[ViewVC] Diff of: OpenMD/trunk/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 1706 by gezelter, Fri Apr 27 20:44:16 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 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();
108	>	PairList* excludes = info_->getExcludedInteractions();
109	>	PairList* oneTwo = info_->getOneTwoInteractions();
110	>	PairList* oneThree = info_->getOneThreeInteractions();
111	>	PairList* oneFour = info_->getOneFourInteractions();
112
113		#ifdef IS_MPI
114
115	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
116	<	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_);
115	>	MPI::Intracomm row = rowComm.getComm();
116	>	MPI::Intracomm col = colComm.getComm();
117
118	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
119	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
120	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
121	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
122	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
118	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
119	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
120	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
121	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
122	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
123
124	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
125	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
126	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
127	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
124	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
125	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
126	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
127	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
128	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
129
130	<	nAtomsInRow_ = AtomCommIntRow->getSize();
131	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
132	<	nGroupsInRow_ = cgCommIntRow->getSize();
133	<	nGroupsInCol_ = cgCommIntColumn->getSize();
130	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
131	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
132	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
133	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
134
135	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
136	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
137	+	nGroupsInRow_ = cgPlanIntRow->getSize();
138	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
139	+
140		// Modify the data storage objects with the correct layouts and sizes:
141		atomRowData.resize(nAtomsInRow_);
142		atomRowData.setStorageLayout(storageLayout_);
#	Line 109 \| Line 150 \| namespace OpenMD {
150		identsRow.resize(nAtomsInRow_);
151		identsCol.resize(nAtomsInCol_);
152
153	<	AtomCommIntRow->gather(idents, identsRow);
154	<	AtomCommIntColumn->gather(idents, identsCol);
153	>	AtomPlanIntRow->gather(idents, identsRow);
154	>	AtomPlanIntColumn->gather(idents, identsCol);
155
156	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
157	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
158	<
118	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
156	>	// allocate memory for the parallel objects
157	>	atypesRow.resize(nAtomsInRow_);
158	>	atypesCol.resize(nAtomsInCol_);
159
160	<	AtomCommRealRow->gather(massFactors, massFactorsRow);
161	<	AtomCommRealColumn->gather(massFactors, massFactorsCol);
160	>	for (int i = 0; i < nAtomsInRow_; i++)
161	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
162	>	for (int i = 0; i < nAtomsInCol_; i++)
163	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
164
165	+	pot_row.resize(nAtomsInRow_);
166	+	pot_col.resize(nAtomsInCol_);
167	+
168	+	AtomRowToGlobal.resize(nAtomsInRow_);
169	+	AtomColToGlobal.resize(nAtomsInCol_);
170	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
171	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
172	+
173	+	cgRowToGlobal.resize(nGroupsInRow_);
174	+	cgColToGlobal.resize(nGroupsInCol_);
