[ViewVC] Diff of: OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC vs.
Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

#	Line 47 \| Line 47 \| namespace OpenMD {
47		using namespace std;
48		namespace OpenMD {
49
50	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
51	+
52	+	// In a parallel computation, row and colum scans must visit all
53	+	// surrounding cells (not just the 14 upper triangular blocks that
54	+	// are used when the processor can see all pairs)
55	+	#ifdef IS_MPI
56	+	cellOffsets_.clear();
57	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
58	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
59	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
60	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
61	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
62	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
63	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
64	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
66	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
67	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
68	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
69	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
70	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
71	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
72	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
73	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
74	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
75	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
76	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
77	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
78	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
79	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
80	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
81	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
82	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
83	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
84	+	#endif
85	+	}
86	+
87	+
88		/**
89		* distributeInitialData is essentially a copy of the older fortran
90		* SimulationSetup
91		*/
54	–
92		void ForceMatrixDecomposition::distributeInitialData() {
93		snap_ = sman_->getCurrentSnapshot();
94		storageLayout_ = sman_->getStorageLayout();
95		ff_ = info_->getForceField();
96		nLocal_ = snap_->getNumberOfAtoms();
97	<
97	>
98		nGroups_ = info_->getNLocalCutoffGroups();
62	–	cerr << "in dId, nGroups = " << nGroups_ << "\n";
99		// gather the information for atomtype IDs (atids):
100		idents = info_->getIdentArray();
101		AtomLocalToGlobal = info_->getGlobalAtomIndices();
102		cgLocalToGlobal = info_->getGlobalGroupIndices();
103		vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
104	+
105		massFactors = info_->getMassFactors();
106
107	<	PairList excludes = info_->getExcludedInteractions();
108	<	PairList oneTwo = info_->getOneTwoInteractions();
109	<	PairList oneThree = info_->getOneThreeInteractions();
110	<	PairList oneFour = info_->getOneFourInteractions();
107	>	PairList* excludes = info_->getExcludedInteractions();
108	>	PairList* oneTwo = info_->getOneTwoInteractions();
109	>	PairList* oneThree = info_->getOneThreeInteractions();
110	>	PairList* oneFour = info_->getOneFourInteractions();
111
112		#ifdef IS_MPI
113
114	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
115	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
79	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
80	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
81	<	AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
114	>	MPI::Intracomm row = rowComm.getComm();
115	>	MPI::Intracomm col = colComm.getComm();
116
117	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
118	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
119	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
120	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
121	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
117	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
118	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
119	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
120	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
121	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
122
123	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
124	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
125	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
126	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
123	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
124	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
125	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
126	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
127	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
128
129	<	nAtomsInRow_ = AtomCommIntRow->getSize();
130	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
131	<	nGroupsInRow_ = cgCommIntRow->getSize();
132	<	nGroupsInCol_ = cgCommIntColumn->getSize();
129	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
130	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
131	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
132	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
133
134	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
135	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
136	+	nGroupsInRow_ = cgPlanIntRow->getSize();
137	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
138	+
139		// Modify the data storage objects with the correct layouts and sizes:
140		atomRowData.resize(nAtomsInRow_);
141		atomRowData.setStorageLayout(storageLayout_);
#	Line 109 \| Line 149 \| namespace OpenMD {
149		identsRow.resize(nAtomsInRow_);
