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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1612 by gezelter, Fri Aug 12 19:59:56 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_.clear();
57	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
58	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
59	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
60	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
61	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
62	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
63	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
64	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
66	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
67	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
68	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
69	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
70	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
71	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
72	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
73	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
74	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
75	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
76	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
77	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
78	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
79	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
80	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
81	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
82	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
83	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
84	+	#endif
85	+	}
86	+
87	+
88		/**
89		* distributeInitialData is essentially a copy of the older fortran
90		* SimulationSetup
91		*/
54	–
92		void ForceMatrixDecomposition::distributeInitialData() {
93		snap_ = sman_->getCurrentSnapshot();
94		storageLayout_ = sman_->getStorageLayout();
95		ff_ = info_->getForceField();
96		nLocal_ = snap_->getNumberOfAtoms();
97	<	nGroups_ = snap_->getNumberOfCutoffGroups();
98	<
97	>
98	>	nGroups_ = info_->getNLocalCutoffGroups();
99		// gather the information for atomtype IDs (atids):
100	<	identsLocal = info_->getIdentArray();
100	>	idents = info_->getIdentArray();
101		AtomLocalToGlobal = info_->getGlobalAtomIndices();
102		cgLocalToGlobal = info_->getGlobalGroupIndices();
103		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();
104
105	+	massFactors = info_->getMassFactors();
106	+
107	+	PairList* excludes = info_->getExcludedInteractions();
108	+	PairList* oneTwo = info_->getOneTwoInteractions();
109	+	PairList* oneThree = info_->getOneThreeInteractions();
110	+	PairList* oneFour = info_->getOneFourInteractions();
111	+
112		#ifdef IS_MPI
113
114	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
115	<	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_);
114	>	MPI::Intracomm row = rowComm.getComm();
115	>	MPI::Intracomm col = colComm.getComm();
116
117	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
118	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
119	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
120	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
121	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
117	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
118	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
119	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
120	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
121	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
122
123	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
124	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
125	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
126	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
123	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
124	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
125	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
126	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
127	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
128
129	<	nAtomsInRow_ = AtomCommIntRow->getSize();
130	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
131	<	nGroupsInRow_ = cgCommIntRow->getSize();
132	<	nGroupsInCol_ = cgCommIntColumn->getSize();
129	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
130	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
131	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
132	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
133
134	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
135	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
136	+	nGroupsInRow_ = cgPlanIntRow->getSize();
137	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
138	+
139		// Modify the data storage objects with the correct layouts and sizes:
140		atomRowData.resize(nAtomsInRow_);
141		atomRowData.setStorageLayout(storageLayout_);
#	Line 104 \| Line 146 \| namespace OpenMD {
146		cgColData.resize(nGroupsInCol_);
147		cgColData.setStorageLayout(DataStorage::dslPosition);
148
149	<	identsRow.reserve(nAtomsInRow_);
150	<	identsCol.reserve(nAtomsInCol_);
149	>	identsRow.resize(nAtomsInRow_);
150	>	identsCol.resize(nAtomsInCol_);
151
152	<	AtomCommIntRow->gather(identsLocal, identsRow);
153	<	AtomCommIntColumn->gather(identsLocal, identsCol);
152	>	AtomPlanIntRow->gather(idents, identsRow);
153	>	AtomPlanIntColumn->gather(idents, identsCol);
154
155	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
156	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
157	<
116	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
117	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
155	>	// allocate memory for the parallel objects
156	>	atypesRow.resize(nAtomsInRow_);
157	>	atypesCol.resize(nAtomsInCol_);
158
159	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
160	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
159	>	for (int i = 0; i < nAtomsInRow_; i++)
160	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
161	>	for (int i = 0; i < nAtomsInCol_; i++)
