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root/OpenMD/branches/development/src/parallel/ForceMatrixDecomposition.cpp

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1586 by gezelter, Tue Jun 21 06:34:35 2011 UTC vs.
Revision 1849 by gezelter, Wed Feb 20 13:52:51 2013 UTC

#	Line 36 | Line 36
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
#	Line 47 | Line 48 | namespace OpenMD {
48		using namespace std;
49		namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	+
53	+	// In a parallel computation, row and colum scans must visit all
54	+	// surrounding cells (not just the 14 upper triangular blocks that
55	+	// are used when the processor can see all pairs)
56	+	#ifdef IS_MPI
57	+	cellOffsets_.clear();
58	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
66	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	+	#endif
86	+	}
87	+
88	+
89		/**
90		* distributeInitialData is essentially a copy of the older fortran
91		* SimulationSetup
92		*/
54	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96		ff_ = info_->getForceField();
97		nLocal_ = snap_->getNumberOfAtoms();
98	<
98	>
99		nGroups_ = info_->getNLocalCutoffGroups();
100		// gather the information for atomtype IDs (atids):
101		idents = info_->getIdentArray();
#	Line 67 | Line 105 | namespace OpenMD {
105
106		massFactors = info_->getMassFactors();
107
108	<	PairList excludes = info_->getExcludedInteractions();
109	<	PairList oneTwo = info_->getOneTwoInteractions();
110	<	PairList oneThree = info_->getOneThreeInteractions();
111	<	PairList oneFour = info_->getOneFourInteractions();
112	<
108	>	PairList* excludes = info_->getExcludedInteractions();
109	>	PairList* oneTwo = info_->getOneTwoInteractions();
110	>	PairList* oneThree = info_->getOneThreeInteractions();
111	>	PairList* oneFour = info_->getOneFourInteractions();
112	>
113	>	if (needVelocities_)
114	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
115	>	DataStorage::dslVelocity);
116	>	else
117	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118	>
119		#ifdef IS_MPI
120
121	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
122	<	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_);
121	>	MPI::Intracomm row = rowComm.getComm();
122	>	MPI::Intracomm col = colComm.getComm();
123
124	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
125	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
126	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
127	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
128	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
124	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
125	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
126	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
127	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
128	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
129
130	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
131	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
132	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
133	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
130	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
131	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
132	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
133	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
134	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
135
136	<	nAtomsInRow_ = AtomCommIntRow->getSize();
137	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
138	<	nGroupsInRow_ = cgCommIntRow->getSize();
139	<	nGroupsInCol_ = cgCommIntColumn->getSize();
136	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
137	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
138	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
139	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
140
141	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
142	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
143	+	nGroupsInRow_ = cgPlanIntRow->getSize();
144	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
145	+
146		// Modify the data storage objects with the correct layouts and sizes:
147		atomRowData.resize(nAtomsInRow_);
148		atomRowData.setStorageLayout(storageLayout_);
#	Line 104 | Line 151 | namespace OpenMD {
151		cgRowData.resize(nGroupsInRow_);
152		cgRowData.setStorageLayout(DataStorage::dslPosition);
153		cgColData.resize(nGroupsInCol_);
154	<	cgColData.setStorageLayout(DataStorage::dslPosition);
155	<
154	>	if (needVelocities_)
155	>	// we only need column velocities if we need them.
156	>	cgColData.setStorageLayout(DataStorage::dslPosition |
157	>	DataStorage::dslVelocity);
158	>	else
159	>	cgColData.setStorageLayout(DataStorage::dslPosition);
160	>
161		identsRow.resize(nAtomsInRow_);
162		identsCol.resize(nAtomsInCol_);
163
164	<	AtomCommIntRow->gather(idents, identsRow);
165	<	AtomCommIntColumn->gather(idents, identsCol);
164	>	AtomPlanIntRow->gather(idents, identsRow);
165	>	AtomPlanIntColumn->gather(idents, identsCol);
166
167	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
168	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
169	<
118	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
167	>	// allocate memory for the parallel objects
168	>	atypesRow.resize(nAtomsInRow_);
169	>	atypesCol.resize(nAtomsInCol_);
170
171	<	AtomCommRealRow->gather(massFactors, massFactorsRow);
172	<	AtomCommRealColumn->gather(massFactors, massFactorsCol);
171	>	for (int i = 0; i < nAtomsInRow_; i++)
172	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
173	>	for (int i = 0; i < nAtomsInCol_; i++)
174	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
175
176	+	pot_row.resize(nAtomsInRow_);
177	+	pot_col.resize(nAtomsInCol_);
178	+
179	+	expot_row.resize(nAtomsInRow_);
180	+	expot_col.resize(nAtomsInCol_);
181	+
182	+	AtomRowToGlobal.resize(nAtomsInRow_);
183	+	AtomColToGlobal.resize(nAtomsInCol_);
184	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
185	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
186	+
187	+	cgRowToGlobal.resize(nGroupsInRow_);
188	+	cgColToGlobal.resize(nGroupsInCol_);
189	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
190	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
191	+
192	+	massFactorsRow.resize(nAtomsInRow_);
193	+	massFactorsCol.resize(nAtomsInCol_);
194	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
195	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
196	+
197		groupListRow_.clear();
198		groupListRow_.resize(nGroupsInRow_);
199		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 143 | Line 216 | namespace OpenMD {