150		identsCol.resize(nAtomsInCol_);
151
152	<	AtomCommIntRow->gather(idents, identsRow);
153	<	AtomCommIntColumn->gather(idents, identsCol);
152	>	AtomPlanIntRow->gather(idents, identsRow);
153	>	AtomPlanIntColumn->gather(idents, identsCol);
154
155	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
156	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
157	<
118	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
155	>	// allocate memory for the parallel objects
156	>	atypesRow.resize(nAtomsInRow_);
157	>	atypesCol.resize(nAtomsInCol_);
158
159	<	AtomCommRealRow->gather(massFactors, massFactorsRow);
160	<	AtomCommRealColumn->gather(massFactors, massFactorsCol);
159	>	for (int i = 0; i < nAtomsInRow_; i++)
160	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
161	>	for (int i = 0; i < nAtomsInCol_; i++)
162	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
163
164	+	pot_row.resize(nAtomsInRow_);
165	+	pot_col.resize(nAtomsInCol_);
166	+
167	+	AtomRowToGlobal.resize(nAtomsInRow_);
168	+	AtomColToGlobal.resize(nAtomsInCol_);
169	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
170	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
171	+
172	+	cgRowToGlobal.resize(nGroupsInRow_);
173	+	cgColToGlobal.resize(nGroupsInCol_);
174	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
176	+
177	+	massFactorsRow.resize(nAtomsInRow_);
178	+	massFactorsCol.resize(nAtomsInCol_);
179	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
180	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
181	+
182		groupListRow_.clear();
183		groupListRow_.resize(nGroupsInRow_);
184		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 143 \| Line 201 \| namespace OpenMD {
201		}
202		}
203
204	<	skipsForAtom.clear();
205	<	skipsForAtom.resize(nAtomsInRow_);
204	>	excludesForAtom.clear();
205	>	excludesForAtom.resize(nAtomsInRow_);
206		toposForAtom.clear();
207		toposForAtom.resize(nAtomsInRow_);
208		topoDist.clear();
#	Line 155 \| Line 213 \| namespace OpenMD {
213		for (int j = 0; j < nAtomsInCol_; j++) {
214		int jglob = AtomColToGlobal[j];
215
216	<	if (excludes.hasPair(iglob, jglob))
217	<	skipsForAtom[i].push_back(j);
216	>	if (excludes->hasPair(iglob, jglob))
217	>	excludesForAtom[i].push_back(j);
218
219	<	if (oneTwo.hasPair(iglob, jglob)) {
219	>	if (oneTwo->hasPair(iglob, jglob)) {
220		toposForAtom[i].push_back(j);
221		topoDist[i].push_back(1);
222		} else {
223	<	if (oneThree.hasPair(iglob, jglob)) {
223	>	if (oneThree->hasPair(iglob, jglob)) {
224		toposForAtom[i].push_back(j);
225		topoDist[i].push_back(2);
226		} else {
227	<	if (oneFour.hasPair(iglob, jglob)) {
227	>	if (oneFour->hasPair(iglob, jglob)) {
228		toposForAtom[i].push_back(j);
229		topoDist[i].push_back(3);
230		}
#	Line 175 \| Line 233 \| namespace OpenMD {
233		}
234		}
235
236	<	#endif
237	<
238	<	groupList_.clear();
181	<	groupList_.resize(nGroups_);
182	<	for (int i = 0; i < nGroups_; i++) {
183	<	int gid = cgLocalToGlobal[i];
184	<	for (int j = 0; j < nLocal_; j++) {
185	<	int aid = AtomLocalToGlobal[j];
186	<	if (globalGroupMembership[aid] == gid) {
187	<	groupList_[i].push_back(j);
188	<	}
189	<	}
190	<	}
191	<
192	<	skipsForAtom.clear();
193	<	skipsForAtom.resize(nLocal_);
236	>	#else
237	>	excludesForAtom.clear();
238	>	excludesForAtom.resize(nLocal_);
239		toposForAtom.clear();
240		toposForAtom.resize(nLocal_);
241		topoDist.clear();
#	Line 202 \| Line 247 \| namespace OpenMD {
247		for (int j = 0; j < nLocal_; j++) {
248		int jglob = AtomLocalToGlobal[j];
249
250	<	if (excludes.hasPair(iglob, jglob))
251	<	skipsForAtom[i].push_back(j);
250	>	if (excludes->hasPair(iglob, jglob))
251	>	excludesForAtom[i].push_back(j);
252
253	<	if (oneTwo.hasPair(iglob, jglob)) {
253	>
254	>	if (oneTwo->hasPair(iglob, jglob)) {
255		toposForAtom[i].push_back(j);
256		topoDist[i].push_back(1);
257		} else {
258	<	if (oneThree.hasPair(iglob, jglob)) {
258	>	if (oneThree->hasPair(iglob, jglob)) {
259		toposForAtom[i].push_back(j);
260		topoDist[i].push_back(2);
261		} else {
262	<	if (oneFour.hasPair(iglob, jglob)) {
262	>	if (oneFour->hasPair(iglob, jglob)) {
263		toposForAtom[i].push_back(j);
264		topoDist[i].push_back(3);
265		}
#	Line 221 \| Line 267 \| namespace OpenMD {
267		}
268		}
269		}
270	<
270	>	#endif
271	>
272	>	// allocate memory for the parallel objects
273	>	atypesLocal.resize(nLocal_);
274	>
275	>	for (int i = 0; i < nLocal_; i++)
276	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
277	>
278	>	groupList_.clear();
279	>	groupList_.resize(nGroups_);
280	>	for (int i = 0; i < nGroups_; i++) {
281	>	int gid = cgLocalToGlobal[i];
282	>	for (int j = 0; j < nLocal_; j++) {
283	>	int aid = AtomLocalToGlobal[j];
284	>	if (globalGroupMembership[aid] == gid) {
285	>	groupList_[i].push_back(j);
286	>	}
287	>	}
288	>	}
289	>
290	>
291		createGtypeCutoffMap();
292	+
293		}
294
295		void ForceMatrixDecomposition::createGtypeCutoffMap() {
296	<
296	>
297		RealType tol = 1e-6;
298	+	largestRcut_ = 0.0;
299		RealType rc;
300		int atid;
301		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302	<	vector<RealType> atypeCutoff;
303	<	atypeCutoff.resize( atypes.size() );
302	>
303	>	map<int, RealType> atypeCutoff;
304
305		for (set<AtomType*>::iterator at = atypes.begin();
306		at != atypes.end(); ++at){
307		atid = (*at)->getIdent();
308	<
241	<	if (userChoseCutoff_)
308	>	if (userChoseCutoff_)
309		atypeCutoff[atid] = userCutoff_;
310		else
311		atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312		}
313	<
313	>
314		vector<RealType> gTypeCutoffs;
248	–
315		// first we do a single loop over the cutoff groups to find the
316		// largest cutoff for any atypes present in this group.