175	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177	+
178	+	massFactorsRow.resize(nAtomsInRow_);
179	+	massFactorsCol.resize(nAtomsInCol_);
180	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
181	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
182	+
183		groupListRow_.clear();
184		groupListRow_.resize(nGroupsInRow_);
185		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 143 \| Line 202 \| namespace OpenMD {
202		}
203		}
204
205	<	skipsForAtom.clear();
206	<	skipsForAtom.resize(nAtomsInRow_);
205	>	excludesForAtom.clear();
206	>	excludesForAtom.resize(nAtomsInRow_);
207		toposForAtom.clear();
208		toposForAtom.resize(nAtomsInRow_);
209		topoDist.clear();
#	Line 155 \| Line 214 \| namespace OpenMD {
214		for (int j = 0; j < nAtomsInCol_; j++) {
215		int jglob = AtomColToGlobal[j];
216
217	<	if (excludes.hasPair(iglob, jglob))
218	<	skipsForAtom[i].push_back(j);
217	>	if (excludes->hasPair(iglob, jglob))
218	>	excludesForAtom[i].push_back(j);
219
220	<	if (oneTwo.hasPair(iglob, jglob)) {
220	>	if (oneTwo->hasPair(iglob, jglob)) {
221		toposForAtom[i].push_back(j);
222		topoDist[i].push_back(1);
223		} else {
224	<	if (oneThree.hasPair(iglob, jglob)) {
224	>	if (oneThree->hasPair(iglob, jglob)) {
225		toposForAtom[i].push_back(j);
226		topoDist[i].push_back(2);
227		} else {
228	<	if (oneFour.hasPair(iglob, jglob)) {
228	>	if (oneFour->hasPair(iglob, jglob)) {
229		toposForAtom[i].push_back(j);
230		topoDist[i].push_back(3);
231		}
#	Line 175 \| Line 234 \| namespace OpenMD {
234		}
235		}
236
237	<	#endif
238	<
239	<	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_);
237	>	#else
238	>	excludesForAtom.clear();
239	>	excludesForAtom.resize(nLocal_);
240		toposForAtom.clear();
241		toposForAtom.resize(nLocal_);
242		topoDist.clear();
#	Line 202 \| Line 248 \| namespace OpenMD {
248		for (int j = 0; j < nLocal_; j++) {
249		int jglob = AtomLocalToGlobal[j];
250
251	<	if (excludes.hasPair(iglob, jglob))
252	<	skipsForAtom[i].push_back(j);
251	>	if (excludes->hasPair(iglob, jglob))
252	>	excludesForAtom[i].push_back(j);
253
254	<	if (oneTwo.hasPair(iglob, jglob)) {
254	>	if (oneTwo->hasPair(iglob, jglob)) {
255		toposForAtom[i].push_back(j);
256		topoDist[i].push_back(1);
257		} else {
258	<	if (oneThree.hasPair(iglob, jglob)) {
258	>	if (oneThree->hasPair(iglob, jglob)) {
259		toposForAtom[i].push_back(j);
260		topoDist[i].push_back(2);
261		} else {
262	<	if (oneFour.hasPair(iglob, jglob)) {
262	>	if (oneFour->hasPair(iglob, jglob)) {
263		toposForAtom[i].push_back(j);
264		topoDist[i].push_back(3);
265		}
#	Line 221 \| Line 267 \| namespace OpenMD {
267		}
268		}
269		}
270	<
270	>	#endif
271	>
272	>	// allocate memory for the parallel objects
273	>	atypesLocal.resize(nLocal_);
274	>
275	>	for (int i = 0; i < nLocal_; i++)
276	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
277	>
278	>	groupList_.clear();
279	>	groupList_.resize(nGroups_);
280	>	for (int i = 0; i < nGroups_; i++) {
281	>	int gid = cgLocalToGlobal[i];
282	>	for (int j = 0; j < nLocal_; j++) {
283	>	int aid = AtomLocalToGlobal[j];
284	>	if (globalGroupMembership[aid] == gid) {
285	>	groupList_[i].push_back(j);
286	>	}
287	>	}
288	>	}
289	>
290	>
291		createGtypeCutoffMap();
292	+
293		}
294
295		void ForceMatrixDecomposition::createGtypeCutoffMap() {
296
297		RealType tol = 1e-6;
298	+	largestRcut_ = 0.0;
299		RealType rc;
300		int atid;
301		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302	<	vector<RealType> atypeCutoff;
303	<	atypeCutoff.resize( atypes.size() );
302	>
303	>	map<int, RealType> atypeCutoff;
304
305		for (set<AtomType*>::iterator at = atypes.begin();
306		at != atypes.end(); ++at){
307		atid = (*at)->getIdent();
308	<
241	<	if (userChoseCutoff_)
308	>	if (userChoseCutoff_)
309		atypeCutoff[atid] = userCutoff_;
310		else
311		atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312		}
313	<
313	>
314		vector<RealType> gTypeCutoffs;
248	–
315		// first we do a single loop over the cutoff groups to find the
316		// largest cutoff for any atypes present in this group.
317		#ifdef IS_MPI
#	Line 303 \| Line 369 \| namespace OpenMD {
369
370		vector<RealType> groupCutoff(nGroups_, 0.0);
371		groupToGtype.resize(nGroups_);
306	–
372		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
308	–
373		groupCutoff[cg1] = 0.0;
374		vector<int> atomList = getAtomsInGroupRow(cg1);
311	–
375		for (vector<int>::iterator ia = atomList.begin();
376		ia != atomList.end(); ++ia) {
377		int atom1 = (*ia);
378		atid = idents[atom1];
379	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
379	>	if (atypeCutoff[atid] > groupCutoff[cg1])
380		groupCutoff[cg1] = atypeCutoff[atid];
318	–	}
381		}
382	<
382	>
383		bool gTypeFound = false;
384		for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
#	Line 325 \| Line 387 \| namespace OpenMD {
387		gTypeFound = true;
388		}
389		}
390	<	if (!gTypeFound) {
390	>	if (!gTypeFound) {
391		gTypeCutoffs.push_back( groupCutoff[cg1] );
392		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393		}
#	Line 334 \| Line 396 \| namespace OpenMD {
396
397		// Now we find the maximum group cutoff value present in the simulation
398
399	<	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
399	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
400	>	gTypeCutoffs.end());
401
402		#ifdef IS_MPI
403	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
403	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
404	>	MPI::MAX);
405		#endif
406
407		RealType tradRcut = groupMax;
#	Line 367 \| Line 431 \| namespace OpenMD {
431
432		pair<int,int> key = make_pair(i,j);
433		gTypeCutoffMap[key].first = thisRcut;
370	–
434		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
372	–
435		gTypeCutoffMap[key].second = thisRcut*thisRcut;
374	–
436		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
376	–
437		// sanity check
438
439		if (userChoseCutoff_) {
#	Line 433 \| Line 493 \| namespace OpenMD {
493		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
494
495		if (storageLayout_ & DataStorage::dslParticlePot) {
496	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
497	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
496	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
497	>	0.0);
498	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
499	>	0.0);
500		}
501
502		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 443 \| Line 505 \| namespace OpenMD {
505		}
506
507		if (storageLayout_ & DataStorage::dslFunctional) {
508	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
509	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
508	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
509	>	0.0);
510	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
511	>	0.0);
512		}
513
514		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 455 \| Line 519 \| namespace OpenMD {
519		}
520
521		if (storageLayout_ & DataStorage::dslSkippedCharge) {
522	<	fill(atomRowData.skippedCharge.begin(), atomRowData.skippedCharge.end(), 0.0);
523	<	fill(atomColData.skippedCharge.begin(), atomColData.skippedCharge.end(), 0.0);
522	>	fill(atomRowData.skippedCharge.begin(),
523	>	atomRowData.skippedCharge.end(), 0.0);
524	>	fill(atomColData.skippedCharge.begin(),
525	>	atomColData.skippedCharge.end(), 0.0);
526		}
527
528	<	#else
529	<
528	>	#endif
529	>	// even in parallel, we need to zero out the local arrays:
530	>
531		if (storageLayout_ & DataStorage::dslParticlePot) {
532		fill(snap_->atomData.particlePot.begin(),
533		snap_->atomData.particlePot.end(), 0.0);
#	Line 470 \| Line 537 \| namespace OpenMD {
537		fill(snap_->atomData.density.begin(),
538		snap_->atomData.density.end(), 0.0);
539		}
540	+
541		if (storageLayout_ & DataStorage::dslFunctional) {
542		fill(snap_->atomData.functional.begin(),
543		snap_->atomData.functional.end(), 0.0);
544		}
545	+
546		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
547		fill(snap_->atomData.functionalDerivative.begin(),
548		snap_->atomData.functionalDerivative.end(), 0.0);
549		}
550	+
551		if (storageLayout_ & DataStorage::dslSkippedCharge) {
552		fill(snap_->atomData.skippedCharge.begin(),
553		snap_->atomData.skippedCharge.end(), 0.0);
554		}
485	–	#endif
486	–
555		}
556
557
#	Line 493 \| Line 561 \| namespace OpenMD {
561		#ifdef IS_MPI
562
563		// gather up the atomic positions
564	<	AtomCommVectorRow->gather(snap_->atomData.position,
564	>	AtomPlanVectorRow->gather(snap_->atomData.position,
565		atomRowData.position);
566	<	AtomCommVectorColumn->gather(snap_->atomData.position,
566	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
567		atomColData.position);
568
569		// gather up the cutoff group positions
570	<	cgCommVectorRow->gather(snap_->cgData.position,
570	>
571	>	cgPlanVectorRow->gather(snap_->cgData.position,
572		cgRowData.position);
573	<	cgCommVectorColumn->gather(snap_->cgData.position,
573	>
574	>	cgPlanVectorColumn->gather(snap_->cgData.position,
575		cgColData.position);
576	+
577
578		// if needed, gather the atomic rotation matrices
579		if (storageLayout_ & DataStorage::dslAmat) {
580	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
580	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
581		atomRowData.aMat);
582	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
582	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
583		atomColData.aMat);
584		}
585
586		// if needed, gather the atomic eletrostatic frames
587		if (storageLayout_ & DataStorage::dslElectroFrame) {
588	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
588	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
589		atomRowData.electroFrame);
590	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
590	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
591		atomColData.electroFrame);
592		}
593	+
594		#endif
595		}
596
#	Line 532 \| Line 604 \| namespace OpenMD {
604
605		if (storageLayout_ & DataStorage::dslDensity) {
606
607	<	AtomCommRealRow->scatter(atomRowData.density,
607	>	AtomPlanRealRow->scatter(atomRowData.density,
608		snap_->atomData.density);
609
610		int n = snap_->atomData.density.size();
611		vector<RealType> rho_tmp(n, 0.0);
612	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
612	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
613		for (int i = 0; i < n; i++)
614		snap_->atomData.density[i] += rho_tmp[i];
615		}
#	Line 553 \| Line 625 \| namespace OpenMD {
625		storageLayout_ = sman_->getStorageLayout();
626		#ifdef IS_MPI
627		if (storageLayout_ & DataStorage::dslFunctional) {
628	<	AtomCommRealRow->gather(snap_->atomData.functional,
628	>	AtomPlanRealRow->gather(snap_->atomData.functional,
629		atomRowData.functional);
630	<	AtomCommRealColumn->gather(snap_->atomData.functional,
630	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
631		atomColData.functional);
632		}
633
634		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
635	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
635	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
636		atomRowData.functionalDerivative);
637	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
637	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
638		atomColData.functionalDerivative);
639		}
640		#endif
#	Line 576 \| Line 648 \| namespace OpenMD {
648		int n = snap_->atomData.force.size();
649		vector<Vector3d> frc_tmp(n, V3Zero);
650
651	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
651	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
652		for (int i = 0; i < n; i++) {
653		snap_->atomData.force[i] += frc_tmp[i];
654		frc_tmp[i] = 0.0;
655		}
656
657	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
658	<	for (int i = 0; i < n; i++)
657	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
658	>	for (int i = 0; i < n; i++) {
659		snap_->atomData.force[i] += frc_tmp[i];
660	<
661	<
660	>	}
661	>
662		if (storageLayout_ & DataStorage::dslTorque) {
663
664	<	int nt = snap_->atomData.force.size();
664	>	int nt = snap_->atomData.torque.size();
665		vector<Vector3d> trq_tmp(nt, V3Zero);
666
667	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
668	<	for (int i = 0; i < n; i++) {
667	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
668	>	for (int i = 0; i < nt; i++) {
669		snap_->atomData.torque[i] += trq_tmp[i];
670		trq_tmp[i] = 0.0;
671		}
672
673	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
674	<	for (int i = 0; i < n; i++)
673	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
674	>	for (int i = 0; i < nt; i++)
675		snap_->atomData.torque[i] += trq_tmp[i];
676		}
677	+
678	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
679	+
680	+	int ns = snap_->atomData.skippedCharge.size();
681	+	vector<RealType> skch_tmp(ns, 0.0);
682	+
683	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
684	+	for (int i = 0; i < ns; i++) {
685	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
686	+	skch_tmp[i] = 0.0;
687	+	}
688	+
689	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
690	+	for (int i = 0; i < ns; i++)
691	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
692	+
693	+	}
694
695		nLocal_ = snap_->getNumberOfAtoms();
696
#	Line 610 \| Line 699 \| namespace OpenMD {
699
700		// scatter/gather pot_row into the members of my column
701
702	<	AtomCommPotRow->scatter(pot_row, pot_temp);
702	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
703
704		for (int ii = 0; ii < pot_temp.size(); ii++ )
705		pairwisePot += pot_temp[ii];
#	Line 618 \| Line 707 \| namespace OpenMD {
707		fill(pot_temp.begin(), pot_temp.end(),
708		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
709
710	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
710	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
711
712		for (int ii = 0; ii < pot_temp.size(); ii++ )
713		pairwisePot += pot_temp[ii];
714	+
715	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
716	+	RealType ploc1 = pairwisePot[ii];
717	+	RealType ploc2 = 0.0;
718	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
719	+	pairwisePot[ii] = ploc2;
720	+	}
721	+
722	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
723	+	RealType ploc1 = embeddingPot[ii];
724	+	RealType ploc2 = 0.0;
725	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
726	+	embeddingPot[ii] = ploc2;
727	+	}
728	+
729		#endif
730
731		}
#	Line 724 \| Line 828 \| namespace OpenMD {
828		return d;
829		}
830
831	<	vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
832	<	return skipsForAtom[atom1];
831	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
832	>	return excludesForAtom[atom1];
833		}
834
835		/**
836	<	* 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
836	>	* We need to exclude some overcounted interactions that result from
837		* the parallel decomposition.
838		*/
839		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
840		int unique_id_1, unique_id_2;
841	<
841	>
842		#ifdef IS_MPI
843		// in MPI, we have to look up the unique IDs for each atom
844		unique_id_1 = AtomRowToGlobal[atom1];
845		unique_id_2 = AtomColToGlobal[atom2];
846	+	#else
847	+	unique_id_1 = AtomLocalToGlobal[atom1];
848	+	unique_id_2 = AtomLocalToGlobal[atom2];
849	+	#endif
850
746	–	// this situation should only arise in MPI simulations
851		if (unique_id_1 == unique_id_2) return true;
852	<
852	>
853	>	#ifdef IS_MPI
854		// this prevents us from doing the pair on multiple processors
855		if (unique_id_1 < unique_id_2) {
856		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
857		} else {
858	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
858	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
859		}
755	–	#else
756	–	// in the normal loop, the atom numbers are unique
757	–	unique_id_1 = atom1;
758	–	unique_id_2 = atom2;
860		#endif
861
862	<	for (vector<int>::iterator i = skipsForAtom[atom1].begin();
863	<	i != skipsForAtom[atom1].end(); ++i) {
864	<	if ( (*i) == unique_id_2 ) return true;
862	>	return false;
863	>	}
864	>
865	>	/**
866	>	* We need to handle the interactions for atoms who are involved in
867	>	* the same rigid body as well as some short range interactions
868	>	* (bonds, bends, torsions) differently from other interactions.
869	>	* We'll still visit the pairwise routines, but with a flag that
870	>	* tells those routines to exclude the pair from direct long range
871	>	* interactions. Some indirect interactions (notably reaction
872	>	* field) must still be handled for these pairs.
873	>	*/
874	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
875	>
876	>	// excludesForAtom was constructed to use row/column indices in the MPI
877	>	// version, and to use local IDs in the non-MPI version:
878	>
879	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
880	>	i != excludesForAtom[atom1].end(); ++i) {
881	>	if ( (*i) == atom2 ) return true;
882		}
883
884		return false;
#	Line 785 \| Line 903 \| namespace OpenMD {
903
904		// filling interaction blocks with pointers
905		void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
906	<	int atom1, int atom2) {
906	>	int atom1, int atom2) {
907	>
908	>	idat.excluded = excludeAtomPair(atom1, atom2);
909	>
910		#ifdef IS_MPI
911	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
912	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
913	+	// ff_->getAtomType(identsCol[atom2]) );
914
791	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
792	–	ff_->getAtomType(identsCol[atom2]) );
793	–
915		if (storageLayout_ & DataStorage::dslAmat) {
916		idat.A1 = &(atomRowData.aMat[atom1]);
917		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 826 \| Line 947 \| namespace OpenMD {
947		idat.particlePot2 = &(atomColData.particlePot[atom2]);
948		}
949
950	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
951	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
952	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
953	+	}
954	+
955		#else
956	+
957
958	<	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
959	<	ff_->getAtomType(idents[atom2]) );
958	>	// cerr << "atoms = " << atom1 << " " << atom2 << "\n";
959	>	// cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
960	>	// cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
961
962	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
963	+	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
964	+	// ff_->getAtomType(idents[atom2]) );
965	+
966		if (storageLayout_ & DataStorage::dslAmat) {
967		idat.A1 = &(snap_->atomData.aMat[atom1]);
968		idat.A2 = &(snap_->atomData.aMat[atom2]);
#	Line 866 \| Line 998 \| namespace OpenMD {
998		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
999		}
1000
1001	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1002	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1003	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1004	+	}
1005		#endif
1006		}
1007
1008
1009		void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1010		#ifdef IS_MPI
1011	<	pot_row[atom1] += 0.5 * *(idat.pot);
1012	<	pot_col[atom2] += 0.5 * *(idat.pot);
1011	>	pot_row[atom1] += RealType(0.5) * *(idat.pot);
1012	>	pot_col[atom2] += RealType(0.5) * *(idat.pot);
1013
1014		atomRowData.force[atom1] += *(idat.f1);
1015		atomColData.force[atom2] -= *(idat.f1);
#	Line 886 \| Line 1022 \| namespace OpenMD {
1022
1023		}
1024
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]);
899	–	}
900	–
901	–	if (storageLayout_ & DataStorage::dslTorque) {
902	–	idat.t1 = &(atomRowData.torque[atom1]);
903	–	idat.t2 = &(atomColData.torque[atom2]);
904	–	}
905	–
906	–	if (storageLayout_ & DataStorage::dslSkippedCharge) {
907	–	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
908	–	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
909	–	}
910	–	#else
911	–	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
912	–	ff_->getAtomType(idents[atom2]) );
913	–
914	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
915	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
916	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
917	–	}
918	–
919	–	if (storageLayout_ & DataStorage::dslTorque) {
920	–	idat.t1 = &(snap_->atomData.torque[atom1]);
921	–	idat.t2 = &(snap_->atomData.torque[atom2]);
922	–	}
923	–
924	–	if (storageLayout_ & DataStorage::dslSkippedCharge) {
925	–	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
926	–	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
927	–	}
928	–	#endif
929	–	}
930	–
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);
938	–	#endif
939	–
940	–	}
941	–
942	–
1025		/*
1026		* buildNeighborList
1027		*
#	Line 950 \| Line 1032 \| namespace OpenMD {
1032
1033		vector<pair<int, int> > neighborList;
1034		groupCutoffs cuts;
1035	+	bool doAllPairs = false;
1036	+
1037		#ifdef IS_MPI
1038		cellListRow_.clear();
1039		cellListCol_.clear();
#	Line 969 \| Line 1053 \| namespace OpenMD {
1053		nCells_.y() = (int) ( Hy.length() )/ rList_;
1054		nCells_.z() = (int) ( Hz.length() )/ rList_;
1055
1056	+	// handle small boxes where the cell offsets can end up repeating cells
1057	+
1058	+	if (nCells_.x() < 3) doAllPairs = true;
1059	+	if (nCells_.y() < 3) doAllPairs = true;
1060	+	if (nCells_.z() < 3) doAllPairs = true;
1061	+
1062		Mat3x3d invHmat = snap_->getInvHmat();
1063		Vector3d rs, scaled, dr;
1064		Vector3i whichCell;
#	Line 982 \| Line 1072 \| namespace OpenMD {
1072		cellList_.resize(nCtot);
1073		#endif
1074
1075	+	if (!doAllPairs) {
1076		#ifdef IS_MPI
986	–	for (int i = 0; i < nGroupsInRow_; i++) {
987	–	rs = cgRowData.position[i];
1077
1078	<	// scaled positions relative to the box vectors
1079	<	scaled = invHmat * rs;
1080	<
1081	<	// wrap the vector back into the unit box by subtracting integer box
1082	<	// numbers
1083	<	for (int j = 0; j < 3; j++) {
1084	<	scaled[j] -= roundMe(scaled[j]);
1085	<	scaled[j] += 0.5;
1078	>	for (int i = 0; i < nGroupsInRow_; i++) {
1079	>	rs = cgRowData.position[i];
1080	>
1081	>	// scaled positions relative to the box vectors
1082	>	scaled = invHmat * rs;
1083	>
1084	>	// wrap the vector back into the unit box by subtracting integer box
1085	>	// numbers
1086	>	for (int j = 0; j < 3; j++) {
1087	>	scaled[j] -= roundMe(scaled[j]);
1088	>	scaled[j] += 0.5;
1089	>	}
1090	>
1091	>	// find xyz-indices of cell that cutoffGroup is in.
1092	>	whichCell.x() = nCells_.x() * scaled.x();
1093	>	whichCell.y() = nCells_.y() * scaled.y();
1094	>	whichCell.z() = nCells_.z() * scaled.z();
1095	>
1096	>	// find single index of this cell:
1097	>	cellIndex = Vlinear(whichCell, nCells_);
1098	>
1099	>	// add this cutoff group to the list of groups in this cell;
1100	>	cellListRow_[cellIndex].push_back(i);
1101		}
1102	<
1103	<	// find xyz-indices of cell that cutoffGroup is in.
1104	<	whichCell.x() = nCells_.x() * scaled.x();
1105	<	whichCell.y() = nCells_.y() * scaled.y();
1106	<	whichCell.z() = nCells_.z() * scaled.z();
1107	<
1108	<	// find single index of this cell:
1109	<	cellIndex = Vlinear(whichCell, nCells_);
1110	<
1111	<	// add this cutoff group to the list of groups in this cell;
1112	<	cellListRow_[cellIndex].push_back(i);
1113	<	}
1114	<
1115	<	for (int i = 0; i < nGroupsInCol_; i++) {
1116	<	rs = cgColData.position[i];
1117	<
1118	<	// scaled positions relative to the box vectors
1119	<	scaled = invHmat * rs;
1120	<
1121	<	// wrap the vector back into the unit box by subtracting integer box
1122	<	// numbers
1123	<	for (int j = 0; j < 3; j++) {
1124	<	scaled[j] -= roundMe(scaled[j]);
1021	<	scaled[j] += 0.5;
1102	>	for (int i = 0; i < nGroupsInCol_; i++) {
1103	>	rs = cgColData.position[i];
1104	>
1105	>	// scaled positions relative to the box vectors
1106	>	scaled = invHmat * rs;
1107	>
1108	>	// wrap the vector back into the unit box by subtracting integer box
1109	>	// numbers
1110	>	for (int j = 0; j < 3; j++) {
1111	>	scaled[j] -= roundMe(scaled[j]);
1112	>	scaled[j] += 0.5;
1113	>	}
1114	>
1115	>	// find xyz-indices of cell that cutoffGroup is in.
1116	>	whichCell.x() = nCells_.x() * scaled.x();
1117	>	whichCell.y() = nCells_.y() * scaled.y();
1118	>	whichCell.z() = nCells_.z() * scaled.z();
1119	>
1120	>	// find single index of this cell:
1121	>	cellIndex = Vlinear(whichCell, nCells_);
1122	>
1123	>	// add this cutoff group to the list of groups in this cell;
1124	>	cellListCol_[cellIndex].push_back(i);
1125		}
1126	<
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	<	}
1126	>
1127		#else
1128	<	for (int i = 0; i < nGroups_; i++) {
1129	<	rs = snap_->cgData.position[i];
1130	<
1131	<	// scaled positions relative to the box vectors
1132	<	scaled = invHmat * rs;
1133	<
1134	<	// wrap the vector back into the unit box by subtracting integer box
1135	<	// numbers
1136	<	for (int j = 0; j < 3; j++) {
1137	<	scaled[j] -= roundMe(scaled[j]);
1138	<	scaled[j] += 0.5;
1128	>	for (int i = 0; i < nGroups_; i++) {
1129	>	rs = snap_->cgData.position[i];
1130	>
1131	>	// scaled positions relative to the box vectors
1132	>	scaled = invHmat * rs;
1133	>
1134	>	// wrap the vector back into the unit box by subtracting integer box
1135	>	// numbers
1136	>	for (int j = 0; j < 3; j++) {
1137	>	scaled[j] -= roundMe(scaled[j]);
1138	>	scaled[j] += 0.5;
1139	>	}
1140	>
1141	>	// find xyz-indices of cell that cutoffGroup is in.
1142	>	whichCell.x() = nCells_.x() * scaled.x();
1143	>	whichCell.y() = nCells_.y() * scaled.y();
1144	>	whichCell.z() = nCells_.z() * scaled.z();
1145	>
1146	>	// find single index of this cell:
1147	>	cellIndex = Vlinear(whichCell, nCells_);
1148	>
1149	>	// add this cutoff group to the list of groups in this cell;
1150	>	cellList_[cellIndex].push_back(i);
1151		}
1152
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	–	}
1153		#endif
1154
1155	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1156	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1157	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1158	<	Vector3i m1v(m1x, m1y, m1z);
1159	<	int m1 = Vlinear(m1v, nCells_);
1067	<
1068	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1069	<	os != cellOffsets_.end(); ++os) {
1155	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1156	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1157	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1158	>	Vector3i m1v(m1x, m1y, m1z);
1159	>	int m1 = Vlinear(m1v, nCells_);
1160
1161	<	Vector3i m2v = m1v + (*os);
1162	<
1163	<	if (m2v.x() >= nCells_.x()) {
1164	<	m2v.x() = 0;
1165	<	} 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_);
1161	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1162	>	os != cellOffsets_.end(); ++os) {
1163	>
1164	>	Vector3i m2v = m1v + (*os);
1165	>
1166
1167	<	#ifdef IS_MPI
1168	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1169	<	j1 != cellListRow_[m1].end(); ++j1) {
1170	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1171	<	j2 != cellListCol_[m2].end(); ++j2) {
1172	<
1173	<	// Always do this if we're in different cells or if
1174	<	// we're in the same cell and the global index of the
1175	<	// j2 cutoff group is less than the j1 cutoff group
1167	>	if (m2v.x() >= nCells_.x()) {
1168	>	m2v.x() = 0;
1169	>	} else if (m2v.x() < 0) {
1170	>	m2v.x() = nCells_.x() - 1;
1171	>	}
1172	>
1173	>	if (m2v.y() >= nCells_.y()) {
1174	>	m2v.y() = 0;
1175	>	} else if (m2v.y() < 0) {
1176	>	m2v.y() = nCells_.y() - 1;
1177	>	}
1178	>
1179	>	if (m2v.z() >= nCells_.z()) {
1180	>	m2v.z() = 0;
1181	>	} else if (m2v.z() < 0) {
1182	>	m2v.z() = nCells_.z() - 1;
1183	>	}
1184
1185	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1185	>	int m2 = Vlinear (m2v, nCells_);
1186	>
1187	>	#ifdef IS_MPI
1188	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1189	>	j1 != cellListRow_[m1].end(); ++j1) {
1190	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1191	>	j2 != cellListCol_[m2].end(); ++j2) {
1192	>
1193	>	// In parallel, we need to visit all pairs of row
1194	>	// & column indicies and will divide labor in the
1195	>	// force evaluation later.
1196		dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1197		snap_->wrapVector(dr);
1198		cuts = getGroupCutoffs( (j1), (j2) );
1199		if (dr.lengthSquare() < cuts.third) {
1200		neighborList.push_back(make_pair((j1), (j2)));
1201	<	}
1201	>	}
1202		}
1203		}
1112	–	}
1204		#else
1205	+	for (vector<int>::iterator j1 = cellList_[m1].begin();
1206	+	j1 != cellList_[m1].end(); ++j1) {
1207	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1208	+	j2 != cellList_[m2].end(); ++j2) {
1209	+
1210	+	// Always do this if we're in different cells or if
1211	+	// we're in the same cell and the global index of
1212	+	// the j2 cutoff group is greater than or equal to
1213	+	// the j1 cutoff group. Note that Rappaport's code
1214	+	// has a "less than" conditional here, but that
1215	+	// deals with atom-by-atom computation. OpenMD
1216	+	// allows atoms within a single cutoff group to
1217	+	// interact with each other.
1218
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) {
1219
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
1220
1221	<	if (m2 != m1 \|\| (j2) < (j1)) {
1222	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1223	<	snap_->wrapVector(dr);
1224	<	cuts = getGroupCutoffs( (j1), (j2) );
1225	<	if (dr.lengthSquare() < cuts.third) {
1226	<	neighborList.push_back(make_pair((j1), (j2)));
1221	>	if (m2 != m1 \|\| (j2) >= (j1) ) {
1222	>
1223	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1224	>	snap_->wrapVector(dr);
1225	>	cuts = getGroupCutoffs( (j1), (j2) );
1226	>	if (dr.lengthSquare() < cuts.third) {
1227	>	neighborList.push_back(make_pair((j1), (j2)));
1228	>	}
1229		}
1230		}
1231		}
1133	–	}
1232		#endif
1233	+	}
1234		}
1235		}
1236		}
1237	+	} else {
1238	+	// branch to do all cutoff group pairs
1239	+	#ifdef IS_MPI
1240	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1241	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1242	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1243	+	snap_->wrapVector(dr);
1244	+	cuts = getGroupCutoffs( j1, j2 );
1245	+	if (dr.lengthSquare() < cuts.third) {
1246	+	neighborList.push_back(make_pair(j1, j2));
1247	+	}
1248	+	}
1249	+	}
1250	+	#else
1251	+	// include all groups here.
1252	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1253	+	// include self group interactions j2 == j1
1254	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1255	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1256	+	snap_->wrapVector(dr);
1257	+	cuts = getGroupCutoffs( j1, j2 );
1258	+	if (dr.lengthSquare() < cuts.third) {
1259	+	neighborList.push_back(make_pair(j1, j2));
1260	+	}
1261	+	}
1262	+	}
1263	+	#endif
1264		}
1265	<
1265	>
1266		// save the local cutoff group positions for the check that is
1267		// done on each loop:
1268		saved_CG_positions_.clear();
1269		for (int i = 0; i < nGroups_; i++)
1270		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1271	<
1271	>
1272		return neighborList;
1273		}
1274		} //end namespace OpenMD

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1586 by gezelter, Tue Jun 21 06:34:35 2011 UTC vs. Revision 1706 by gezelter, Fri Apr 27 20:44:16 2012 UTC

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1586 by gezelter, Tue Jun 21 06:34:35 2011 UTC vs.
Revision 1706 by gezelter, Fri Apr 27 20:44:16 2012 UTC