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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1591 by gezelter, Tue Jul 12 15:25:07 2011 UTC

#	Line 57 \| Line 57 \| namespace OpenMD {
57		storageLayout_ = sman_->getStorageLayout();
58		ff_ = info_->getForceField();
59		nLocal_ = snap_->getNumberOfAtoms();
60	<	nGroups_ = snap_->getNumberOfCutoffGroups();
61	<
60	>
61	>	nGroups_ = info_->getNLocalCutoffGroups();
62		// gather the information for atomtype IDs (atids):
63	<	identsLocal = info_->getIdentArray();
63	>	idents = info_->getIdentArray();
64		AtomLocalToGlobal = info_->getGlobalAtomIndices();
65		cgLocalToGlobal = info_->getGlobalGroupIndices();
66		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();
67
68	+	massFactors = info_->getMassFactors();
69	+
70	+	PairList* excludes = info_->getExcludedInteractions();
71	+	PairList* oneTwo = info_->getOneTwoInteractions();
72	+	PairList* oneThree = info_->getOneThreeInteractions();
73	+	PairList* oneFour = info_->getOneFourInteractions();
74	+
75		#ifdef IS_MPI
76
77		AtomCommIntRow = new Communicator<Row,int>(nLocal_);
#	Line 104 \| Line 106 \| namespace OpenMD {
106		cgColData.resize(nGroupsInCol_);
107		cgColData.setStorageLayout(DataStorage::dslPosition);
108
109	<	identsRow.reserve(nAtomsInRow_);
110	<	identsCol.reserve(nAtomsInCol_);
109	>	identsRow.resize(nAtomsInRow_);
110	>	identsCol.resize(nAtomsInCol_);
111
112	<	AtomCommIntRow->gather(identsLocal, identsRow);
113	<	AtomCommIntColumn->gather(identsLocal, identsCol);
112	>	AtomCommIntRow->gather(idents, identsRow);
113	>	AtomCommIntColumn->gather(idents, identsCol);
114
115	+	// allocate memory for the parallel objects
116	+	atypesRow.resize(nAtomsInRow_);
117	+	atypesCol.resize(nAtomsInCol_);
118	+
119	+	for (int i = 0; i < nAtomsInRow_; i++)
120	+	atypesRow[i] = ff_->getAtomType(identsRow[i]);
121	+	for (int i = 0; i < nAtomsInCol_; i++)
122	+	atypesCol[i] = ff_->getAtomType(identsCol[i]);
123	+
124	+	pot_row.resize(nAtomsInRow_);
125	+	pot_col.resize(nAtomsInCol_);
126	+
127	+	AtomRowToGlobal.resize(nAtomsInRow_);
128	+	AtomColToGlobal.resize(nAtomsInCol_);
129		AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
130		AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
131
132	+	cgRowToGlobal.resize(nGroupsInRow_);
133	+	cgColToGlobal.resize(nGroupsInCol_);
134		cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
135		cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
136
137	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
138	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
137	>	massFactorsRow.resize(nAtomsInRow_);
138	>	massFactorsCol.resize(nAtomsInCol_);
139	>	AtomCommRealRow->gather(massFactors, massFactorsRow);
140	>	AtomCommRealColumn->gather(massFactors, massFactorsCol);
141
142		groupListRow_.clear();
143	<	groupListRow_.reserve(nGroupsInRow_);
143	>	groupListRow_.resize(nGroupsInRow_);
144		for (int i = 0; i < nGroupsInRow_; i++) {
145		int gid = cgRowToGlobal[i];
146		for (int j = 0; j < nAtomsInRow_; j++) {
#	Line 131 \| Line 151 \| namespace OpenMD {
151		}
152
153		groupListCol_.clear();
154	<	groupListCol_.reserve(nGroupsInCol_);
154	>	groupListCol_.resize(nGroupsInCol_);
155		for (int i = 0; i < nGroupsInCol_; i++) {
156		int gid = cgColToGlobal[i];
157		for (int j = 0; j < nAtomsInCol_; j++) {
#	Line 141 \| Line 161 \| namespace OpenMD {
161		}
162		}
163
164	<	skipsForRowAtom.clear();
165	<	skipsForRowAtom.reserve(nAtomsInRow_);
164	>	excludesForAtom.clear();
165	>	excludesForAtom.resize(nAtomsInRow_);
166	>	toposForAtom.clear();
167	>	toposForAtom.resize(nAtomsInRow_);
168	>	topoDist.clear();
169	>	topoDist.resize(nAtomsInRow_);
170		for (int i = 0; i < nAtomsInRow_; i++) {
171		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	–	}
172
155	–	toposForRowAtom.clear();