317		#ifdef IS_MPI
#	Line 303 \| Line 369 \| namespace OpenMD {
369
370		vector<RealType> groupCutoff(nGroups_, 0.0);
371		groupToGtype.resize(nGroups_);
306	–
307	–	cerr << "nGroups = " << nGroups_ << "\n";
372		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
309	–
373		groupCutoff[cg1] = 0.0;
374		vector<int> atomList = getAtomsInGroupRow(cg1);
312	–
375		for (vector<int>::iterator ia = atomList.begin();
376		ia != atomList.end(); ++ia) {
377		int atom1 = (*ia);
378		atid = idents[atom1];
379	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
379	>	if (atypeCutoff[atid] > groupCutoff[cg1])
380		groupCutoff[cg1] = atypeCutoff[atid];
319	–	}
381		}
382	<
382	>
383		bool gTypeFound = false;
384		for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
#	Line 326 \| Line 387 \| namespace OpenMD {
387		gTypeFound = true;
388		}
389		}
390	<	if (!gTypeFound) {
390	>	if (!gTypeFound) {
391		gTypeCutoffs.push_back( groupCutoff[cg1] );
392		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393		}
394		}
395		#endif
396
336	–	cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
397		// Now we find the maximum group cutoff value present in the simulation
398
399	<	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
399	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
400	>	gTypeCutoffs.end());
401
402		#ifdef IS_MPI
403	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
403	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
404	>	MPI::MAX);
405		#endif
406
407		RealType tradRcut = groupMax;
#	Line 369 \| Line 431 \| namespace OpenMD {
431
432		pair<int,int> key = make_pair(i,j);
433		gTypeCutoffMap[key].first = thisRcut;
372	–
434		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
374	–
435		gTypeCutoffMap[key].second = thisRcut*thisRcut;
376	–
436		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
378	–
437		// sanity check
438
439		if (userChoseCutoff_) {
#	Line 435 \| Line 493 \| namespace OpenMD {
493		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
494
495		if (storageLayout_ & DataStorage::dslParticlePot) {
496	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
497	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
496	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
497	>	0.0);
498	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
499	>	0.0);
500		}
501
502		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 445 \| Line 505 \| namespace OpenMD {
505		}
506
507		if (storageLayout_ & DataStorage::dslFunctional) {
508	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
509	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
508	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
509	>	0.0);
510	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
511	>	0.0);
512		}
513
514		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 456 \| Line 518 \| namespace OpenMD {
518		atomColData.functionalDerivative.end(), 0.0);
519		}
520
521	<	#else
522	<
521	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
522	>	fill(atomRowData.skippedCharge.begin(),
523	>	atomRowData.skippedCharge.end(), 0.0);
524	>	fill(atomColData.skippedCharge.begin(),
525	>	atomColData.skippedCharge.end(), 0.0);
526	>	}
527	>
528	>	#endif
529	>	// even in parallel, we need to zero out the local arrays:
530	>
531		if (storageLayout_ & DataStorage::dslParticlePot) {
532		fill(snap_->atomData.particlePot.begin(),
533		snap_->atomData.particlePot.end(), 0.0);
#	Line 475 \| Line 545 \| namespace OpenMD {
545		fill(snap_->atomData.functionalDerivative.begin(),
546		snap_->atomData.functionalDerivative.end(), 0.0);
547		}
548	<	#endif
548	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
549	>	fill(snap_->atomData.skippedCharge.begin(),
550	>	snap_->atomData.skippedCharge.end(), 0.0);
551	>	}
552
553		}
554
#	Line 486 \| Line 559 \| namespace OpenMD {
559		#ifdef IS_MPI
560
561		// gather up the atomic positions
562	<	AtomCommVectorRow->gather(snap_->atomData.position,
562	>	AtomPlanVectorRow->gather(snap_->atomData.position,
563		atomRowData.position);
564	<	AtomCommVectorColumn->gather(snap_->atomData.position,
564	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
565		atomColData.position);
566
567		// gather up the cutoff group positions
568	<	cgCommVectorRow->gather(snap_->cgData.position,
568	>
569	>	cgPlanVectorRow->gather(snap_->cgData.position,
570		cgRowData.position);
571	<	cgCommVectorColumn->gather(snap_->cgData.position,
571	>
572	>	cgPlanVectorColumn->gather(snap_->cgData.position,
573		cgColData.position);
574	+
575
576		// if needed, gather the atomic rotation matrices
577		if (storageLayout_ & DataStorage::dslAmat) {
578	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
578	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
579		atomRowData.aMat);
580	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
580	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
581		atomColData.aMat);
582		}
583
584		// if needed, gather the atomic eletrostatic frames
585		if (storageLayout_ & DataStorage::dslElectroFrame) {
586	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
586	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
587		atomRowData.electroFrame);
588	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
588	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
589		atomColData.electroFrame);
590		}
591	+
592		#endif
593		}
594
#	Line 525 \| Line 602 \| namespace OpenMD {
602
603		if (storageLayout_ & DataStorage::dslDensity) {
604
605	<	AtomCommRealRow->scatter(atomRowData.density,
605	>	AtomPlanRealRow->scatter(atomRowData.density,
606		snap_->atomData.density);
607
608		int n = snap_->atomData.density.size();
609		vector<RealType> rho_tmp(n, 0.0);
610	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
610	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
611		for (int i = 0; i < n; i++)
612		snap_->atomData.density[i] += rho_tmp[i];
613		}
#	Line 546 \| Line 623 \| namespace OpenMD {
623		storageLayout_ = sman_->getStorageLayout();
624		#ifdef IS_MPI
625		if (storageLayout_ & DataStorage::dslFunctional) {
626	<	AtomCommRealRow->gather(snap_->atomData.functional,
626	>	AtomPlanRealRow->gather(snap_->atomData.functional,
627		atomRowData.functional);
628	<	AtomCommRealColumn->gather(snap_->atomData.functional,
628	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
629		atomColData.functional);
630		}
631
632		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
633	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
633	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
634		atomRowData.functionalDerivative);
635	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
635	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
636		atomColData.functionalDerivative);
637		}
638		#endif
#	Line 569 \| Line 646 \| namespace OpenMD {
646		int n = snap_->atomData.force.size();
647		vector<Vector3d> frc_tmp(n, V3Zero);
648
649	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
649	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
650		for (int i = 0; i < n; i++) {
651		snap_->atomData.force[i] += frc_tmp[i];
652		frc_tmp[i] = 0.0;
653		}
654
655	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
656	<	for (int i = 0; i < n; i++)
655	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
656	>	for (int i = 0; i < n; i++) {
657		snap_->atomData.force[i] += frc_tmp[i];
658	<
659	<
658	>	}
659	>
660		if (storageLayout_ & DataStorage::dslTorque) {
661
662	<	int nt = snap_->atomData.force.size();
662	>	int nt = snap_->atomData.torque.size();
663		vector<Vector3d> trq_tmp(nt, V3Zero);
664
665	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
666	<	for (int i = 0; i < n; i++) {
665	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
666	>	for (int i = 0; i < nt; i++) {
667		snap_->atomData.torque[i] += trq_tmp[i];
668		trq_tmp[i] = 0.0;
669		}
670
671	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
672	<	for (int i = 0; i < n; i++)
671	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
672	>	for (int i = 0; i < nt; i++)
673		snap_->atomData.torque[i] += trq_tmp[i];
674		}
675	+
676	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
677	+
678	+	int ns = snap_->atomData.skippedCharge.size();
679	+	vector<RealType> skch_tmp(ns, 0.0);
680	+
681	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
682	+	for (int i = 0; i < ns; i++) {
683	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
684	+	skch_tmp[i] = 0.0;
685	+	}
686	+
687	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
688	+	for (int i = 0; i < ns; i++)
689	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
690	+
691	+	}
692
693		nLocal_ = snap_->getNumberOfAtoms();
694
#	Line 603 \| Line 697 \| namespace OpenMD {
697
698		// scatter/gather pot_row into the members of my column
699
700	<	AtomCommPotRow->scatter(pot_row, pot_temp);
700	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
701
702		for (int ii = 0; ii < pot_temp.size(); ii++ )
703		pairwisePot += pot_temp[ii];
#	Line 611 \| Line 705 \| namespace OpenMD {
705		fill(pot_temp.begin(), pot_temp.end(),
706		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
707
708	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
708	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
709
710		for (int ii = 0; ii < pot_temp.size(); ii++ )
711		pairwisePot += pot_temp[ii];
712	+
713	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
714	+	RealType ploc1 = pairwisePot[ii];
715	+	RealType ploc2 = 0.0;
716	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
717	+	pairwisePot[ii] = ploc2;
718	+	}
719	+
720	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
721	+	RealType ploc1 = embeddingPot[ii];
722	+	RealType ploc2 = 0.0;
723	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
724	+	embeddingPot[ii] = ploc2;
725	+	}
726	+
727		#endif
728
729		}
#	Line 691 \| Line 800 \| namespace OpenMD {
800		#ifdef IS_MPI
801		return massFactorsRow[atom1];
802		#else
694	–	cerr << "mfs = " << massFactors.size() << " atom1 = " << atom1 << "\n";
803		return massFactors[atom1];
804		#endif
805		}
#	Line 718 \| Line 826 \| namespace OpenMD {
826		return d;
827		}
828
829	<	vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
830	<	return skipsForAtom[atom1];
829	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
830	>	return excludesForAtom[atom1];
831		}
832
833		/**
834	<	* There are a number of reasons to skip a pair or a
727	<	* particle. Mostly we do this to exclude atoms who are involved in
728	<	* short range interactions (bonds, bends, torsions), but we also
729	<	* need to exclude some overcounted interactions that result from
834	>	* We need to exclude some overcounted interactions that result from
835		* the parallel decomposition.