162	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
163
164	+	pot_row.resize(nAtomsInRow_);
165	+	pot_col.resize(nAtomsInCol_);
166	+
167	+	AtomRowToGlobal.resize(nAtomsInRow_);
168	+	AtomColToGlobal.resize(nAtomsInCol_);
169	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
170	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
171	+
172	+	cgRowToGlobal.resize(nGroupsInRow_);
173	+	cgColToGlobal.resize(nGroupsInCol_);
174	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
176	+
177	+	massFactorsRow.resize(nAtomsInRow_);
178	+	massFactorsCol.resize(nAtomsInCol_);
179	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
180	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
181	+
182		groupListRow_.clear();
183	<	groupListRow_.reserve(nGroupsInRow_);
183	>	groupListRow_.resize(nGroupsInRow_);
184		for (int i = 0; i < nGroupsInRow_; i++) {
185		int gid = cgRowToGlobal[i];
186		for (int j = 0; j < nAtomsInRow_; j++) {
#	Line 131 \| Line 191 \| namespace OpenMD {
191		}
192
193		groupListCol_.clear();
194	<	groupListCol_.reserve(nGroupsInCol_);
194	>	groupListCol_.resize(nGroupsInCol_);
195		for (int i = 0; i < nGroupsInCol_; i++) {
196		int gid = cgColToGlobal[i];
197		for (int j = 0; j < nAtomsInCol_; j++) {
#	Line 141 \| Line 201 \| namespace OpenMD {
201		}
202		}
203
204	<	skipsForRowAtom.clear();
205	<	skipsForRowAtom.reserve(nAtomsInRow_);
204	>	excludesForAtom.clear();
205	>	excludesForAtom.resize(nAtomsInRow_);
206	>	toposForAtom.clear();
207	>	toposForAtom.resize(nAtomsInRow_);
208	>	topoDist.clear();
209	>	topoDist.resize(nAtomsInRow_);
210		for (int i = 0; i < nAtomsInRow_; i++) {
211		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	–	}
212
155	–	toposForRowAtom.clear();
156	–	toposForRowAtom.reserve(nAtomsInRow_);
157	–	for (int i = 0; i < nAtomsInRow_; i++) {
158	–	int iglob = AtomRowToGlobal[i];
159	–	int nTopos = 0;
213		for (int j = 0; j < nAtomsInCol_; j++) {
214	<	int jglob = AtomColToGlobal[j];
215	<	if (oneTwo.hasPair(iglob, jglob)) {
216	<	toposForRowAtom[i].push_back(j);
217	<	topoDistRow[i][nTopos] = 1;
218	<	nTopos++;
214	>	int jglob = AtomColToGlobal[j];
215	>
216	>	if (excludes->hasPair(iglob, jglob))
217	>	excludesForAtom[i].push_back(j);
218	>
219	>	if (oneTwo->hasPair(iglob, jglob)) {
220	>	toposForAtom[i].push_back(j);
221	>	topoDist[i].push_back(1);
222	>	} else {
223	>	if (oneThree->hasPair(iglob, jglob)) {
224	>	toposForAtom[i].push_back(j);
225	>	topoDist[i].push_back(2);
226	>	} else {
227	>	if (oneFour->hasPair(iglob, jglob)) {
228	>	toposForAtom[i].push_back(j);
229	>	topoDist[i].push_back(3);
230	>	}
231	>	}
232		}
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	–	}
233		}
234		}
235
236		#endif
237
238	+	// allocate memory for the parallel objects
239	+	atypesLocal.resize(nLocal_);
240	+
241	+	for (int i = 0; i < nLocal_; i++)
242	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
243	+
244		groupList_.clear();
245	<	groupList_.reserve(nGroups_);
245	>	groupList_.resize(nGroups_);
246		for (int i = 0; i < nGroups_; i++) {
247		int gid = cgLocalToGlobal[i];
248		for (int j = 0; j < nLocal_; j++) {
249		int aid = AtomLocalToGlobal[j];
250	<	if (globalGroupMembership[aid] == gid)
250	>	if (globalGroupMembership[aid] == gid) {
251		groupList_[i].push_back(j);
252	+	}
253		}
254		}
255
256	<	skipsForLocalAtom.clear();
257	<	skipsForLocalAtom.reserve(nLocal_);
256	>	excludesForAtom.clear();
257	>	excludesForAtom.resize(nLocal_);
258	>	toposForAtom.clear();
259	>	toposForAtom.resize(nLocal_);
260	>	topoDist.clear();
261	>	topoDist.resize(nLocal_);
262
263		for (int i = 0; i < nLocal_; i++) {
264		int iglob = AtomLocalToGlobal[i];
198	–	for (int j = 0; j < nLocal_; j++) {
199	–	int jglob = AtomLocalToGlobal[j];
200	–	if (excludes.hasPair(iglob, jglob))
201	–	skipsForLocalAtom[i].push_back(j);
202	–	}
203	–	}
265
205	–	toposForLocalAtom.clear();
206	–	toposForLocalAtom.reserve(nLocal_);
207	–	for (int i = 0; i < nLocal_; i++) {
208	–	int iglob = AtomLocalToGlobal[i];
209	–	int nTopos = 0;
266		for (int j = 0; j < nLocal_; j++) {
267	<	int jglob = AtomLocalToGlobal[j];
268	<	if (oneTwo.hasPair(iglob, jglob)) {
269	<	toposForLocalAtom[i].push_back(j);
270	<	topoDistLocal[i][nTopos] = 1;
271	<	nTopos++;
272	<	}
273	<	if (oneThree.hasPair(iglob, jglob)) {
274	<	toposForLocalAtom[i].push_back(j);
275	<	topoDistLocal[i][nTopos] = 2;
276	<	nTopos++;
277	<	}
278	<	if (oneFour.hasPair(iglob, jglob)) {
279	<	toposForLocalAtom[i].push_back(j);
280	<	topoDistLocal[i][nTopos] = 3;
281	<	nTopos++;
267	>	int jglob = AtomLocalToGlobal[j];
268	>
269	>	if (excludes->hasPair(iglob, jglob))
270	>	excludesForAtom[i].push_back(j);
271	>
272	>	if (oneTwo->hasPair(iglob, jglob)) {
273	>	toposForAtom[i].push_back(j);
274	>	topoDist[i].push_back(1);
275	>	} else {
276	>	if (oneThree->hasPair(iglob, jglob)) {
277	>	toposForAtom[i].push_back(j);
278	>	topoDist[i].push_back(2);
279	>	} else {
280	>	if (oneFour->hasPair(iglob, jglob)) {
281	>	toposForAtom[i].push_back(j);
282	>	topoDist[i].push_back(3);
283	>	}
284	>	}
285		}
286		}
287	<	}
287	>	}
288	>
289	>	createGtypeCutoffMap();
290
291		}
292
293		void ForceMatrixDecomposition::createGtypeCutoffMap() {
294	<
294	>
295		RealType tol = 1e-6;
296	+	largestRcut_ = 0.0;
297		RealType rc;
298		int atid;
299		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
300	<	vector<RealType> atypeCutoff;
301	<	atypeCutoff.reserve( atypes.size() );
302	<
303	<	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
304	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
300	>
301	>	map<int, RealType> atypeCutoff;
302	>
303	>	for (set<AtomType*>::iterator at = atypes.begin();
304	>	at != atypes.end(); ++at){
305		atid = (*at)->getIdent();
306	<	atypeCutoff[atid] = rc;
306	>	if (userChoseCutoff_)
307	>	atypeCutoff[atid] = userCutoff_;
308	>	else
309	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
310		}
311	<
311	>
312		vector<RealType> gTypeCutoffs;
248	–
313		// first we do a single loop over the cutoff groups to find the
314		// largest cutoff for any atypes present in this group.
