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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1589 by gezelter, Sun Jul 10 16:05:34 2011 UTC vs.
Revision 1772 by gezelter, Tue Jul 31 14:00:05 2012 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 71 \| Line 109 \| namespace OpenMD {
109		PairList* oneTwo = info_->getOneTwoInteractions();
110		PairList* oneThree = info_->getOneThreeInteractions();
111		PairList* oneFour = info_->getOneFourInteractions();
112	<
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		// allocate memory for the parallel objects
168	+	atypesRow.resize(nAtomsInRow_);
169	+	atypesCol.resize(nAtomsInCol_);
170	+
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	<	pot_row.resize(nAtomsInRow_);
195	<	pot_col.resize(nAtomsInCol_);
194	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
195	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
196
125	–	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
126	–	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
127	–
128	–	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
129	–	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
130	–
131	–	AtomCommRealRow->gather(massFactors, massFactorsRow);
132	–	AtomCommRealColumn->gather(massFactors, massFactorsCol);
133	–
197		groupListRow_.clear();
198		groupListRow_.resize(nGroupsInRow_);
199		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 185 \| Line 248 \| namespace OpenMD {
248		}
249		}
250
251	<	#endif
189	<
190	<	groupList_.clear();
191	<	groupList_.resize(nGroups_);
192	<	for (int i = 0; i < nGroups_; i++) {
193	<	int gid = cgLocalToGlobal[i];
194	<	for (int j = 0; j < nLocal_; j++) {
195	<	int aid = AtomLocalToGlobal[j];
196	<	if (globalGroupMembership[aid] == gid) {
197	<	groupList_[i].push_back(j);
198	<	}
199	<	}
200	<	}
201	<
251	>	#else
252		excludesForAtom.clear();
253		excludesForAtom.resize(nLocal_);
254		toposForAtom.clear();
#	Line 231 \| 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		}
#	Line 239 \| Line 309 \| namespace OpenMD {
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	+
316		map<int, RealType> atypeCutoff;
317
318		for (set<AtomType*>::iterator at = atypes.begin();
#	Line 249 \| Line 320 \| namespace OpenMD {
320		atid = (*at)->getIdent();
321		if (userChoseCutoff_)
322		atypeCutoff[atid] = userCutoff_;
323	<	else
323	>	else
324		atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
325		}
326	<
326	>
327		vector<RealType> gTypeCutoffs;
328		// first we do a single loop over the cutoff groups to find the
329		// largest cutoff for any atypes present in this group.
#	Line 312 \| Line 383 \| namespace OpenMD {
383		vector<RealType> groupCutoff(nGroups_, 0.0);
384		groupToGtype.resize(nGroups_);
385		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
315	–
386		groupCutoff[cg1] = 0.0;
387		vector<int> atomList = getAtomsInGroupRow(cg1);
318	–
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]) {
393	<	groupCutoff[cg1] = atypeCutoff[atid];
325	<	}
392	>	if (atypeCutoff[atid] > groupCutoff[cg1])
393	>	groupCutoff[cg1] = atypeCutoff[atid];
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 341 \| 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 374 \| Line 444 \| namespace OpenMD {
444
445		pair<int,int> key = make_pair(i,j);
446		gTypeCutoffMap[key].first = thisRcut;
377	–
447		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
379	–
448		gTypeCutoffMap[key].second = thisRcut*thisRcut;
381	–
449		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
383	–
450		// sanity check
451
452		if (userChoseCutoff_) {
#	Line 397 \| Line 463 \| namespace OpenMD {
463		}
464		}
465
400	–
466		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467		int i, j;
468		#ifdef IS_MPI
#	Line 411 \| 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 421 \| 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 439 \| 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 450 \| 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 468 \| Line 545 \| namespace OpenMD {
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	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
563	>	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
564	>	0.0);
565	>	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
566	>	0.0);
567	>	}
568	>
569	>	#endif
570	>	// even in parallel, we need to zero out the local arrays:
571	>
572		if (storageLayout_ & DataStorage::dslParticlePot) {
573		fill(snap_->atomData.particlePot.begin(),
574		snap_->atomData.particlePot.end(), 0.0);
#	Line 479 \| Line 578 \| namespace OpenMD {
578		fill(snap_->atomData.density.begin(),
579		snap_->atomData.density.end(), 0.0);
580		}
581	+
582		if (storageLayout_ & DataStorage::dslFunctional) {
583		fill(snap_->atomData.functional.begin(),
584		snap_->atomData.functional.end(), 0.0);
585		}
586	+
587		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
588		fill(snap_->atomData.functionalDerivative.begin(),
589		snap_->atomData.functionalDerivative.end(), 0.0);
590		}
591	+
592		if (storageLayout_ & DataStorage::dslSkippedCharge) {
593		fill(snap_->atomData.skippedCharge.begin(),
594		snap_->atomData.skippedCharge.end(), 0.0);
595		}
596	<	#endif
597	<
596	>
597	>	if (storageLayout_ & DataStorage::dslElectricField) {
598	>	fill(snap_->atomData.electricField.begin(),
599	>	snap_->atomData.electricField.end(), V3Zero);
600	>	}
601		}
602
603
#	Line 502 \| Line 607 \| namespace OpenMD {
607		#ifdef IS_MPI
608
609		// gather up the atomic positions
610	<	AtomCommVectorRow->gather(snap_->atomData.position,
610	>	AtomPlanVectorRow->gather(snap_->atomData.position,
611		atomRowData.position);
612	<	AtomCommVectorColumn->gather(snap_->atomData.position,
612	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
613		atomColData.position);
614
615		// gather up the cutoff group positions
616	<	cgCommVectorRow->gather(snap_->cgData.position,
616	>
617	>	cgPlanVectorRow->gather(snap_->cgData.position,
618		cgRowData.position);
619	<	cgCommVectorColumn->gather(snap_->cgData.position,
619	>
620	>	cgPlanVectorColumn->gather(snap_->cgData.position,
621		cgColData.position);
622	+
623	+
624	+
625	+	if (needVelocities_) {
626	+	// gather up the atomic velocities
627	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
628	+	atomColData.velocity);
629	+
630	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
631	+	cgColData.velocity);
632	+	}
633	+
634
635		// if needed, gather the atomic rotation matrices
636		if (storageLayout_ & DataStorage::dslAmat) {
637	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
637	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
638		atomRowData.aMat);
639	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
639	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
640		atomColData.aMat);
641		}
642
643		// if needed, gather the atomic eletrostatic frames
644		if (storageLayout_ & DataStorage::dslElectroFrame) {
645	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
645	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
646		atomRowData.electroFrame);
647	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
647	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
648		atomColData.electroFrame);
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 541 \| 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	+	if (storageLayout_ & DataStorage::dslElectricField) {
683	+
684	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
685	+	snap_->atomData.electricField);
686	+
687	+	int n = snap_->atomData.electricField.size();
688	+	vector<Vector3d> field_tmp(n, V3Zero);
689	+	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
690	+	for (int i = 0; i < n; i++)
691	+	snap_->atomData.electricField[i] += field_tmp[i];
692	+	}
693		#endif
694		}
695
#	Line 562 \| Line 702 \| namespace OpenMD {
702		storageLayout_ = sman_->getStorageLayout();
703		#ifdef IS_MPI
704		if (storageLayout_ & DataStorage::dslFunctional) {
705	<	AtomCommRealRow->gather(snap_->atomData.functional,
705	>	AtomPlanRealRow->gather(snap_->atomData.functional,
706		atomRowData.functional);
707	<	AtomCommRealColumn->gather(snap_->atomData.functional,
707	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
708		atomColData.functional);
709		}
710
711		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
712	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
712	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
713		atomRowData.functionalDerivative);
714	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
714	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
715		atomColData.functionalDerivative);
716		}
717		#endif
#	Line 585 \| Line 725 \| namespace OpenMD {
725		int n = snap_->atomData.force.size();
726		vector<Vector3d> frc_tmp(n, V3Zero);
727
728	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
728	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
729		for (int i = 0; i < n; i++) {
730		snap_->atomData.force[i] += frc_tmp[i];
731		frc_tmp[i] = 0.0;
732		}
733
734	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
735	<	for (int i = 0; i < n; i++)
734	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
735	>	for (int i = 0; i < n; i++) {
736		snap_->atomData.force[i] += frc_tmp[i];
737	<
738	<
737	>	}
738	>
739		if (storageLayout_ & DataStorage::dslTorque) {
740
741		int nt = snap_->atomData.torque.size();
742		vector<Vector3d> trq_tmp(nt, V3Zero);
743
744	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
744	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
745		for (int i = 0; i < nt; i++) {
746		snap_->atomData.torque[i] += trq_tmp[i];
747		trq_tmp[i] = 0.0;
748		}
749
750	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
750	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
751		for (int i = 0; i < nt; i++)
752		snap_->atomData.torque[i] += trq_tmp[i];
753		}
#	Line 617 \| Line 757 \| namespace OpenMD {
757		int ns = snap_->atomData.skippedCharge.size();
758		vector<RealType> skch_tmp(ns, 0.0);
759
760	<	AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
760	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
761		for (int i = 0; i < ns; i++) {
762	<	snap_->atomData.skippedCharge[i] = skch_tmp[i];
762	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
763		skch_tmp[i] = 0.0;
764		}
765
766	<	AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
767	<	for (int i = 0; i < ns; i++)
766	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
767	>	for (int i = 0; i < ns; i++)
768		snap_->atomData.skippedCharge[i] += skch_tmp[i];
769	+
770		}
771
772	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
773	+
774	+	int nq = snap_->atomData.flucQFrc.size();
775	+	vector<RealType> fqfrc_tmp(nq, 0.0);
776	+
777	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
778	+	for (int i = 0; i < nq; i++) {
779	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
780	+	fqfrc_tmp[i] = 0.0;
781	+	}
782	+
783	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
784	+	for (int i = 0; i < nq; i++)
785	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
786	+
787	+	}
788	+
789		nLocal_ = snap_->getNumberOfAtoms();
790
791		vector<potVec> pot_temp(nLocal_,
792		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
793	+	vector<potVec> expot_temp(nLocal_,
794	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
795
796		// scatter/gather pot_row into the members of my column
797
798	<	AtomCommPotRow->scatter(pot_row, pot_temp);
798	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
799	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
800
801	<	for (int ii = 0; ii < pot_temp.size(); ii++ )
801	>	for (int ii = 0; ii < pot_temp.size(); ii++ )
802		pairwisePot += pot_temp[ii];
803	<
803	>
804	>	for (int ii = 0; ii < expot_temp.size(); ii++ )
805	>	excludedPot += expot_temp[ii];
806	>
807	>	if (storageLayout_ & DataStorage::dslParticlePot) {
808	>	// This is the pairwise contribution to the particle pot. The
809	>	// embedding contribution is added in each of the low level
810	>	// non-bonded routines. In single processor, this is done in
811	>	// unpackInteractionData, not in collectData.
812	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
813	>	for (int i = 0; i < nLocal_; i++) {
814	>	// factor of two is because the total potential terms are divided
815	>	// by 2 in parallel due to row/ column scatter
816	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
817	>	}
818	>	}
819	>	}
820	>
821		fill(pot_temp.begin(), pot_temp.end(),
822		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
823	+	fill(expot_temp.begin(), expot_temp.end(),
824	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
825
826	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
826	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
827	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
828
829		for (int ii = 0; ii < pot_temp.size(); ii++ )
830		pairwisePot += pot_temp[ii];
831	+
832	+	for (int ii = 0; ii < expot_temp.size(); ii++ )
833	+	excludedPot += expot_temp[ii];
834	+
835	+	if (storageLayout_ & DataStorage::dslParticlePot) {
836	+	// This is the pairwise contribution to the particle pot. The
837	+	// embedding contribution is added in each of the low level
838	+	// non-bonded routines. In single processor, this is done in
839	+	// unpackInteractionData, not in collectData.
840	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
841	+	for (int i = 0; i < nLocal_; i++) {
842	+	// factor of two is because the total potential terms are divided
843	+	// by 2 in parallel due to row/ column scatter
844	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
845	+	}
846	+	}
847	+	}
848	+
849	+	if (storageLayout_ & DataStorage::dslParticlePot) {
850	+	int npp = snap_->atomData.particlePot.size();
851	+	vector<RealType> ppot_temp(npp, 0.0);
852	+
853	+	// This is the direct or embedding contribution to the particle
854	+	// pot.
855	+
856	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
857	+	for (int i = 0; i < npp; i++) {
858	+	snap_->atomData.particlePot[i] += ppot_temp[i];
859	+	}
860	+
861	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
862	+
863	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
864	+	for (int i = 0; i < npp; i++) {
865	+	snap_->atomData.particlePot[i] += ppot_temp[i];
866	+	}
867	+	}
868	+
869	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
870	+	RealType ploc1 = pairwisePot[ii];
871	+	RealType ploc2 = 0.0;
872	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
873	+	pairwisePot[ii] = ploc2;
874	+	}
875	+
876	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
877	+	RealType ploc1 = excludedPot[ii];
878	+	RealType ploc2 = 0.0;
879	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
880	+	excludedPot[ii] = ploc2;
881	+	}
882	+
883	+	// Here be dragons.
884	+	MPI::Intracomm col = colComm.getComm();
885	+
886	+	col.Allreduce(MPI::IN_PLACE,
887	+	&snap_->frameData.conductiveHeatFlux[0], 3,
888	+	MPI::REALTYPE, MPI::SUM);
889	+
890	+
891		#endif
892
893		}
894
895	+	/**
896	+	* Collects information obtained during the post-pair (and embedding
897	+	* functional) loops onto local data structures.
898	+	*/
899	+	void ForceMatrixDecomposition::collectSelfData() {
900	+	snap_ = sman_->getCurrentSnapshot();
901	+	storageLayout_ = sman_->getStorageLayout();
902	+
903	+	#ifdef IS_MPI
904	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
905	+	RealType ploc1 = embeddingPot[ii];
906	+	RealType ploc2 = 0.0;
907	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
908	+	embeddingPot[ii] = ploc2;
909	+	}
910	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
911	+	RealType ploc1 = excludedSelfPot[ii];
912	+	RealType ploc2 = 0.0;
913	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
914	+	excludedSelfPot[ii] = ploc2;
915	+	}
916	+	#endif
917	+
918	+	}
919	+
920	+
921	+
922		int ForceMatrixDecomposition::getNAtomsInRow() {
923		#ifdef IS_MPI
924		return nAtomsInRow_;
#	Line 691 \| Line 959 \| namespace OpenMD {
959		return d;
960		}
961
962	+	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
963	+	#ifdef IS_MPI
964	+	return cgColData.velocity[cg2];
965	+	#else
966	+	return snap_->cgData.velocity[cg2];
967	+	#endif
968	+	}
969
970	+	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
971	+	#ifdef IS_MPI
972	+	return atomColData.velocity[atom2];
973	+	#else
974	+	return snap_->atomData.velocity[atom2];
975	+	#endif
976	+	}
977	+
978	+
979		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
980
981		Vector3d d;
#	Line 757 \| Line 1041 \| namespace OpenMD {
1041		* We need to exclude some overcounted interactions that result from
1042		* the parallel decomposition.
1043		*/
1044	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1045	<	int unique_id_1, unique_id_2;
1046	<
1044	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1045	>	int unique_id_1, unique_id_2, group1, group2;
1046	>
1047		#ifdef IS_MPI
1048		// in MPI, we have to look up the unique IDs for each atom
1049		unique_id_1 = AtomRowToGlobal[atom1];
1050		unique_id_2 = AtomColToGlobal[atom2];
1051	<
1052	<	// this situation should only arise in MPI simulations
1051	>	group1 = cgRowToGlobal[cg1];
1052	>	group2 = cgColToGlobal[cg2];
1053	>	#else
1054	>	unique_id_1 = AtomLocalToGlobal[atom1];
1055	>	unique_id_2 = AtomLocalToGlobal[atom2];
1056	>	group1 = cgLocalToGlobal[cg1];
1057	>	group2 = cgLocalToGlobal[cg2];
1058	>	#endif
1059	>
1060		if (unique_id_1 == unique_id_2) return true;
1061	<
1061	>
1062	>	#ifdef IS_MPI
1063		// this prevents us from doing the pair on multiple processors
1064		if (unique_id_1 < unique_id_2) {
1065		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1066		} else {
1067	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1067	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1068		}
1069	+	#endif
1070	+
1071	+	#ifndef IS_MPI
1072	+	if (group1 == group2) {
1073	+	if (unique_id_1 < unique_id_2) return true;
1074	+	}
1075		#endif
1076	+
1077		return false;
1078		}
1079
#	Line 788 \| Line 1087 \| namespace OpenMD {
1087		* field) must still be handled for these pairs.
1088		*/
1089		bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1090	<	int unique_id_2;
1090	>
1091	>	// excludesForAtom was constructed to use row/column indices in the MPI
1092	>	// version, and to use local IDs in the non-MPI version:
1093
793	–	#ifdef IS_MPI
794	–	// in MPI, we have to look up the unique IDs for the row atom.
795	–	unique_id_2 = AtomColToGlobal[atom2];
796	–	#else
797	–	// in the normal loop, the atom numbers are unique
798	–	unique_id_2 = atom2;
799	–	#endif
800	–
1094		for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1095		i != excludesForAtom[atom1].end(); ++i) {
1096	<	if ( (*i) == unique_id_2 ) return true;
1096	>	if ( (*i) == atom2 ) return true;
1097		}
1098
1099		return false;
#	Line 830 \| Line 1123 \| namespace OpenMD {
1123		idat.excluded = excludeAtomPair(atom1, atom2);
1124
1125		#ifdef IS_MPI
1126	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1127	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1128	+	// ff_->getAtomType(identsCol[atom2]) );
1129
834	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
835	–	ff_->getAtomType(identsCol[atom2]) );
836	–
1130		if (storageLayout_ & DataStorage::dslAmat) {
1131		idat.A1 = &(atomRowData.aMat[atom1]);
1132		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 874 \| Line 1167 \| namespace OpenMD {
1167		idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1168		}
1169
1170	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1171	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1172	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1173	+	}
1174	+
1175		#else
1176	+
1177	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1178
879	–	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
880	–	ff_->getAtomType(idents[atom2]) );
881	–
1179		if (storageLayout_ & DataStorage::dslAmat) {
1180		idat.A1 = &(snap_->atomData.aMat[atom1]);
1181		idat.A2 = &(snap_->atomData.aMat[atom2]);
#	Line 918 \| Line 1215 \| namespace OpenMD {
1215		idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1216		idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1217		}
1218	+
1219	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1220	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1221	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1222	+	}
1223	+
1224		#endif
1225		}
1226
1227
1228		void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1229		#ifdef IS_MPI
1230	<	pot_row[atom1] += 0.5 * *(idat.pot);
1231	<	pot_col[atom2] += 0.5 * *(idat.pot);
1230	>	pot_row[atom1] += RealType(0.5) * *(idat.pot);
1231	>	pot_col[atom2] += RealType(0.5) * *(idat.pot);
1232	>	expot_row[atom1] += RealType(0.5) * *(idat.excludedPot);
1233	>	expot_col[atom2] += RealType(0.5) * *(idat.excludedPot);
1234
1235		atomRowData.force[atom1] += *(idat.f1);
1236		atomColData.force[atom2] -= *(idat.f1);
1237	+
1238	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1239	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1240	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1241	+	}
1242	+
1243	+	if (storageLayout_ & DataStorage::dslElectricField) {
1244	+	atomRowData.electricField[atom1] += *(idat.eField1);
1245	+	atomColData.electricField[atom2] += *(idat.eField2);
1246	+	}
1247	+
1248		#else
1249		pairwisePot += *(idat.pot);
1250	+	excludedPot += *(idat.excludedPot);
1251
1252		snap_->atomData.force[atom1] += *(idat.f1);
1253		snap_->atomData.force[atom2] -= *(idat.f1);
1254	+
1255	+	if (idat.doParticlePot) {
1256	+	// This is the pairwise contribution to the particle pot. The
1257	+	// embedding contribution is added in each of the low level
1258	+	// non-bonded routines. In parallel, this calculation is done
1259	+	// in collectData, not in unpackInteractionData.
1260	+	snap_->atomData.particlePot[atom1] += (idat.vpair) *(idat.sw);
1261	+	snap_->atomData.particlePot[atom2] += (idat.vpair) *(idat.sw);
1262	+	}
1263	+
1264	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1265	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1266	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1267	+	}
1268	+
1269	+	if (storageLayout_ & DataStorage::dslElectricField) {
1270	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1271	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1272	+	}
1273	+
1274		#endif
1275
1276		}
#	Line 1002 \| Line 1339 \| namespace OpenMD {
1339		for (int j = 0; j < 3; j++) {
1340		scaled[j] -= roundMe(scaled[j]);
1341		scaled[j] += 0.5;
1342	+	// Handle the special case when an object is exactly on the
1343	+	// boundary (a scaled coordinate of 1.0 is the same as
1344	+	// scaled coordinate of 0.0)
1345	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1346		}
1347
1348		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1015 \| Line 1356 \| namespace OpenMD {
1356		// add this cutoff group to the list of groups in this cell;
1357		cellListRow_[cellIndex].push_back(i);
1358		}
1018	–
1359		for (int i = 0; i < nGroupsInCol_; i++) {
1360		rs = cgColData.position[i];
1361
#	Line 1027 \| Line 1367 \| namespace OpenMD {
1367		for (int j = 0; j < 3; j++) {
1368		scaled[j] -= roundMe(scaled[j]);
1369		scaled[j] += 0.5;
1370	+	// Handle the special case when an object is exactly on the
1371	+	// boundary (a scaled coordinate of 1.0 is the same as
1372	+	// scaled coordinate of 0.0)
1373	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1374		}
1375
1376		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1040 \| Line 1384 \| namespace OpenMD {
1384		// add this cutoff group to the list of groups in this cell;
1385		cellListCol_[cellIndex].push_back(i);
1386		}
1387	+
1388		#else
1389		for (int i = 0; i < nGroups_; i++) {
1390		rs = snap_->cgData.position[i];
#	Line 1052 \| Line 1397 \| namespace OpenMD {
1397		for (int j = 0; j < 3; j++) {
1398		scaled[j] -= roundMe(scaled[j]);
1399		scaled[j] += 0.5;
1400	+	// Handle the special case when an object is exactly on the
1401	+	// boundary (a scaled coordinate of 1.0 is the same as
1402	+	// scaled coordinate of 0.0)
1403	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1404		}
1405
1406		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1060 \| Line 1409 \| namespace OpenMD {
1409		whichCell.z() = nCells_.z() * scaled.z();
1410
1411		// find single index of this cell:
1412	<	cellIndex = Vlinear(whichCell, nCells_);
1412	>	cellIndex = Vlinear(whichCell, nCells_);
1413
1414		// add this cutoff group to the list of groups in this cell;
1415		cellList_[cellIndex].push_back(i);
1416		}
1417	+
1418		#endif
1419
1420		for (int m1z = 0; m1z < nCells_.z(); m1z++) {
#	Line 1077 \| Line 1427 \| namespace OpenMD {
1427		os != cellOffsets_.end(); ++os) {
1428
1429		Vector3i m2v = m1v + (*os);
1430	<
1430	>
1431	>
1432		if (m2v.x() >= nCells_.x()) {
1433		m2v.x() = 0;
1434		} else if (m2v.x() < 0) {
#	Line 1095 \| Line 1446 \| namespace OpenMD {
1446		} else if (m2v.z() < 0) {
1447		m2v.z() = nCells_.z() - 1;
1448		}
1449	<
1449	>
1450		int m2 = Vlinear (m2v, nCells_);
1451
1452		#ifdef IS_MPI
#	Line 1104 \| Line 1455 \| namespace OpenMD {
1455		for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1456		j2 != cellListCol_[m2].end(); ++j2) {
1457
1458	<	// Always do this if we're in different cells or if
1459	<	// we're in the same cell and the global index of the
1460	<	// j2 cutoff group is less than the j1 cutoff group
1461	<
1462	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1463	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1464	<	snap_->wrapVector(dr);
1465	<	cuts = getGroupCutoffs( (j1), (j2) );
1466	<	if (dr.lengthSquare() < cuts.third) {
1116	<	neighborList.push_back(make_pair((j1), (j2)));
1117	<	}
1118	<	}
1458	>	// In parallel, we need to visit all pairs of row
1459	>	// & column indicies and will divide labor in the
1460	>	// force evaluation later.
1461	>	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1462	>	snap_->wrapVector(dr);
1463	>	cuts = getGroupCutoffs( (j1), (j2) );
1464	>	if (dr.lengthSquare() < cuts.third) {
1465	>	neighborList.push_back(make_pair((j1), (j2)));
1466	>	}
1467		}
1468		}
1469		#else
1122	–
1470		for (vector<int>::iterator j1 = cellList_[m1].begin();
1471		j1 != cellList_[m1].end(); ++j1) {
1472		for (vector<int>::iterator j2 = cellList_[m2].begin();
1473		j2 != cellList_[m2].end(); ++j2) {
1474	<
1474	>
1475		// Always do this if we're in different cells or if
1476	<	// we're in the same cell and the global index of the
1477	<	// j2 cutoff group is less than the j1 cutoff group
1478	<
1479	<	if (m2 != m1 \|\| (j2) < (j1)) {
1476	>	// we're in the same cell and the global index of
1477	>	// the j2 cutoff group is greater than or equal to
1478	>	// the j1 cutoff group. Note that Rappaport's code
1479	>	// has a "less than" conditional here, but that
1480	>	// deals with atom-by-atom computation. OpenMD
1481	>	// allows atoms within a single cutoff group to
1482	>	// interact with each other.
1483	>
1484	>
1485	>
1486	>	if (m2 != m1 \|\| (j2) >= (j1) ) {
1487	>
1488		dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1489		snap_->wrapVector(dr);
1490		cuts = getGroupCutoffs( (j1), (j2) );
#	Line 1148 \| Line 1503 \| namespace OpenMD {
1503		// branch to do all cutoff group pairs
1504		#ifdef IS_MPI
1505		for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1506	<	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1506	>	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1507		dr = cgColData.position[j2] - cgRowData.position[j1];
1508		snap_->wrapVector(dr);
1509		cuts = getGroupCutoffs( j1, j2 );
#	Line 1156 \| Line 1511 \| namespace OpenMD {
1511		neighborList.push_back(make_pair(j1, j2));
1512		}
1513		}
1514	<	}
1514	>	}
1515		#else
1516	<	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1517	<	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1516	>	// include all groups here.
1517	>	for (int j1 = 0; j1 < nGroups_; j1++) {
1518	>	// include self group interactions j2 == j1
1519	>	for (int j2 = j1; j2 < nGroups_; j2++) {
1520		dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1521		snap_->wrapVector(dr);
1522		cuts = getGroupCutoffs( j1, j2 );
1523		if (dr.lengthSquare() < cuts.third) {
1524		neighborList.push_back(make_pair(j1, j2));
1525		}
1526	<	}
1527	<	}
1526	>	}
1527	>	}
1528		#endif
1529		}
1530

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1589 by gezelter, Sun Jul 10 16:05:34 2011 UTC vs. Revision 1772 by gezelter, Tue Jul 31 14:00:05 2012 UTC

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1589 by gezelter, Sun Jul 10 16:05:34 2011 UTC vs.
Revision 1772 by gezelter, Tue Jul 31 14:00:05 2012 UTC