836		*/
837		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
838		int unique_id_1, unique_id_2;
839	<
839	>
840		#ifdef IS_MPI
841		// in MPI, we have to look up the unique IDs for each atom
842		unique_id_1 = AtomRowToGlobal[atom1];
#	Line 746 \| Line 851 \| namespace OpenMD {
851		} else {
852		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
853		}
749	–	#else
750	–	// in the normal loop, the atom numbers are unique
751	–	unique_id_1 = atom1;
752	–	unique_id_2 = atom2;
854		#endif
855	+	return false;
856	+	}
857	+
858	+	/**
859	+	* We need to handle the interactions for atoms who are involved in
860	+	* the same rigid body as well as some short range interactions
861	+	* (bonds, bends, torsions) differently from other interactions.
862	+	* We'll still visit the pairwise routines, but with a flag that
863	+	* tells those routines to exclude the pair from direct long range
864	+	* interactions. Some indirect interactions (notably reaction
865	+	* field) must still be handled for these pairs.
866	+	*/
867	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
868	+
869	+	// excludesForAtom was constructed to use row/column indices in the MPI
870	+	// version, and to use local IDs in the non-MPI version:
871
872	<	for (vector<int>::iterator i = skipsForAtom[atom1].begin();
873	<	i != skipsForAtom[atom1].end(); ++i) {
874	<	if ( (*i) == unique_id_2 ) return true;
872	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
873	>	i != excludesForAtom[atom1].end(); ++i) {
874	>	if ( (*i) == atom2 ) return true;
875		}
876
877		return false;
#	Line 779 \| Line 896 \| namespace OpenMD {
896
897		// filling interaction blocks with pointers
898		void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
899	<	int atom1, int atom2) {
899	>	int atom1, int atom2) {
900	>
901	>	idat.excluded = excludeAtomPair(atom1, atom2);
902	>
903		#ifdef IS_MPI
904	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
905	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
906	+	// ff_->getAtomType(identsCol[atom2]) );
907
785	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
786	–	ff_->getAtomType(identsCol[atom2]) );
787	–
908		if (storageLayout_ & DataStorage::dslAmat) {
909		idat.A1 = &(atomRowData.aMat[atom1]);
910		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 820 \| Line 940 \| namespace OpenMD {
940		idat.particlePot2 = &(atomColData.particlePot[atom2]);
941		}
942
943	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
944	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
945	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
946	+	}
947	+
948		#else
949
950	<	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
951	<	ff_->getAtomType(idents[atom2]) );
950	>	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
951	>	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
952	>	// ff_->getAtomType(idents[atom2]) );
953
954		if (storageLayout_ & DataStorage::dslAmat) {
955		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 860 \| Line 986 \| namespace OpenMD {
986		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
987		}
988
989	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
990	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
991	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
992	+	}
993		#endif
994		}
995
#	Line 877 \| Line 1007 \| namespace OpenMD {
1007		snap_->atomData.force[atom1] += *(idat.f1);
1008		snap_->atomData.force[atom2] -= *(idat.f1);
1009		#endif
1010	<
1010	>
1011		}
1012
883	–
884	–	void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
885	–	int atom1, int atom2) {
886	–	#ifdef IS_MPI
887	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
888	–	ff_->getAtomType(identsCol[atom2]) );
889	–
890	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
891	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
892	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
893	–	}
894	–
895	–	if (storageLayout_ & DataStorage::dslTorque) {
896	–	idat.t1 = &(atomRowData.torque[atom1]);
897	–	idat.t2 = &(atomColData.torque[atom2]);
898	–	}
899	–
900	–	if (storageLayout_ & DataStorage::dslSkippedCharge) {
901	–	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
902	–	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
903	–	}
904	–	#else
905	–	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
906	–	ff_->getAtomType(idents[atom2]) );
907	–
908	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
909	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
910	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
911	–	}
912	–
913	–	if (storageLayout_ & DataStorage::dslTorque) {
914	–	idat.t1 = &(snap_->atomData.torque[atom1]);
915	–	idat.t2 = &(snap_->atomData.torque[atom2]);
916	–	}
917	–
918	–	if (storageLayout_ & DataStorage::dslSkippedCharge) {
919	–	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
920	–	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
921	–	}
922	–	#endif
923	–	}
924	–
925	–
926	–	void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {
927	–	#ifdef IS_MPI
928	–	pot_row[atom1] += 0.5 * *(idat.pot);
929	–	pot_col[atom2] += 0.5 * *(idat.pot);
930	–	#else
931	–	pairwisePot += *(idat.pot);
932	–	#endif
933	–
934	–	}
935	–
936	–
1013		/*
1014		* buildNeighborList
1015		*
#	Line 944 \| Line 1020 \| namespace OpenMD {
1020
1021		vector<pair<int, int> > neighborList;
1022		groupCutoffs cuts;
1023	+	bool doAllPairs = false;
1024	+
1025		#ifdef IS_MPI
1026		cellListRow_.clear();
1027		cellListCol_.clear();
#	Line 963 \| Line 1041 \| namespace OpenMD {
1041		nCells_.y() = (int) ( Hy.length() )/ rList_;
1042		nCells_.z() = (int) ( Hz.length() )/ rList_;
1043
1044	+	// handle small boxes where the cell offsets can end up repeating cells
1045	+
1046	+	if (nCells_.x() < 3) doAllPairs = true;
1047	+	if (nCells_.y() < 3) doAllPairs = true;
1048	+	if (nCells_.z() < 3) doAllPairs = true;
1049	+
1050		Mat3x3d invHmat = snap_->getInvHmat();
1051		Vector3d rs, scaled, dr;
1052		Vector3i whichCell;
#	Line 976 \| Line 1060 \| namespace OpenMD {
1060		cellList_.resize(nCtot);
1061		#endif
1062
1063	+	if (!doAllPairs) {
1064		#ifdef IS_MPI
980	–	for (int i = 0; i < nGroupsInRow_; i++) {
981	–	rs = cgRowData.position[i];
1065
1066	<	// scaled positions relative to the box vectors
1067	<	scaled = invHmat * rs;
1068	<
1069	<	// wrap the vector back into the unit box by subtracting integer box
1070	<	// numbers
1071	<	for (int j = 0; j < 3; j++) {
1072	<	scaled[j] -= roundMe(scaled[j]);
1073	<	scaled[j] += 0.5;
1066	>	for (int i = 0; i < nGroupsInRow_; i++) {
1067	>	rs = cgRowData.position[i];
1068	>
1069	>	// scaled positions relative to the box vectors
1070	>	scaled = invHmat * rs;
1071	>
1072	>	// wrap the vector back into the unit box by subtracting integer box
1073	>	// numbers
1074	>	for (int j = 0; j < 3; j++) {
1075	>	scaled[j] -= roundMe(scaled[j]);
1076	>	scaled[j] += 0.5;
1077	>	}
1078	>
1079	>	// find xyz-indices of cell that cutoffGroup is in.
1080	>	whichCell.x() = nCells_.x() * scaled.x();
1081	>	whichCell.y() = nCells_.y() * scaled.y();
1082	>	whichCell.z() = nCells_.z() * scaled.z();
1083	>
1084	>	// find single index of this cell:
1085	>	cellIndex = Vlinear(whichCell, nCells_);
1086	>
1087	>	// add this cutoff group to the list of groups in this cell;
1088	>	cellListRow_[cellIndex].push_back(i);
1089		}
1090	<
1091	<	// find xyz-indices of cell that cutoffGroup is in.
1092	<	whichCell.x() = nCells_.x() * scaled.x();
1093	<	whichCell.y() = nCells_.y() * scaled.y();
1094	<	whichCell.z() = nCells_.z() * scaled.z();
1095	<
1096	<	// find single index of this cell:
1097	<	cellIndex = Vlinear(whichCell, nCells_);
1098	<
1099	<	// add this cutoff group to the list of groups in this cell;
1100	<	cellListRow_[cellIndex].push_back(i);
1101	<	}
1102	<
1103	<	for (int i = 0; i < nGroupsInCol_; i++) {
1104	<	rs = cgColData.position[i];
1105	<
1106	<	// scaled positions relative to the box vectors
1107	<	scaled = invHmat * rs;
1108	<
1109	<	// wrap the vector back into the unit box by subtracting integer box
1110	<	// numbers
1111	<	for (int j = 0; j < 3; j++) {
1112	<	scaled[j] -= roundMe(scaled[j]);
1015	<	scaled[j] += 0.5;
1090	>	for (int i = 0; i < nGroupsInCol_; i++) {
1091	>	rs = cgColData.position[i];
1092	>
1093	>	// scaled positions relative to the box vectors
1094	>	scaled = invHmat * rs;
1095	>
1096	>	// wrap the vector back into the unit box by subtracting integer box
1097	>	// numbers
1098	>	for (int j = 0; j < 3; j++) {
1099	>	scaled[j] -= roundMe(scaled[j]);
1100	>	scaled[j] += 0.5;
1101	>	}
1102	>
1103	>	// find xyz-indices of cell that cutoffGroup is in.
1104	>	whichCell.x() = nCells_.x() * scaled.x();
1105	>	whichCell.y() = nCells_.y() * scaled.y();
1106	>	whichCell.z() = nCells_.z() * scaled.z();
1107	>
1108	>	// find single index of this cell:
1109	>	cellIndex = Vlinear(whichCell, nCells_);
1110	>
1111	>	// add this cutoff group to the list of groups in this cell;
1112	>	cellListCol_[cellIndex].push_back(i);
1113		}
1114	<
1018	<	// find xyz-indices of cell that cutoffGroup is in.
1019	<	whichCell.x() = nCells_.x() * scaled.x();
1020	<	whichCell.y() = nCells_.y() * scaled.y();
1021	<	whichCell.z() = nCells_.z() * scaled.z();
1022	<
1023	<	// find single index of this cell:
1024	<	cellIndex = Vlinear(whichCell, nCells_);
1025	<
1026	<	// add this cutoff group to the list of groups in this cell;
1027	<	cellListCol_[cellIndex].push_back(i);
1028	<	}
1114	>
1115		#else
1116	<	for (int i = 0; i < nGroups_; i++) {
1117	<	rs = snap_->cgData.position[i];
1118	<
1119	<	// scaled positions relative to the box vectors
1120	<	scaled = invHmat * rs;
1121	<
1122	<	// wrap the vector back into the unit box by subtracting integer box
1123	<	// numbers
1124	<	for (int j = 0; j < 3; j++) {
1125	<	scaled[j] -= roundMe(scaled[j]);
1126	<	scaled[j] += 0.5;
1116	>	for (int i = 0; i < nGroups_; i++) {
1117	>	rs = snap_->cgData.position[i];
1118	>
1119	>	// scaled positions relative to the box vectors
1120	>	scaled = invHmat * rs;
1121	>
1122	>	// wrap the vector back into the unit box by subtracting integer box
1123	>	// numbers
1124	>	for (int j = 0; j < 3; j++) {
1125	>	scaled[j] -= roundMe(scaled[j]);
1126	>	scaled[j] += 0.5;
1127	>	}
1128	>
1129	>	// find xyz-indices of cell that cutoffGroup is in.
1130	>	whichCell.x() = nCells_.x() * scaled.x();
1131	>	whichCell.y() = nCells_.y() * scaled.y();
1132	>	whichCell.z() = nCells_.z() * scaled.z();
1133	>
1134	>	// find single index of this cell:
1135	>	cellIndex = Vlinear(whichCell, nCells_);
1136	>
1137	>	// add this cutoff group to the list of groups in this cell;
1138	>	cellList_[cellIndex].push_back(i);
1139		}
1140
1043	–	// find xyz-indices of cell that cutoffGroup is in.
1044	–	whichCell.x() = nCells_.x() * scaled.x();
1045	–	whichCell.y() = nCells_.y() * scaled.y();
1046	–	whichCell.z() = nCells_.z() * scaled.z();
1047	–
1048	–	// find single index of this cell:
1049	–	cellIndex = Vlinear(whichCell, nCells_);
1050	–
1051	–	// add this cutoff group to the list of groups in this cell;
1052	–	cellList_[cellIndex].push_back(i);
1053	–	}
1141		#endif
1142
1143	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1144	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1145	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1146	<	Vector3i m1v(m1x, m1y, m1z);
1147	<	int m1 = Vlinear(m1v, nCells_);
1061	<
1062	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1063	<	os != cellOffsets_.end(); ++os) {
1143	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1144	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1145	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1146	>	Vector3i m1v(m1x, m1y, m1z);
1147	>	int m1 = Vlinear(m1v, nCells_);
1148
1149	<	Vector3i m2v = m1v + (*os);
1150	<
1151	<	if (m2v.x() >= nCells_.x()) {
1152	<	m2v.x() = 0;
1153	<	} else if (m2v.x() < 0) {
1070	<	m2v.x() = nCells_.x() - 1;
1071	<	}
1072	<
1073	<	if (m2v.y() >= nCells_.y()) {
1074	<	m2v.y() = 0;
1075	<	} else if (m2v.y() < 0) {
1076	<	m2v.y() = nCells_.y() - 1;
1077	<	}
1078	<
1079	<	if (m2v.z() >= nCells_.z()) {
1080	<	m2v.z() = 0;
1081	<	} else if (m2v.z() < 0) {
1082	<	m2v.z() = nCells_.z() - 1;
1083	<	}
1084	<
1085	<	int m2 = Vlinear (m2v, nCells_);
1149	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1150	>	os != cellOffsets_.end(); ++os) {
1151	>
1152	>	Vector3i m2v = m1v + (*os);
1153	>
1154
1155	<	#ifdef IS_MPI
1156	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1157	<	j1 != cellListRow_[m1].end(); ++j1) {
1158	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1159	<	j2 != cellListCol_[m2].end(); ++j2) {
1160	<
1161	<	// Always do this if we're in different cells or if
1162	<	// we're in the same cell and the global index of the
1163	<	// j2 cutoff group is less than the j1 cutoff group
1155	>	if (m2v.x() >= nCells_.x()) {
1156	>	m2v.x() = 0;
1157	>	} else if (m2v.x() < 0) {
1158	>	m2v.x() = nCells_.x() - 1;
1159	>	}
1160	>
1161	>	if (m2v.y() >= nCells_.y()) {
1162	>	m2v.y() = 0;
1163	>	} else if (m2v.y() < 0) {
1164	>	m2v.y() = nCells_.y() - 1;
1165	>	}
1166	>
1167	>	if (m2v.z() >= nCells_.z()) {
1168	>	m2v.z() = 0;
1169	>	} else if (m2v.z() < 0) {
1170	>	m2v.z() = nCells_.z() - 1;
1171	>	}
1172
1173	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1173	>	int m2 = Vlinear (m2v, nCells_);
1174	>
1175	>	#ifdef IS_MPI
1176	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1177	>	j1 != cellListRow_[m1].end(); ++j1) {
1178	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1179	>	j2 != cellListCol_[m2].end(); ++j2) {
1180	>
1181	>	// In parallel, we need to visit all pairs of row
1182	>	// & column indicies and will divide labor in the
1183	>	// force evaluation later.
1184		dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1185		snap_->wrapVector(dr);
1186		cuts = getGroupCutoffs( (j1), (j2) );
1187		if (dr.lengthSquare() < cuts.third) {
1188		neighborList.push_back(make_pair((j1), (j2)));
1189	<	}
1189	>	}
1190		}
1191		}
1106	–	}
1192		#else
1193	<
1194	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1195	<	j1 != cellList_[m1].end(); ++j1) {
1196	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1197	<	j2 != cellList_[m2].end(); ++j2) {
1198	<
1199	<	// Always do this if we're in different cells or if
1200	<	// we're in the same cell and the global index of the
1201	<	// j2 cutoff group is less than the j1 cutoff group
1202	<
1203	<	if (m2 != m1 \|\| (j2) < (j1)) {
1204	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1205	<	snap_->wrapVector(dr);
1206	<	cuts = getGroupCutoffs( (j1), (j2) );
1207	<	if (dr.lengthSquare() < cuts.third) {
1208	<	neighborList.push_back(make_pair((j1), (j2)));
1193	>
1194	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1195	>	j1 != cellList_[m1].end(); ++j1) {
1196	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1197	>	j2 != cellList_[m2].end(); ++j2) {
1198	>
1199	>	// Always do this if we're in different cells or if
1200	>	// we're in the same cell and the global index of the
1201	>	// j2 cutoff group is less than the j1 cutoff group
1202	>
1203	>	if (m2 != m1 \|\| (j2) < (j1)) {
1204	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1205	>	snap_->wrapVector(dr);
1206	>	cuts = getGroupCutoffs( (j1), (j2) );
1207	>	if (dr.lengthSquare() < cuts.third) {
1208	>	neighborList.push_back(make_pair((j1), (j2)));
1209	>	}
1210		}
1211		}
1212		}
1127	–	}
1213		#endif
1214	+	}
1215		}
1216		}
1217		}
1218	+	} else {
1219	+	// branch to do all cutoff group pairs
1220	+	#ifdef IS_MPI
1221	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1222	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1223	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1224	+	snap_->wrapVector(dr);
1225	+	cuts = getGroupCutoffs( j1, j2 );
1226	+	if (dr.lengthSquare() < cuts.third) {
1227	+	neighborList.push_back(make_pair(j1, j2));
1228	+	}
1229	+	}
1230	+	}
1231	+	#else
1232	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1233	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1234	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1235	+	snap_->wrapVector(dr);
1236	+	cuts = getGroupCutoffs( j1, j2 );
1237	+	if (dr.lengthSquare() < cuts.third) {
1238	+	neighborList.push_back(make_pair(j1, j2));
1239	+	}
1240	+	}
1241	+	}
1242	+	#endif
1243		}
1244	<
1244	>
1245		// save the local cutoff group positions for the check that is
1246		// done on each loop:
1247		saved_CG_positions_.clear();
1248		for (int i = 0; i < nGroups_; i++)
1249		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1250	<
1250	>
1251		return neighborList;
1252		}
1253		} //end namespace OpenMD

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC vs. Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC vs.
Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC