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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs.
Revision 1601 by gezelter, Thu Aug 4 20:04:35 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();
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();
67	–	vector<RealType> massFactorsLocal = info_->getMassFactors();
68	–	PairList excludes = info_->getExcludedInteractions();
69	–	PairList oneTwo = info_->getOneTwoInteractions();
70	–	PairList oneThree = info_->getOneThreeInteractions();
71	–	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_);
77	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
78	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
79	<	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 107 \| 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	<
116	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
117	<	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	+	cgRowToGlobal.resize(nGroupsInRow_);
158	+	cgColToGlobal.resize(nGroupsInCol_);
159	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
160	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
161	+
162	+	massFactorsRow.resize(nAtomsInRow_);
163	+	massFactorsCol.resize(nAtomsInCol_);
164	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
165	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
166	+
167		groupListRow_.clear();
168		groupListRow_.resize(nGroupsInRow_);
169		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 141 \| Line 186 \| namespace OpenMD {
186		}
187		}
188
189	<	skipsForRowAtom.clear();
190	<	skipsForRowAtom.resize(nAtomsInRow_);
189	>	excludesForAtom.clear();
190	>	excludesForAtom.resize(nAtomsInRow_);
191	>	toposForAtom.clear();
192	>	toposForAtom.resize(nAtomsInRow_);
193	>	topoDist.clear();
194	>	topoDist.resize(nAtomsInRow_);
195		for (int i = 0; i < nAtomsInRow_; i++) {
196		int iglob = AtomRowToGlobal[i];
148	–	for (int j = 0; j < nAtomsInCol_; j++) {
149	–	int jglob = AtomColToGlobal[j];
150	–	if (excludes.hasPair(iglob, jglob))
151	–	skipsForRowAtom[i].push_back(j);
152	–	}
153	–	}
197
155	–	toposForRowAtom.clear();
156	–	toposForRowAtom.resize(nAtomsInRow_);
157	–	for (int i = 0; i < nAtomsInRow_; i++) {
158	–	int iglob = AtomRowToGlobal[i];
159	–	int nTopos = 0;
198		for (int j = 0; j < nAtomsInCol_; j++) {
199	<	int jglob = AtomColToGlobal[j];
200	<	if (oneTwo.hasPair(iglob, jglob)) {
201	<	toposForRowAtom[i].push_back(j);
202	<	topoDistRow[i][nTopos] = 1;
203	<	nTopos++;
199	>	int jglob = AtomColToGlobal[j];
200	>
201	>	if (excludes->hasPair(iglob, jglob))
202	>	excludesForAtom[i].push_back(j);
203	>
204	>	if (oneTwo->hasPair(iglob, jglob)) {
205	>	toposForAtom[i].push_back(j);
206	>	topoDist[i].push_back(1);
207	>	} else {
208	>	if (oneThree->hasPair(iglob, jglob)) {
209	>	toposForAtom[i].push_back(j);
210	>	topoDist[i].push_back(2);
211	>	} else {
212	>	if (oneFour->hasPair(iglob, jglob)) {
213	>	toposForAtom[i].push_back(j);
214	>	topoDist[i].push_back(3);
215	>	}
216	>	}
217		}
167	–	if (oneThree.hasPair(iglob, jglob)) {
168	–	toposForRowAtom[i].push_back(j);
169	–	topoDistRow[i][nTopos] = 2;
170	–	nTopos++;
171	–	}
172	–	if (oneFour.hasPair(iglob, jglob)) {
173	–	toposForRowAtom[i].push_back(j);
174	–	topoDistRow[i][nTopos] = 3;
175	–	nTopos++;
176	–	}
218		}
219		}
220
221		#endif
222	+
223	+	// allocate memory for the parallel objects
224	+	atypesLocal.resize(nLocal_);
225	+
226	+	for (int i = 0; i < nLocal_; i++)
227	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
228	+
229		groupList_.clear();
230		groupList_.resize(nGroups_);
231		for (int i = 0; i < nGroups_; i++) {
#	Line 186 \| Line 234 \| namespace OpenMD {
234		int aid = AtomLocalToGlobal[j];
235		if (globalGroupMembership[aid] == gid) {
236		groupList_[i].push_back(j);
189	–
237		}
238		}
239		}
240
241	<	skipsForLocalAtom.clear();
242	<	skipsForLocalAtom.resize(nLocal_);
241	>	excludesForAtom.clear();
242	>	excludesForAtom.resize(nLocal_);
243	>	toposForAtom.clear();
244	>	toposForAtom.resize(nLocal_);
245	>	topoDist.clear();
246	>	topoDist.resize(nLocal_);
247
248		for (int i = 0; i < nLocal_; i++) {
249		int iglob = AtomLocalToGlobal[i];
250	+
251		for (int j = 0; j < nLocal_; j++) {
252	<	int jglob = AtomLocalToGlobal[j];
253	<	if (excludes.hasPair(iglob, jglob))
254	<	skipsForLocalAtom[i].push_back(j);
255	<	}
256	<	}
257	<	toposForLocalAtom.clear();
258	<	toposForLocalAtom.resize(nLocal_);
259	<	for (int i = 0; i < nLocal_; i++) {
260	<	int iglob = AtomLocalToGlobal[i];
261	<	int nTopos = 0;
262	<	for (int j = 0; j < nLocal_; j++) {
263	<	int jglob = AtomLocalToGlobal[j];
264	<	if (oneTwo.hasPair(iglob, jglob)) {
265	<	toposForLocalAtom[i].push_back(j);
266	<	topoDistLocal[i][nTopos] = 1;
267	<	nTopos++;
252	>	int jglob = AtomLocalToGlobal[j];
253	>
254	>	if (excludes->hasPair(iglob, jglob))
255	>	excludesForAtom[i].push_back(j);
256	>
257	>	if (oneTwo->hasPair(iglob, jglob)) {
258	>	toposForAtom[i].push_back(j);
259	>	topoDist[i].push_back(1);
260	>	} else {
261	>	if (oneThree->hasPair(iglob, jglob)) {
262	>	toposForAtom[i].push_back(j);
