques();
92	>	atom->zeroForcesAndTorques();
93		}
94	<
94	>
95		//change the positions of atoms which belong to the rigidbodies
96	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
97	<	rb->zeroForcesAndTorques();
98	<	}
96	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
97	>	rb = mol->nextRigidBody(rbIter)) {
98	>	rb->zeroForcesAndTorques();
99	>	}
100	>
101		}
102	<
102	>
103	>	// Zero out the stress tensor
104	>	tau *= 0.0;
105	>
106		}
107
108		void ForceManager::calcShortRangeInteraction() {
#	Line 152 | Line 111 | namespace oopse {
111		Bond* bond;
112		Bend* bend;
113		Torsion* torsion;
114	+	Inversion* inversion;
115		SimInfo::MoleculeIterator mi;
116		Molecule::RigidBodyIterator rbIter;
117		Molecule::BondIterator bondIter;;
118		Molecule::BendIterator  bendIter;
119		Molecule::TorsionIterator  torsionIter;
120	<	double bondPotential = 0.0;
121	<	double bendPotential = 0.0;
122	<	double torsionPotential = 0.0;
120	>	Molecule::InversionIterator  inversionIter;
121	>	RealType bondPotential = 0.0;
122	>	RealType bendPotential = 0.0;
123	>	RealType torsionPotential = 0.0;
124	>	RealType inversionPotential = 0.0;
125
126	<	//calculate short range interactions
127	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
126	>	//calculate short range interactions
127	>	for (mol = info_->beginMolecule(mi); mol != NULL;
128	>	mol = info_->nextMolecule(mi)) {
129
130		//change the positions of atoms which belong to the rigidbodies
131	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
132	<	rb->updateAtoms();
131	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
132	>	rb = mol->nextRigidBody(rbIter)) {
133	>	rb->updateAtoms();
134		}
135
136	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
136	>	for (bond = mol->beginBond(bondIter); bond != NULL;
137	>	bond = mol->nextBond(bondIter)) {
138		bond->calcForce();
139		bondPotential += bond->getPotential();
140		}
141
142	+	for (bend = mol->beginBend(bendIter); bend != NULL;
143	+	bend = mol->nextBend(bendIter)) {
144
145	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
145	>	RealType angle;
146	>	bend->calcForce(angle);
147	>	RealType currBendPot = bend->getPotential();
148
149	<	double angle;
150	<	bend->calcForce(angle);
151	<	double currBendPot = bend->getPotential();
152	<	bendPotential += bend->getPotential();
153	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
154	<	if (i == bendDataSets.end()) {
155	<	BendDataSet dataSet;
156	<	dataSet.prev.angle = dataSet.curr.angle = angle;
157	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
158	<	dataSet.deltaV = 0.0;
159	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
160	<	}else {
161	<	i->second.prev.angle = i->second.curr.angle;
162	<	i->second.prev.potential = i->second.curr.potential;
163	<	i->second.curr.angle = angle;
164	<	i->second.curr.potential = currBendPot;
196	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
197	<	}
149	>	bendPotential += bend->getPotential();
150	>	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
151	>	if (i == bendDataSets.end()) {
152	>	BendDataSet dataSet;
153	>	dataSet.prev.angle = dataSet.curr.angle = angle;
154	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
155	>	dataSet.deltaV = 0.0;
156	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
157	>	}else {
158	>	i->second.prev.angle = i->second.curr.angle;
159	>	i->second.prev.potential = i->second.curr.potential;
160	>	i->second.curr.angle = angle;
161	>	i->second.curr.potential = currBendPot;
162	>	i->second.deltaV =  fabs(i->second.curr.potential -
163	>	i->second.prev.potential);
164	>	}
165		}
166
167	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
168	<	double angle;
169	<	torsion->calcForce(angle);
170	<	double currTorsionPot = torsion->getPotential();
171	<	torsionPotential += torsion->getPotential();
172	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
173	<	if (i == torsionDataSets.end()) {
174	<	TorsionDataSet dataSet;
175	<	dataSet.prev.angle = dataSet.curr.angle = angle;
176	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
177	<	dataSet.deltaV = 0.0;
178	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
179	<	}else {
180	<	i->second.prev.angle = i->second.curr.angle;
181	<	i->second.prev.potential = i->second.curr.potential;
182	<	i->second.curr.angle = angle;
183	<	i->second.curr.potential = currTorsionPot;
184	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
185	<	}
167	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
168	>	torsion = mol->nextTorsion(torsionIter)) {
169	>	RealType angle;
170	>	torsion->calcForce(angle);
171	>	RealType currTorsionPot = torsion->getPotential();
172	>	torsionPotential += torsion->getPotential();
173	>	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
174	>	if (i == torsionDataSets.end()) {
175	>	TorsionDataSet dataSet;
176	>	dataSet.prev.angle = dataSet.curr.angle = angle;
177	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
178	>	dataSet.deltaV = 0.0;
179	>	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
180	>	}else {
181	>	i->second.prev.angle = i->second.curr.angle;
182	>	i->second.prev.potential = i->second.curr.potential;
183	>	i->second.curr.angle = angle;
184	>	i->second.curr.potential = currTorsionPot;
185	>	i->second.deltaV =  fabs(i->second.curr.potential -
186	>	i->second.prev.potential);
187	>	}
188		}
189
190	+	for (inversion = mol->beginInversion(inversionIter);
191	+	inversion != NULL;
192	+	inversion = mol->nextInversion(inversionIter)) {
193	+	RealType angle;
194	+	inversion->calcForce(angle);
195	+	RealType currInversionPot = inversion->getPotential();
196	+	inversionPotential += inversion->getPotential();
197	+	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
198	+	if (i == inversionDataSets.end()) {
199	+	InversionDataSet dataSet;
200	+	dataSet.prev.angle = dataSet.curr.angle = angle;
201	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
202	+	dataSet.deltaV = 0.0;
203	+	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
204	+	}else {
205	+	i->second.prev.angle = i->second.curr.angle;
206	+	i->second.prev.potential = i->second.curr.potential;
207	+	i->second.curr.angle = angle;
208	+	i->second.curr.potential = currInversionPot;
209	+	i->second.deltaV =  fabs(i->second.curr.potential -
210	+	i->second.prev.potential);
211	+	}
212	+	}
213		}
214	<
215	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
214	>
215	>	RealType  shortRangePotential = bondPotential + bendPotential +
216	>	torsionPotential +  inversionPotential;
217		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
218		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
219		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
220		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
221		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
222	<
222	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
223	>
224		}
225
226	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
226	>	void ForceManager::calcLongRangeInteraction() {
227		Snapshot* curSnapshot;
228		DataStorage* config;
229	<	double* frc;
230	<	double* pos;
231	<	double* trq;
232	<	double* A;
233	<	double* electroFrame;
234	<	double* rc;
235	<
229	>	RealType* frc;
230	>	RealType* pos;
231	>	RealType* vel;
232	>	RealType* trq;
233	>	RealType* A;
234	>	RealType* electroFrame;
235	>	RealType* rc;
236	>	RealType* vc;
237	>	RealType* particlePot;
238	>
239		//get current snapshot from SimInfo
240		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
241
#	Line 246 | Line 243 | namespace oopse {
243		config = &(curSnapshot->atomData);
244		frc = config->getArrayPointer(DataStorage::dslForce);
245		pos = config->getArrayPointer(DataStorage::dslPosition);
246	+	vel = config->getArrayPointer(DataStorage::dslVelocity);
247		trq = config->getArrayPointer(DataStorage::dslTorque);
248		A   = config->getArrayPointer(DataStorage::dslAmat);
249		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
250	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
251
252		//calculate the center of mass of cutoff group
253		SimInfo::MoleculeIterator mi;
#	Line 256 | Line 255 | namespace oopse {
255		Molecule::CutoffGroupIterator ci;
256		CutoffGroup* cg;
257		Vector3d com;
258	+	Vector3d comv;
259		std::vector<Vector3d> rcGroup;
260	+	std::vector<Vector3d> vcGroup;
261
262		if(info_->getNCutoffGroups() > 0){
263	<
264	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
265	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
266	<	cg->getCOM(com);
267	<	rcGroup.push_back(com);
263	>
264	>	for (mol = info_->beginMolecule(mi); mol != NULL;
265	>	mol = info_->nextMolecule(mi)) {
266	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
267	>	cg = mol->nextCutoffGroup(ci)) {
268	>	cg->getCOM(com);
269	>	cg->getCOMV(comv);
270	>	rcGroup.push_back(com);
271	>	vcGroup.push_back(comv);
272		}
273		}// end for (mol)
274	<
274	>
275		rc = rcGroup[0].getArrayPointer();
276	+	vc = vcGroup[0].getArrayPointer();
277		} else {
278	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
278	>	// center of mass of the group is the same as position of the atom
279	>	// if cutoff group does not exist
280		rc = pos;
281	+	vc = vel;
282		}
283	<
283	>
284		//initialize data before passing to fortran
285	<	double longRangePotential[LR_POT_TYPES];
286	<	double lrPot = 0.0;
285	>	RealType longRangePotential[LR_POT_TYPES];
286	>	RealType lrPot = 0.0;
287	>	Vector3d totalDipole;
288	>	Jv_ = 0.0;
289	>
290
291	<	Mat3x3d tau;
281	<	short int passedCalcPot = needPotential;
282	<	short int passedCalcStress = needStress;
291	>
292		int isError = 0;
293
294		for (int i=0; i<LR_POT_TYPES;i++){
295		longRangePotential[i]=0.0; //Initialize array
296		}
297
298	<	doForceLoop( pos,
299	<	rc,
300	<	A,
301	<	electroFrame,
302	<	frc,
303	<	trq,
304	<	tau.getArrayPointer(),
305	<	longRangePotential,
306	<	&passedCalcPot,
307	<	&passedCalcStress,
308	<	&isError );
298	>	doForceLoop(pos,
299	>	vel,
300	>	rc,
301	>	vc,
302	>	A,
303	>	electroFrame,
304	>	frc,
305	>	trq,
306	>	tau.getArrayPointer(),
307	>	Jv_.getArrayPointer(),
308	>	longRangePotential,
309	>	particlePot,
310	>	&isError );
311
312		if( isError ){
313		sprintf( painCave.errMsg,
314	<	"Error returned from the fortran force calculation.\n" );
314	>	"Error returned from the fortran force calculation.\n" );
315		painCave.isFatal = 1;
316		simError();
317		}
#	Line 308 | Line 319 | namespace oopse {
319		lrPot += longRangePotential[i]; //Quick hack
320		}
321
322	<	//store the tau and long range potential
322	>	// grab the simulation box dipole moment if specified
323	>	if (info_->getCalcBoxDipole()){
324	>	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
325	>
326	>	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
327	>	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
328	>	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
329	>	}
330	>
331	>	//store the tau and long range potential
332		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
333		curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
334		curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315	–
316	–	curSnapshot->statData.setTau(tau);
335		}
336
337
#	Line 322 | Line 340 | namespace oopse {
340		Molecule* mol;
341		Molecule::RigidBodyIterator rbIter;
342		RigidBody* rb;
343	<
343	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
344	>
345		// collect the atomic forces onto rigid bodies
346	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
347	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
348	<	rb->calcForcesAndTorques();
346	>
347	>	for (mol = info_->beginMolecule(mi); mol != NULL;
348	>	mol = info_->nextMolecule(mi)) {
349	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
350	>	rb = mol->nextRigidBody(rbIter)) {
351	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
352	>	tau += rbTau;
353		}
354		}
355
356	+	#ifdef IS_MPI
357	+	Mat3x3d tmpTau(tau);
358	+	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
359	+	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
360	+	#endif
361	+	curSnapshot->statData.setTau(tau);
362	+	curSnapshot->statData.setJv(Jv_);
363		}
364
365	<	} //end namespace oopse
365	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/heatflux/src/brains/ForceManager.cpp (property svn:keywords), Revision 1682 by chuckv, Tue Feb 28 23:11:22 2012 UTC

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