315		#ifdef IS_MPI
316		vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
317	+	groupRowToGtype.resize(nGroupsInRow_);
318		for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
319		vector<int> atomListRow = getAtomsInGroupRow(cg1);
320		for (vector<int>::iterator ia = atomListRow.begin();
#	Line 275 \| Line 340 \| namespace OpenMD {
340
341		}
342		vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
343	+	groupColToGtype.resize(nGroupsInCol_);
344		for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
345		vector<int> atomListCol = getAtomsInGroupColumn(cg2);
346		for (vector<int>::iterator jb = atomListCol.begin();
#	Line 298 \| Line 364 \| namespace OpenMD {
364		}
365		}
366		#else
367	+
368		vector<RealType> groupCutoff(nGroups_, 0.0);
369	+	groupToGtype.resize(nGroups_);
370		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
371		groupCutoff[cg1] = 0.0;
372		vector<int> atomList = getAtomsInGroupRow(cg1);
373		for (vector<int>::iterator ia = atomList.begin();
374		ia != atomList.end(); ++ia) {
375		int atom1 = (*ia);
376	<	atid = identsLocal[atom1];
377	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
376	>	atid = idents[atom1];
377	>	if (atypeCutoff[atid] > groupCutoff[cg1])
378		groupCutoff[cg1] = atypeCutoff[atid];
311	–	}
379		}
380	<
380	>
381		bool gTypeFound = false;
382		for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
383		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
#	Line 318 \| Line 385 \| namespace OpenMD {
385		gTypeFound = true;
386		}
387		}
388	<	if (!gTypeFound) {
388	>	if (!gTypeFound) {
389		gTypeCutoffs.push_back( groupCutoff[cg1] );
390		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
391		}
#	Line 327 \| Line 394 \| namespace OpenMD {
394
395		// Now we find the maximum group cutoff value present in the simulation
396
397	<	vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
398	<	RealType groupMax = *groupMaxLoc;
397	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
398	>	gTypeCutoffs.end());
399
400		#ifdef IS_MPI
401	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
401	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
402	>	MPI::MAX);
403		#endif
404
405		RealType tradRcut = groupMax;
406
407		for (int i = 0; i < gTypeCutoffs.size(); i++) {
408	<	for (int j = 0; j < gTypeCutoffs.size(); j++) {
341	<
408	>	for (int j = 0; j < gTypeCutoffs.size(); j++) {
409		RealType thisRcut;
410		switch(cutoffPolicy_) {
411		case TRADITIONAL:
412		thisRcut = tradRcut;
413	+	break;
414		case MIX:
415		thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
416	+	break;
417		case MAX:
418		thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
419	+	break;
420		default:
421		sprintf(painCave.errMsg,
422		"ForceMatrixDecomposition::createGtypeCutoffMap "
423		"hit an unknown cutoff policy!\n");
424		painCave.severity = OPENMD_ERROR;
425		painCave.isFatal = 1;
426	<	simError();
426	>	simError();
427	>	break;
428		}
429
430		pair<int,int> key = make_pair(i,j);
431		gTypeCutoffMap[key].first = thisRcut;
361	–
432		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
363	–
433		gTypeCutoffMap[key].second = thisRcut*thisRcut;
365	–
434		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
367	–
435		// sanity check
436
437		if (userChoseCutoff_) {
438		if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
439		sprintf(painCave.errMsg,
440		"ForceMatrixDecomposition::createGtypeCutoffMap "
441	<	"user-specified rCut does not match computed group Cutoff\n");
441	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
442		painCave.severity = OPENMD_ERROR;
443		painCave.isFatal = 1;
444		simError();
#	Line 383 \| Line 450 \| namespace OpenMD {
450
451
452		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
453	<	int i, j;
387	<
453	>	int i, j;
454		#ifdef IS_MPI
455		i = groupRowToGtype[cg1];
456		j = groupColToGtype[cg2];
457		#else
458		i = groupToGtype[cg1];
459		j = groupToGtype[cg2];
460	<	#endif
395	<
460	>	#endif
461		return gTypeCutoffMap[make_pair(i,j)];
462		}
463
464	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
465	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
466	+	if (toposForAtom[atom1][j] == atom2)
467	+	return topoDist[atom1][j];
468	+	}
469	+	return 0;
470	+	}
471
472		void ForceMatrixDecomposition::zeroWorkArrays() {
473	+	pairwisePot = 0.0;
474	+	embeddingPot = 0.0;
475
402	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403	–	longRangePot_[j] = 0.0;
404	–	}
405	–
476		#ifdef IS_MPI
477		if (storageLayout_ & DataStorage::dslForce) {
478		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 418 \| Line 488 \| namespace OpenMD {
488		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
489
490		fill(pot_col.begin(), pot_col.end(),
491	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422	<
423	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
491	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
492
493		if (storageLayout_ & DataStorage::dslParticlePot) {
494	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
495	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
494	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
495	>	0.0);
496	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
497	>	0.0);
498		}
499
500		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 433 \| Line 503 \| namespace OpenMD {
503		}
504
505		if (storageLayout_ & DataStorage::dslFunctional) {
506	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
507	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
506	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
507	>	0.0);
508	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
509	>	0.0);
510		}
511
512		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 444 \| Line 516 \| namespace OpenMD {
516		atomColData.functionalDerivative.end(), 0.0);
517		}
518
519	<	#else
520	<
519	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
520	>	fill(atomRowData.skippedCharge.begin(),
521	>	atomRowData.skippedCharge.end(), 0.0);
522	>	fill(atomColData.skippedCharge.begin(),
523	>	atomColData.skippedCharge.end(), 0.0);
524	>	}
525	>
526	>	#endif
527	>	// even in parallel, we need to zero out the local arrays:
528	>
529		if (storageLayout_ & DataStorage::dslParticlePot) {
530		fill(snap_->atomData.particlePot.begin(),
531		snap_->atomData.particlePot.end(), 0.0);
#	Line 463 \| Line 543 \| namespace OpenMD {
543		fill(snap_->atomData.functionalDerivative.begin(),
544		snap_->atomData.functionalDerivative.end(), 0.0);
545		}
546	<	#endif
546	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
547	>	fill(snap_->atomData.skippedCharge.begin(),
548	>	snap_->atomData.skippedCharge.end(), 0.0);
549	>	}
550
551		}
552
#	Line 474 \| Line 557 \| namespace OpenMD {
557		#ifdef IS_MPI
558
559		// gather up the atomic positions
560	<	AtomCommVectorRow->gather(snap_->atomData.position,
560	>	AtomPlanVectorRow->gather(snap_->atomData.position,
561		atomRowData.position);
562	<	AtomCommVectorColumn->gather(snap_->atomData.position,
562	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
563		atomColData.position);
564
565		// gather up the cutoff group positions
566	<	cgCommVectorRow->gather(snap_->cgData.position,
566	>
567	>	cgPlanVectorRow->gather(snap_->cgData.position,
568		cgRowData.position);
569	<	cgCommVectorColumn->gather(snap_->cgData.position,
569	>
570	>	cgPlanVectorColumn->gather(snap_->cgData.position,
571		cgColData.position);
572	+
573
574		// if needed, gather the atomic rotation matrices
575		if (storageLayout_ & DataStorage::dslAmat) {
576	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
576	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
577		atomRowData.aMat);
578	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
578	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
579		atomColData.aMat);
580		}
581
582		// if needed, gather the atomic eletrostatic frames
583		if (storageLayout_ & DataStorage::dslElectroFrame) {
584	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
584	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
585		atomRowData.electroFrame);
586	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
586	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
587		atomColData.electroFrame);
588		}
589	+
590		#endif
591		}
592
#	Line 513 \| Line 600 \| namespace OpenMD {
600
601		if (storageLayout_ & DataStorage::dslDensity) {
602
603	<	AtomCommRealRow->scatter(atomRowData.density,
603	>	AtomPlanRealRow->scatter(atomRowData.density,
604		snap_->atomData.density);
605
606		int n = snap_->atomData.density.size();
607		vector<RealType> rho_tmp(n, 0.0);
608	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
608	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
609		for (int i = 0; i < n; i++)
610		snap_->atomData.density[i] += rho_tmp[i];
611		}
#	Line 534 \| Line 621 \| namespace OpenMD {
621		storageLayout_ = sman_->getStorageLayout();
622		#ifdef IS_MPI
623		if (storageLayout_ & DataStorage::dslFunctional) {
624	<	AtomCommRealRow->gather(snap_->atomData.functional,
624	>	AtomPlanRealRow->gather(snap_->atomData.functional,
625		atomRowData.functional);
626	<	AtomCommRealColumn->gather(snap_->atomData.functional,
626	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
627		atomColData.functional);
628		}
629
630		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
631	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
631	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
632		atomRowData.functionalDerivative);
633	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
633	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
634		atomColData.functionalDerivative);
635		}
636		#endif
#	Line 557 \| Line 644 \| namespace OpenMD {
644		int n = snap_->atomData.force.size();
645		vector<Vector3d> frc_tmp(n, V3Zero);
646
647	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
647	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
648		for (int i = 0; i < n; i++) {
649		snap_->atomData.force[i] += frc_tmp[i];
650		frc_tmp[i] = 0.0;
651		}
652
653	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
654	<	for (int i = 0; i < n; i++)
653	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
654	>	for (int i = 0; i < n; i++) {
655		snap_->atomData.force[i] += frc_tmp[i];
656	<
657	<
656	>	}
657	>
658		if (storageLayout_ & DataStorage::dslTorque) {
659
660	<	int nt = snap_->atomData.force.size();
660	>	int nt = snap_->atomData.torque.size();
661		vector<Vector3d> trq_tmp(nt, V3Zero);
662
663	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
664	<	for (int i = 0; i < n; i++) {
663	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
664	>	for (int i = 0; i < nt; i++) {
665		snap_->atomData.torque[i] += trq_tmp[i];
666		trq_tmp[i] = 0.0;
667		}
668
669	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
670	<	for (int i = 0; i < n; i++)
669	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
670	>	for (int i = 0; i < nt; i++)
671		snap_->atomData.torque[i] += trq_tmp[i];
672		}
673	+
674	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
675	+
676	+	int ns = snap_->atomData.skippedCharge.size();
677	+	vector<RealType> skch_tmp(ns, 0.0);
678	+
679	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
680	+	for (int i = 0; i < ns; i++) {
681	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
682	+	skch_tmp[i] = 0.0;
683	+	}
684	+
685	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
686	+	for (int i = 0; i < ns; i++)
687	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
688	+	}
689
690		nLocal_ = snap_->getNumberOfAtoms();
691
#	Line 591 \| Line 694 \| namespace OpenMD {
694
695		// scatter/gather pot_row into the members of my column
696
697	<	AtomCommPotRow->scatter(pot_row, pot_temp);
697	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
698
699		for (int ii = 0; ii < pot_temp.size(); ii++ )
700	<	pot_local += pot_temp[ii];
700	>	pairwisePot += pot_temp[ii];
701
702		fill(pot_temp.begin(), pot_temp.end(),
703		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
704
705	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
705	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
706
707		for (int ii = 0; ii < pot_temp.size(); ii++ )
708	<	pot_local += pot_temp[ii];
708	>	pairwisePot += pot_temp[ii];
709
710	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
711	+	RealType ploc1 = pairwisePot[ii];
712	+	RealType ploc2 = 0.0;
713	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
714	+	pairwisePot[ii] = ploc2;
715	+	}
716	+
717		#endif
718	+
719		}
720
721		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 679 \| Line 790 \| namespace OpenMD {
790		#ifdef IS_MPI
791		return massFactorsRow[atom1];
792		#else
793	<	return massFactorsLocal[atom1];
793	>	return massFactors[atom1];
794		#endif
795		}
796
#	Line 687 \| Line 798 \| namespace OpenMD {
798		#ifdef IS_MPI
799		return massFactorsCol[atom2];
800		#else
801	<	return massFactorsLocal[atom2];
801	>	return massFactors[atom2];
802		#endif
803
804		}
#	Line 705 \| Line 816 \| namespace OpenMD {
816		return d;
817		}
818
819	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
820	<	#ifdef IS_MPI
710	<	return skipsForRowAtom[atom1];
711	<	#else
712	<	return skipsForLocalAtom[atom1];
713	<	#endif
819	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
820	>	return excludesForAtom[atom1];
821		}
822
823		/**
824	<	* 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
824	>	* We need to exclude some overcounted interactions that result from
825		* the parallel decomposition.
826		*/
827		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
828		int unique_id_1, unique_id_2;
829	<
829	>
830		#ifdef IS_MPI
831		// in MPI, we have to look up the unique IDs for each atom
832		unique_id_1 = AtomRowToGlobal[atom1];
#	Line 737 \| Line 841 \| namespace OpenMD {
841		} else {
842		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
843		}
844	+	#endif
845	+	return false;
846	+	}
847	+
848	+	/**
849	+	* We need to handle the interactions for atoms who are involved in
850	+	* the same rigid body as well as some short range interactions
851	+	* (bonds, bends, torsions) differently from other interactions.
852	+	* We'll still visit the pairwise routines, but with a flag that
853	+	* tells those routines to exclude the pair from direct long range
854	+	* interactions. Some indirect interactions (notably reaction
855	+	* field) must still be handled for these pairs.
856	+	*/
857	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
858	+	int unique_id_2;
859	+	#ifdef IS_MPI
860	+	// in MPI, we have to look up the unique IDs for the row atom.
