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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs.
Revision 1593 by gezelter, Fri Jul 15 21:35:14 2011 UTC

#	Line 47 \| Line 47 \| namespace OpenMD {
47		using namespace std;
48		namespace OpenMD {
49
50	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
51	+
52	+	// In a parallel computation, row and colum scans must visit all
53	+	// surrounding cells (not just the 14 upper triangular blocks that
54	+	// are used when the processor can see all pairs)
55	+	#ifdef IS_MPI
56	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
57	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
58	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
59	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
60	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
62	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
63	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
64	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
66	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
68	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
69	+	#endif
70	+	}
71	+
72	+
73		/**
74		* distributeInitialData is essentially a copy of the older fortran
75		* SimulationSetup
76		*/
54	–
77		void ForceMatrixDecomposition::distributeInitialData() {
78		snap_ = sman_->getCurrentSnapshot();
79		storageLayout_ = sman_->getStorageLayout();
80		ff_ = info_->getForceField();
81		nLocal_ = snap_->getNumberOfAtoms();
82	<
82	>
83		nGroups_ = info_->getNLocalCutoffGroups();
62	–	cerr << "in dId, nGroups = " << nGroups_ << "\n";
84		// gather the information for atomtype IDs (atids):
85	<	identsLocal = info_->getIdentArray();
85	>	idents = info_->getIdentArray();
86		AtomLocalToGlobal = info_->getGlobalAtomIndices();
87		cgLocalToGlobal = info_->getGlobalGroupIndices();
88		vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68	–	vector<RealType> massFactorsLocal = info_->getMassFactors();
69	–	PairList excludes = info_->getExcludedInteractions();
70	–	PairList oneTwo = info_->getOneTwoInteractions();
71	–	PairList oneThree = info_->getOneThreeInteractions();
72	–	PairList oneFour = info_->getOneFourInteractions();
89
90	+	massFactors = info_->getMassFactors();
91	+
92	+	PairList* excludes = info_->getExcludedInteractions();
93	+	PairList* oneTwo = info_->getOneTwoInteractions();
94	+	PairList* oneThree = info_->getOneThreeInteractions();
95	+	PairList* oneFour = info_->getOneFourInteractions();
96	+
97		#ifdef IS_MPI
98
99	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
100	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
78	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
79	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
80	<	AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
99	>	MPI::Intracomm row = rowComm.getComm();
100	>	MPI::Intracomm col = colComm.getComm();
101
102	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
103	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
104	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
105	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
106	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
102	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
103	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
104	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
105	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
106	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
107
108	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
109	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
110	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
111	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
108	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
109	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
110	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
111	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
112	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
113
114	<	nAtomsInRow_ = AtomCommIntRow->getSize();
115	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
116	<	nGroupsInRow_ = cgCommIntRow->getSize();
117	<	nGroupsInCol_ = cgCommIntColumn->getSize();
114	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
115	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
116	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
117	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
118
119	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
120	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
121	+	nGroupsInRow_ = cgPlanIntRow->getSize();
122	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
123	+
124		// Modify the data storage objects with the correct layouts and sizes:
125		atomRowData.resize(nAtomsInRow_);
126		atomRowData.setStorageLayout(storageLayout_);
#	Line 108 \| Line 134 \| namespace OpenMD {
134		identsRow.resize(nAtomsInRow_);
135		identsCol.resize(nAtomsInCol_);
136
137	<	AtomCommIntRow->gather(identsLocal, identsRow);
138	<	AtomCommIntColumn->gather(identsLocal, identsCol);
137	>	AtomPlanIntRow->gather(idents, identsRow);
138	>	AtomPlanIntColumn->gather(idents, identsCol);
139
140	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
141	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
142	<
117	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
118	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
140	>	// allocate memory for the parallel objects
141	>	atypesRow.resize(nAtomsInRow_);
142	>	atypesCol.resize(nAtomsInCol_);
143
144	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
145	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
144	>	for (int i = 0; i < nAtomsInRow_; i++)
145	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
146	>	for (int i = 0; i < nAtomsInCol_; i++)
147	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
148
149	+	pot_row.resize(nAtomsInRow_);
150	+	pot_col.resize(nAtomsInCol_);
151	+
152	+	AtomRowToGlobal.resize(nAtomsInRow_);
153	+	AtomColToGlobal.resize(nAtomsInCol_);
154	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156	+
157	+	cerr << "Atoms in Local:\n";
158	+	for (int i = 0; i < AtomLocalToGlobal.size(); i++) {
159	+	cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
160	+	}
161	+	cerr << "Atoms in Row:\n";
162	+	for (int i = 0; i < AtomRowToGlobal.size(); i++) {
163	+	cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
164	+	}
165	+	cerr << "Atoms in Col:\n";
166	+	for (int i = 0; i < AtomColToGlobal.size(); i++) {
167	+	cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
168	+	}
169	+
170	+	cgRowToGlobal.resize(nGroupsInRow_);
171	+	cgColToGlobal.resize(nGroupsInCol_);
172	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
173	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
174	+
175	+	cerr << "Gruops in Local:\n";
176	+	for (int i = 0; i < cgLocalToGlobal.size(); i++) {
177	+	cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
178	+	}
179	+	cerr << "Groups in Row:\n";
180	+	for (int i = 0; i < cgRowToGlobal.size(); i++) {
181	+	cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
182	+	}
183	+	cerr << "Groups in Col:\n";
184	+	for (int i = 0; i < cgColToGlobal.size(); i++) {
185	+	cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
186	+	}
187	+
188	+
189	+	massFactorsRow.resize(nAtomsInRow_);
190	+	massFactorsCol.resize(nAtomsInCol_);
191	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
192	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
193	+
194		groupListRow_.clear();
195		groupListRow_.resize(nGroupsInRow_);
196		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 142 \| Line 213 \| namespace OpenMD {
213		}
214		}
215
216	<	skipsForAtom.clear();
217	<	skipsForAtom.resize(nAtomsInRow_);
216	>	excludesForAtom.clear();
217	>	excludesForAtom.resize(nAtomsInRow_);
218		toposForAtom.clear();
219		toposForAtom.resize(nAtomsInRow_);
220		topoDist.clear();
#	Line 154 \| Line 225 \| namespace OpenMD {
225		for (int j = 0; j < nAtomsInCol_; j++) {
226		int jglob = AtomColToGlobal[j];
227
228	<	if (excludes.hasPair(iglob, jglob))
229	<	skipsForAtom[i].push_back(j);
228	>	if (excludes->hasPair(iglob, jglob))
229	>	excludesForAtom[i].push_back(j);
230
231	<	if (oneTwo.hasPair(iglob, jglob)) {
231	>	if (oneTwo->hasPair(iglob, jglob)) {
232		toposForAtom[i].push_back(j);
233		topoDist[i].push_back(1);
234		} else {
235	<	if (oneThree.hasPair(iglob, jglob)) {
235	>	if (oneThree->hasPair(iglob, jglob)) {
236		toposForAtom[i].push_back(j);
237		topoDist[i].push_back(2);
238		} else {
239	<	if (oneFour.hasPair(iglob, jglob)) {
239	>	if (oneFour->hasPair(iglob, jglob)) {
240		toposForAtom[i].push_back(j);
241		topoDist[i].push_back(3);
242		}
#	Line 176 \| Line 247 \| namespace OpenMD {
247
248		#endif
249
250	+	// allocate memory for the parallel objects
251	+	atypesLocal.resize(nLocal_);
252	+
253	+	for (int i = 0; i < nLocal_; i++)
254	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
255	+
256		groupList_.clear();
257		groupList_.resize(nGroups_);
258		for (int i = 0; i < nGroups_; i++) {
#	Line 188 \| Line 265 \| namespace OpenMD {
265		}
266		}
267
268	<	skipsForAtom.clear();
269	<	skipsForAtom.resize(nLocal_);
268	>	excludesForAtom.clear();
269	>	excludesForAtom.resize(nLocal_);
270		toposForAtom.clear();
271		toposForAtom.resize(nLocal_);
272		topoDist.clear();
#	Line 201 \| Line 278 \| namespace OpenMD {
278		for (int j = 0; j < nLocal_; j++) {
279		int jglob = AtomLocalToGlobal[j];
280
281	<	if (excludes.hasPair(iglob, jglob))
282	<	skipsForAtom[i].push_back(j);
281	>	if (excludes->hasPair(iglob, jglob))
282	>	excludesForAtom[i].push_back(j);
283
284	<	if (oneTwo.hasPair(iglob, jglob)) {
284	>	if (oneTwo->hasPair(iglob, jglob)) {
285		toposForAtom[i].push_back(j);
286		topoDist[i].push_back(1);
287		} else {
288	<	if (oneThree.hasPair(iglob, jglob)) {
288	>	if (oneThree->hasPair(iglob, jglob)) {
289		toposForAtom[i].push_back(j);
290		topoDist[i].push_back(2);
291		} else {
292	<	if (oneFour.hasPair(iglob, jglob)) {
292	>	if (oneFour->hasPair(iglob, jglob)) {
293		toposForAtom[i].push_back(j);
294		topoDist[i].push_back(3);
295		}
#	Line 222 \| Line 299 \| namespace OpenMD {
299		}
300
301		createGtypeCutoffMap();
302	+
303		}
304
305		void ForceMatrixDecomposition::createGtypeCutoffMap() {
306	<
306	>
307		RealType tol = 1e-6;
308	+	largestRcut_ = 0.0;
309		RealType rc;
310		int atid;
311		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
312	<	vector<RealType> atypeCutoff;
313	<	atypeCutoff.resize( atypes.size() );
314	<
312	>
313	>	map<int, RealType> atypeCutoff;
314	>
315		for (set<AtomType*>::iterator at = atypes.begin();
316		at != atypes.end(); ++at){
238	–	rc = interactionMan_->getSuggestedCutoffRadius(*at);
317		atid = (*at)->getIdent();
318	<	atypeCutoff[atid] = rc;
318	>	if (userChoseCutoff_)
319	>	atypeCutoff[atid] = userCutoff_;
320	>	else
321	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
322		}
323	<
323	>
324		vector<RealType> gTypeCutoffs;
244	–
325		// first we do a single loop over the cutoff groups to find the
326		// largest cutoff for any atypes present in this group.
327		#ifdef IS_MPI
#	Line 299 \| Line 379 \| namespace OpenMD {
379
380		vector<RealType> groupCutoff(nGroups_, 0.0);
381		groupToGtype.resize(nGroups_);
302	–
303	–	cerr << "nGroups = " << nGroups_ << "\n";
382		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305	–
383		groupCutoff[cg1] = 0.0;
384		vector<int> atomList = getAtomsInGroupRow(cg1);
308	–
385		for (vector<int>::iterator ia = atomList.begin();
386		ia != atomList.end(); ++ia) {
387		int atom1 = (*ia);
388	<	atid = identsLocal[atom1];
389	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
390	<	groupCutoff[cg1] = atypeCutoff[atid];
315	<	}
388	>	atid = idents[atom1];
389	>	if (atypeCutoff[atid] > groupCutoff[cg1])
390	>	groupCutoff[cg1] = atypeCutoff[atid];
391		}
392	<
392	>
393		bool gTypeFound = false;
394		for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
395		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
#	Line 322 \| Line 397 \| namespace OpenMD {
397		gTypeFound = true;
398		}
399		}
400	<	if (!gTypeFound) {
400	>	if (!gTypeFound) {
401		gTypeCutoffs.push_back( groupCutoff[cg1] );
402		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
403		}
404		}
405		#endif
406
332	–	cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
407		// Now we find the maximum group cutoff value present in the simulation
408
409	<	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
409	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
410	>	gTypeCutoffs.end());
411
412		#ifdef IS_MPI
413	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
413	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
414	>	MPI::MAX);
415		#endif
416
417		RealType tradRcut = groupMax;
#	Line 365 \| Line 441 \| namespace OpenMD {
441
442		pair<int,int> key = make_pair(i,j);
443		gTypeCutoffMap[key].first = thisRcut;
368	–
444		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
370	–
445		gTypeCutoffMap[key].second = thisRcut*thisRcut;
372	–
446		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
374	–
447		// sanity check
448
449		if (userChoseCutoff_) {
450		if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
451		sprintf(painCave.errMsg,
452		"ForceMatrixDecomposition::createGtypeCutoffMap "
453	<	"user-specified rCut does not match computed group Cutoff\n");
453	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
454		painCave.severity = OPENMD_ERROR;
455		painCave.isFatal = 1;
456		simError();
#	Line 410 \| Line 482 \| namespace OpenMD {
482		}
483
484		void ForceMatrixDecomposition::zeroWorkArrays() {
485	+	pairwisePot = 0.0;
486	+	embeddingPot = 0.0;
487
414	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
415	–	longRangePot_[j] = 0.0;
416	–	}
417	–
488		#ifdef IS_MPI
489		if (storageLayout_ & DataStorage::dslForce) {
490		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 430 \| Line 500 \| namespace OpenMD {
500		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
501
502		fill(pot_col.begin(), pot_col.end(),
503	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434	<
435	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
503	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
504
505		if (storageLayout_ & DataStorage::dslParticlePot) {
506	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
507	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
506	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
507	>	0.0);
508	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
509	>	0.0);
510		}
511
512		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 445 \| Line 515 \| namespace OpenMD {
515		}
516
517		if (storageLayout_ & DataStorage::dslFunctional) {
518	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
519	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
518	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
519	>	0.0);
520	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
521	>	0.0);
522		}
523
524		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 456 \| Line 528 \| namespace OpenMD {
528		atomColData.functionalDerivative.end(), 0.0);
529		}
530
531	<	#else
532	<
531	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
532	>	fill(atomRowData.skippedCharge.begin(),
533	>	atomRowData.skippedCharge.end(), 0.0);
534	>	fill(atomColData.skippedCharge.begin(),
535	>	atomColData.skippedCharge.end(), 0.0);
536	>	}
537	>
538	>	#endif
539	>	// even in parallel, we need to zero out the local arrays:
540	>
541		if (storageLayout_ & DataStorage::dslParticlePot) {
542		fill(snap_->atomData.particlePot.begin(),
543		snap_->atomData.particlePot.end(), 0.0);
#	Line 475 \| Line 555 \| namespace OpenMD {
555		fill(snap_->atomData.functionalDerivative.begin(),
556		snap_->atomData.functionalDerivative.end(), 0.0);
557		}
558	<	#endif
558	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
559	>	fill(snap_->atomData.skippedCharge.begin(),
560	>	snap_->atomData.skippedCharge.end(), 0.0);
561	>	}
562
563		}
564
#	Line 486 \| Line 569 \| namespace OpenMD {
569		#ifdef IS_MPI
570
571		// gather up the atomic positions
572	<	AtomCommVectorRow->gather(snap_->atomData.position,
572	>	AtomPlanVectorRow->gather(snap_->atomData.position,
573		atomRowData.position);
574	<	AtomCommVectorColumn->gather(snap_->atomData.position,
574	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
575		atomColData.position);
576
577		// gather up the cutoff group positions
578	<	cgCommVectorRow->gather(snap_->cgData.position,
578	>
579	>	cerr << "before gather\n";
580	>	for (int i = 0; i < snap_->cgData.position.size(); i++) {
581	>	cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
582	>	}
583	>
584	>	cgPlanVectorRow->gather(snap_->cgData.position,
585		cgRowData.position);
586	<	cgCommVectorColumn->gather(snap_->cgData.position,
586	>
587	>	cerr << "after gather\n";
588	>	for (int i = 0; i < cgRowData.position.size(); i++) {
589	>	cerr << "cgRpos = " << cgRowData.position[i] << "\n";
590	>	}
591	>
592	>	cgPlanVectorColumn->gather(snap_->cgData.position,
593		cgColData.position);
594	+	for (int i = 0; i < cgColData.position.size(); i++) {
595	+	cerr << "cgCpos = " << cgColData.position[i] << "\n";
596	+	}
597	+
598
599		// if needed, gather the atomic rotation matrices
600		if (storageLayout_ & DataStorage::dslAmat) {
601	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
601	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
602		atomRowData.aMat);
603	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
603	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
604		atomColData.aMat);
605		}
606
607		// if needed, gather the atomic eletrostatic frames
608		if (storageLayout_ & DataStorage::dslElectroFrame) {
609	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
609	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
610		atomRowData.electroFrame);
611	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
611	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
612		atomColData.electroFrame);
613		}
614	+
615		#endif
616		}
617
#	Line 525 \| Line 625 \| namespace OpenMD {
625
626		if (storageLayout_ & DataStorage::dslDensity) {
627
628	<	AtomCommRealRow->scatter(atomRowData.density,
628	>	AtomPlanRealRow->scatter(atomRowData.density,
629		snap_->atomData.density);
630
631		int n = snap_->atomData.density.size();
632		vector<RealType> rho_tmp(n, 0.0);
633	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
633	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
634		for (int i = 0; i < n; i++)
635		snap_->atomData.density[i] += rho_tmp[i];
636		}
#	Line 546 \| Line 646 \| namespace OpenMD {
646		storageLayout_ = sman_->getStorageLayout();
647		#ifdef IS_MPI
648		if (storageLayout_ & DataStorage::dslFunctional) {
649	<	AtomCommRealRow->gather(snap_->atomData.functional,
649	>	AtomPlanRealRow->gather(snap_->atomData.functional,
650		atomRowData.functional);
651	<	AtomCommRealColumn->gather(snap_->atomData.functional,
651	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
652		atomColData.functional);
653		}
654
655		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
656	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
656	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
657		atomRowData.functionalDerivative);
658	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
658	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
659		atomColData.functionalDerivative);
660		}
661		#endif
#	Line 569 \| Line 669 \| namespace OpenMD {
669		int n = snap_->atomData.force.size();
670		vector<Vector3d> frc_tmp(n, V3Zero);
671
672	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
672	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
673		for (int i = 0; i < n; i++) {
674		snap_->atomData.force[i] += frc_tmp[i];
675		frc_tmp[i] = 0.0;
676		}
677
678	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
679	<	for (int i = 0; i < n; i++)
678	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
679	>	for (int i = 0; i < n; i++) {
680		snap_->atomData.force[i] += frc_tmp[i];
681	<
682	<
681	>	}
682	>
683		if (storageLayout_ & DataStorage::dslTorque) {
684
685	<	int nt = snap_->atomData.force.size();
685	>	int nt = snap_->atomData.torque.size();
686		vector<Vector3d> trq_tmp(nt, V3Zero);
687
688	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
689	<	for (int i = 0; i < n; i++) {
688	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
689	>	for (int i = 0; i < nt; i++) {
690		snap_->atomData.torque[i] += trq_tmp[i];
691		trq_tmp[i] = 0.0;
692		}
693
694	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
695	<	for (int i = 0; i < n; i++)
694	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
695	>	for (int i = 0; i < nt; i++)
696		snap_->atomData.torque[i] += trq_tmp[i];
697		}
698	+
699	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
700	+
701	+	int ns = snap_->atomData.skippedCharge.size();
702	+	vector<RealType> skch_tmp(ns, 0.0);
703	+
704	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
705	+	for (int i = 0; i < ns; i++) {
706	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
707	+	skch_tmp[i] = 0.0;
708	+	}
709	+
710	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
711	+	for (int i = 0; i < ns; i++)
712	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
713	+	}
714
715		nLocal_ = snap_->getNumberOfAtoms();
716
#	Line 603 \| Line 719 \| namespace OpenMD {
719
720		// scatter/gather pot_row into the members of my column
721
722	<	AtomCommPotRow->scatter(pot_row, pot_temp);
722	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
723
724		for (int ii = 0; ii < pot_temp.size(); ii++ )
725	<	pot_local += pot_temp[ii];
725	>	pairwisePot += pot_temp[ii];
726
727		fill(pot_temp.begin(), pot_temp.end(),
728		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
729
730	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
730	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
731
732		for (int ii = 0; ii < pot_temp.size(); ii++ )
733	<	pot_local += pot_temp[ii];
618	<
733	>	pairwisePot += pot_temp[ii];
734		#endif
735	+
736	+	cerr << "pairwisePot = " << pairwisePot << "\n";
737		}
738
739		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 651 \| Line 768 \| namespace OpenMD {
768
769		#ifdef IS_MPI
770		d = cgColData.position[cg2] - cgRowData.position[cg1];
771	+	cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
772	+	cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
773		#else
774		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
775	+	cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
776	+	cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
777		#endif
778
779		snap_->wrapVector(d);
#	Line 691 \| Line 812 \| namespace OpenMD {
812		#ifdef IS_MPI
813		return massFactorsRow[atom1];
814		#else
815	<	return massFactorsLocal[atom1];
815	>	return massFactors[atom1];
816		#endif
817		}
818
#	Line 699 \| Line 820 \| namespace OpenMD {
820		#ifdef IS_MPI
821		return massFactorsCol[atom2];
822		#else
823	<	return massFactorsLocal[atom2];
823	>	return massFactors[atom2];
824		#endif
825
826		}
#	Line 717 \| Line 838 \| namespace OpenMD {
838		return d;
839		}
840
841	<	vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
842	<	return skipsForAtom[atom1];
841	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
842	>	return excludesForAtom[atom1];
843		}
844
845		/**
846	<	* There are a number of reasons to skip a pair or a
726	<	* particle. Mostly we do this to exclude atoms who are involved in
727	<	* short range interactions (bonds, bends, torsions), but we also
728	<	* need to exclude some overcounted interactions that result from
846	>	* We need to exclude some overcounted interactions that result from
847		* the parallel decomposition.
848		*/
849		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
850		int unique_id_1, unique_id_2;
851	+
852
853	+	cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
854		#ifdef IS_MPI
855		// in MPI, we have to look up the unique IDs for each atom
856		unique_id_1 = AtomRowToGlobal[atom1];
857		unique_id_2 = AtomColToGlobal[atom2];
858
859	+	cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
860		// this situation should only arise in MPI simulations
861		if (unique_id_1 == unique_id_2) return true;
862
#	Line 745 \| Line 866 \| namespace OpenMD {
866		} else {
867		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
868		}
869	+	#endif
870	+	return false;
871	+	}
872	+
873	+	/**
874	+	* We need to handle the interactions for atoms who are involved in
875	+	* the same rigid body as well as some short range interactions
876	+	* (bonds, bends, torsions) differently from other interactions.
877	+	* We'll still visit the pairwise routines, but with a flag that
878	+	* tells those routines to exclude the pair from direct long range
879	+	* interactions. Some indirect interactions (notably reaction
880	+	* field) must still be handled for these pairs.
881	+	*/
882	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
883	+	int unique_id_2;
884	+	#ifdef IS_MPI
885	+	// in MPI, we have to look up the unique IDs for the row atom.
886	+	unique_id_2 = AtomColToGlobal[atom2];
887		#else
888		// in the normal loop, the atom numbers are unique
750	–	unique_id_1 = atom1;
889		unique_id_2 = atom2;
890		#endif
891
892	<	for (vector<int>::iterator i = skipsForAtom[atom1].begin();
893	<	i != skipsForAtom[atom1].end(); ++i) {
892	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
893	>	i != excludesForAtom[atom1].end(); ++i) {
894		if ( (*i) == unique_id_2 ) return true;
895	<	}
895	>	}
896
897	+	return false;
898		}
899
900
#	Line 776 \| Line 915 \| namespace OpenMD {
915		}
916
917		// filling interaction blocks with pointers
918	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
919	<	InteractionData idat;
918	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
919	>	int atom1, int atom2) {
920
921	+	idat.excluded = excludeAtomPair(atom1, atom2);
922	+
923		#ifdef IS_MPI
924	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
925	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
926	+	// ff_->getAtomType(identsCol[atom2]) );
927
784	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
785	–	ff_->getAtomType(identsCol[atom2]) );
786	–
787	–
928		if (storageLayout_ & DataStorage::dslAmat) {
929		idat.A1 = &(atomRowData.aMat[atom1]);
930		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 820 \| Line 960 \| namespace OpenMD {
960		idat.particlePot2 = &(atomColData.particlePot[atom2]);
961		}
962
963	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
964	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
965	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
966	+	}
967	+
968		#else
969
970	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
971	<	ff_->getAtomType(identsLocal[atom2]) );
970	>	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
971	>	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
972	>	// ff_->getAtomType(idents[atom2]) );
973
974		if (storageLayout_ & DataStorage::dslAmat) {
975		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 840 \| Line 986 \| namespace OpenMD {
986		idat.t2 = &(snap_->atomData.torque[atom2]);
987		}
988
989	<	if (storageLayout_ & DataStorage::dslDensity) {
989	>	if (storageLayout_ & DataStorage::dslDensity) {
990		idat.rho1 = &(snap_->atomData.density[atom1]);
991		idat.rho2 = &(snap_->atomData.density[atom2]);
992		}
#	Line 860 \| Line 1006 \| namespace OpenMD {
1006		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1007		}
1008
1009	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1010	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1011	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1012	+	}
1013		#endif
864	–	return idat;
1014		}
1015
1016
1017	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
1017	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1018		#ifdef IS_MPI
1019		pot_row[atom1] += 0.5 * *(idat.pot);
1020		pot_col[atom2] += 0.5 * *(idat.pot);
#	Line 873 \| Line 1022 \| namespace OpenMD {
1022		atomRowData.force[atom1] += *(idat.f1);
1023		atomColData.force[atom2] -= *(idat.f1);
1024		#else
1025	<	longRangePot_ += *(idat.pot);
1026	<
1025	>	pairwisePot += *(idat.pot);
1026	>
1027		snap_->atomData.force[atom1] += *(idat.f1);
1028		snap_->atomData.force[atom2] -= *(idat.f1);
1029		#endif
1030	<
1030	>
1031		}
1032
884	–
885	–	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
886	–
887	–	InteractionData idat;
888	–	#ifdef IS_MPI
889	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
890	–	ff_->getAtomType(identsCol[atom2]) );
891	–
892	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
893	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
894	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
895	–	}
896	–	if (storageLayout_ & DataStorage::dslTorque) {
897	–	idat.t1 = &(atomRowData.torque[atom1]);
898	–	idat.t2 = &(atomColData.torque[atom2]);
899	–	}
900	–	#else
901	–	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
902	–	ff_->getAtomType(identsLocal[atom2]) );
903	–
904	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
905	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
906	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
907	–	}
908	–	if (storageLayout_ & DataStorage::dslTorque) {
909	–	idat.t1 = &(snap_->atomData.torque[atom1]);
910	–	idat.t2 = &(snap_->atomData.torque[atom2]);
911	–	}
912	–	#endif
913	–	}
914	–
1033		/*
1034		* buildNeighborList
1035		*
#	Line 922 \| Line 1040 \| namespace OpenMD {
1040
1041		vector<pair<int, int> > neighborList;
1042		groupCutoffs cuts;
1043	+	bool doAllPairs = false;
1044	+
1045		#ifdef IS_MPI
1046		cellListRow_.clear();
1047		cellListCol_.clear();
#	Line 940 \| Line 1060 \| namespace OpenMD {
1060		nCells_.x() = (int) ( Hx.length() )/ rList_;
1061		nCells_.y() = (int) ( Hy.length() )/ rList_;
1062		nCells_.z() = (int) ( Hz.length() )/ rList_;
1063	+
1064	+	// handle small boxes where the cell offsets can end up repeating cells
1065	+
1066	+	if (nCells_.x() < 3) doAllPairs = true;
1067	+	if (nCells_.y() < 3) doAllPairs = true;
1068	+	if (nCells_.z() < 3) doAllPairs = true;
1069
1070		Mat3x3d invHmat = snap_->getInvHmat();
1071		Vector3d rs, scaled, dr;
#	Line 954 \| Line 1080 \| namespace OpenMD {
1080		cellList_.resize(nCtot);
1081		#endif
1082
1083	+	if (!doAllPairs) {
1084		#ifdef IS_MPI
958	–	for (int i = 0; i < nGroupsInRow_; i++) {
959	–	rs = cgRowData.position[i];
960	–	// scaled positions relative to the box vectors
961	–	scaled = invHmat * rs;
962	–	// wrap the vector back into the unit box by subtracting integer box
963	–	// numbers
964	–	for (int j = 0; j < 3; j++)
965	–	scaled[j] -= roundMe(scaled[j]);
966	–
967	–	// find xyz-indices of cell that cutoffGroup is in.
968	–	whichCell.x() = nCells_.x() * scaled.x();
969	–	whichCell.y() = nCells_.y() * scaled.y();
970	–	whichCell.z() = nCells_.z() * scaled.z();
1085
1086	<	// find single index of this cell:
1087	<	cellIndex = Vlinear(whichCell, nCells_);
1088	<	// add this cutoff group to the list of groups in this cell;
1089	<	cellListRow_[cellIndex].push_back(i);
1090	<	}
1091	<
1092	<	for (int i = 0; i < nGroupsInCol_; i++) {
1093	<	rs = cgColData.position[i];
1094	<	// scaled positions relative to the box vectors
1095	<	scaled = invHmat * rs;
1096	<	// wrap the vector back into the unit box by subtracting integer box
1097	<	// numbers
1098	<	for (int j = 0; j < 3; j++)
1099	<	scaled[j] -= roundMe(scaled[j]);
1100	<
1101	<	// find xyz-indices of cell that cutoffGroup is in.
1102	<	whichCell.x() = nCells_.x() * scaled.x();
1103	<	whichCell.y() = nCells_.y() * scaled.y();
1104	<	whichCell.z() = nCells_.z() * scaled.z();
1105	<
1106	<	// find single index of this cell:
1107	<	cellIndex = Vlinear(whichCell, nCells_);
1108	<	// add this cutoff group to the list of groups in this cell;
1109	<	cellListCol_[cellIndex].push_back(i);
1110	<	}
1086	>	for (int i = 0; i < nGroupsInRow_; i++) {
1087	>	rs = cgRowData.position[i];
1088	>
1089	>	// scaled positions relative to the box vectors
1090	>	scaled = invHmat * rs;
1091	>
1092	>	// wrap the vector back into the unit box by subtracting integer box
1093	>	// numbers
1094	>	for (int j = 0; j < 3; j++) {
1095	>	scaled[j] -= roundMe(scaled[j]);
1096	>	scaled[j] += 0.5;
1097	>	}
1098	>
1099	>	// find xyz-indices of cell that cutoffGroup is in.
1100	>	whichCell.x() = nCells_.x() * scaled.x();
1101	>	whichCell.y() = nCells_.y() * scaled.y();
1102	>	whichCell.z() = nCells_.z() * scaled.z();
1103	>
1104	>	// find single index of this cell:
1105	>	cellIndex = Vlinear(whichCell, nCells_);
1106	>
1107	>	// add this cutoff group to the list of groups in this cell;
1108	>	cellListRow_[cellIndex].push_back(i);
1109	>	}
1110	>	for (int i = 0; i < nGroupsInCol_; i++) {
1111	>	rs = cgColData.position[i];
1112	>
1113	>	// scaled positions relative to the box vectors
1114	>	scaled = invHmat * rs;
1115	>
1116	>	// wrap the vector back into the unit box by subtracting integer box
1117	>	// numbers
1118	>	for (int j = 0; j < 3; j++) {
1119	>	scaled[j] -= roundMe(scaled[j]);
1120	>	scaled[j] += 0.5;
1121	>	}
1122	>
1123	>	// find xyz-indices of cell that cutoffGroup is in.
1124	>	whichCell.x() = nCells_.x() * scaled.x();
1125	>	whichCell.y() = nCells_.y() * scaled.y();
1126	>	whichCell.z() = nCells_.z() * scaled.z();
1127	>
1128	>	// find single index of this cell:
1129	>	cellIndex = Vlinear(whichCell, nCells_);
1130	>
1131	>	// add this cutoff group to the list of groups in this cell;
1132	>	cellListCol_[cellIndex].push_back(i);
1133	>	}
1134		#else
1135	<	for (int i = 0; i < nGroups_; i++) {
1136	<	rs = snap_->cgData.position[i];
1137	<	// scaled positions relative to the box vectors
1138	<	scaled = invHmat * rs;
1139	<	// wrap the vector back into the unit box by subtracting integer box
1140	<	// numbers
1141	<	for (int j = 0; j < 3; j++)
1142	<	scaled[j] -= roundMe(scaled[j]);
1143	<
1144	<	// find xyz-indices of cell that cutoffGroup is in.
1145	<	whichCell.x() = nCells_.x() * scaled.x();
1146	<	whichCell.y() = nCells_.y() * scaled.y();
1147	<	whichCell.z() = nCells_.z() * scaled.z();
1148	<
1149	<	// find single index of this cell:
1150	<	cellIndex = Vlinear(whichCell, nCells_);
1151	<	// add this cutoff group to the list of groups in this cell;
1152	<	cellList_[cellIndex].push_back(i);
1153	<	}
1135	>	for (int i = 0; i < nGroups_; i++) {
1136	>	rs = snap_->cgData.position[i];
1137	>
1138	>	// scaled positions relative to the box vectors
1139	>	scaled = invHmat * rs;
1140	>
1141	>	// wrap the vector back into the unit box by subtracting integer box
1142	>	// numbers
1143	>	for (int j = 0; j < 3; j++) {
1144	>	scaled[j] -= roundMe(scaled[j]);
1145	>	scaled[j] += 0.5;
1146	>	}
1147	>
1148	>	// find xyz-indices of cell that cutoffGroup is in.
1149	>	whichCell.x() = nCells_.x() * scaled.x();
1150	>	whichCell.y() = nCells_.y() * scaled.y();
1151	>	whichCell.z() = nCells_.z() * scaled.z();
1152	>
1153	>	// find single index of this cell:
1154	>	cellIndex = Vlinear(whichCell, nCells_);
1155	>
1156	>	// add this cutoff group to the list of groups in this cell;
1157	>	cellList_[cellIndex].push_back(i);
1158	>	}
1159		#endif
1160
1161	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1162	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1163	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1164	<	Vector3i m1v(m1x, m1y, m1z);
1165	<	int m1 = Vlinear(m1v, nCells_);
1024	<
1025	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1026	<	os != cellOffsets_.end(); ++os) {
1161	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1162	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1163	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1164	>	Vector3i m1v(m1x, m1y, m1z);
1165	>	int m1 = Vlinear(m1v, nCells_);
1166
1167	<	Vector3i m2v = m1v + (*os);
1168	<
1169	<	if (m2v.x() >= nCells_.x()) {
1170	<	m2v.x() = 0;
1171	<	} else if (m2v.x() < 0) {
1172	<	m2v.x() = nCells_.x() - 1;
1173	<	}
1174	<
1175	<	if (m2v.y() >= nCells_.y()) {
1176	<	m2v.y() = 0;
1177	<	} else if (m2v.y() < 0) {
1178	<	m2v.y() = nCells_.y() - 1;
1179	<	}
1180	<
1181	<	if (m2v.z() >= nCells_.z()) {
1182	<	m2v.z() = 0;
1183	<	} else if (m2v.z() < 0) {
1184	<	m2v.z() = nCells_.z() - 1;
1185	<	}
1186	<
1187	<	int m2 = Vlinear (m2v, nCells_);
1188	<
1167	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1168	>	os != cellOffsets_.end(); ++os) {
1169	>
1170	>	Vector3i m2v = m1v + (*os);
1171	>
1172	>	if (m2v.x() >= nCells_.x()) {
1173	>	m2v.x() = 0;
1174	>	} else if (m2v.x() < 0) {
1175	>	m2v.x() = nCells_.x() - 1;
1176	>	}
1177	>
1178	>	if (m2v.y() >= nCells_.y()) {
1179	>	m2v.y() = 0;
1180	>	} else if (m2v.y() < 0) {
1181	>	m2v.y() = nCells_.y() - 1;
1182	>	}
1183	>
1184	>	if (m2v.z() >= nCells_.z()) {
1185	>	m2v.z() = 0;
1186	>	} else if (m2v.z() < 0) {
1187	>	m2v.z() = nCells_.z() - 1;
1188	>	}
1189	>
1190	>	int m2 = Vlinear (m2v, nCells_);
1191	>
1192		#ifdef IS_MPI
1193	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1194	<	j1 != cellListRow_[m1].end(); ++j1) {
1195	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1196	<	j2 != cellListCol_[m2].end(); ++j2) {
1197	<
1198	<	// Always do this if we're in different cells or if
1199	<	// we're in the same cell and the global index of the
1058	<	// j2 cutoff group is less than the j1 cutoff group
1059	<
1060	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1193	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1194	>	j1 != cellListRow_[m1].end(); ++j1) {
1195	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1196	>	j2 != cellListCol_[m2].end(); ++j2) {
1197	>
1198	>	// In parallel, we need to visit all pairs of row &
1199	>	// column indicies and will truncate later on.
1200		dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1201		snap_->wrapVector(dr);
1202		cuts = getGroupCutoffs( (j1), (j2) );
1203		if (dr.lengthSquare() < cuts.third) {
1204		neighborList.push_back(make_pair((j1), (j2)));
1205	<	}
1205	>	}
1206		}
1207		}
1069	–	}
1208		#else
1209	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1210	<	j1 != cellList_[m1].end(); ++j1) {
1211	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1212	<	j2 != cellList_[m2].end(); ++j2) {
1213	<
1214	<	// Always do this if we're in different cells or if
1215	<	// we're in the same cell and the global index of the
1216	<	// j2 cutoff group is less than the j1 cutoff group
1217	<
1218	<	if (m2 != m1 \|\| (j2) < (j1)) {
1219	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1220	<	snap_->wrapVector(dr);
1221	<	cuts = getGroupCutoffs( (j1), (j2) );
1222	<	if (dr.lengthSquare() < cuts.third) {
1223	<	neighborList.push_back(make_pair((j1), (j2)));
1209	>
1210	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1211	>	j1 != cellList_[m1].end(); ++j1) {
1212	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1213	>	j2 != cellList_[m2].end(); ++j2) {
1214	>
1215	>	// Always do this if we're in different cells or if
1216	>	// we're in the same cell and the global index of the
1217	>	// j2 cutoff group is less than the j1 cutoff group
1218	>
1219	>	if (m2 != m1 \|\| (j2) < (j1)) {
1220	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1221	>	snap_->wrapVector(dr);
1222	>	cuts = getGroupCutoffs( (j1), (j2) );
1223	>	if (dr.lengthSquare() < cuts.third) {
1224	>	neighborList.push_back(make_pair((j1), (j2)));
1225	>	}
1226		}
1227		}
1228		}
1089	–	}
1229		#endif
1230	+	}
1231		}
1232		}
1233		}
1234	+	} else {
1235	+	// branch to do all cutoff group pairs
1236	+	#ifdef IS_MPI
1237	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1238	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1239	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1240	+	snap_->wrapVector(dr);
1241	+	cuts = getGroupCutoffs( j1, j2 );
1242	+	if (dr.lengthSquare() < cuts.third) {
1243	+	neighborList.push_back(make_pair(j1, j2));
1244	+	}
1245	+	}
1246	+	}
1247	+	#else
1248	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1249	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1250	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1251	+	snap_->wrapVector(dr);
1252	+	cuts = getGroupCutoffs( j1, j2 );
1253	+	if (dr.lengthSquare() < cuts.third) {
1254	+	neighborList.push_back(make_pair(j1, j2));
1255	+	}
1256	+	}
1257	+	}
1258	+	#endif
1259		}
1260	<
1260	>
1261		// save the local cutoff group positions for the check that is
1262		// done on each loop:
1263		saved_CG_positions_.clear();
1264		for (int i = 0; i < nGroups_; i++)
1265		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1266	<
1266	>
1267		return neighborList;
1268		}
1269		} //end namespace OpenMD

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs. Revision 1593 by gezelter, Fri Jul 15 21:35:14 2011 UTC

Diff Legend

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs.
Revision 1593 by gezelter, Fri Jul 15 21:35:14 2011 UTC