216		}
217		}
218
219	<	skipsForAtom.clear();
220	<	skipsForAtom.resize(nAtomsInRow_);
219	>	excludesForAtom.clear();
220	>	excludesForAtom.resize(nAtomsInRow_);
221		toposForAtom.clear();
222		toposForAtom.resize(nAtomsInRow_);
223		topoDist.clear();
#	Line 155 | Line 228 | namespace OpenMD {
228		for (int j = 0; j < nAtomsInCol_; j++) {
229		int jglob = AtomColToGlobal[j];
230
231	<	if (excludes.hasPair(iglob, jglob))
232	<	skipsForAtom[i].push_back(j);
231	>	if (excludes->hasPair(iglob, jglob))
232	>	excludesForAtom[i].push_back(j);
233
234	<	if (oneTwo.hasPair(iglob, jglob)) {
234	>	if (oneTwo->hasPair(iglob, jglob)) {
235		toposForAtom[i].push_back(j);
236		topoDist[i].push_back(1);
237		} else {
238	<	if (oneThree.hasPair(iglob, jglob)) {
238	>	if (oneThree->hasPair(iglob, jglob)) {
239		toposForAtom[i].push_back(j);
240		topoDist[i].push_back(2);
241		} else {
242	<	if (oneFour.hasPair(iglob, jglob)) {
242	>	if (oneFour->hasPair(iglob, jglob)) {
243		toposForAtom[i].push_back(j);
244		topoDist[i].push_back(3);
245		}
#	Line 175 | Line 248 | namespace OpenMD {
248		}
249		}
250
251	<	#endif
252	<
253	<	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_);
251	>	#else
252	>	excludesForAtom.clear();
253	>	excludesForAtom.resize(nLocal_);
254		toposForAtom.clear();
255		toposForAtom.resize(nLocal_);
256		topoDist.clear();
#	Line 202 | Line 262 | namespace OpenMD {
262		for (int j = 0; j < nLocal_; j++) {
263		int jglob = AtomLocalToGlobal[j];
264
265	<	if (excludes.hasPair(iglob, jglob))
266	<	skipsForAtom[i].push_back(j);
265	>	if (excludes->hasPair(iglob, jglob))
266	>	excludesForAtom[i].push_back(j);
267
268	<	if (oneTwo.hasPair(iglob, jglob)) {
268	>	if (oneTwo->hasPair(iglob, jglob)) {
269		toposForAtom[i].push_back(j);
270		topoDist[i].push_back(1);
271		} else {
272	<	if (oneThree.hasPair(iglob, jglob)) {
272	>	if (oneThree->hasPair(iglob, jglob)) {
273		toposForAtom[i].push_back(j);
274		topoDist[i].push_back(2);
275		} else {
276	<	if (oneFour.hasPair(iglob, jglob)) {
276	>	if (oneFour->hasPair(iglob, jglob)) {
277		toposForAtom[i].push_back(j);
278		topoDist[i].push_back(3);
279		}
#	Line 221 | Line 281 | namespace OpenMD {
281		}
282		}
283		}
284	<
284	>	#endif
285	>
286	>	// allocate memory for the parallel objects
287	>	atypesLocal.resize(nLocal_);
288	>
289	>	for (int i = 0; i < nLocal_; i++)
290	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
291	>
292	>	groupList_.clear();
293	>	groupList_.resize(nGroups_);
294	>	for (int i = 0; i < nGroups_; i++) {
295	>	int gid = cgLocalToGlobal[i];
296	>	for (int j = 0; j < nLocal_; j++) {
297	>	int aid = AtomLocalToGlobal[j];
298	>	if (globalGroupMembership[aid] == gid) {
299	>	groupList_[i].push_back(j);
300	>	}
301	>	}
302	>	}
303	>
304	>
305		createGtypeCutoffMap();
306	+
307		}
308
309		void ForceMatrixDecomposition::createGtypeCutoffMap() {
310
311		RealType tol = 1e-6;
312	<	RealType rc;
312	>	largestRcut_ = 0.0;
313		int atid;
314		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315	<	vector<RealType> atypeCutoff;
316	<	atypeCutoff.resize( atypes.size() );
315	>
316	>	map<int, RealType> atypeCutoff;
317
318		for (set<AtomType*>::iterator at = atypes.begin();
319		at != atypes.end(); ++at){
320		atid = (*at)->getIdent();
321	<
241	<	if (userChoseCutoff_)
321	>	if (userChoseCutoff_)
322		atypeCutoff[atid] = userCutoff_;
323		else
324		atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
325		}
326	<
326	>
327		vector<RealType> gTypeCutoffs;
248	–
328		// first we do a single loop over the cutoff groups to find the
329		// largest cutoff for any atypes present in this group.
330		#ifdef IS_MPI
#	Line 303 | Line 382 | namespace OpenMD {
382
383		vector<RealType> groupCutoff(nGroups_, 0.0);
384		groupToGtype.resize(nGroups_);
306	–
385		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
308	–
386		groupCutoff[cg1] = 0.0;
387		vector<int> atomList = getAtomsInGroupRow(cg1);
311	–
388		for (vector<int>::iterator ia = atomList.begin();
389		ia != atomList.end(); ++ia) {
390		int atom1 = (*ia);
391		atid = idents[atom1];
392	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
392	>	if (atypeCutoff[atid] > groupCutoff[cg1])
393		groupCutoff[cg1] = atypeCutoff[atid];
318	–	}
394		}
395	<
395	>
396		bool gTypeFound = false;
397	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
397	>	for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
398		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
399		groupToGtype[cg1] = gt;
400		gTypeFound = true;
401		}
402		}
403	<	if (!gTypeFound) {
403	>	if (!gTypeFound) {
404		gTypeCutoffs.push_back( groupCutoff[cg1] );
405		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
406		}
#	Line 334 | Line 409 | namespace OpenMD {
409
410		// Now we find the maximum group cutoff value present in the simulation
411
412	<	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
412	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
413	>	gTypeCutoffs.end());
414
415		#ifdef IS_MPI
416	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
416	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
417	>	MPI::MAX);
418		#endif
419
420		RealType tradRcut = groupMax;
421
422	<	for (int i = 0; i < gTypeCutoffs.size();  i++) {
423	<	for (int j = 0; j < gTypeCutoffs.size();  j++) {
422	>	for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
423	>	for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {
424		RealType thisRcut;
425		switch(cutoffPolicy_) {
426		case TRADITIONAL:
#	Line 367 | Line 444 | namespace OpenMD {
444
445		pair<int,int> key = make_pair(i,j);
446		gTypeCutoffMap[key].first = thisRcut;
370	–
447		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
372	–
448		gTypeCutoffMap[key].second = thisRcut*thisRcut;
374	–
449		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
376	–
450		// sanity check
451
452		if (userChoseCutoff_) {
#	Line 390 | Line 463 | namespace OpenMD {
463		}
464		}
465
393	–
466		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467		int i, j;
468		#ifdef IS_MPI
#	Line 404 | Line 476 | namespace OpenMD {
476		}
477
478		int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
479	<	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
479	>	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
480		if (toposForAtom[atom1][j] == atom2)
481		return topoDist[atom1][j];
482		}
#	Line 414 | Line 486 | namespace OpenMD {
486		void ForceMatrixDecomposition::zeroWorkArrays() {
487		pairwisePot = 0.0;
488		embeddingPot = 0.0;
489	+	excludedPot = 0.0;
490	+	excludedSelfPot = 0.0;
491
492		#ifdef IS_MPI
493		if (storageLayout_ & DataStorage::dslForce) {
#	Line 432 | Line 506 | namespace OpenMD {
506		fill(pot_col.begin(), pot_col.end(),
507		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
508
509	+	fill(expot_row.begin(), expot_row.end(),
510	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
511	+
512	+	fill(expot_col.begin(), expot_col.end(),
513	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
514	+
515		if (storageLayout_ & DataStorage::dslParticlePot) {
516	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
517	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
516	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
517	>	0.0);
518	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
519	>	0.0);
520		}
521
522		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 443 | Line 525 | namespace OpenMD {
525		}
526
527		if (storageLayout_ & DataStorage::dslFunctional) {
528	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
529	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
528	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
529	>	0.0);
530	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
531	>	0.0);
532		}
533
534		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 455 | Line 539 | namespace OpenMD {
539		}
540
541		if (storageLayout_ & DataStorage::dslSkippedCharge) {
542	<	fill(atomRowData.skippedCharge.begin(), atomRowData.skippedCharge.end(), 0.0);
543	<	fill(atomColData.skippedCharge.begin(), atomColData.skippedCharge.end(), 0.0);
542	>	fill(atomRowData.skippedCharge.begin(),
543	>	atomRowData.skippedCharge.end(), 0.0);
544	>	fill(atomColData.skippedCharge.begin(),
545	>	atomColData.skippedCharge.end(), 0.0);
546		}
547
548	<	#else
549	<
548	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
549	>	fill(atomRowData.flucQFrc.begin(),
550	>	atomRowData.flucQFrc.end(), 0.0);
551	>	fill(atomColData.flucQFrc.begin(),
552	>	atomColData.flucQFrc.end(), 0.0);
553	>	}
554	>
555	>	if (storageLayout_ & DataStorage::dslElectricField) {
556	>	fill(atomRowData.electricField.begin(),
557	>	atomRowData.electricField.end(), V3Zero);
558	>	fill(atomColData.electricField.begin(),
559	>	atomColData.electricField.end(), V3Zero);
560	>	}
561	>
562	>	#endif
563	>	// even in parallel, we need to zero out the local arrays:
564	>
565		if (storageLayout_ & DataStorage::dslParticlePot) {
566		fill(snap_->atomData.particlePot.begin(),
567		snap_->atomData.particlePot.end(), 0.0);
#	Line 470 | Line 571 | namespace OpenMD {
571		fill(snap_->atomData.density.begin(),
572		snap_->atomData.density.end(), 0.0);
573		}
574	+
575		if (storageLayout_ & DataStorage::dslFunctional) {
576		fill(snap_->atomData.functional.begin(),
577		snap_->atomData.functional.end(), 0.0);
578		}
579	+
580		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
581		fill(snap_->atomData.functionalDerivative.begin(),
582		snap_->atomData.functionalDerivative.end(), 0.0);
583		}
584	+
585		if (storageLayout_ & DataStorage::dslSkippedCharge) {
586		fill(snap_->atomData.skippedCharge.begin(),
587		snap_->atomData.skippedCharge.end(), 0.0);
588		}
589	<	#endif
590	<
589	>
590	>	if (storageLayout_ & DataStorage::dslElectricField) {
591	>	fill(snap_->atomData.electricField.begin(),
592	>	snap_->atomData.electricField.end(), V3Zero);
593	>	}
594		}
595
596
#	Line 493 | Line 600 | namespace OpenMD {
600		#ifdef IS_MPI
601
602		// gather up the atomic positions
603	<	AtomCommVectorRow->gather(snap_->atomData.position,
603	>	AtomPlanVectorRow->gather(snap_->atomData.position,
604		atomRowData.position);
605	<	AtomCommVectorColumn->gather(snap_->atomData.position,
605	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
606		atomColData.position);
607
608		// gather up the cutoff group positions
609	<	cgCommVectorRow->gather(snap_->cgData.position,
609	>
610	>	cgPlanVectorRow->gather(snap_->cgData.position,
611		cgRowData.position);
612	<	cgCommVectorColumn->gather(snap_->cgData.position,
612	>
613	>	cgPlanVectorColumn->gather(snap_->cgData.position,
614		cgColData.position);
615	+
616	+
617	+
618	+	if (needVelocities_) {
619	+	// gather up the atomic velocities
620	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
621	+	atomColData.velocity);
622	+
623	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
624	+	cgColData.velocity);
625	+	}
626	+
627
628		// if needed, gather the atomic rotation matrices
629		if (storageLayout_ & DataStorage::dslAmat) {
630	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
630	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
631		atomRowData.aMat);
632	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
632	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
633		atomColData.aMat);
634		}
635	<
636	<	// if needed, gather the atomic eletrostatic frames
637	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
638	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
639	<	atomRowData.electroFrame);
640	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
641	<	atomColData.electroFrame);
635	>
636	>	// if needed, gather the atomic eletrostatic information
637	>	if (storageLayout_ & DataStorage::dslDipole) {
638	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
639	>	atomRowData.dipole);
640	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
641	>	atomColData.dipole);
642		}
643	+
644	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
645	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
646	+	atomRowData.quadrupole);
647	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
648	+	atomColData.quadrupole);
649	+	}
650	+
651	+	// if needed, gather the atomic fluctuating charge values
652	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
653	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
654	+	atomRowData.flucQPos);
655	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
656	+	atomColData.flucQPos);
657	+	}
658	+
659		#endif
660		}
661
#	Line 532 | Line 669 | namespace OpenMD {
669
670		if (storageLayout_ & DataStorage::dslDensity) {
671
672	<	AtomCommRealRow->scatter(atomRowData.density,
672	>	AtomPlanRealRow->scatter(atomRowData.density,
673		snap_->atomData.density);
674
675		int n = snap_->atomData.density.size();
676		vector<RealType> rho_tmp(n, 0.0);
677	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
677	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
678		for (int i = 0; i < n; i++)
679		snap_->atomData.density[i] += rho_tmp[i];
680		}
681	+
682	+	// this isn't necessary if we don't have polarizable atoms, but
683	+	// we'll leave it here for now.
684	+	if (storageLayout_ & DataStorage::dslElectricField) {
685	+
686	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
687	+	snap_->atomData.electricField);
688	+
689	+	int n = snap_->atomData.electricField.size();
690	+	vector<Vector3d> field_tmp(n, V3Zero);
691	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
692	+	field_tmp);
693	+	for (int i = 0; i < n; i++)
694	+	snap_->atomData.electricField[i] += field_tmp[i];
695	+	}
696		#endif
697		}
698
#	Line 553 | Line 705 | namespace OpenMD {
705		storageLayout_ = sman_->getStorageLayout();
706		#ifdef IS_MPI
707		if (storageLayout_ & DataStorage::dslFunctional) {
708	<	AtomCommRealRow->gather(snap_->atomData.functional,
708	>	AtomPlanRealRow->gather(snap_->atomData.functional,
709		atomRowData.functional);
710	<	AtomCommRealColumn->gather(snap_->atomData.functional,
710	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
711		atomColData.functional);
712		}
713
714		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
715	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
715	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
716		atomRowData.functionalDerivative);
717	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
717	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
718		atomColData.functionalDerivative);
719		}
720		#endif
#	Line 576 | Line 728 | namespace OpenMD {
728		int n = snap_->atomData.force.size();
729		vector<Vector3d> frc_tmp(n, V3Zero);
730
731	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
731	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
732		for (int i = 0; i < n; i++) {
733		snap_->atomData.force[i] += frc_tmp[i];
734		frc_tmp[i] = 0.0;
735		}
736
737	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
738	<	for (int i = 0; i < n; i++)
737	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
738	>	for (int i = 0; i < n; i++) {
739		snap_->atomData.force[i] += frc_tmp[i];
740	<
741	<
740	>	}
741	>
742		if (storageLayout_ & DataStorage::dslTorque) {
743
744	<	int nt = snap_->atomData.force.size();
744	>	int nt = snap_->atomData.torque.size();
745		vector<Vector3d> trq_tmp(nt, V3Zero);
746
747	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
748	<	for (int i = 0; i < n; i++) {
747	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
748	>	for (int i = 0; i < nt; i++) {
749		snap_->atomData.torque[i] += trq_tmp[i];
750		trq_tmp[i] = 0.0;
751		}
752
753	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
754	<	for (int i = 0; i < n; i++)
753	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
754	>	for (int i = 0; i < nt; i++)
755		snap_->atomData.torque[i] += trq_tmp[i];
756		}
757	+
758	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
759	+
760	+	int ns = snap_->atomData.skippedCharge.size();
761	+	vector<RealType> skch_tmp(ns, 0.0);
762	+
763	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
764	+	for (int i = 0; i < ns; i++) {
765	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
766	+	skch_tmp[i] = 0.0;
767	+	}
768	+
769	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
770	+	for (int i = 0; i < ns; i++)
771	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
772	+
773	+	}
774
775	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
776	+
777	+	int nq = snap_->atomData.flucQFrc.size();
778	+	vector<RealType> fqfrc_tmp(nq, 0.0);
779	+
780	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
781	+	for (int i = 0; i < nq; i++) {
782	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
783	+	fqfrc_tmp[i] = 0.0;
784	+	}
785	+
786	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
787	+	for (int i = 0; i < nq; i++)
788	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
789	+
790	+	}
791	+
792	+	if (storageLayout_ & DataStorage::dslElectricField) {
793	+
794	+	int nef = snap_->atomData.electricField.size();
795	+	vector<Vector3d> efield_tmp(nef, V3Zero);
796	+
797	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
798	+	for (int i = 0; i < nef; i++) {
799	+	snap_->atomData.electricField[i] += efield_tmp[i];
800	+	efield_tmp[i] = 0.0;
801	+	}
802	+
803	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
804	+	for (int i = 0; i < nef; i++)
805	+	snap_->atomData.electricField[i] += efield_tmp[i];
806	+	}
807	+
808	+
809		nLocal_ = snap_->getNumberOfAtoms();
810
811		vector<potVec> pot_temp(nLocal_,
812		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
813	+	vector<potVec> expot_temp(nLocal_,
814	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
815
816		// scatter/gather pot_row into the members of my column
817
818	<	AtomCommPotRow->scatter(pot_row, pot_temp);
818	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
819	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
820
821	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
821	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
822		pairwisePot += pot_temp[ii];
823	<
823	>
824	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
825	>	excludedPot += expot_temp[ii];
826	>
827	>	if (storageLayout_ & DataStorage::dslParticlePot) {
828	>	// This is the pairwise contribution to the particle pot.  The
829	>	// embedding contribution is added in each of the low level
830	>	// non-bonded routines.  In single processor, this is done in
831	>	// unpackInteractionData, not in collectData.
832	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
833	>	for (int i = 0; i < nLocal_; i++) {
834	>	// factor of two is because the total potential terms are divided
835	>	// by 2 in parallel due to row/ column scatter
836	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
837	>	}
838	>	}
839	>	}
840	>
841		fill(pot_temp.begin(), pot_temp.end(),
842		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
843	+	fill(expot_temp.begin(), expot_temp.end(),
844	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
845
846	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
846	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
847	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
848
849		for (int ii = 0;  ii < pot_temp.size(); ii++ )
850		pairwisePot += pot_temp[ii];
851	+
852	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
853	+	excludedPot += expot_temp[ii];
854	+
855	+	if (storageLayout_ & DataStorage::dslParticlePot) {
856	+	// This is the pairwise contribution to the particle pot.  The
857	+	// embedding contribution is added in each of the low level
858	+	// non-bonded routines.  In single processor, this is done in
859	+	// unpackInteractionData, not in collectData.
860	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
861	+	for (int i = 0; i < nLocal_; i++) {
862	+	// factor of two is because the total potential terms are divided
863	+	// by 2 in parallel due to row/ column scatter
864	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
865	+	}
866	+	}
867	+	}
868	+
869	+	if (storageLayout_ & DataStorage::dslParticlePot) {
870	+	int npp = snap_->atomData.particlePot.size();
871	+	vector<RealType> ppot_temp(npp, 0.0);
872	+
873	+	// This is the direct or embedding contribution to the particle
874	+	// pot.
875	+
876	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
877	+	for (int i = 0; i < npp; i++) {
878	+	snap_->atomData.particlePot[i] += ppot_temp[i];
879	+	}
880	+
881	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
882	+
883	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
884	+	for (int i = 0; i < npp; i++) {
885	+	snap_->atomData.particlePot[i] += ppot_temp[i];
886	+	}
887	+	}
888	+
889	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
890	+	RealType ploc1 = pairwisePot[ii];
891	+	RealType ploc2 = 0.0;
892	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
893	+	pairwisePot[ii] = ploc2;
894	+	}
895	+
896	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
897	+	RealType ploc1 = excludedPot[ii];
898	+	RealType ploc2 = 0.0;
899	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
900	+	excludedPot[ii] = ploc2;
901	+	}
902	+
903	+	// Here be dragons.
904	+	MPI::Intracomm col = colComm.getComm();
905	+
906	+	col.Allreduce(MPI::IN_PLACE,
907	+	&snap_->frameData.conductiveHeatFlux[0], 3,
908	+	MPI::REALTYPE, MPI::SUM);
909	+
910	+
911		#endif
912
913	+	}
914	+
915	+	/**
916	+	* Collects information obtained during the post-pair (and embedding
917	+	* functional) loops onto local data structures.
918	+	*/
919	+	void ForceMatrixDecomposition::collectSelfData() {
920	+	snap_ = sman_->getCurrentSnapshot();
921	+	storageLayout_ = sman_->getStorageLayout();
922	+
923	+	#ifdef IS_MPI
924	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
925	+	RealType ploc1 = embeddingPot[ii];
926	+	RealType ploc2 = 0.0;
927	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
928	+	embeddingPot[ii] = ploc2;
929	+	}
930	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
931	+	RealType ploc1 = excludedSelfPot[ii];
932	+	RealType ploc2 = 0.0;
933	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
934	+	excludedSelfPot[ii] = ploc2;
935	+	}
936	+	#endif
937	+
938		}
939
940	+
941	+
942		int ForceMatrixDecomposition::getNAtomsInRow() {
943		#ifdef IS_MPI
944		return nAtomsInRow_;
#	Line 666 | Line 979 | namespace OpenMD {
979		return d;
980		}
981
982	+	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
983	+	#ifdef IS_MPI
984	+	return cgColData.velocity[cg2];
985	+	#else
986	+	return snap_->cgData.velocity[cg2];
987	+	#endif
988	+	}
989
990	+	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
991	+	#ifdef IS_MPI
992	+	return atomColData.velocity[atom2];
993	+	#else
994	+	return snap_->atomData.velocity[atom2];
995	+	#endif
996	+	}
997	+
998	+
999		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
1000
1001		Vector3d d;
#	Line 724 | Line 1053 | namespace OpenMD {
1053		return d;
1054		}
1055
1056	<	vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
1057	<	return skipsForAtom[atom1];
1056	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1057	>	return excludesForAtom[atom1];
1058		}
1059
1060		/**
1061	<	* There are a number of reasons to skip a pair or a
733	<	* particle. Mostly we do this to exclude atoms who are involved in
734	<	* short range interactions (bonds, bends, torsions), but we also
735	<	* need to exclude some overcounted interactions that result from
1061	>	* We need to exclude some overcounted interactions that result from
1062		* the parallel decomposition.
1063		*/
1064	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1064	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1065		int unique_id_1, unique_id_2;
1066	<
1066	>
1067		#ifdef IS_MPI
1068		// in MPI, we have to look up the unique IDs for each atom
1069		unique_id_1 = AtomRowToGlobal[atom1];
1070		unique_id_2 = AtomColToGlobal[atom2];
1071	+	// group1 = cgRowToGlobal[cg1];
1072	+	// group2 = cgColToGlobal[cg2];
1073	+	#else
1074	+	unique_id_1 = AtomLocalToGlobal[atom1];
1075	+	unique_id_2 = AtomLocalToGlobal[atom2];
1076	+	int group1 = cgLocalToGlobal[cg1];
1077	+	int group2 = cgLocalToGlobal[cg2];
1078	+	#endif
1079
746	–	// this situation should only arise in MPI simulations
1080		if (unique_id_1 == unique_id_2) return true;
1081	<
1081	>
1082	>	#ifdef IS_MPI
1083		// this prevents us from doing the pair on multiple processors
1084		if (unique_id_1 < unique_id_2) {
1085		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1086		} else {
1087	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1087	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1088		}
1089	<	#else
1090	<	// in the normal loop, the atom numbers are unique
1091	<	unique_id_1 = atom1;
1092	<	unique_id_2 = atom2;
1089	>	#endif
1090	>
1091	>	#ifndef IS_MPI
1092	>	if (group1 == group2) {
1093	>	if (unique_id_1 < unique_id_2) return true;
1094	>	}
1095		#endif
1096
1097	<	for (vector<int>::iterator i = skipsForAtom[atom1].begin();
1098	<	i != skipsForAtom[atom1].end(); ++i) {
1099	<	if ( (*i) == unique_id_2 ) return true;
1097	>	return false;
1098	>	}
1099	>
1100	>	/**
1101	>	* We need to handle the interactions for atoms who are involved in
1102	>	* the same rigid body as well as some short range interactions
1103	>	* (bonds, bends, torsions) differently from other interactions.
1104	>	* We'll still visit the pairwise routines, but with a flag that
1105	>	* tells those routines to exclude the pair from direct long range
1106	>	* interactions.  Some indirect interactions (notably reaction
1107	>	* field) must still be handled for these pairs.
1108	>	*/
1109	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1110	>
1111	>	// excludesForAtom was constructed to use row/column indices in the MPI
1112	>	// version, and to use local IDs in the non-MPI version:
1113	>
1114	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1115	>	i != excludesForAtom[atom1].end(); ++i) {
1116	>	if ( (*i) == atom2 ) return true;
1117		}
1118
1119		return false;
#	Line 785 | Line 1138 | namespace OpenMD {
1138
1139		// filling interaction blocks with pointers
1140		void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1141	<	int atom1, int atom2) {
1141	>	int atom1, int atom2) {
1142	>
1143	>	idat.excluded = excludeAtomPair(atom1, atom2);
1144	>
1145		#ifdef IS_MPI
1146	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1147	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1148	+	//                         ff_->getAtomType(identsCol[atom2]) );
1149
791	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
792	–	ff_->getAtomType(identsCol[atom2]) );
793	–
1150		if (storageLayout_ & DataStorage::dslAmat) {
1151		idat.A1 = &(atomRowData.aMat[atom1]);
1152		idat.A2 = &(atomColData.aMat[atom2]);
1153		}
1154
799	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
800	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
801	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
802	–	}
803	–
1155		if (storageLayout_ & DataStorage::dslTorque) {
1156		idat.t1 = &(atomRowData.torque[atom1]);
1157		idat.t2 = &(atomColData.torque[atom2]);
1158		}
1159
1160	+	if (storageLayout_ & DataStorage::dslDipole) {
1161	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1162	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1163	+	}
1164	+
1165	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1166	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1167	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1168	+	}
1169	+
1170		if (storageLayout_ & DataStorage::dslDensity) {
1171		idat.rho1 = &(atomRowData.density[atom1]);
1172		idat.rho2 = &(atomColData.density[atom2]);
#	Line 826 | Line 1187 | namespace OpenMD {
1187		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1188		}
1189
1190	<	#else
1190	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1191	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1192	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1193	>	}
1194
1195	<	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1196	<	ff_->getAtomType(idents[atom2]) );
1195	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1196	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1197	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1198	>	}
1199
1200	+	#else
1201	+
1202	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1203	+
1204		if (storageLayout_ & DataStorage::dslAmat) {
1205		idat.A1 = &(snap_->atomData.aMat[atom1]);
1206		idat.A2 = &(snap_->atomData.aMat[atom2]);
1207		}
1208
1209	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
840	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
841	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
842	<	}
1209	>	RealType ct = dot(idat.A1->getColumn(2), idat.A2->getColumn(2));
1210
1211		if (storageLayout_ & DataStorage::dslTorque) {
1212		idat.t1 = &(snap_->atomData.torque[atom1]);
1213		idat.t2 = &(snap_->atomData.torque[atom2]);
1214	+	}
1215	+
1216	+	if (storageLayout_ & DataStorage::dslDipole) {
1217	+	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1218	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1219	+	}
1220	+
1221	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1222	+	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1223	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1224		}
1225
1226		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 866 | Line 1243 | namespace OpenMD {
1243		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1244		}
1245
1246	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1247	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1248	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1249	+	}
1250	+
1251	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1252	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1253	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1254	+	}
1255	+
1256		#endif
1257		}
1258
1259
1260		void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1261		#ifdef IS_MPI
1262	<	pot_row[atom1] += 0.5 *  *(idat.pot);
1263	<	pot_col[atom2] += 0.5 *  *(idat.pot);
1262	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1263	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1264	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1265	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1266
1267		atomRowData.force[atom1] += *(idat.f1);
1268		atomColData.force[atom2] -= *(idat.f1);
880	–	#else
881	–	pairwisePot += *(idat.pot);
1269
1270	<	snap_->atomData.force[atom1] += *(idat.f1);
1271	<	snap_->atomData.force[atom2] -= *(idat.f1);
1272	<	#endif
886	<
887	<	}
888	<
889	<
890	<	void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
891	<	int atom1, int atom2) {
892	<	#ifdef IS_MPI
893	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
894	<	ff_->getAtomType(identsCol[atom2]) );
895	<
896	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
897	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
898	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1270	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1271	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1272	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1273		}
1274
1275	<	if (storageLayout_ & DataStorage::dslTorque) {
1276	<	idat.t1 = &(atomRowData.torque[atom1]);
1277	<	idat.t2 = &(atomColData.torque[atom2]);
1275	>	if (storageLayout_ & DataStorage::dslElectricField) {
1276	>	atomRowData.electricField[atom1] += *(idat.eField1);
1277	>	atomColData.electricField[atom2] += *(idat.eField2);
1278		}
1279
906	–	if (storageLayout_ & DataStorage::dslSkippedCharge) {
907	–	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
908	–	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
909	–	}
1280		#else
1281	<	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1282	<	ff_->getAtomType(idents[atom2]) );
1281	>	pairwisePot += *(idat.pot);
1282	>	excludedPot += *(idat.excludedPot);
1283
1284	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1285	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
916	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
917	<	}
1284	>	snap_->atomData.force[atom1] += *(idat.f1);
1285	>	snap_->atomData.force[atom2] -= *(idat.f1);
1286
1287	<	if (storageLayout_ & DataStorage::dslTorque) {
1288	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1289	<	idat.t2 = &(snap_->atomData.torque[atom2]);
1287	>	if (idat.doParticlePot) {
1288	>	// This is the pairwise contribution to the particle pot.  The
1289	>	// embedding contribution is added in each of the low level
1290	>	// non-bonded routines.  In parallel, this calculation is done
1291	>	// in collectData, not in unpackInteractionData.
1292	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1293	>	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1294		}
1295	+
1296	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1297	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1298	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1299	+	}
1300
1301	<	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1302	<	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1303	<	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1301	>	if (storageLayout_ & DataStorage::dslElectricField) {
1302	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1303	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1304		}
928	–	#endif
929	–	}
1305
931	–
932	–	void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {
933	–	#ifdef IS_MPI
934	–	pot_row[atom1] += 0.5 *  *(idat.pot);
935	–	pot_col[atom2] += 0.5 *  *(idat.pot);
936	–	#else
937	–	pairwisePot += *(idat.pot);
1306		#endif
1307	<
1307	>
1308		}
1309
942	–
1310		/*
1311		* buildNeighborList
1312		*
#	Line 950 | Line 1317 | namespace OpenMD {
1317
1318		vector<pair<int, int> > neighborList;
1319		groupCutoffs cuts;
1320	+	bool doAllPairs = false;
1321	+
1322		#ifdef IS_MPI
1323		cellListRow_.clear();
1324		cellListCol_.clear();
#	Line 958 | Line 1327 | namespace OpenMD {
1327		#endif
1328
1329		RealType rList_ = (largestRcut_ + skinThickness_);
961	–	RealType rl2 = rList_ * rList_;
1330		Snapshot* snap_ = sman_->getCurrentSnapshot();
1331		Mat3x3d Hmat = snap_->getHmat();
1332		Vector3d Hx = Hmat.getColumn(0);
#	Line 969 | Line 1337 | namespace OpenMD {
1337		nCells_.y() = (int) ( Hy.length() )/ rList_;
1338		nCells_.z() = (int) ( Hz.length() )/ rList_;
1339
1340	+	// handle small boxes where the cell offsets can end up repeating cells
1341	+
1342	+	if (nCells_.x() < 3) doAllPairs = true;
1343	+	if (nCells_.y() < 3) doAllPairs = true;
1344	+	if (nCells_.z() < 3) doAllPairs = true;
1345	+
1346		Mat3x3d invHmat = snap_->getInvHmat();
1347		Vector3d rs, scaled, dr;
1348		Vector3i whichCell;
#	Line 982 | Line 1356 | namespace OpenMD {
1356		cellList_.resize(nCtot);
1357		#endif
1358
1359	+	if (!doAllPairs) {
1360		#ifdef IS_MPI
986	–	for (int i = 0; i < nGroupsInRow_; i++) {
987	–	rs = cgRowData.position[i];
1361
1362	<	// scaled positions relative to the box vectors
1363	<	scaled = invHmat * rs;
1364	<
1365	<	// wrap the vector back into the unit box by subtracting integer box
1366	<	// numbers
1367	<	for (int j = 0; j < 3; j++) {
1368	<	scaled[j] -= roundMe(scaled[j]);
1369	<	scaled[j] += 0.5;
1362	>	for (int i = 0; i < nGroupsInRow_; i++) {
1363	>	rs = cgRowData.position[i];
1364	>
1365	>	// scaled positions relative to the box vectors
1366	>	scaled = invHmat * rs;
1367	>
1368	>	// wrap the vector back into the unit box by subtracting integer box
1369	>	// numbers
1370	>	for (int j = 0; j < 3; j++) {
1371	>	scaled[j] -= roundMe(scaled[j]);
1372	>	scaled[j] += 0.5;
1373	>	// Handle the special case when an object is exactly on the
1374	>	// boundary (a scaled coordinate of 1.0 is the same as
1375	>	// scaled coordinate of 0.0)
1376	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1377	>	}
1378	>
1379	>	// find xyz-indices of cell that cutoffGroup is in.
1380	>	whichCell.x() = nCells_.x() * scaled.x();
1381	>	whichCell.y() = nCells_.y() * scaled.y();
1382	>	whichCell.z() = nCells_.z() * scaled.z();
1383	>
1384	>	// find single index of this cell:
1385	>	cellIndex = Vlinear(whichCell, nCells_);
1386	>
1387	>	// add this cutoff group to the list of groups in this cell;
1388	>	cellListRow_[cellIndex].push_back(i);
1389		}
1390	<
1391	<	// find xyz-indices of cell that cutoffGroup is in.
1392	<	whichCell.x() = nCells_.x() * scaled.x();
1393	<	whichCell.y() = nCells_.y() * scaled.y();
1394	<	whichCell.z() = nCells_.z() * scaled.z();
1395	<
1396	<	// find single index of this cell:
1397	<	cellIndex = Vlinear(whichCell, nCells_);
1398	<
1399	<	// add this cutoff group to the list of groups in this cell;
1400	<	cellListRow_[cellIndex].push_back(i);
1401	<	}
1402	<
1403	<	for (int i = 0; i < nGroupsInCol_; i++) {
1404	<	rs = cgColData.position[i];
1405	<
1406	<	// scaled positions relative to the box vectors
1407	<	scaled = invHmat * rs;
1408	<
1409	<	// wrap the vector back into the unit box by subtracting integer box
1410	<	// numbers
1411	<	for (int j = 0; j < 3; j++) {
1412	<	scaled[j] -= roundMe(scaled[j]);
1413	<	scaled[j] += 0.5;
1390	>	for (int i = 0; i < nGroupsInCol_; i++) {
1391	>	rs = cgColData.position[i];
1392	>
1393	>	// scaled positions relative to the box vectors
1394	>	scaled = invHmat * rs;
1395	>
1396	>	// wrap the vector back into the unit box by subtracting integer box
1397	>	// numbers
1398	>	for (int j = 0; j < 3; j++) {
1399	>	scaled[j] -= roundMe(scaled[j]);
1400	>	scaled[j] += 0.5;
1401	>	// Handle the special case when an object is exactly on the
1402	>	// boundary (a scaled coordinate of 1.0 is the same as
1403	>	// scaled coordinate of 0.0)
1404	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1405	>	}
1406	>
1407	>	// find xyz-indices of cell that cutoffGroup is in.
1408	>	whichCell.x() = nCells_.x() * scaled.x();
1409	>	whichCell.y() = nCells_.y() * scaled.y();
1410	>	whichCell.z() = nCells_.z() * scaled.z();
1411	>
1412	>	// find single index of this cell:
1413	>	cellIndex = Vlinear(whichCell, nCells_);
1414	>
1415	>	// add this cutoff group to the list of groups in this cell;
1416	>	cellListCol_[cellIndex].push_back(i);
1417		}
1418	<
1024	<	// find xyz-indices of cell that cutoffGroup is in.
1025	<	whichCell.x() = nCells_.x() * scaled.x();
1026	<	whichCell.y() = nCells_.y() * scaled.y();
1027	<	whichCell.z() = nCells_.z() * scaled.z();
1028	<
1029	<	// find single index of this cell:
1030	<	cellIndex = Vlinear(whichCell, nCells_);
1031	<
1032	<	// add this cutoff group to the list of groups in this cell;
1033	<	cellListCol_[cellIndex].push_back(i);
1034	<	}
1418	>
1419		#else
1420	<	for (int i = 0; i < nGroups_; i++) {
1421	<	rs = snap_->cgData.position[i];
1422	<
1423	<	// scaled positions relative to the box vectors
1424	<	scaled = invHmat * rs;
1425	<
1426	<	// wrap the vector back into the unit box by subtracting integer box
1427	<	// numbers
1428	<	for (int j = 0; j < 3; j++) {
1429	<	scaled[j] -= roundMe(scaled[j]);
1430	<	scaled[j] += 0.5;
1420	>	for (int i = 0; i < nGroups_; i++) {
1421	>	rs = snap_->cgData.position[i];
1422	>
1423	>	// scaled positions relative to the box vectors
1424	>	scaled = invHmat * rs;
1425	>
1426	>	// wrap the vector back into the unit box by subtracting integer box
1427	>	// numbers
1428	>	for (int j = 0; j < 3; j++) {
1429	>	scaled[j] -= roundMe(scaled[j]);
1430	>	scaled[j] += 0.5;
1431	>	// Handle the special case when an object is exactly on the
1432	>	// boundary (a scaled coordinate of 1.0 is the same as
1433	>	// scaled coordinate of 0.0)
1434	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1435	>	}
1436	>
1437	>	// find xyz-indices of cell that cutoffGroup is in.
1438	>	whichCell.x() = nCells_.x() * scaled.x();
1439	>	whichCell.y() = nCells_.y() * scaled.y();
1440	>	whichCell.z() = nCells_.z() * scaled.z();
1441	>
1442	>	// find single index of this cell:
1443	>	cellIndex = Vlinear(whichCell, nCells_);
1444	>
1445	>	// add this cutoff group to the list of groups in this cell;
1446	>	cellList_[cellIndex].push_back(i);
1447		}
1448
1049	–	// find xyz-indices of cell that cutoffGroup is in.
1050	–	whichCell.x() = nCells_.x() * scaled.x();
1051	–	whichCell.y() = nCells_.y() * scaled.y();
1052	–	whichCell.z() = nCells_.z() * scaled.z();
1053	–
1054	–	// find single index of this cell:
1055	–	cellIndex = Vlinear(whichCell, nCells_);
1056	–
1057	–	// add this cutoff group to the list of groups in this cell;
1058	–	cellList_[cellIndex].push_back(i);
1059	–	}
1449		#endif
1450
1451	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1452	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1453	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1454	<	Vector3i m1v(m1x, m1y, m1z);
1455	<	int m1 = Vlinear(m1v, nCells_);
1067	<
1068	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1069	<	os != cellOffsets_.end(); ++os) {
1451	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1452	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1453	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1454	>	Vector3i m1v(m1x, m1y, m1z);
1455	>	int m1 = Vlinear(m1v, nCells_);
1456
1457	<	Vector3i m2v = m1v + (*os);
1458	<
1459	<	if (m2v.x() >= nCells_.x()) {
1460	<	m2v.x() = 0;
1461	<	} else if (m2v.x() < 0) {
1076	<	m2v.x() = nCells_.x() - 1;
1077	<	}
1078	<
1079	<	if (m2v.y() >= nCells_.y()) {
1080	<	m2v.y() = 0;
1081	<	} else if (m2v.y() < 0) {
1082	<	m2v.y() = nCells_.y() - 1;
1083	<	}
1084	<
1085	<	if (m2v.z() >= nCells_.z()) {
1086	<	m2v.z() = 0;
1087	<	} else if (m2v.z() < 0) {
1088	<	m2v.z() = nCells_.z() - 1;
1089	<	}
1090	<
1091	<	int m2 = Vlinear (m2v, nCells_);
1457	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1458	>	os != cellOffsets_.end(); ++os) {
1459	>
1460	>	Vector3i m2v = m1v + (*os);
1461	>
1462
1463	<	#ifdef IS_MPI
1464	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1465	<	j1 != cellListRow_[m1].end(); ++j1) {
1466	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1467	<	j2 != cellListCol_[m2].end(); ++j2) {
1468	<
1469	<	// Always do this if we're in different cells or if
1470	<	// we're in the same cell and the global index of the
1471	<	// j2 cutoff group is less than the j1 cutoff group
1463	>	if (m2v.x() >= nCells_.x()) {
1464	>	m2v.x() = 0;
1465	>	} else if (m2v.x() < 0) {
1466	>	m2v.x() = nCells_.x() - 1;
1467	>	}
1468	>
1469	>	if (m2v.y() >= nCells_.y()) {
1470	>	m2v.y() = 0;
1471	>	} else if (m2v.y() < 0) {
1472	>	m2v.y() = nCells_.y() - 1;
1473	>	}
1474	>
1475	>	if (m2v.z() >= nCells_.z()) {
1476	>	m2v.z() = 0;
1477	>	} else if (m2v.z() < 0) {
1478	>	m2v.z() = nCells_.z() - 1;
1479	>	}
1480
1481	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1481	>	int m2 = Vlinear (m2v, nCells_);
1482	>
1483	>	#ifdef IS_MPI
1484	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1485	>	j1 != cellListRow_[m1].end(); ++j1) {
1486	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1487	>	j2 != cellListCol_[m2].end(); ++j2) {
1488	>
1489	>	// In parallel, we need to visit *all* pairs of row
1490	>	// & column indicies and will divide labor in the
1491	>	// force evaluation later.
1492		dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1493		snap_->wrapVector(dr);
1494		cuts = getGroupCutoffs( (*j1), (*j2) );
1495		if (dr.lengthSquare() < cuts.third) {
1496		neighborList.push_back(make_pair((*j1), (*j2)));
1497	<	}
1497	>	}
1498		}
1499		}
1112	–	}
1500		#else
1501	+	for (vector<int>::iterator j1 = cellList_[m1].begin();
1502	+	j1 != cellList_[m1].end(); ++j1) {
1503	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1504	+	j2 != cellList_[m2].end(); ++j2) {
1505	+
1506	+	// Always do this if we're in different cells or if
1507	+	// we're in the same cell and the global index of
1508	+	// the j2 cutoff group is greater than or equal to
1509	+	// the j1 cutoff group.  Note that Rappaport's code
1510	+	// has a "less than" conditional here, but that
1511	+	// deals with atom-by-atom computation.  OpenMD
1512	+	// allows atoms within a single cutoff group to
1513	+	// interact with each other.
1514
1115	–	for (vector<int>::iterator j1 = cellList_[m1].begin();
1116	–	j1 != cellList_[m1].end(); ++j1) {
1117	–	for (vector<int>::iterator j2 = cellList_[m2].begin();
1118	–	j2 != cellList_[m2].end(); ++j2) {
1515
1120	–	// Always do this if we're in different cells or if
1121	–	// we're in the same cell and the global index of the
1122	–	// j2 cutoff group is less than the j1 cutoff group
1516
1517	<	if (m2 != m1 || (*j2) < (*j1)) {
1518	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1519	<	snap_->wrapVector(dr);
1520	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1521	<	if (dr.lengthSquare() < cuts.third) {
1522	<	neighborList.push_back(make_pair((*j1), (*j2)));
1517	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1518	>
1519	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1520	>	snap_->wrapVector(dr);
1521	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1522	>	if (dr.lengthSquare() < cuts.third) {
1523	>	neighborList.push_back(make_pair((*j1), (*j2)));
1524	>	}
1525		}
1526		}
1527		}
1133	–	}
1528		#endif
1529	+	}
1530		}
1531		}
1532		}
1533	+	} else {
1534	+	// branch to do all cutoff group pairs
1535	+	#ifdef IS_MPI
1536	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1537	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1538	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1539	+	snap_->wrapVector(dr);
1540	+	cuts = getGroupCutoffs( j1, j2 );
1541	+	if (dr.lengthSquare() < cuts.third) {
1542	+	neighborList.push_back(make_pair(j1, j2));
1543	+	}
1544	+	}
1545	+	}
1546	+	#else
1547	+	// include all groups here.
1548	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1549	+	// include self group interactions j2 == j1
1550	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1551	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1552	+	snap_->wrapVector(dr);
1553	+	cuts = getGroupCutoffs( j1, j2 );
1554	+	if (dr.lengthSquare() < cuts.third) {
1555	+	neighborList.push_back(make_pair(j1, j2));
1556	+	}
1557	+	}
1558	+	}
1559	+	#endif
1560		}
1561	<
1561	>
1562		// save the local cutoff group positions for the check that is
1563		// done on each loop:
1564		saved_CG_positions_.clear();
1565		for (int i = 0; i < nGroups_; i++)
1566		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1567	<
1567	>
1568		return neighborList;
1569		}
1570		} //end namespace OpenMD

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