861	+	unique_id_2 = AtomColToGlobal[atom2];
862		#else
863		// in the normal loop, the atom numbers are unique
742	–	unique_id_1 = atom1;
864		unique_id_2 = atom2;
865		#endif
866
867	<	#ifdef IS_MPI
868	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748	<	i != skipsForRowAtom[atom1].end(); ++i) {
867	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
868	>	i != excludesForAtom[atom1].end(); ++i) {
869		if ( (*i) == unique_id_2 ) return true;
870	<	}
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	<	}
870	>	}
871
872	<	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];
764	<	}
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
770	<
771	<	// zero is default for unconnected (i.e. normal) pair interactions
772	<	return 0;
872	>	return false;
873		}
874
875	+
876		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
877		#ifdef IS_MPI
878		atomRowData.force[atom1] += fg;
#	Line 789 \| Line 890 \| namespace OpenMD {
890		}
891
892		// filling interaction blocks with pointers
893	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
894	<	InteractionData idat;
893	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
894	>	int atom1, int atom2) {
895
896	+	idat.excluded = excludeAtomPair(atom1, atom2);
897	+
898		#ifdef IS_MPI
899	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
900	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
901	+	// ff_->getAtomType(identsCol[atom2]) );
902
797	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
798	–	ff_->getAtomType(identsCol[atom2]) );
799	–
800	–
903		if (storageLayout_ & DataStorage::dslAmat) {
904		idat.A1 = &(atomRowData.aMat[atom1]);
905		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 833 \| Line 935 \| namespace OpenMD {
935		idat.particlePot2 = &(atomColData.particlePot[atom2]);
936		}
937
938	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
939	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
940	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
941	+	}
942	+
943		#else
944
945	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
946	<	ff_->getAtomType(identsLocal[atom2]) );
945	>	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
946	>	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
947	>	// ff_->getAtomType(idents[atom2]) );
948
949		if (storageLayout_ & DataStorage::dslAmat) {
950		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 853 \| Line 961 \| namespace OpenMD {
961		idat.t2 = &(snap_->atomData.torque[atom2]);
962		}
963
964	<	if (storageLayout_ & DataStorage::dslDensity) {
964	>	if (storageLayout_ & DataStorage::dslDensity) {
965		idat.rho1 = &(snap_->atomData.density[atom1]);
966		idat.rho2 = &(snap_->atomData.density[atom2]);
967		}
#	Line 873 \| Line 981 \| namespace OpenMD {
981		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
982		}
983
984	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
985	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
986	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
987	+	}
988		#endif
877	–	return idat;
989		}
990
991
992	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
992	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
993		#ifdef IS_MPI
994		pot_row[atom1] += 0.5 * *(idat.pot);
995		pot_col[atom2] += 0.5 * *(idat.pot);
#	Line 886 \| Line 997 \| namespace OpenMD {
997		atomRowData.force[atom1] += *(idat.f1);
998		atomColData.force[atom2] -= *(idat.f1);
999		#else
1000	<	longRangePot_ += *(idat.pot);
1001	<
1000	>	pairwisePot += *(idat.pot);
1001	>
1002		snap_->atomData.force[atom1] += *(idat.f1);
1003		snap_->atomData.force[atom2] -= *(idat.f1);
1004		#endif
1005	<
1005	>
1006		}
1007
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
926	–	}
927	–
1008		/*
1009		* buildNeighborList
1010		*
#	Line 935 \| Line 1015 \| namespace OpenMD {
1015
1016		vector<pair<int, int> > neighborList;
1017		groupCutoffs cuts;
1018	+	bool doAllPairs = false;
1019	+
1020		#ifdef IS_MPI
1021		cellListRow_.clear();
1022		cellListCol_.clear();
#	Line 954 \| Line 1036 \| namespace OpenMD {
1036		nCells_.y() = (int) ( Hy.length() )/ rList_;
1037		nCells_.z() = (int) ( Hz.length() )/ rList_;
1038
1039	+	// handle small boxes where the cell offsets can end up repeating cells
1040	+
1041	+	if (nCells_.x() < 3) doAllPairs = true;
1042	+	if (nCells_.y() < 3) doAllPairs = true;
1043	+	if (nCells_.z() < 3) doAllPairs = true;
1044	+
1045		Mat3x3d invHmat = snap_->getInvHmat();
1046		Vector3d rs, scaled, dr;
1047		Vector3i whichCell;
1048		int cellIndex;
1049	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1050
1051		#ifdef IS_MPI
1052	<	for (int i = 0; i < nGroupsInRow_; i++) {
1053	<	rs = cgRowData.position[i];
1054	<	// scaled positions relative to the box vectors
1055	<	scaled = invHmat * rs;
1056	<	// 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();
1052	>	cellListRow_.resize(nCtot);
1053	>	cellListCol_.resize(nCtot);
1054	>	#else
1055	>	cellList_.resize(nCtot);
1056	>	#endif
1057
1058	<	// find single index of this cell:
1059	<	cellIndex = Vlinear(whichCell, nCells_);
979	<	// add this cutoff group to the list of groups in this cell;
980	<	cellListRow_[cellIndex].push_back(i);
981	<	}
1058	>	if (!doAllPairs) {
1059	>	#ifdef IS_MPI
1060
1061	<	for (int i = 0; i < nGroupsInCol_; i++) {
1062	<	rs = cgColData.position[i];
1063	<	// scaled positions relative to the box vectors
1064	<	scaled = invHmat * rs;
1065	<	// wrap the vector back into the unit box by subtracting integer box
1066	<	// numbers
1067	<	for (int j = 0; j < 3; j++)
1068	<	scaled[j] -= roundMe(scaled[j]);
1069	<
1070	<	// find xyz-indices of cell that cutoffGroup is in.
1071	<	whichCell.x() = nCells_.x() * scaled.x();
1072	<	whichCell.y() = nCells_.y() * scaled.y();
1073	<	whichCell.z() = nCells_.z() * scaled.z();
1074	<
1075	<	// find single index of this cell:
1076	<	cellIndex = Vlinear(whichCell, nCells_);
1077	<	// add this cutoff group to the list of groups in this cell;
1078	<	cellListCol_[cellIndex].push_back(i);
1079	<	}
1061	>	for (int i = 0; i < nGroupsInRow_; i++) {
1062	>	rs = cgRowData.position[i];
1063	>
1064	>	// scaled positions relative to the box vectors
1065	>	scaled = invHmat * rs;
1066	>
1067	>	// wrap the vector back into the unit box by subtracting integer box
1068	>	// numbers
1069	>	for (int j = 0; j < 3; j++) {
1070	>	scaled[j] -= roundMe(scaled[j]);
1071	>	scaled[j] += 0.5;
1072	>	}
1073	>
1074	>	// find xyz-indices of cell that cutoffGroup is in.
1075	>	whichCell.x() = nCells_.x() * scaled.x();
1076	>	whichCell.y() = nCells_.y() * scaled.y();
1077	>	whichCell.z() = nCells_.z() * scaled.z();
1078	>
1079	>	// find single index of this cell:
1080	>	cellIndex = Vlinear(whichCell, nCells_);
1081	>
1082	>	// add this cutoff group to the list of groups in this cell;
1083	>	cellListRow_[cellIndex].push_back(i);
1084	>	}
1085	>	for (int i = 0; i < nGroupsInCol_; i++) {
1086	>	rs = cgColData.position[i];
1087	>
1088	>	// scaled positions relative to the box vectors
1089	>	scaled = invHmat * rs;
1090	>
1091	>	// wrap the vector back into the unit box by subtracting integer box
1092	>	// numbers
1093	>	for (int j = 0; j < 3; j++) {
1094	>	scaled[j] -= roundMe(scaled[j]);
1095	>	scaled[j] += 0.5;
1096	>	}
1097	>
1098	>	// find xyz-indices of cell that cutoffGroup is in.
1099	>	whichCell.x() = nCells_.x() * scaled.x();
1100	>	whichCell.y() = nCells_.y() * scaled.y();
1101	>	whichCell.z() = nCells_.z() * scaled.z();
1102	>
1103	>	// find single index of this cell:
1104	>	cellIndex = Vlinear(whichCell, nCells_);
1105	>
1106	>	// add this cutoff group to the list of groups in this cell;
1107	>	cellListCol_[cellIndex].push_back(i);
1108	>	}
1109	>
1110		#else
1111	<	for (int i = 0; i < nGroups_; i++) {
1112	<	rs = snap_->cgData.position[i];
1113	<	// scaled positions relative to the box vectors
1114	<	scaled = invHmat * rs;
1115	<	// wrap the vector back into the unit box by subtracting integer box
1116	<	// numbers
1117	<	for (int j = 0; j < 3; j++)
1118	<	scaled[j] -= roundMe(scaled[j]);
1111	>	for (int i = 0; i < nGroups_; i++) {
1112	>	rs = snap_->cgData.position[i];
1113	>
1114	>	// scaled positions relative to the box vectors
1115	>	scaled = invHmat * rs;
1116	>
1117	>	// wrap the vector back into the unit box by subtracting integer box
1118	>	// numbers
1119	>	for (int j = 0; j < 3; j++) {
1120	>	scaled[j] -= roundMe(scaled[j]);
1121	>	scaled[j] += 0.5;
1122	>	}
1123	>
1124	>	// find xyz-indices of cell that cutoffGroup is in.
1125	>	whichCell.x() = nCells_.x() * scaled.x();
1126	>	whichCell.y() = nCells_.y() * scaled.y();
1127	>	whichCell.z() = nCells_.z() * scaled.z();
1128	>
1129	>	// find single index of this cell:
1130	>	cellIndex = Vlinear(whichCell, nCells_);
1131	>
1132	>	// add this cutoff group to the list of groups in this cell;
1133	>	cellList_[cellIndex].push_back(i);
1134	>	}
1135
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	–	}
1136		#endif
1137
1138	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1139	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1140	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1141	<	Vector3i m1v(m1x, m1y, m1z);
1142	<	int m1 = Vlinear(m1v, nCells_);
1029	<
1030	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1031	<	os != cellOffsets_.end(); ++os) {
1138	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1139	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1140	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1141	>	Vector3i m1v(m1x, m1y, m1z);
1142	>	int m1 = Vlinear(m1v, nCells_);
1143
1144	<	Vector3i m2v = m1v + (*os);
1145	<
1146	<	if (m2v.x() >= nCells_.x()) {
1147	<	m2v.x() = 0;
1148	<	} else if (m2v.x() < 0) {
1038	<	m2v.x() = nCells_.x() - 1;
1039	<	}
1040	<
1041	<	if (m2v.y() >= nCells_.y()) {
1042	<	m2v.y() = 0;
1043	<	} else if (m2v.y() < 0) {
1044	<	m2v.y() = nCells_.y() - 1;
1045	<	}
1046	<
1047	<	if (m2v.z() >= nCells_.z()) {
1048	<	m2v.z() = 0;
1049	<	} else if (m2v.z() < 0) {
1050	<	m2v.z() = nCells_.z() - 1;
1051	<	}
1052	<
1053	<	int m2 = Vlinear (m2v, nCells_);
1144	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1145	>	os != cellOffsets_.end(); ++os) {
1146	>
1147	>	Vector3i m2v = m1v + (*os);
1148	>
1149
1150	<	#ifdef IS_MPI
1151	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1152	<	j1 != cellListRow_[m1].end(); ++j1) {
1153	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1154	<	j2 != cellListCol_[m2].end(); ++j2) {
1155	<
1156	<	// Always do this if we're in different cells or if
1157	<	// we're in the same cell and the global index of the
1158	<	// j2 cutoff group is less than the j1 cutoff group
1150	>	if (m2v.x() >= nCells_.x()) {
1151	>	m2v.x() = 0;
1152	>	} else if (m2v.x() < 0) {
1153	>	m2v.x() = nCells_.x() - 1;
1154	>	}
1155	>
1156	>	if (m2v.y() >= nCells_.y()) {
1157	>	m2v.y() = 0;
1158	>	} else if (m2v.y() < 0) {
1159	>	m2v.y() = nCells_.y() - 1;
1160	>	}
1161	>
1162	>	if (m2v.z() >= nCells_.z()) {
1163	>	m2v.z() = 0;
1164	>	} else if (m2v.z() < 0) {
1165	>	m2v.z() = nCells_.z() - 1;
1166	>	}
1167
1168	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1168	>	int m2 = Vlinear (m2v, nCells_);
1169	>
1170	>	#ifdef IS_MPI
1171	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1172	>	j1 != cellListRow_[m1].end(); ++j1) {
1173	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1174	>	j2 != cellListCol_[m2].end(); ++j2) {
1175	>
1176	>	// In parallel, we need to visit all pairs of row
1177	>	// & column indicies and will divide labor in the
1178	>	// force evaluation later.
1179		dr = cgColData.position[(j2)] - cgRowData.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)));
1184	<	}
1184	>	}
1185		}
1186		}
1074	–	}
1187		#else
1188	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1189	<	j1 != cellList_[m1].end(); ++j1) {
1190	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1191	<	j2 != cellList_[m2].end(); ++j2) {
1192	<
1193	<	// Always do this if we're in different cells or if
1194	<	// we're in the same cell and the global index of the
1195	<	// j2 cutoff group is less than the j1 cutoff group
1196	<
1197	<	if (m2 != m1 \|\| (j2) < (j1)) {
1198	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1199	<	snap_->wrapVector(dr);
1200	<	cuts = getGroupCutoffs( (j1), (j2) );
1201	<	if (dr.lengthSquare() < cuts.third) {
1202	<	neighborList.push_back(make_pair((j1), (j2)));
1188	>
1189	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1190	>	j1 != cellList_[m1].end(); ++j1) {
1191	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1192	>	j2 != cellList_[m2].end(); ++j2) {
1193	>
1194	>	// Always do this if we're in different cells or if
1195	>	// we're in the same cell and the global index of the
1196	>	// j2 cutoff group is less than the j1 cutoff group
1197	>
1198	>	if (m2 != m1 \|\| (j2) < (j1)) {
1199	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.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		}
1094	–	}
1208		#endif
1209	+	}
1210		}
1211		}
1212		}
1213	+	} else {
1214	+	// branch to do all cutoff group pairs
1215	+	#ifdef IS_MPI
1216	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1217	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1218	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1219	+	snap_->wrapVector(dr);
1220	+	cuts = getGroupCutoffs( j1, j2 );
1221	+	if (dr.lengthSquare() < cuts.third) {
1222	+	neighborList.push_back(make_pair(j1, j2));
1223	+	}
1224	+	}
1225	+	}
1226	+	#else
1227	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1228	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1229	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1230	+	snap_->wrapVector(dr);
1231	+	cuts = getGroupCutoffs( j1, j2 );
1232	+	if (dr.lengthSquare() < cuts.third) {
1233	+	neighborList.push_back(make_pair(j1, j2));
1234	+	}
1235	+	}
1236	+	}
1237	+	#endif
1238		}
1239	<
1239	>
1240		// save the local cutoff group positions for the check that is
1241		// done on each loop:
1242		saved_CG_positions_.clear();
1243		for (int i = 0; i < nGroups_; i++)
1244		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1245	<
1245	>
1246		return neighborList;
1247		}
1248		} //end namespace OpenMD

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs. Revision 1612 by gezelter, Fri Aug 12 19:59:56 2011 UTC

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1612 by gezelter, Fri Aug 12 19:59:56 2011 UTC