263	>	topoDist[i].push_back(2);
264	>	} else {
265	>	if (oneFour->hasPair(iglob, jglob)) {
266	>	toposForAtom[i].push_back(j);
267	>	topoDist[i].push_back(3);
268	>	}
269	>	}
270		}
217	–	if (oneThree.hasPair(iglob, jglob)) {
218	–	toposForLocalAtom[i].push_back(j);
219	–	topoDistLocal[i][nTopos] = 2;
220	–	nTopos++;
221	–	}
222	–	if (oneFour.hasPair(iglob, jglob)) {
223	–	toposForLocalAtom[i].push_back(j);
224	–	topoDistLocal[i][nTopos] = 3;
225	–	nTopos++;
226	–	}
271		}
272	<	}
272	>	}
273	>
274	>	createGtypeCutoffMap();
275
276		}
277
278		void ForceMatrixDecomposition::createGtypeCutoffMap() {
279	<
279	>
280		RealType tol = 1e-6;
281	+	largestRcut_ = 0.0;
282		RealType rc;
283		int atid;
284		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
285	<	vector<RealType> atypeCutoff;
286	<	atypeCutoff.resize( atypes.size() );
287	<
288	<	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
289	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
285	>
286	>	map<int, RealType> atypeCutoff;
287	>
288	>	for (set<AtomType*>::iterator at = atypes.begin();
289	>	at != atypes.end(); ++at){
290		atid = (*at)->getIdent();
291	<	atypeCutoff[atid] = rc;
291	>	if (userChoseCutoff_)
292	>	atypeCutoff[atid] = userCutoff_;
293	>	else
294	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
295		}
296	<
296	>
297		vector<RealType> gTypeCutoffs;
248	–
298		// first we do a single loop over the cutoff groups to find the
299		// largest cutoff for any atypes present in this group.
300		#ifdef IS_MPI
301		vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
302	+	groupRowToGtype.resize(nGroupsInRow_);
303		for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
304		vector<int> atomListRow = getAtomsInGroupRow(cg1);
305		for (vector<int>::iterator ia = atomListRow.begin();
#	Line 275 \| Line 325 \| namespace OpenMD {
325
326		}
327		vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
328	+	groupColToGtype.resize(nGroupsInCol_);
329		for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
330		vector<int> atomListCol = getAtomsInGroupColumn(cg2);
331		for (vector<int>::iterator jb = atomListCol.begin();
#	Line 298 \| Line 349 \| namespace OpenMD {
349		}
350		}
351		#else
352	+
353		vector<RealType> groupCutoff(nGroups_, 0.0);
354	+	groupToGtype.resize(nGroups_);
355		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
356		groupCutoff[cg1] = 0.0;
357		vector<int> atomList = getAtomsInGroupRow(cg1);
358		for (vector<int>::iterator ia = atomList.begin();
359		ia != atomList.end(); ++ia) {
360		int atom1 = (*ia);
361	<	atid = identsLocal[atom1];
362	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
361	>	atid = idents[atom1];
362	>	if (atypeCutoff[atid] > groupCutoff[cg1])
363		groupCutoff[cg1] = atypeCutoff[atid];
311	–	}
364		}
365	<
365	>
366		bool gTypeFound = false;
367		for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
368		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
#	Line 318 \| Line 370 \| namespace OpenMD {
370		gTypeFound = true;
371		}
372		}
373	<	if (!gTypeFound) {
373	>	if (!gTypeFound) {
374		gTypeCutoffs.push_back( groupCutoff[cg1] );
375		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
376		}
#	Line 327 \| Line 379 \| namespace OpenMD {
379
380		// Now we find the maximum group cutoff value present in the simulation
381
382	<	vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
383	<	RealType groupMax = *groupMaxLoc;
382	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
383	>	gTypeCutoffs.end());
384
385		#ifdef IS_MPI
386	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
386	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
387	>	MPI::MAX);
388		#endif
389
390		RealType tradRcut = groupMax;
391
392		for (int i = 0; i < gTypeCutoffs.size(); i++) {
393	<	for (int j = 0; j < gTypeCutoffs.size(); j++) {
341	<
393	>	for (int j = 0; j < gTypeCutoffs.size(); j++) {
394		RealType thisRcut;
395		switch(cutoffPolicy_) {
396		case TRADITIONAL:
397		thisRcut = tradRcut;
398	+	break;
399		case MIX:
400		thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
401	+	break;
402		case MAX:
403		thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
404	+	break;
405		default:
406		sprintf(painCave.errMsg,
407		"ForceMatrixDecomposition::createGtypeCutoffMap "
408		"hit an unknown cutoff policy!\n");
409		painCave.severity = OPENMD_ERROR;
410		painCave.isFatal = 1;
411	<	simError();
411	>	simError();
412	>	break;
413		}
414
415		pair<int,int> key = make_pair(i,j);
416		gTypeCutoffMap[key].first = thisRcut;
361	–
417		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
363	–
418		gTypeCutoffMap[key].second = thisRcut*thisRcut;
365	–
419		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
367	–
420		// sanity check
421
422		if (userChoseCutoff_) {
423		if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
424		sprintf(painCave.errMsg,
425		"ForceMatrixDecomposition::createGtypeCutoffMap "
426	<	"user-specified rCut does not match computed group Cutoff\n");
426	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
427		painCave.severity = OPENMD_ERROR;
428		painCave.isFatal = 1;
429		simError();
#	Line 383 \| Line 435 \| namespace OpenMD {
435
436
437		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
438	<	int i, j;
387	<
438	>	int i, j;
439		#ifdef IS_MPI
440		i = groupRowToGtype[cg1];
441		j = groupColToGtype[cg2];
442		#else
443		i = groupToGtype[cg1];
444		j = groupToGtype[cg2];
445	<	#endif
395	<
445	>	#endif
446		return gTypeCutoffMap[make_pair(i,j)];
447		}
448
449	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
450	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
451	+	if (toposForAtom[atom1][j] == atom2)
452	+	return topoDist[atom1][j];
453	+	}
454	+	return 0;
455	+	}
456
457		void ForceMatrixDecomposition::zeroWorkArrays() {
458	+	pairwisePot = 0.0;
459	+	embeddingPot = 0.0;
460
402	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403	–	longRangePot_[j] = 0.0;
404	–	}
405	–
461		#ifdef IS_MPI
462		if (storageLayout_ & DataStorage::dslForce) {
463		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 418 \| Line 473 \| namespace OpenMD {
473		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
474
475		fill(pot_col.begin(), pot_col.end(),
476	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422	<
423	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
476	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
477
478		if (storageLayout_ & DataStorage::dslParticlePot) {
479	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
480	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
479	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
480	>	0.0);
481	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
482	>	0.0);
483		}
484
485		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 433 \| Line 488 \| namespace OpenMD {
488		}
489
490		if (storageLayout_ & DataStorage::dslFunctional) {
491	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
492	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
491	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
492	>	0.0);
493	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
494	>	0.0);
495		}
496
497		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 444 \| Line 501 \| namespace OpenMD {
501		atomColData.functionalDerivative.end(), 0.0);
502		}
503
504	<	#else
505	<
504	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
505	>	fill(atomRowData.skippedCharge.begin(),
506	>	atomRowData.skippedCharge.end(), 0.0);
507	>	fill(atomColData.skippedCharge.begin(),
508	>	atomColData.skippedCharge.end(), 0.0);
509	>	}
510	>
511	>	#endif
512	>	// even in parallel, we need to zero out the local arrays:
513	>
514		if (storageLayout_ & DataStorage::dslParticlePot) {
515		fill(snap_->atomData.particlePot.begin(),
516		snap_->atomData.particlePot.end(), 0.0);
#	Line 463 \| Line 528 \| namespace OpenMD {
528		fill(snap_->atomData.functionalDerivative.begin(),
529		snap_->atomData.functionalDerivative.end(), 0.0);
530		}
531	<	#endif
531	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
532	>	fill(snap_->atomData.skippedCharge.begin(),
533	>	snap_->atomData.skippedCharge.end(), 0.0);
534	>	}
535
536		}
537
#	Line 474 \| Line 542 \| namespace OpenMD {
542		#ifdef IS_MPI
543
544		// gather up the atomic positions
545	<	AtomCommVectorRow->gather(snap_->atomData.position,
545	>	AtomPlanVectorRow->gather(snap_->atomData.position,
546		atomRowData.position);
547	<	AtomCommVectorColumn->gather(snap_->atomData.position,
547	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
548		atomColData.position);
549
550		// gather up the cutoff group positions
551	<	cgCommVectorRow->gather(snap_->cgData.position,
551	>
552	>	cgPlanVectorRow->gather(snap_->cgData.position,
553		cgRowData.position);
554	<	cgCommVectorColumn->gather(snap_->cgData.position,
554	>
555	>	cgPlanVectorColumn->gather(snap_->cgData.position,
556		cgColData.position);
557	+
558
559		// if needed, gather the atomic rotation matrices
560		if (storageLayout_ & DataStorage::dslAmat) {
561	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
561	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
562		atomRowData.aMat);
563	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
563	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
564		atomColData.aMat);
565		}
566
567		// if needed, gather the atomic eletrostatic frames
568		if (storageLayout_ & DataStorage::dslElectroFrame) {
569	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
569	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
570		atomRowData.electroFrame);
571	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
571	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
572		atomColData.electroFrame);
573		}
574	+
575		#endif
576		}
577
#	Line 513 \| Line 585 \| namespace OpenMD {
585
586		if (storageLayout_ & DataStorage::dslDensity) {
587
588	<	AtomCommRealRow->scatter(atomRowData.density,
588	>	AtomPlanRealRow->scatter(atomRowData.density,
589		snap_->atomData.density);
590
591		int n = snap_->atomData.density.size();
592		vector<RealType> rho_tmp(n, 0.0);
593	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
593	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
594		for (int i = 0; i < n; i++)
595		snap_->atomData.density[i] += rho_tmp[i];
596		}
#	Line 534 \| Line 606 \| namespace OpenMD {
606		storageLayout_ = sman_->getStorageLayout();
607		#ifdef IS_MPI
608		if (storageLayout_ & DataStorage::dslFunctional) {
609	<	AtomCommRealRow->gather(snap_->atomData.functional,
609	>	AtomPlanRealRow->gather(snap_->atomData.functional,
610		atomRowData.functional);
611	<	AtomCommRealColumn->gather(snap_->atomData.functional,
611	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
612		atomColData.functional);
613		}
614
615		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
616	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
616	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
617		atomRowData.functionalDerivative);
618	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
618	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
619		atomColData.functionalDerivative);
620		}
621		#endif
#	Line 557 \| Line 629 \| namespace OpenMD {
629		int n = snap_->atomData.force.size();
630		vector<Vector3d> frc_tmp(n, V3Zero);
631
632	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
632	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
633		for (int i = 0; i < n; i++) {
634		snap_->atomData.force[i] += frc_tmp[i];
635		frc_tmp[i] = 0.0;
636		}
637
638	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
639	<	for (int i = 0; i < n; i++)
638	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
639	>	for (int i = 0; i < n; i++) {
640		snap_->atomData.force[i] += frc_tmp[i];
641	<
642	<
641	>	}
642	>
643		if (storageLayout_ & DataStorage::dslTorque) {
644
645	<	int nt = snap_->atomData.force.size();
645	>	int nt = snap_->atomData.torque.size();
646		vector<Vector3d> trq_tmp(nt, V3Zero);
647
648	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
649	<	for (int i = 0; i < n; i++) {
648	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
649	>	for (int i = 0; i < nt; i++) {
650		snap_->atomData.torque[i] += trq_tmp[i];
651		trq_tmp[i] = 0.0;
652		}
653
654	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
655	<	for (int i = 0; i < n; i++)
654	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
655	>	for (int i = 0; i < nt; i++)
656		snap_->atomData.torque[i] += trq_tmp[i];
657		}
658	+
659	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
660	+
661	+	int ns = snap_->atomData.skippedCharge.size();
662	+	vector<RealType> skch_tmp(ns, 0.0);
663	+
664	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
665	+	for (int i = 0; i < ns; i++) {
666	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
667	+	skch_tmp[i] = 0.0;
668	+	}
669	+
670	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
671	+	for (int i = 0; i < ns; i++)
672	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
673	+	}
674
675		nLocal_ = snap_->getNumberOfAtoms();
676
#	Line 591 \| Line 679 \| namespace OpenMD {
679
680		// scatter/gather pot_row into the members of my column
681
682	<	AtomCommPotRow->scatter(pot_row, pot_temp);
682	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
683
684		for (int ii = 0; ii < pot_temp.size(); ii++ )
685	<	pot_local += pot_temp[ii];
685	>	pairwisePot += pot_temp[ii];
686
687		fill(pot_temp.begin(), pot_temp.end(),
688		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
689
690	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
690	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
691
692		for (int ii = 0; ii < pot_temp.size(); ii++ )
693	<	pot_local += pot_temp[ii];
693	>	pairwisePot += pot_temp[ii];
694
695	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
696	+	RealType ploc1 = pairwisePot[ii];
697	+	RealType ploc2 = 0.0;
698	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
699	+	pairwisePot[ii] = ploc2;
700	+	}
701	+
702		#endif
703	+
704		}
705
706		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 679 \| Line 775 \| namespace OpenMD {
775		#ifdef IS_MPI
776		return massFactorsRow[atom1];
777		#else
778	<	return massFactorsLocal[atom1];
778	>	return massFactors[atom1];
779		#endif
780		}
781
#	Line 687 \| Line 783 \| namespace OpenMD {
783		#ifdef IS_MPI
784		return massFactorsCol[atom2];
785		#else
786	<	return massFactorsLocal[atom2];
786	>	return massFactors[atom2];
787		#endif
788
789		}
#	Line 705 \| Line 801 \| namespace OpenMD {
801		return d;
802		}
803
804	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
805	<	#ifdef IS_MPI
710	<	return skipsForRowAtom[atom1];
711	<	#else
712	<	return skipsForLocalAtom[atom1];
713	<	#endif
804	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
805	>	return excludesForAtom[atom1];
806		}
807
808		/**
809	<	* There are a number of reasons to skip a pair or a
718	<	* particle. Mostly we do this to exclude atoms who are involved in
719	<	* short range interactions (bonds, bends, torsions), but we also
720	<	* need to exclude some overcounted interactions that result from
809	>	* We need to exclude some overcounted interactions that result from
810		* the parallel decomposition.
811		*/
812		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
813		int unique_id_1, unique_id_2;
814	<
814	>
815		#ifdef IS_MPI
816		// in MPI, we have to look up the unique IDs for each atom
817		unique_id_1 = AtomRowToGlobal[atom1];
#	Line 737 \| Line 826 \| namespace OpenMD {
826		} else {
827		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
828		}
829	+	#endif
830	+	return false;
831	+	}
832	+
833	+	/**
834	+	* We need to handle the interactions for atoms who are involved in
835	+	* the same rigid body as well as some short range interactions
836	+	* (bonds, bends, torsions) differently from other interactions.
837	+	* We'll still visit the pairwise routines, but with a flag that
838	+	* tells those routines to exclude the pair from direct long range
839	+	* interactions. Some indirect interactions (notably reaction
840	+	* field) must still be handled for these pairs.
841	+	*/
842	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
843	+	int unique_id_2;
844	+	#ifdef IS_MPI
845	+	// in MPI, we have to look up the unique IDs for the row atom.
846	+	unique_id_2 = AtomColToGlobal[atom2];
847		#else
848		// in the normal loop, the atom numbers are unique
742	–	unique_id_1 = atom1;
849		unique_id_2 = atom2;
850		#endif
851
852	<	#ifdef IS_MPI
853	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748	<	i != skipsForRowAtom[atom1].end(); ++i) {
852	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
853	>	i != excludesForAtom[atom1].end(); ++i) {
854		if ( (*i) == unique_id_2 ) return true;
750	–	}
751	–	#else
752	–	for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
753	–	i != skipsForLocalAtom[atom1].end(); ++i) {
754	–	if ( (*i) == unique_id_2 ) return true;
755	–	}
756	–	#endif
757	–	}
758	–
759	–	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
760	–
761	–	#ifdef IS_MPI
762	–	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
763	–	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
855		}
765	–	#else
766	–	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
767	–	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
768	–	}
769	–	#endif
856
857	<	// zero is default for unconnected (i.e. normal) pair interactions
772	<	return 0;
857	>	return false;
858		}
859
860	+
861		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
862		#ifdef IS_MPI
863		atomRowData.force[atom1] += fg;
#	Line 789 \| Line 875 \| namespace OpenMD {
875		}
876
877		// filling interaction blocks with pointers
878	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
879	<	InteractionData idat;
878	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
879	>	int atom1, int atom2) {
880
881	+	idat.excluded = excludeAtomPair(atom1, atom2);
882	+
883		#ifdef IS_MPI
884	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
885	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
886	+	// ff_->getAtomType(identsCol[atom2]) );
887
797	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
798	–	ff_->getAtomType(identsCol[atom2]) );
799	–
800	–
888		if (storageLayout_ & DataStorage::dslAmat) {
889		idat.A1 = &(atomRowData.aMat[atom1]);
890		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 833 \| Line 920 \| namespace OpenMD {
920		idat.particlePot2 = &(atomColData.particlePot[atom2]);
921		}
922
923	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
924	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
925	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
926	+	}
927	+
928		#else
929
930	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
931	<	ff_->getAtomType(identsLocal[atom2]) );
930	>	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
931	>	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
932	>	// ff_->getAtomType(idents[atom2]) );
933
934		if (storageLayout_ & DataStorage::dslAmat) {
935		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 853 \| Line 946 \| namespace OpenMD {
946		idat.t2 = &(snap_->atomData.torque[atom2]);
947		}
948
949	<	if (storageLayout_ & DataStorage::dslDensity) {
949	>	if (storageLayout_ & DataStorage::dslDensity) {
950		idat.rho1 = &(snap_->atomData.density[atom1]);
951		idat.rho2 = &(snap_->atomData.density[atom2]);
952		}
#	Line 873 \| Line 966 \| namespace OpenMD {
966		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
967		}
968
969	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
970	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
971	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
972	+	}
973		#endif
877	–	return idat;
974		}
975
976
977	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
977	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
978		#ifdef IS_MPI
979		pot_row[atom1] += 0.5 * *(idat.pot);
980		pot_col[atom2] += 0.5 * *(idat.pot);
#	Line 886 \| Line 982 \| namespace OpenMD {
982		atomRowData.force[atom1] += *(idat.f1);
983		atomColData.force[atom2] -= *(idat.f1);
984		#else
985	<	longRangePot_ += *(idat.pot);
986	<
985	>	pairwisePot += *(idat.pot);
986	>
987		snap_->atomData.force[atom1] += *(idat.f1);
988		snap_->atomData.force[atom2] -= *(idat.f1);
989		#endif
990	<
895	<	}
896	<
897	<
898	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
899	<
900	<	InteractionData idat;
901	<	#ifdef IS_MPI
902	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
903	<	ff_->getAtomType(identsCol[atom2]) );
904	<
905	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
906	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
907	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
908	<	}
909	<	if (storageLayout_ & DataStorage::dslTorque) {
910	<	idat.t1 = &(atomRowData.torque[atom1]);
911	<	idat.t2 = &(atomColData.torque[atom2]);
912	<	}
913	<	#else
914	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
915	<	ff_->getAtomType(identsLocal[atom2]) );
916	<
917	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
918	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
919	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
920	<	}
921	<	if (storageLayout_ & DataStorage::dslTorque) {
922	<	idat.t1 = &(snap_->atomData.torque[atom1]);
923	<	idat.t2 = &(snap_->atomData.torque[atom2]);
924	<	}
925	<	#endif
990	>
991		}
992
993		/*
#	Line 935 \| Line 1000 \| namespace OpenMD {
1000
1001		vector<pair<int, int> > neighborList;
1002		groupCutoffs cuts;
1003	+	bool doAllPairs = false;
1004	+
1005		#ifdef IS_MPI
1006		cellListRow_.clear();
1007		cellListCol_.clear();
#	Line 954 \| Line 1021 \| namespace OpenMD {
1021		nCells_.y() = (int) ( Hy.length() )/ rList_;
1022		nCells_.z() = (int) ( Hz.length() )/ rList_;
1023
1024	+	// handle small boxes where the cell offsets can end up repeating cells
1025	+
1026	+	if (nCells_.x() < 3) doAllPairs = true;
1027	+	if (nCells_.y() < 3) doAllPairs = true;
1028	+	if (nCells_.z() < 3) doAllPairs = true;
1029	+
1030		Mat3x3d invHmat = snap_->getInvHmat();
1031		Vector3d rs, scaled, dr;
1032		Vector3i whichCell;
1033		int cellIndex;
1034	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1035
1036		#ifdef IS_MPI
1037	<	for (int i = 0; i < nGroupsInRow_; i++) {
1038	<	rs = cgRowData.position[i];
965	<	// scaled positions relative to the box vectors
966	<	scaled = invHmat * rs;
967	<	// wrap the vector back into the unit box by subtracting integer box
968	<	// numbers
969	<	for (int j = 0; j < 3; j++)
970	<	scaled[j] -= roundMe(scaled[j]);
971	<
972	<	// find xyz-indices of cell that cutoffGroup is in.
973	<	whichCell.x() = nCells_.x() * scaled.x();
974	<	whichCell.y() = nCells_.y() * scaled.y();
975	<	whichCell.z() = nCells_.z() * scaled.z();
976	<
977	<	// find single index of this cell:
978	<	cellIndex = Vlinear(whichCell, nCells_);
979	<	// add this cutoff group to the list of groups in this cell;
980	<	cellListRow_[cellIndex].push_back(i);
981	<	}
982	<
983	<	for (int i = 0; i < nGroupsInCol_; i++) {
984	<	rs = cgColData.position[i];
985	<	// scaled positions relative to the box vectors
986	<	scaled = invHmat * rs;
987	<	// wrap the vector back into the unit box by subtracting integer box
988	<	// numbers
989	<	for (int j = 0; j < 3; j++)
990	<	scaled[j] -= roundMe(scaled[j]);
991	<
992	<	// find xyz-indices of cell that cutoffGroup is in.
993	<	whichCell.x() = nCells_.x() * scaled.x();
994	<	whichCell.y() = nCells_.y() * scaled.y();
995	<	whichCell.z() = nCells_.z() * scaled.z();
996	<
997	<	// find single index of this cell:
998	<	cellIndex = Vlinear(whichCell, nCells_);
999	<	// add this cutoff group to the list of groups in this cell;
1000	<	cellListCol_[cellIndex].push_back(i);
1001	<	}
1037	>	cellListRow_.resize(nCtot);
1038	>	cellListCol_.resize(nCtot);
1039		#else
1040	<	for (int i = 0; i < nGroups_; i++) {
1004	<	rs = snap_->cgData.position[i];
1005	<	// scaled positions relative to the box vectors
1006	<	scaled = invHmat * rs;
1007	<	// wrap the vector back into the unit box by subtracting integer box
1008	<	// numbers
1009	<	for (int j = 0; j < 3; j++)
1010	<	scaled[j] -= roundMe(scaled[j]);
1011	<
1012	<	// find xyz-indices of cell that cutoffGroup is in.
1013	<	whichCell.x() = nCells_.x() * scaled.x();
1014	<	whichCell.y() = nCells_.y() * scaled.y();
1015	<	whichCell.z() = nCells_.z() * scaled.z();
1016	<
1017	<	// find single index of this cell:
1018	<	cellIndex = Vlinear(whichCell, nCells_);
1019	<	// add this cutoff group to the list of groups in this cell;
1020	<	cellList_[cellIndex].push_back(i);
1021	<	}
1040	>	cellList_.resize(nCtot);
1041		#endif
1042
1043	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1044	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1026	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1027	<	Vector3i m1v(m1x, m1y, m1z);
1028	<	int m1 = Vlinear(m1v, nCells_);
1043	>	if (!doAllPairs) {
1044	>	#ifdef IS_MPI
1045
1046	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1047	<	os != cellOffsets_.end(); ++os) {
1048	<
1049	<	Vector3i m2v = m1v + (*os);
1050	<
1051	<	if (m2v.x() >= nCells_.x()) {
1052	<	m2v.x() = 0;
1053	<	} else if (m2v.x() < 0) {
1054	<	m2v.x() = nCells_.x() - 1;
1055	<	}
1056	<
1057	<	if (m2v.y() >= nCells_.y()) {
1058	<	m2v.y() = 0;
1059	<	} else if (m2v.y() < 0) {
1060	<	m2v.y() = nCells_.y() - 1;
1061	<	}
1062	<
1063	<	if (m2v.z() >= nCells_.z()) {
1064	<	m2v.z() = 0;
1065	<	} else if (m2v.z() < 0) {
1066	<	m2v.z() = nCells_.z() - 1;
1067	<	}
1068	<
1069	<	int m2 = Vlinear (m2v, nCells_);
1046	>	for (int i = 0; i < nGroupsInRow_; i++) {
1047	>	rs = cgRowData.position[i];
1048	>
1049	>	// scaled positions relative to the box vectors
1050	>	scaled = invHmat * rs;
1051	>
1052	>	// wrap the vector back into the unit box by subtracting integer box
1053	>	// numbers
1054	>	for (int j = 0; j < 3; j++) {
1055	>	scaled[j] -= roundMe(scaled[j]);
1056	>	scaled[j] += 0.5;
1057	>	}
1058	>
1059	>	// find xyz-indices of cell that cutoffGroup is in.
1060	>	whichCell.x() = nCells_.x() * scaled.x();
1061	>	whichCell.y() = nCells_.y() * scaled.y();
1062	>	whichCell.z() = nCells_.z() * scaled.z();
1063	>
1064	>	// find single index of this cell:
1065	>	cellIndex = Vlinear(whichCell, nCells_);
1066	>
1067	>	// add this cutoff group to the list of groups in this cell;
1068	>	cellListRow_[cellIndex].push_back(i);
1069	>	}
1070	>	for (int i = 0; i < nGroupsInCol_; i++) {
1071	>	rs = cgColData.position[i];
1072	>
1073	>	// scaled positions relative to the box vectors
1074	>	scaled = invHmat * rs;
1075	>
1076	>	// wrap the vector back into the unit box by subtracting integer box
1077	>	// numbers
1078	>	for (int j = 0; j < 3; j++) {
1079	>	scaled[j] -= roundMe(scaled[j]);
1080	>	scaled[j] += 0.5;
1081	>	}
1082	>
1083	>	// find xyz-indices of cell that cutoffGroup is in.
1084	>	whichCell.x() = nCells_.x() * scaled.x();
1085	>	whichCell.y() = nCells_.y() * scaled.y();
1086	>	whichCell.z() = nCells_.z() * scaled.z();
1087	>
1088	>	// find single index of this cell:
1089	>	cellIndex = Vlinear(whichCell, nCells_);
1090	>
1091	>	// add this cutoff group to the list of groups in this cell;
1092	>	cellListCol_[cellIndex].push_back(i);
1093	>	}
1094	>	#else
1095	>	for (int i = 0; i < nGroups_; i++) {
1096	>	rs = snap_->cgData.position[i];
1097	>
1098	>	// scaled positions relative to the box vectors
1099	>	scaled = invHmat * rs;
1100	>
1101	>	// wrap the vector back into the unit box by subtracting integer box
1102	>	// numbers
1103	>	for (int j = 0; j < 3; j++) {
1104	>	scaled[j] -= roundMe(scaled[j]);
1105	>	scaled[j] += 0.5;
1106	>	}
1107	>
1108	>	// find xyz-indices of cell that cutoffGroup is in.
1109	>	whichCell.x() = nCells_.x() * scaled.x();
1110	>	whichCell.y() = nCells_.y() * scaled.y();
1111	>	whichCell.z() = nCells_.z() * scaled.z();
1112	>
1113	>	// find single index of this cell:
1114	>	cellIndex = Vlinear(whichCell, nCells_);
1115	>
1116	>	// add this cutoff group to the list of groups in this cell;
1117	>	cellList_[cellIndex].push_back(i);
1118	>	}
1119	>	#endif
1120
1121	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1122	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1123	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1124	+	Vector3i m1v(m1x, m1y, m1z);
1125	+	int m1 = Vlinear(m1v, nCells_);
1126	+
1127	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1128	+	os != cellOffsets_.end(); ++os) {
1129	+
1130	+	Vector3i m2v = m1v + (*os);
1131	+
1132	+	if (m2v.x() >= nCells_.x()) {
1133	+	m2v.x() = 0;
1134	+	} else if (m2v.x() < 0) {
1135	+	m2v.x() = nCells_.x() - 1;
1136	+	}
1137	+
1138	+	if (m2v.y() >= nCells_.y()) {
1139	+	m2v.y() = 0;
1140	+	} else if (m2v.y() < 0) {
1141	+	m2v.y() = nCells_.y() - 1;
1142	+	}
1143	+
1144	+	if (m2v.z() >= nCells_.z()) {
1145	+	m2v.z() = 0;
1146	+	} else if (m2v.z() < 0) {
1147	+	m2v.z() = nCells_.z() - 1;
1148	+	}
1149	+
1150	+	int m2 = Vlinear (m2v, nCells_);
1151	+
1152		#ifdef IS_MPI
1153	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1154	<	j1 != cellListRow_[m1].end(); ++j1) {
1155	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1156	<	j2 != cellListCol_[m2].end(); ++j2) {
1157	<
1158	<	// Always do this if we're in different cells or if
1159	<	// we're in the same cell and the global index of the
1063	<	// j2 cutoff group is less than the j1 cutoff group
1064	<
1065	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1153	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1154	>	j1 != cellListRow_[m1].end(); ++j1) {
1155	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1156	>	j2 != cellListCol_[m2].end(); ++j2) {
1157	>
1158	>	// In parallel, we need to visit all pairs of row &
1159	>	// column indicies and will truncate later on.
1160		dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1161		snap_->wrapVector(dr);
1162		cuts = getGroupCutoffs( (j1), (j2) );
1163		if (dr.lengthSquare() < cuts.third) {
1164		neighborList.push_back(make_pair((j1), (j2)));
1165	<	}
1165	>	}
1166		}
1167		}
1074	–	}
1168		#else
1169	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1170	<	j1 != cellList_[m1].end(); ++j1) {
1171	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1172	<	j2 != cellList_[m2].end(); ++j2) {
1173	<
1174	<	// Always do this if we're in different cells or if
1175	<	// we're in the same cell and the global index of the
1176	<	// j2 cutoff group is less than the j1 cutoff group
1177	<
1178	<	if (m2 != m1 \|\| (j2) < (j1)) {
1179	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1180	<	snap_->wrapVector(dr);
1181	<	cuts = getGroupCutoffs( (j1), (j2) );
1182	<	if (dr.lengthSquare() < cuts.third) {
1183	<	neighborList.push_back(make_pair((j1), (j2)));
1169	>
1170	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1171	>	j1 != cellList_[m1].end(); ++j1) {
1172	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1173	>	j2 != cellList_[m2].end(); ++j2) {
1174	>
1175	>	// Always do this if we're in different cells or if
1176	>	// we're in the same cell and the global index of the
1177	>	// j2 cutoff group is less than the j1 cutoff group
1178	>
1179	>	if (m2 != m1 \|\| (j2) < (j1)) {
1180	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1181	>	snap_->wrapVector(dr);
1182	>	cuts = getGroupCutoffs( (j1), (j2) );
1183	>	if (dr.lengthSquare() < cuts.third) {
1184	>	neighborList.push_back(make_pair((j1), (j2)));
1185	>	}
1186		}
1187		}
1188		}
1094	–	}
1189		#endif
1190	+	}
1191		}
1192		}
1193		}
1194	+	} else {
1195	+	// branch to do all cutoff group pairs
1196	+	#ifdef IS_MPI
1197	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1198	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1199	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1200	+	snap_->wrapVector(dr);
1201	+	cuts = getGroupCutoffs( j1, j2 );
1202	+	if (dr.lengthSquare() < cuts.third) {
1203	+	neighborList.push_back(make_pair(j1, j2));
1204	+	}
1205	+	}
1206	+	}
1207	+	#else
1208	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1209	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1210	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1211	+	snap_->wrapVector(dr);
1212	+	cuts = getGroupCutoffs( j1, j2 );
1213	+	if (dr.lengthSquare() < cuts.third) {
1214	+	neighborList.push_back(make_pair(j1, j2));
1215	+	}
1216	+	}
1217	+	}
1218	+	#endif
1219		}
1220	<
1220	>
1221		// save the local cutoff group positions for the check that is
1222		// done on each loop:
1223		saved_CG_positions_.clear();
1224		for (int i = 0; i < nGroups_; i++)
1225		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1226	<
1226	>
1227		return neighborList;
1228		}
1229		} //end namespace OpenMD

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs. Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs.
Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC