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root/OpenMD/branches/development/src/brains/SimInfo.cpp

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trunk/src/brains/SimInfo.cpp (file contents), Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
branches/development/src/brains/SimInfo.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		/**
#	Line 48 | Line 49
49
50		#include <algorithm>
51		#include <set>
52	+	#include <map>
53
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61	<
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "UseTheForce/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
64	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<
70	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	<	ForceField* ff, Globals* simParams) :
72	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
79	<
78	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
80	<	MoleculeStamp* molStamp;
81	<	int nMolWithSameStamp;
82	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
84	<	CutoffGroupStamp* cgStamp;
85	<	RigidBodyStamp* rbStamp;
86	<	int nRigidAtoms = 0;
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80
81	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
82	<	molStamp = i->first;
83	<	nMolWithSameStamp = i->second;
84	<
85	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
86	<
87	<	//calculate atoms in molecules
88	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
89	<
90	<
91	<	//calculate atoms in cutoff groups
92	<	int nAtomsInGroups = 0;
93	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
94	<
95	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
96	<	cgStamp = molStamp->getCutoffGroup(j);
97	<	nAtomsInGroups += cgStamp->getNMembers();
98	<	}
99	<
100	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
101	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
102	<
103	<	//calculate atoms in rigid bodies
104	<	int nAtomsInRigidBodies = 0;
105	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
106	<
114	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
115	<	rbStamp = molStamp->getRigidBody(j);
116	<	nAtomsInRigidBodies += rbStamp->getNMembers();
117	<	}
118	<
119	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121	<
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107		}
108	<
109	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
110	<	//therefore the total number of cutoff groups in the system is equal to
111	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
112	<	//file plus the number of cutoff groups defined in meta-data file
113	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
114	<
115	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
116	<	//therefore the total number of  integrable objects in the system is equal to
117	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
118	<	//file plus the number of  rigid bodies defined in meta-data file
119	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
120	<
121	<	nGlobalMols_ = molStampIds_.size();
122	<
123	<	#ifdef IS_MPI
124	<	molToProcMap_.resize(nGlobalMols_);
140	<	#endif
141	<
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
133	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	+
135	+	//every free atom (atom does not belong to rigid bodies) is an
136	+	//integrable object therefore the total number of integrable objects
137	+	//in the system is equal to the total number of atoms minus number of
138	+	//atoms belong to rigid body defined in meta-data file plus the number
139	+	//of rigid bodies defined in meta-data file
140	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	+	+ nGlobalRigidBodies_;
142	+
143	+	nGlobalMols_ = molStampIds_.size();
144	+	molToProcMap_.resize(nGlobalMols_);
145	+	}
146	+
147		SimInfo::~SimInfo() {
148	<	std::map<int, Molecule*>::iterator i;
148	>	map<int, Molecule*>::iterator i;
149		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150		delete i->second;
151		}
152		molecules_.clear();
153
151	–	delete stamps_;
154		delete sman_;
155		delete simParams_;
156		delete forceField_;
157		}
158
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
159
160		bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168		nAtoms_ += mol->getNAtoms();
169		nBonds_ += mol->getNBonds();
170		nBends_ += mol->getNBends();
171		nTorsions_ += mol->getNTorsions();
172	+	nInversions_ += mol->getNInversions();
173		nRigidBodies_ += mol->getNRigidBodies();
174		nIntegrableObjects_ += mol->getNIntegrableObjects();
175		nCutoffGroups_ += mol->getNCutoffGroups();
176		nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
177	>
178	>	addInteractionPairs(mol);
179	>
180		return true;
181		} else {
182		return false;
183		}
184		}
185	<
185	>
186		bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
#	Line 202 | Line 195 | namespace oopse {
195		nBonds_ -= mol->getNBonds();
196		nBends_ -= mol->getNBends();
197		nTorsions_ -= mol->getNTorsions();
198	+	nInversions_ -= mol->getNInversions();
199		nRigidBodies_ -= mol->getNRigidBodies();
200		nIntegrableObjects_ -= mol->getNIntegrableObjects();
201		nCutoffGroups_ -= mol->getNCutoffGroups();
202		nConstraints_ -= mol->getNConstraintPairs();
203
204	<	removeExcludePairs(mol);
204	>	removeInteractionPairs(mol);
205		molecules_.erase(mol->getGlobalIndex());
206
207		delete mol;
#	Line 216 | Line 210 | namespace oopse {
210		} else {
211		return false;
212		}
219	–
220	–
213		}
214
215
#	Line 235 | Line 227 | namespace oopse {
227		void SimInfo::calcNdf() {
228		int ndf_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231		Molecule* mol;
232		StuntDouble* integrableObject;
233
#	Line 255 | Line 247 | namespace oopse {
247		}
248		}
249
250	<	}//end for (integrableObject)
251	<	}// end for (mol)
250	>	}
251	>	}
252
253		// n_constraints is local, so subtract them on each processor
254		ndf_local -= nConstraints_;
#	Line 273 | Line 265 | namespace oopse {
265
266		}
267
268	+	int SimInfo::getFdf() {
269	+	#ifdef IS_MPI
270	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	+	#else
272	+	fdf_ = fdf_local;
273	+	#endif
274	+	return fdf_;
275	+	}
276	+
277	+	unsigned int SimInfo::getNLocalCutoffGroups(){
278	+	int nLocalCutoffAtoms = 0;
279	+	Molecule* mol;
280	+	MoleculeIterator mi;
281	+	CutoffGroup* cg;
282	+	Molecule::CutoffGroupIterator ci;
283	+
284	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
285	+
286	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
287	+	cg = mol->nextCutoffGroup(ci)) {
288	+	nLocalCutoffAtoms += cg->getNumAtom();
289	+
290	+	}
291	+	}
292	+
293	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
294	+	}
295	+
296		void SimInfo::calcNdfRaw() {
297		int ndfRaw_local;
298
299		MoleculeIterator i;
300	<	std::vector<StuntDouble*>::iterator j;
300	>	vector<StuntDouble*>::iterator j;
301		Molecule* mol;
302		StuntDouble* integrableObject;
303
#	Line 324 | Line 344 | namespace oopse {
344
345		}
346
347	<	void SimInfo::addExcludePairs(Molecule* mol) {
348	<	std::vector<Bond*>::iterator bondIter;
349	<	std::vector<Bend*>::iterator bendIter;
350	<	std::vector<Torsion*>::iterator torsionIter;
347	>	void SimInfo::addInteractionPairs(Molecule* mol) {
348	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
349	>	vector<Bond*>::iterator bondIter;
350	>	vector<Bend*>::iterator bendIter;
351	>	vector<Torsion*>::iterator torsionIter;
352	>	vector<Inversion*>::iterator inversionIter;
353		Bond* bond;
354		Bend* bend;
355		Torsion* torsion;
356	+	Inversion* inversion;
357		int a;
358		int b;
359		int c;
360		int d;
361	+
362	+	// atomGroups can be used to add special interaction maps between
363	+	// groups of atoms that are in two separate rigid bodies.
364	+	// However, most site-site interactions between two rigid bodies
365	+	// are probably not special, just the ones between the physically
366	+	// bonded atoms.  Interactions *within* a single rigid body should
367	+	// always be excluded.  These are done at the bottom of this
368	+	// function.
369	+
370	+	map<int, set<int> > atomGroups;
371	+	Molecule::RigidBodyIterator rbIter;
372	+	RigidBody* rb;
373	+	Molecule::IntegrableObjectIterator ii;
374	+	StuntDouble* integrableObject;
375
376	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
376	>	for (integrableObject = mol->beginIntegrableObject(ii);
377	>	integrableObject != NULL;
378	>	integrableObject = mol->nextIntegrableObject(ii)) {
379	>
380	>	if (integrableObject->isRigidBody()) {
381	>	rb = static_cast<RigidBody*>(integrableObject);
382	>	vector<Atom*> atoms = rb->getAtoms();
383	>	set<int> rigidAtoms;
384	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
385	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
386	>	}
387	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
388	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
389	>	}
390	>	} else {
391	>	set<int> oneAtomSet;
392	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
393	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
394	>	}
395	>	}
396	>
397	>	for (bond= mol->beginBond(bondIter); bond != NULL;
398	>	bond = mol->nextBond(bondIter)) {
399	>
400		a = bond->getAtomA()->getGlobalIndex();
401	<	b = bond->getAtomB()->getGlobalIndex();
402	<	exclude_.addPair(a, b);
401	>	b = bond->getAtomB()->getGlobalIndex();
402	>
403	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
404	>	oneTwoInteractions_.addPair(a, b);
405	>	} else {
406	>	excludedInteractions_.addPair(a, b);
407	>	}
408		}
409
410	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
410	>	for (bend= mol->beginBend(bendIter); bend != NULL;
411	>	bend = mol->nextBend(bendIter)) {
412	>
413		a = bend->getAtomA()->getGlobalIndex();
414		b = bend->getAtomB()->getGlobalIndex();
415		c = bend->getAtomC()->getGlobalIndex();
416	+
417	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
418	+	oneTwoInteractions_.addPair(a, b);
419	+	oneTwoInteractions_.addPair(b, c);
420	+	} else {
421	+	excludedInteractions_.addPair(a, b);
422	+	excludedInteractions_.addPair(b, c);
423	+	}
424
425	<	exclude_.addPair(a, b);
426	<	exclude_.addPair(a, c);
427	<	exclude_.addPair(b, c);
425	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
426	>	oneThreeInteractions_.addPair(a, c);
427	>	} else {
428	>	excludedInteractions_.addPair(a, c);
429	>	}
430		}
431
432	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
432	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
433	>	torsion = mol->nextTorsion(torsionIter)) {
434	>
435		a = torsion->getAtomA()->getGlobalIndex();
436		b = torsion->getAtomB()->getGlobalIndex();
437		c = torsion->getAtomC()->getGlobalIndex();
438	<	d = torsion->getAtomD()->getGlobalIndex();
438	>	d = torsion->getAtomD()->getGlobalIndex();
439
440	<	exclude_.addPair(a, b);
441	<	exclude_.addPair(a, c);
442	<	exclude_.addPair(a, d);
443	<	exclude_.addPair(b, c);
444	<	exclude_.addPair(b, d);
445	<	exclude_.addPair(c, d);
440	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
441	>	oneTwoInteractions_.addPair(a, b);
442	>	oneTwoInteractions_.addPair(b, c);
443	>	oneTwoInteractions_.addPair(c, d);
444	>	} else {
445	>	excludedInteractions_.addPair(a, b);
446	>	excludedInteractions_.addPair(b, c);
447	>	excludedInteractions_.addPair(c, d);
448	>	}
449	>
450	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
451	>	oneThreeInteractions_.addPair(a, c);
452	>	oneThreeInteractions_.addPair(b, d);
453	>	} else {
454	>	excludedInteractions_.addPair(a, c);
455	>	excludedInteractions_.addPair(b, d);
456	>	}
457	>
458	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
459	>	oneFourInteractions_.addPair(a, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, d);
462	>	}
463		}
464
465	<	Molecule::RigidBodyIterator rbIter;
466	<	RigidBody* rb;
467	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
468	<	std::vector<Atom*> atoms = rb->getAtoms();
469	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
470	<	for (int j = i + 1; j < atoms.size(); ++j) {
465	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
466	>	inversion = mol->nextInversion(inversionIter)) {
467	>
468	>	a = inversion->getAtomA()->getGlobalIndex();
469	>	b = inversion->getAtomB()->getGlobalIndex();
470	>	c = inversion->getAtomC()->getGlobalIndex();
471	>	d = inversion->getAtomD()->getGlobalIndex();
472	>
473	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
474	>	oneTwoInteractions_.addPair(a, b);
475	>	oneTwoInteractions_.addPair(a, c);
476	>	oneTwoInteractions_.addPair(a, d);
477	>	} else {
478	>	excludedInteractions_.addPair(a, b);
479	>	excludedInteractions_.addPair(a, c);
480	>	excludedInteractions_.addPair(a, d);
481	>	}
482	>
483	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
484	>	oneThreeInteractions_.addPair(b, c);
485	>	oneThreeInteractions_.addPair(b, d);
486	>	oneThreeInteractions_.addPair(c, d);
487	>	} else {
488	>	excludedInteractions_.addPair(b, c);
489	>	excludedInteractions_.addPair(b, d);
490	>	excludedInteractions_.addPair(c, d);
491	>	}
492	>	}
493	>
494	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
495	>	rb = mol->nextRigidBody(rbIter)) {
496	>	vector<Atom*> atoms = rb->getAtoms();
497	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
498	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
499		a = atoms[i]->getGlobalIndex();
500		b = atoms[j]->getGlobalIndex();
501	<	exclude_.addPair(a, b);
501	>	excludedInteractions_.addPair(a, b);
502		}
503		}
504		}
505
506		}
507
508	<	void SimInfo::removeExcludePairs(Molecule* mol) {
509	<	std::vector<Bond*>::iterator bondIter;
510	<	std::vector<Bend*>::iterator bendIter;
511	<	std::vector<Torsion*>::iterator torsionIter;
508	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
509	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
510	>	vector<Bond*>::iterator bondIter;
511	>	vector<Bend*>::iterator bendIter;
512	>	vector<Torsion*>::iterator torsionIter;
513	>	vector<Inversion*>::iterator inversionIter;
514		Bond* bond;
515		Bend* bend;
516		Torsion* torsion;
517	+	Inversion* inversion;
518		int a;
519		int b;
520		int c;
521		int d;
522	+
523	+	map<int, set<int> > atomGroups;
524	+	Molecule::RigidBodyIterator rbIter;
525	+	RigidBody* rb;
526	+	Molecule::IntegrableObjectIterator ii;
527	+	StuntDouble* integrableObject;
528
529	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
529	>	for (integrableObject = mol->beginIntegrableObject(ii);
530	>	integrableObject != NULL;
531	>	integrableObject = mol->nextIntegrableObject(ii)) {
532	>
533	>	if (integrableObject->isRigidBody()) {
534	>	rb = static_cast<RigidBody*>(integrableObject);
535	>	vector<Atom*> atoms = rb->getAtoms();
536	>	set<int> rigidAtoms;
537	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
538	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
539	>	}
540	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
541	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
542	>	}
543	>	} else {
544	>	set<int> oneAtomSet;
545	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
546	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
547	>	}
548	>	}
549	>
550	>	for (bond= mol->beginBond(bondIter); bond != NULL;
551	>	bond = mol->nextBond(bondIter)) {
552	>
553		a = bond->getAtomA()->getGlobalIndex();
554	<	b = bond->getAtomB()->getGlobalIndex();
555	<	exclude_.removePair(a, b);
554	>	b = bond->getAtomB()->getGlobalIndex();
555	>
556	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
557	>	oneTwoInteractions_.removePair(a, b);
558	>	} else {
559	>	excludedInteractions_.removePair(a, b);
560	>	}
561		}
562
563	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
563	>	for (bend= mol->beginBend(bendIter); bend != NULL;
564	>	bend = mol->nextBend(bendIter)) {
565	>
566		a = bend->getAtomA()->getGlobalIndex();
567		b = bend->getAtomB()->getGlobalIndex();
568		c = bend->getAtomC()->getGlobalIndex();
569	+
570	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	+	oneTwoInteractions_.removePair(a, b);
572	+	oneTwoInteractions_.removePair(b, c);
573	+	} else {
574	+	excludedInteractions_.removePair(a, b);
575	+	excludedInteractions_.removePair(b, c);
576	+	}
577
578	<	exclude_.removePair(a, b);
579	<	exclude_.removePair(a, c);
580	<	exclude_.removePair(b, c);
578	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
579	>	oneThreeInteractions_.removePair(a, c);
580	>	} else {
581	>	excludedInteractions_.removePair(a, c);
582	>	}
583		}
584
585	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
585	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
586	>	torsion = mol->nextTorsion(torsionIter)) {
587	>
588		a = torsion->getAtomA()->getGlobalIndex();
589		b = torsion->getAtomB()->getGlobalIndex();
590		c = torsion->getAtomC()->getGlobalIndex();
591	<	d = torsion->getAtomD()->getGlobalIndex();
591	>	d = torsion->getAtomD()->getGlobalIndex();
592	>
593	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
594	>	oneTwoInteractions_.removePair(a, b);
595	>	oneTwoInteractions_.removePair(b, c);
596	>	oneTwoInteractions_.removePair(c, d);
597	>	} else {
598	>	excludedInteractions_.removePair(a, b);
599	>	excludedInteractions_.removePair(b, c);
600	>	excludedInteractions_.removePair(c, d);
601	>	}
602
603	<	exclude_.removePair(a, b);
604	<	exclude_.removePair(a, c);
605	<	exclude_.removePair(a, d);
606	<	exclude_.removePair(b, c);
607	<	exclude_.removePair(b, d);
608	<	exclude_.removePair(c, d);
603	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
604	>	oneThreeInteractions_.removePair(a, c);
605	>	oneThreeInteractions_.removePair(b, d);
606	>	} else {
607	>	excludedInteractions_.removePair(a, c);
608	>	excludedInteractions_.removePair(b, d);
609	>	}
610	>
611	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
612	>	oneFourInteractions_.removePair(a, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, d);
615	>	}
616		}
617
618	<	Molecule::RigidBodyIterator rbIter;
619	<	RigidBody* rb;
620	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
621	<	std::vector<Atom*> atoms = rb->getAtoms();
622	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
623	<	for (int j = i + 1; j < atoms.size(); ++j) {
618	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
619	>	inversion = mol->nextInversion(inversionIter)) {
620	>
621	>	a = inversion->getAtomA()->getGlobalIndex();
622	>	b = inversion->getAtomB()->getGlobalIndex();
623	>	c = inversion->getAtomC()->getGlobalIndex();
624	>	d = inversion->getAtomD()->getGlobalIndex();
625	>
626	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
627	>	oneTwoInteractions_.removePair(a, b);
628	>	oneTwoInteractions_.removePair(a, c);
629	>	oneTwoInteractions_.removePair(a, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, b);
632	>	excludedInteractions_.removePair(a, c);
633	>	excludedInteractions_.removePair(a, d);
634	>	}
635	>
636	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
637	>	oneThreeInteractions_.removePair(b, c);
638	>	oneThreeInteractions_.removePair(b, d);
639	>	oneThreeInteractions_.removePair(c, d);
640	>	} else {
641	>	excludedInteractions_.removePair(b, c);
642	>	excludedInteractions_.removePair(b, d);
643	>	excludedInteractions_.removePair(c, d);
644	>	}
645	>	}
646	>
647	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
648	>	rb = mol->nextRigidBody(rbIter)) {
649	>	vector<Atom*> atoms = rb->getAtoms();
650	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
651	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
652		a = atoms[i]->getGlobalIndex();
653		b = atoms[j]->getGlobalIndex();
654	<	exclude_.removePair(a, b);
654	>	excludedInteractions_.removePair(a, b);
655		}
656		}
657		}
658	<
658	>
659		}
660	<
661	<
660	>
661	>
662		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
663		int curStampId;
664	<
664	>
665		//index from 0
666		curStampId = moleculeStamps_.size();
667
#	Line 449 | Line 669 | namespace oopse {
669		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
670		}
671
452	–	void SimInfo::update() {
672
673	<	setupSimType();
674	<
675	<	#ifdef IS_MPI
676	<	setupFortranParallel();
677	<	#endif
678	<
679	<	setupFortranSim();
680	<
681	<	//setup fortran force field
463	<	/** @deprecate */
464	<	int isError = 0;
465	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
466	<	if(isError){
467	<	sprintf( painCave.errMsg,
468	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
469	<	painCave.isFatal = 1;
470	<	simError();
471	<	}
472	<
473	<
474	<	setupCutoff();
475	<
673	>	/**
674	>	* update
675	>	*
676	>	*  Performs the global checks and variable settings after the
677	>	*  objects have been created.
678	>	*
679	>	*/
680	>	void SimInfo::update() {
681	>	setupSimVariables();
682		calcNdf();
683		calcNdfRaw();
684		calcNdfTrans();
479	–
480	–	fortranInitialized_ = true;
685		}
686	<
687	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
686	>
687	>	/**
688	>	* getSimulatedAtomTypes
689	>	*
690	>	* Returns an STL set of AtomType* that are actually present in this
691	>	* simulation.  Must query all processors to assemble this information.
692	>	*
693	>	*/
694	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
695		SimInfo::MoleculeIterator mi;
696		Molecule* mol;
697		Molecule::AtomIterator ai;
698		Atom* atom;
699	<	std::set<AtomType*> atomTypes;
700	<
699	>	set<AtomType*> atomTypes;
700	>
701		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
702	<
703	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
702	>	for(atom = mol->beginAtom(ai); atom != NULL;
703	>	atom = mol->nextAtom(ai)) {
704		atomTypes.insert(atom->getAtomType());
705	<	}
706	<
705	>	}
706	>	}
707	>
708	>	#ifdef IS_MPI
709	>
710	>	// loop over the found atom types on this processor, and add their
711	>	// numerical idents to a vector:
712	>
713	>	vector<int> foundTypes;
714	>	set<AtomType*>::iterator i;
715	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
716	>	foundTypes.push_back( (*i)->getIdent() );
717	>
718	>	// count_local holds the number of found types on this processor
719	>	int count_local = foundTypes.size();
720	>
721	>	int nproc = MPI::COMM_WORLD.Get_size();
722	>
723	>	// we need arrays to hold the counts and displacement vectors for
724	>	// all processors
725	>	vector<int> counts(nproc, 0);
726	>	vector<int> disps(nproc, 0);
727	>
728	>	// fill the counts array
729	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
730	>	1, MPI::INT);
731	>
732	>	// use the processor counts to compute the displacement array
733	>	disps[0] = 0;
734	>	int totalCount = counts[0];
735	>	for (int iproc = 1; iproc < nproc; iproc++) {
736	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
737	>	totalCount += counts[iproc];
738		}
739
740	+	// we need a (possibly redundant) set of all found types:
741	+	vector<int> ftGlobal(totalCount);
742	+
743	+	// now spray out the foundTypes to all the other processors:
744	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
745	+	&ftGlobal[0], &counts[0], &disps[0],
746	+	MPI::INT);
747	+
748	+	vector<int>::iterator j;
749	+
750	+	// foundIdents is a stl set, so inserting an already found ident
751	+	// will have no effect.
752	+	set<int> foundIdents;
753	+
754	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
755	+	foundIdents.insert((*j));
756	+
757	+	// now iterate over the foundIdents and get the actual atom types
758	+	// that correspond to these:
759	+	set<int>::iterator it;
760	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
761	+	atomTypes.insert( forceField_->getAtomType((*it)) );
762	+
763	+	#endif
764	+
765		return atomTypes;
766		}
767
768	<	void SimInfo::setupSimType() {
769	<	std::set<AtomType*>::iterator i;
770	<	std::set<AtomType*> atomTypes;
771	<	atomTypes = getUniqueAtomTypes();
768	>	void SimInfo::setupSimVariables() {
769	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
770	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
771	>	calcBoxDipole_ = false;
772	>	if ( simParams_->haveAccumulateBoxDipole() )
773	>	if ( simParams_->getAccumulateBoxDipole() ) {
774	>	calcBoxDipole_ = true;
775	>	}
776
777	<	int useLennardJones = 0;
778	<	int useElectrostatic = 0;
779	<	int useEAM = 0;
780	<	int useCharge = 0;
781	<	int useDirectional = 0;
782	<	int useDipole = 0;
512	<	int useGayBerne = 0;
513	<	int useSticky = 0;
514	<	int useStickyPower = 0;
515	<	int useShape = 0;
516	<	int useFLARB = 0; //it is not in AtomType yet
517	<	int useDirectionalAtom = 0;
518	<	int useElectrostatics = 0;
519	<	//usePBC and useRF are from simParams
520	<	int usePBC = simParams_->getPBC();
521	<	int useRF = simParams_->getUseRF();
522	<
777	>	set<AtomType*>::iterator i;
778	>	set<AtomType*> atomTypes;
779	>	atomTypes = getSimulatedAtomTypes();
780	>	int usesElectrostatic = 0;
781	>	int usesMetallic = 0;
782	>	int usesDirectional = 0;
783		//loop over all of the atom types
784		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785	<	useLennardJones |= (*i)->isLennardJones();
786	<	useElectrostatic |= (*i)->isElectrostatic();
787	<	useEAM |= (*i)->isEAM();
528	<	useCharge |= (*i)->isCharge();
529	<	useDirectional |= (*i)->isDirectional();
530	<	useDipole |= (*i)->isDipole();
531	<	useGayBerne |= (*i)->isGayBerne();
532	<	useSticky |= (*i)->isSticky();
533	<	useStickyPower |= (*i)->isStickyPower();
534	<	useShape |= (*i)->isShape();
785	>	usesElectrostatic |= (*i)->isElectrostatic();
786	>	usesMetallic |= (*i)->isMetal();
787	>	usesDirectional |= (*i)->isDirectional();
788		}
789	<
537	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
538	<	useDirectionalAtom = 1;
539	<	}
540	<
541	<	if (useCharge || useDipole) {
542	<	useElectrostatics = 1;
543	<	}
544	<
789	>
790		#ifdef IS_MPI
791		int temp;
792	+	temp = usesDirectional;
793	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
794	+
795	+	temp = usesMetallic;
796	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
797	+
798	+	temp = usesElectrostatic;
799	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800	+	#else
801
802	<	temp = usePBC;
803	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	>	usesDirectionalAtoms_ = usesDirectional;
803	>	usesMetallicAtoms_ = usesMetallic;
804	>	usesElectrostaticAtoms_ = usesElectrostatic;
805
806	<	temp = useDirectionalAtom;
552	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	<
554	<	temp = useLennardJones;
555	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556	<
557	<	temp = useElectrostatics;
558	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
559	<
560	<	temp = useCharge;
561	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
562	<
563	<	temp = useDipole;
564	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
565	<
566	<	temp = useSticky;
567	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568	<
569	<	temp = useStickyPower;
570	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	#endif
807
808	<	temp = useGayBerne;
809	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
809	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
810	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
811	>	}
812
575	–	temp = useEAM;
576	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useShape;
815	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	vector<int> SimInfo::getGlobalAtomIndices() {
815	>	SimInfo::MoleculeIterator mi;
816	>	Molecule* mol;
817	>	Molecule::AtomIterator ai;
818	>	Atom* atom;
819
820	<	temp = useFLARB;
582	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
583	<
584	<	temp = useRF;
585	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
821
822	<	#endif
822	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
823	>
824	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
825	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
826	>	}
827	>	}
828	>	return GlobalAtomIndices;
829	>	}
830
589	–	fInfo_.SIM_uses_PBC = usePBC;
590	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
591	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
592	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
593	–	fInfo_.SIM_uses_Charges = useCharge;
594	–	fInfo_.SIM_uses_Dipoles = useDipole;
595	–	fInfo_.SIM_uses_Sticky = useSticky;
596	–	fInfo_.SIM_uses_StickyPower = useStickyPower;
597	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
598	–	fInfo_.SIM_uses_EAM = useEAM;
599	–	fInfo_.SIM_uses_Shapes = useShape;
600	–	fInfo_.SIM_uses_FLARB = useFLARB;
601	–	fInfo_.SIM_uses_RF = useRF;
831
832	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
832	>	vector<int> SimInfo::getGlobalGroupIndices() {
833	>	SimInfo::MoleculeIterator mi;
834	>	Molecule* mol;
835	>	Molecule::CutoffGroupIterator ci;
836	>	CutoffGroup* cg;
837
838	<	if (simParams_->haveDielectric()) {
839	<	fInfo_.dielect = simParams_->getDielectric();
840	<	} else {
841	<	sprintf(painCave.errMsg,
842	<	"SimSetup Error: No Dielectric constant was set.\n"
843	<	"\tYou are trying to use Reaction Field without"
844	<	"\tsetting a dielectric constant!\n");
845	<	painCave.isFatal = 1;
846	<	simError();
847	<	}
615	<
616	<	} else {
617	<	fInfo_.dielect = 0.0;
838	>	vector<int> GlobalGroupIndices;
839	>
840	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
841	>
842	>	//local index of cutoff group is trivial, it only depends on the
843	>	//order of travesing
844	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
845	>	cg = mol->nextCutoffGroup(ci)) {
846	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
847	>	}
848		}
849	<
849	>	return GlobalGroupIndices;
850		}
851
622	–	void SimInfo::setupFortranSim() {
623	–	int isError;
624	–	int nExclude;
625	–	std::vector<int> fortranGlobalGroupMembership;
626	–
627	–	nExclude = exclude_.getSize();
628	–	isError = 0;
852
853	<	//globalGroupMembership_ is filled by SimCreator
854	<	for (int i = 0; i < nGlobalAtoms_; i++) {
632	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
633	<	}
853	>	void SimInfo::prepareTopology() {
854	>	int nExclude, nOneTwo, nOneThree, nOneFour;
855
856		//calculate mass ratio of cutoff group
636	–	std::vector<double> mfact;
857		SimInfo::MoleculeIterator mi;
858		Molecule* mol;
859		Molecule::CutoffGroupIterator ci;
860		CutoffGroup* cg;
861		Molecule::AtomIterator ai;
862		Atom* atom;
863	<	double totalMass;
863	>	RealType totalMass;
864
865	<	//to avoid memory reallocation, reserve enough space for mfact
866	<	mfact.reserve(getNCutoffGroups());
865	>	/**
866	>	* The mass factor is the relative mass of an atom to the total
867	>	* mass of the cutoff group it belongs to.  By default, all atoms
868	>	* are their own cutoff groups, and therefore have mass factors of
869	>	* 1.  We need some special handling for massless atoms, which
870	>	* will be treated as carrying the entire mass of the cutoff
871	>	* group.
872	>	*/
873	>	massFactors_.clear();
874	>	massFactors_.resize(getNAtoms(), 1.0);
875
876		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
877	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
877	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
878	>	cg = mol->nextCutoffGroup(ci)) {
879
880		totalMass = cg->getMass();
881		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
882	<	mfact.push_back(atom->getMass()/totalMass);
882	>	// Check for massless groups - set mfact to 1 if true
883	>	if (totalMass != 0)
884	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
885	>	else
886	>	massFactors_[atom->getLocalIndex()] = 1.0;
887		}
655	–
888		}
889		}
890
891	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
660	<	std::vector<int> identArray;
891	>	// Build the identArray_
892
893	<	//to avoid memory reallocation, reserve enough space identArray
894	<	identArray.reserve(getNAtoms());
664	<
893	>	identArray_.clear();
894	>	identArray_.reserve(getNAtoms());
895		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
896		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
897	<	identArray.push_back(atom->getIdent());
897	>	identArray_.push_back(atom->getIdent());
898		}
899		}
670	–
671	–	//fill molMembershipArray
672	–	//molMembershipArray is filled by SimCreator
673	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
674	–	for (int i = 0; i < nGlobalAtoms_; i++) {
675	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
676	–	}
900
901	<	//setup fortran simulation
679	<	int nGlobalExcludes = 0;
680	<	int* globalExcludes = NULL;
681	<	int* excludeList = exclude_.getExcludeList();
682	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
683	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
684	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
901	>	//scan topology
902
903	<	if( isError ){
903	>	nExclude = excludedInteractions_.getSize();
904	>	nOneTwo = oneTwoInteractions_.getSize();
905	>	nOneThree = oneThreeInteractions_.getSize();
906	>	nOneFour = oneFourInteractions_.getSize();
907
908	<	sprintf( painCave.errMsg,
909	<	"There was an error setting the simulation information in fortran.\n" );
910	<	painCave.isFatal = 1;
911	<	painCave.severity = OOPSE_ERROR;
692	<	simError();
693	<	}
908	>	int* excludeList = excludedInteractions_.getPairList();
909	>	int* oneTwoList = oneTwoInteractions_.getPairList();
910	>	int* oneThreeList = oneThreeInteractions_.getPairList();
911	>	int* oneFourList = oneFourInteractions_.getPairList();
912
913	<	#ifdef IS_MPI
696	<	sprintf( checkPointMsg,
697	<	"succesfully sent the simulation information to fortran.\n");
698	<	MPIcheckPoint();
699	<	#endif // is_mpi
700	<	}
701	<
702	<
703	<	#ifdef IS_MPI
704	<	void SimInfo::setupFortranParallel() {
705	<
706	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
707	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
708	<	std::vector<int> localToGlobalCutoffGroupIndex;
709	<	SimInfo::MoleculeIterator mi;
710	<	Molecule::AtomIterator ai;
711	<	Molecule::CutoffGroupIterator ci;
712	<	Molecule* mol;
713	<	Atom* atom;
714	<	CutoffGroup* cg;
715	<	mpiSimData parallelData;
716	<	int isError;
717	<
718	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
719	<
720	<	//local index(index in DataStorge) of atom is important
721	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
722	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
723	<	}
724	<
725	<	//local index of cutoff group is trivial, it only depends on the order of travesing
726	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
727	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
728	<	}
729	<
730	<	}
731	<
732	<	//fill up mpiSimData struct
733	<	parallelData.nMolGlobal = getNGlobalMolecules();
734	<	parallelData.nMolLocal = getNMolecules();
735	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
736	<	parallelData.nAtomsLocal = getNAtoms();
737	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
738	<	parallelData.nGroupsLocal = getNCutoffGroups();
739	<	parallelData.myNode = worldRank;
740	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
741	<
742	<	//pass mpiSimData struct and index arrays to fortran
743	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
744	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
745	<	&localToGlobalCutoffGroupIndex[0], &isError);
746	<
747	<	if (isError) {
748	<	sprintf(painCave.errMsg,
749	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
750	<	painCave.isFatal = 1;
751	<	simError();
752	<	}
753	<
754	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
755	<	MPIcheckPoint();
756	<
757	<
913	>	topologyDone_ = true;
914		}
915
760	–	#endif
761	–
762	–	double SimInfo::calcMaxCutoffRadius() {
763	–
764	–
765	–	std::set<AtomType*> atomTypes;
766	–	std::set<AtomType*>::iterator i;
767	–	std::vector<double> cutoffRadius;
768	–
769	–	//get the unique atom types
770	–	atomTypes = getUniqueAtomTypes();
771	–
772	–	//query the max cutoff radius among these atom types
773	–	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774	–	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
775	–	}
776	–
777	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
778	–	#ifdef IS_MPI
779	–	//pick the max cutoff radius among the processors
780	–	#endif
781	–
782	–	return maxCutoffRadius;
783	–	}
784	–
785	–	void SimInfo::getCutoff(double& rcut, double& rsw) {
786	–
787	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
788	–
789	–	if (!simParams_->haveRcut()){
790	–	sprintf(painCave.errMsg,
791	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
792	–	"\tOOPSE will use a default value of 15.0 angstroms"
793	–	"\tfor the cutoffRadius.\n");
794	–	painCave.isFatal = 0;
795	–	simError();
796	–	rcut = 15.0;
797	–	} else{
798	–	rcut = simParams_->getRcut();
799	–	}
800	–
801	–	if (!simParams_->haveRsw()){
802	–	sprintf(painCave.errMsg,
803	–	"SimCreator Warning: No value was set for switchingRadius.\n"
804	–	"\tOOPSE will use a default value of\n"
805	–	"\t0.95 * cutoffRadius for the switchingRadius\n");
806	–	painCave.isFatal = 0;
807	–	simError();
808	–	rsw = 0.95 * rcut;
809	–	} else{
810	–	rsw = simParams_->getRsw();
811	–	}
812	–
813	–	} else {
814	–	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
815	–	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
816	–
817	–	if (simParams_->haveRcut()) {
818	–	rcut = simParams_->getRcut();
819	–	} else {
820	–	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821	–	rcut = calcMaxCutoffRadius();
822	–	}
823	–
824	–	if (simParams_->haveRsw()) {
825	–	rsw  = simParams_->getRsw();
826	–	} else {
827	–	rsw = rcut;
828	–	}
829	–
830	–	}
831	–	}
832	–
833	–	void SimInfo::setupCutoff() {
834	–	getCutoff(rcut_, rsw_);
835	–	double rnblist = rcut_ + 1; // skin of neighbor list
836	–
837	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
838	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
839	–	}
840	–
916		void SimInfo::addProperty(GenericData* genData) {
917		properties_.addProperty(genData);
918		}
919
920	<	void SimInfo::removeProperty(const std::string& propName) {
920	>	void SimInfo::removeProperty(const string& propName) {
921		properties_.removeProperty(propName);
922		}
923
#	Line 850 | Line 925 | namespace oopse {
925		properties_.clearProperties();
926		}
927
928	<	std::vector<std::string> SimInfo::getPropertyNames() {
928	>	vector<string> SimInfo::getPropertyNames() {
929		return properties_.getPropertyNames();
930		}
931
932	<	std::vector<GenericData*> SimInfo::getProperties() {
932	>	vector<GenericData*> SimInfo::getProperties() {
933		return properties_.getProperties();
934		}
935
936	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
936	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
937		return properties_.getPropertyByName(propName);
938		}
939
#	Line 872 | Line 947 | namespace oopse {
947		Molecule* mol;
948		RigidBody* rb;
949		Atom* atom;
950	+	CutoffGroup* cg;
951		SimInfo::MoleculeIterator mi;
952		Molecule::RigidBodyIterator rbIter;
953	<	Molecule::AtomIterator atomIter;;
953	>	Molecule::AtomIterator atomIter;
954	>	Molecule::CutoffGroupIterator cgIter;
955
956		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
957
#	Line 885 | Line 962 | namespace oopse {
962		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
963		rb->setSnapshotManager(sman_);
964		}
965	+
966	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
967	+	cg->setSnapshotManager(sman_);
968	+	}
969		}
970
971		}
#	Line 894 | Line 975 | namespace oopse {
975		Molecule* mol;
976
977		Vector3d comVel(0.0);
978	<	double totalMass = 0.0;
978	>	RealType totalMass = 0.0;
979
980
981		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
982	<	double mass = mol->getMass();
982	>	RealType mass = mol->getMass();
983		totalMass += mass;
984		comVel += mass * mol->getComVel();
985		}
986
987		#ifdef IS_MPI
988	<	double tmpMass = totalMass;
988	>	RealType tmpMass = totalMass;
989		Vector3d tmpComVel(comVel);
990	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
991	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
990	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
991	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
992		#endif
993
994		comVel /= totalMass;
#	Line 920 | Line 1001 | namespace oopse {
1001		Molecule* mol;
1002
1003		Vector3d com(0.0);
1004	<	double totalMass = 0.0;
1004	>	RealType totalMass = 0.0;
1005
1006		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1007	<	double mass = mol->getMass();
1007	>	RealType mass = mol->getMass();
1008		totalMass += mass;
1009		com += mass * mol->getCom();
1010		}
1011
1012		#ifdef IS_MPI
1013	<	double tmpMass = totalMass;
1013	>	RealType tmpMass = totalMass;
1014		Vector3d tmpCom(com);
1015	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1016	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1015	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1016	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1017		#endif
1018
1019		com /= totalMass;
#	Line 941 | Line 1022 | namespace oopse {
1022
1023		}
1024
1025	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1025	>	ostream& operator <<(ostream& o, SimInfo& info) {
1026
1027		return o;
1028		}
#	Line 956 | Line 1037 | namespace oopse {
1037		Molecule* mol;
1038
1039
1040	<	double totalMass = 0.0;
1040	>	RealType totalMass = 0.0;
1041
1042
1043		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1044	<	double mass = mol->getMass();
1044	>	RealType mass = mol->getMass();
1045		totalMass += mass;
1046		com += mass * mol->getCom();
1047		comVel += mass * mol->getComVel();
1048		}
1049
1050		#ifdef IS_MPI
1051	<	double tmpMass = totalMass;
1051	>	RealType tmpMass = totalMass;
1052		Vector3d tmpCom(com);
1053		Vector3d tmpComVel(comVel);
1054	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1055	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1056	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1054	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1056	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1057		#endif
1058
1059		com /= totalMass;
#	Line 981 | Line 1062 | namespace oopse {
1062
1063		/*
1064		Return intertia tensor for entire system and angular momentum Vector.
1065	+
1066	+
1067	+	[  Ixx -Ixy  -Ixz ]
1068	+	J =| -Iyx  Iyy  -Iyz |
1069	+	[ -Izx -Iyz   Izz ]
1070		*/
1071
1072		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1073
1074
1075	<	double xx = 0.0;
1076	<	double yy = 0.0;
1077	<	double zz = 0.0;
1078	<	double xy = 0.0;
1079	<	double xz = 0.0;
1080	<	double yz = 0.0;
1075	>	RealType xx = 0.0;
1076	>	RealType yy = 0.0;
1077	>	RealType zz = 0.0;
1078	>	RealType xy = 0.0;
1079	>	RealType xz = 0.0;
1080	>	RealType yz = 0.0;
1081		Vector3d com(0.0);
1082		Vector3d comVel(0.0);
1083
#	Line 1003 | Line 1089 | namespace oopse {
1089		Vector3d thisq(0.0);
1090		Vector3d thisv(0.0);
1091
1092	<	double thisMass = 0.0;
1092	>	RealType thisMass = 0.0;
1093
1094
1095
#	Line 1032 | Line 1118 | namespace oopse {
1118		inertiaTensor(0,1) = -xy;
1119		inertiaTensor(0,2) = -xz;
1120		inertiaTensor(1,0) = -xy;
1121	<	inertiaTensor(2,0) = xx + zz;
1121	>	inertiaTensor(1,1) = xx + zz;
1122		inertiaTensor(1,2) = -yz;
1123		inertiaTensor(2,0) = -xz;
1124		inertiaTensor(2,1) = -yz;
#	Line 1041 | Line 1127 | namespace oopse {
1127		#ifdef IS_MPI
1128		Mat3x3d tmpI(inertiaTensor);
1129		Vector3d tmpAngMom;
1130	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1131	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1130	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1131	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1132		#endif
1133
1134		return;
#	Line 1060 | Line 1146 | namespace oopse {
1146		SimInfo::MoleculeIterator i;
1147		Molecule* mol;
1148
1149	<	Vector3d thisq(0.0);
1150	<	Vector3d thisv(0.0);
1149	>	Vector3d thisr(0.0);
1150	>	Vector3d thisp(0.0);
1151
1152	<	double thisMass = 0.0;
1152	>	RealType thisMass;
1153
1154		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1155	<	thisq = mol->getCom()-com;
1156	<	thisv = mol->getComVel()-comVel;
1157	<	thisMass = mol->getMass();
1072	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1155	>	thisMass = mol->getMass();
1156	>	thisr = mol->getCom()-com;
1157	>	thisp = (mol->getComVel()-comVel)*thisMass;
1158
1159	+	angularMomentum += cross( thisr, thisp );
1160	+
1161		}
1162
1163		#ifdef IS_MPI
1164		Vector3d tmpAngMom;
1165	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1165	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1166		#endif
1167
1168		return angularMomentum;
1169		}
1170
1171	<
1172	<	}//end namespace oopse
1171	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1172	>	return IOIndexToIntegrableObject.at(index);
1173	>	}
1174	>
1175	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1176	>	IOIndexToIntegrableObject= v;
1177	>	}
1178
1179	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1180	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1181	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1182	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1183	+	*/
1184	+	void SimInfo::getGyrationalVolume(RealType &volume){
1185	+	Mat3x3d intTensor;
1186	+	RealType det;
1187	+	Vector3d dummyAngMom;
1188	+	RealType sysconstants;
1189	+	RealType geomCnst;
1190	+
1191	+	geomCnst = 3.0/2.0;
1192	+	/* Get the inertial tensor and angular momentum for free*/
1193	+	getInertiaTensor(intTensor,dummyAngMom);
1194	+
1195	+	det = intTensor.determinant();
1196	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1197	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1198	+	return;
1199	+	}
1200	+
1201	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1202	+	Mat3x3d intTensor;
1203	+	Vector3d dummyAngMom;
1204	+	RealType sysconstants;
1205	+	RealType geomCnst;
1206	+
1207	+	geomCnst = 3.0/2.0;
1208	+	/* Get the inertial tensor and angular momentum for free*/
1209	+	getInertiaTensor(intTensor,dummyAngMom);
1210	+
1211	+	detI = intTensor.determinant();
1212	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1213	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1214	+	return;
1215	+	}
1216	+	/*
1217	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1218	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1219	+	sdByGlobalIndex_ = v;
1220	+	}
1221	+
1222	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1223	+	//assert(index < nAtoms_ + nRigidBodies_);
1224	+	return sdByGlobalIndex_.at(index);
1225	+	}
1226	+	*/
1227	+	int SimInfo::getNGlobalConstraints() {
1228	+	int nGlobalConstraints;
1229	+	#ifdef IS_MPI
1230	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1231	+	MPI_COMM_WORLD);
1232	+	#else
1233	+	nGlobalConstraints =  nConstraints_;
1234	+	#endif
1235	+	return nGlobalConstraints;
1236	+	}
1237	+
1238	+	}//end namespace OpenMD
1239	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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