156	–	toposForRowAtom.reserve(nAtomsInRow_);
157	–	for (int i = 0; i < nAtomsInRow_; i++) {
158	–	int iglob = AtomRowToGlobal[i];
159	–	int nTopos = 0;
173		for (int j = 0; j < nAtomsInCol_; j++) {
174	<	int jglob = AtomColToGlobal[j];
175	<	if (oneTwo.hasPair(iglob, jglob)) {
176	<	toposForRowAtom[i].push_back(j);
177	<	topoDistRow[i][nTopos] = 1;
178	<	nTopos++;
174	>	int jglob = AtomColToGlobal[j];
175	>
176	>	if (excludes->hasPair(iglob, jglob))
177	>	excludesForAtom[i].push_back(j);
178	>
179	>	if (oneTwo->hasPair(iglob, jglob)) {
180	>	toposForAtom[i].push_back(j);
181	>	topoDist[i].push_back(1);
182	>	} else {
183	>	if (oneThree->hasPair(iglob, jglob)) {
184	>	toposForAtom[i].push_back(j);
185	>	topoDist[i].push_back(2);
186	>	} else {
187	>	if (oneFour->hasPair(iglob, jglob)) {
188	>	toposForAtom[i].push_back(j);
189	>	topoDist[i].push_back(3);
190	>	}
191	>	}
192		}
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	–	}
193		}
194		}
195
196		#endif
197
198	+	// allocate memory for the parallel objects
199	+	atypesLocal.resize(nLocal_);
200	+
201	+	for (int i = 0; i < nLocal_; i++)
202	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
203	+
204		groupList_.clear();
205	<	groupList_.reserve(nGroups_);
205	>	groupList_.resize(nGroups_);
206		for (int i = 0; i < nGroups_; i++) {
207		int gid = cgLocalToGlobal[i];
208		for (int j = 0; j < nLocal_; j++) {
209		int aid = AtomLocalToGlobal[j];
210	<	if (globalGroupMembership[aid] == gid)
210	>	if (globalGroupMembership[aid] == gid) {
211		groupList_[i].push_back(j);
212	+	}
213		}
214		}
215
216	<	skipsForLocalAtom.clear();
217	<	skipsForLocalAtom.reserve(nLocal_);
216	>	excludesForAtom.clear();
217	>	excludesForAtom.resize(nLocal_);
218	>	toposForAtom.clear();
219	>	toposForAtom.resize(nLocal_);
220	>	topoDist.clear();
221	>	topoDist.resize(nLocal_);
222
223		for (int i = 0; i < nLocal_; i++) {
224		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	–	}
225
205	–	toposForLocalAtom.clear();
206	–	toposForLocalAtom.reserve(nLocal_);
207	–	for (int i = 0; i < nLocal_; i++) {
208	–	int iglob = AtomLocalToGlobal[i];
209	–	int nTopos = 0;
226		for (int j = 0; j < nLocal_; j++) {
227	<	int jglob = AtomLocalToGlobal[j];
228	<	if (oneTwo.hasPair(iglob, jglob)) {
229	<	toposForLocalAtom[i].push_back(j);
230	<	topoDistLocal[i][nTopos] = 1;
231	<	nTopos++;
227	>	int jglob = AtomLocalToGlobal[j];
228	>
229	>	if (excludes->hasPair(iglob, jglob))
230	>	excludesForAtom[i].push_back(j);
231	>
232	>	if (oneTwo->hasPair(iglob, jglob)) {
233	>	toposForAtom[i].push_back(j);
234	>	topoDist[i].push_back(1);
235	>	} else {
236	>	if (oneThree->hasPair(iglob, jglob)) {
237	>	toposForAtom[i].push_back(j);
238	>	topoDist[i].push_back(2);
239	>	} else {
240	>	if (oneFour->hasPair(iglob, jglob)) {
241	>	toposForAtom[i].push_back(j);
242	>	topoDist[i].push_back(3);
243	>	}
244	>	}
245		}
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	–	}
246		}
247		}
248	+
249	+	createGtypeCutoffMap();
250	+
251		}
252
253	<	void ForceMatrixDecomposition::zeroWorkArrays() {
253	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
254	>
255	>	RealType tol = 1e-6;
256	>	RealType rc;
257	>	int atid;
258	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
259	>	map<int, RealType> atypeCutoff;
260	>
261	>	for (set<AtomType*>::iterator at = atypes.begin();
262	>	at != atypes.end(); ++at){
263	>	atid = (*at)->getIdent();
264	>	if (userChoseCutoff_)
265	>	atypeCutoff[atid] = userCutoff_;
266	>	else
267	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
268	>	}
269
270	<	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
271	<	longRangePot_[j] = 0.0;
270	>	vector<RealType> gTypeCutoffs;
271	>	// first we do a single loop over the cutoff groups to find the
272	>	// largest cutoff for any atypes present in this group.
273	>	#ifdef IS_MPI
274	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
275	>	groupRowToGtype.resize(nGroupsInRow_);
276	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
277	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
278	>	for (vector<int>::iterator ia = atomListRow.begin();
279	>	ia != atomListRow.end(); ++ia) {
280	>	int atom1 = (*ia);
281	>	atid = identsRow[atom1];
282	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
283	>	groupCutoffRow[cg1] = atypeCutoff[atid];
284	>	}
285	>	}
286	>
287	>	bool gTypeFound = false;
288	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
289	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
290	>	groupRowToGtype[cg1] = gt;
291	>	gTypeFound = true;
292	>	}
293	>	}
294	>	if (!gTypeFound) {
295	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
296	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
297	>	}
298	>
299		}
300	+	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
301	+	groupColToGtype.resize(nGroupsInCol_);
302	+	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
303	+	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
304	+	for (vector<int>::iterator jb = atomListCol.begin();
305	+	jb != atomListCol.end(); ++jb) {
306	+	int atom2 = (*jb);
307	+	atid = identsCol[atom2];
308	+	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
309	+	groupCutoffCol[cg2] = atypeCutoff[atid];
310	+	}
311	+	}
312	+	bool gTypeFound = false;
313	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
314	+	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
315	+	groupColToGtype[cg2] = gt;
316	+	gTypeFound = true;
317	+	}
318	+	}
319	+	if (!gTypeFound) {
320	+	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
321	+	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
322	+	}
323	+	}
324	+	#else
325	+
326	+	vector<RealType> groupCutoff(nGroups_, 0.0);
327	+	groupToGtype.resize(nGroups_);
328	+	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
329	+
330	+	groupCutoff[cg1] = 0.0;
331	+	vector<int> atomList = getAtomsInGroupRow(cg1);
332	+
333	+	for (vector<int>::iterator ia = atomList.begin();
334	+	ia != atomList.end(); ++ia) {
335	+	int atom1 = (*ia);
336	+	atid = idents[atom1];
337	+	if (atypeCutoff[atid] > groupCutoff[cg1]) {
338	+	groupCutoff[cg1] = atypeCutoff[atid];
339	+	}
340	+	}
341	+
342	+	bool gTypeFound = false;
343	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
344	+	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
345	+	groupToGtype[cg1] = gt;
346	+	gTypeFound = true;
347	+	}
348	+	}
349	+	if (!gTypeFound) {
350	+	gTypeCutoffs.push_back( groupCutoff[cg1] );
351	+	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
352	+	}
353	+	}
354	+	#endif
355	+
356	+	// Now we find the maximum group cutoff value present in the simulation
357	+
358	+	RealType groupMax = *max_element(gTypeCutoffs.begin(),
359	+	gTypeCutoffs.end());
360	+
361	+	#ifdef IS_MPI
362	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
363	+	MPI::MAX);
364	+	#endif
365	+
366	+	RealType tradRcut = groupMax;
367	+
368	+	for (int i = 0; i < gTypeCutoffs.size(); i++) {
369	+	for (int j = 0; j < gTypeCutoffs.size(); j++) {
370	+	RealType thisRcut;
371	+	switch(cutoffPolicy_) {
372	+	case TRADITIONAL:
373	+	thisRcut = tradRcut;
374	+	break;
375	+	case MIX:
376	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
377	+	break;
378	+	case MAX:
379	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
380	+	break;
381	+	default:
382	+	sprintf(painCave.errMsg,
383	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
384	+	"hit an unknown cutoff policy!\n");
385	+	painCave.severity = OPENMD_ERROR;
386	+	painCave.isFatal = 1;
387	+	simError();
388	+	break;
389	+	}
390	+
391	+	pair<int,int> key = make_pair(i,j);
392	+	gTypeCutoffMap[key].first = thisRcut;
393	+
394	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
395	+
396	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
397	+
398	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
399	+
400	+	// sanity check
401	+
402	+	if (userChoseCutoff_) {
403	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
404	+	sprintf(painCave.errMsg,
405	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
406	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
407	+	painCave.severity = OPENMD_ERROR;
408	+	painCave.isFatal = 1;
409	+	simError();
410	+	}
411	+	}
412	+	}
413	+	}
414	+	}
415	+
416	+
417	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
418	+	int i, j;
419	+	#ifdef IS_MPI
420	+	i = groupRowToGtype[cg1];
421	+	j = groupColToGtype[cg2];
422	+	#else
423	+	i = groupToGtype[cg1];
424	+	j = groupToGtype[cg2];
425	+	#endif
426	+	return gTypeCutoffMap[make_pair(i,j)];
427	+	}
428
429	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
430	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
431	+	if (toposForAtom[atom1][j] == atom2)
432	+	return topoDist[atom1][j];
433	+	}
434	+	return 0;
435	+	}
436	+
437	+	void ForceMatrixDecomposition::zeroWorkArrays() {
438	+	pairwisePot = 0.0;
439	+	embeddingPot = 0.0;
440	+
441		#ifdef IS_MPI
442		if (storageLayout_ & DataStorage::dslForce) {
443		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 249 \| Line 453 \| namespace OpenMD {
453		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
454
455		fill(pot_col.begin(), pot_col.end(),
456	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
253	<
254	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
456	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
457
458		if (storageLayout_ & DataStorage::dslParticlePot) {
459	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
460	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
459	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
460	>	0.0);
461	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
462	>	0.0);
463		}
464
465		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 264 \| Line 468 \| namespace OpenMD {
468		}
469
470		if (storageLayout_ & DataStorage::dslFunctional) {
471	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
472	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
471	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
472	>	0.0);
473	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
474	>	0.0);
475		}
476
477		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 275 \| Line 481 \| namespace OpenMD {
481		atomColData.functionalDerivative.end(), 0.0);
482		}
483
484	<	#else
485	<
484	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
485	>	fill(atomRowData.skippedCharge.begin(),
486	>	atomRowData.skippedCharge.end(), 0.0);
487	>	fill(atomColData.skippedCharge.begin(),
488	>	atomColData.skippedCharge.end(), 0.0);
489	>	}
490	>
491	>	#endif
492	>	// even in parallel, we need to zero out the local arrays:
493	>
494		if (storageLayout_ & DataStorage::dslParticlePot) {
495		fill(snap_->atomData.particlePot.begin(),
496		snap_->atomData.particlePot.end(), 0.0);
#	Line 294 \| Line 508 \| namespace OpenMD {
508		fill(snap_->atomData.functionalDerivative.begin(),
509		snap_->atomData.functionalDerivative.end(), 0.0);
510		}
511	<	#endif
511	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
512	>	fill(snap_->atomData.skippedCharge.begin(),
513	>	snap_->atomData.skippedCharge.end(), 0.0);
514	>	}
515
516		}
517
#	Line 331 \| Line 548 \| namespace OpenMD {
548		AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
549		atomColData.electroFrame);
550		}
551	+
552		#endif
553		}
554
#	Line 397 \| Line 615 \| namespace OpenMD {
615		AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
616		for (int i = 0; i < n; i++)
617		snap_->atomData.force[i] += frc_tmp[i];
618	<
401	<
618	>
619		if (storageLayout_ & DataStorage::dslTorque) {
620
621	<	int nt = snap_->atomData.force.size();
621	>	int nt = snap_->atomData.torque.size();
622		vector<Vector3d> trq_tmp(nt, V3Zero);
623
624		AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
625	<	for (int i = 0; i < n; i++) {
625	>	for (int i = 0; i < nt; i++) {
626		snap_->atomData.torque[i] += trq_tmp[i];
627		trq_tmp[i] = 0.0;
628		}
629
630		AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
631	<	for (int i = 0; i < n; i++)
631	>	for (int i = 0; i < nt; i++)
632		snap_->atomData.torque[i] += trq_tmp[i];
633	+	}
634	+
635	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
636	+
637	+	int ns = snap_->atomData.skippedCharge.size();
638	+	vector<RealType> skch_tmp(ns, 0.0);
639	+
640	+	AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
641	+	for (int i = 0; i < ns; i++) {
642	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
643	+	skch_tmp[i] = 0.0;
644	+	}
645	+
646	+	AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
647	+	for (int i = 0; i < ns; i++)
648	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
649		}
650
651		nLocal_ = snap_->getNumberOfAtoms();
#	Line 425 \| Line 658 \| namespace OpenMD {
658		AtomCommPotRow->scatter(pot_row, pot_temp);
659
660		for (int ii = 0; ii < pot_temp.size(); ii++ )
661	<	pot_local += pot_temp[ii];
661	>	pairwisePot += pot_temp[ii];
662
663		fill(pot_temp.begin(), pot_temp.end(),
664		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
#	Line 433 \| Line 666 \| namespace OpenMD {
666		AtomCommPotColumn->scatter(pot_col, pot_temp);
667
668		for (int ii = 0; ii < pot_temp.size(); ii++ )
669	<	pot_local += pot_temp[ii];
437	<
669	>	pairwisePot += pot_temp[ii];
670		#endif
671	+
672		}
673
674		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 510 \| Line 743 \| namespace OpenMD {
743		#ifdef IS_MPI
744		return massFactorsRow[atom1];
745		#else
746	<	return massFactorsLocal[atom1];
746	>	return massFactors[atom1];
747		#endif
748		}
749
#	Line 518 \| Line 751 \| namespace OpenMD {
751		#ifdef IS_MPI
752		return massFactorsCol[atom2];
753		#else
754	<	return massFactorsLocal[atom2];
754	>	return massFactors[atom2];
755		#endif
756
757		}
#	Line 536 \| Line 769 \| namespace OpenMD {
769		return d;
770		}
771
772	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
773	<	#ifdef IS_MPI
541	<	return skipsForRowAtom[atom1];
542	<	#else
543	<	return skipsForLocalAtom[atom1];
544	<	#endif
772	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
773	>	return excludesForAtom[atom1];
774		}
775
776		/**
777	<	* There are a number of reasons to skip a pair or a
549	<	* particle. Mostly we do this to exclude atoms who are involved in
550	<	* short range interactions (bonds, bends, torsions), but we also
551	<	* need to exclude some overcounted interactions that result from
777	>	* We need to exclude some overcounted interactions that result from
778		* the parallel decomposition.
779		*/
780		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
#	Line 568 \| Line 794 \| namespace OpenMD {
794		} else {
795		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
796		}
797	+	#endif
798	+	return false;
799	+	}
800	+
801	+	/**
802	+	* We need to handle the interactions for atoms who are involved in
803	+	* the same rigid body as well as some short range interactions
804	+	* (bonds, bends, torsions) differently from other interactions.
805	+	* We'll still visit the pairwise routines, but with a flag that
806	+	* tells those routines to exclude the pair from direct long range
807	+	* interactions. Some indirect interactions (notably reaction
808	+	* field) must still be handled for these pairs.
809	+	*/
810	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
811	+	int unique_id_2;
812	+
813	+	#ifdef IS_MPI
814	+	// in MPI, we have to look up the unique IDs for the row atom.
815	+	unique_id_2 = AtomColToGlobal[atom2];
816		#else
817		// in the normal loop, the atom numbers are unique
573	–	unique_id_1 = atom1;
818		unique_id_2 = atom2;
819		#endif
820
821	<	#ifdef IS_MPI
822	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
579	<	i != skipsForRowAtom[atom1].end(); ++i) {
821	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
822	>	i != excludesForAtom[atom1].end(); ++i) {
823		if ( (*i) == unique_id_2 ) return true;
581	–	}
582	–	#else
583	–	for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
584	–	i != skipsForLocalAtom[atom1].end(); ++i) {
585	–	if ( (*i) == unique_id_2 ) return true;
586	–	}
587	–	#endif
588	–	}
589	–
590	–	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
591	–
592	–	#ifdef IS_MPI
593	–	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
594	–	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
824		}
596	–	#else
597	–	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
598	–	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
599	–	}
600	–	#endif
825
826	<	// zero is default for unconnected (i.e. normal) pair interactions
603	<	return 0;
826	>	return false;
827		}
828
829	+
830		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
831		#ifdef IS_MPI
832		atomRowData.force[atom1] += fg;
#	Line 620 \| Line 844 \| namespace OpenMD {
844		}
845
846		// filling interaction blocks with pointers
847	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
848	<	InteractionData idat;
847	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
848	>	int atom1, int atom2) {
849
850	+	idat.excluded = excludeAtomPair(atom1, atom2);
851	+
852		#ifdef IS_MPI
853	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
854	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
855	+	// ff_->getAtomType(identsCol[atom2]) );
856
628	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
629	–	ff_->getAtomType(identsCol[atom2]) );
630	–
631	–
857		if (storageLayout_ & DataStorage::dslAmat) {
858		idat.A1 = &(atomRowData.aMat[atom1]);
859		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 664 \| Line 889 \| namespace OpenMD {
889		idat.particlePot2 = &(atomColData.particlePot[atom2]);
890		}
891
892	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
893	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
894	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
895	+	}
896	+
897		#else
898
899	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
900	<	ff_->getAtomType(identsLocal[atom2]) );
899	>	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
900	>	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
901	>	// ff_->getAtomType(idents[atom2]) );
902
903		if (storageLayout_ & DataStorage::dslAmat) {
904		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 684 \| Line 915 \| namespace OpenMD {
915		idat.t2 = &(snap_->atomData.torque[atom2]);
916		}
917
918	<	if (storageLayout_ & DataStorage::dslDensity) {
918	>	if (storageLayout_ & DataStorage::dslDensity) {
919		idat.rho1 = &(snap_->atomData.density[atom1]);
920		idat.rho2 = &(snap_->atomData.density[atom2]);
921		}
#	Line 704 \| Line 935 \| namespace OpenMD {
935		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
936		}
937
938	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
939	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
940	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
941	+	}
942		#endif
708	–	return idat;
943		}
944
945
946	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
946	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
947		#ifdef IS_MPI
948		pot_row[atom1] += 0.5 * *(idat.pot);
949		pot_col[atom2] += 0.5 * *(idat.pot);
#	Line 717 \| Line 951 \| namespace OpenMD {
951		atomRowData.force[atom1] += *(idat.f1);
952		atomColData.force[atom2] -= *(idat.f1);
953		#else
954	<	longRangePot_ += *(idat.pot);
955	<
954	>	pairwisePot += *(idat.pot);
955	>
956		snap_->atomData.force[atom1] += *(idat.f1);
957		snap_->atomData.force[atom2] -= *(idat.f1);
958		#endif
959	<
726	<	}
727	<
728	<
729	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
730	<
731	<	InteractionData idat;
732	<	#ifdef IS_MPI
733	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
734	<	ff_->getAtomType(identsCol[atom2]) );
735	<
736	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
737	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
738	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
739	<	}
740	<	if (storageLayout_ & DataStorage::dslTorque) {
741	<	idat.t1 = &(atomRowData.torque[atom1]);
742	<	idat.t2 = &(atomColData.torque[atom2]);
743	<	}
744	<	#else
745	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
746	<	ff_->getAtomType(identsLocal[atom2]) );
747	<
748	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
749	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
750	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
751	<	}
752	<	if (storageLayout_ & DataStorage::dslTorque) {
753	<	idat.t1 = &(snap_->atomData.torque[atom1]);
754	<	idat.t2 = &(snap_->atomData.torque[atom2]);
755	<	}
756	<	#endif
959	>
960		}
961
962		/*
#	Line 765 \| Line 968 \| namespace OpenMD {
968		vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
969
970		vector<pair<int, int> > neighborList;
971	+	groupCutoffs cuts;
972	+	bool doAllPairs = false;
973	+
974		#ifdef IS_MPI
975		cellListRow_.clear();
976		cellListCol_.clear();
#	Line 772 \| Line 978 \| namespace OpenMD {
978		cellList_.clear();
979		#endif
980
981	<	// dangerous to not do error checking.
776	<	RealType rCut_;
777	<
778	<	RealType rList_ = (rCut_ + skinThickness_);
981	>	RealType rList_ = (largestRcut_ + skinThickness_);
982		RealType rl2 = rList_ * rList_;
983		Snapshot* snap_ = sman_->getCurrentSnapshot();
984		Mat3x3d Hmat = snap_->getHmat();
#	Line 787 \| Line 990 \| namespace OpenMD {
990		nCells_.y() = (int) ( Hy.length() )/ rList_;
991		nCells_.z() = (int) ( Hz.length() )/ rList_;
992
993	+	// handle small boxes where the cell offsets can end up repeating cells
994	+
995	+	if (nCells_.x() < 3) doAllPairs = true;
996	+	if (nCells_.y() < 3) doAllPairs = true;
997	+	if (nCells_.z() < 3) doAllPairs = true;
998	+
999		Mat3x3d invHmat = snap_->getInvHmat();
1000		Vector3d rs, scaled, dr;
1001		Vector3i whichCell;
1002		int cellIndex;
1003	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1004
1005		#ifdef IS_MPI
1006	<	for (int i = 0; i < nGroupsInRow_; i++) {
1007	<	rs = cgRowData.position[i];
798	<	// scaled positions relative to the box vectors
799	<	scaled = invHmat * rs;
800	<	// wrap the vector back into the unit box by subtracting integer box
801	<	// numbers
802	<	for (int j = 0; j < 3; j++)
803	<	scaled[j] -= roundMe(scaled[j]);
804	<
805	<	// find xyz-indices of cell that cutoffGroup is in.
806	<	whichCell.x() = nCells_.x() * scaled.x();
807	<	whichCell.y() = nCells_.y() * scaled.y();
808	<	whichCell.z() = nCells_.z() * scaled.z();
809	<
810	<	// find single index of this cell:
811	<	cellIndex = Vlinear(whichCell, nCells_);
812	<	// add this cutoff group to the list of groups in this cell;
813	<	cellListRow_[cellIndex].push_back(i);
814	<	}
815	<
816	<	for (int i = 0; i < nGroupsInCol_; i++) {
817	<	rs = cgColData.position[i];
818	<	// scaled positions relative to the box vectors
819	<	scaled = invHmat * rs;
820	<	// wrap the vector back into the unit box by subtracting integer box
821	<	// numbers
822	<	for (int j = 0; j < 3; j++)
823	<	scaled[j] -= roundMe(scaled[j]);
824	<
825	<	// find xyz-indices of cell that cutoffGroup is in.
826	<	whichCell.x() = nCells_.x() * scaled.x();
827	<	whichCell.y() = nCells_.y() * scaled.y();
828	<	whichCell.z() = nCells_.z() * scaled.z();
829	<
830	<	// find single index of this cell:
831	<	cellIndex = Vlinear(whichCell, nCells_);
832	<	// add this cutoff group to the list of groups in this cell;
833	<	cellListCol_[cellIndex].push_back(i);
834	<	}
1006	>	cellListRow_.resize(nCtot);
1007	>	cellListCol_.resize(nCtot);
1008		#else
1009	<	for (int i = 0; i < nGroups_; i++) {
837	<	rs = snap_->cgData.position[i];
838	<	// scaled positions relative to the box vectors
839	<	scaled = invHmat * rs;
840	<	// wrap the vector back into the unit box by subtracting integer box
841	<	// numbers
842	<	for (int j = 0; j < 3; j++)
843	<	scaled[j] -= roundMe(scaled[j]);
844	<
845	<	// find xyz-indices of cell that cutoffGroup is in.
846	<	whichCell.x() = nCells_.x() * scaled.x();
847	<	whichCell.y() = nCells_.y() * scaled.y();
848	<	whichCell.z() = nCells_.z() * scaled.z();
849	<
850	<	// find single index of this cell:
851	<	cellIndex = Vlinear(whichCell, nCells_);
852	<	// add this cutoff group to the list of groups in this cell;
853	<	cellList_[cellIndex].push_back(i);
854	<	}
1009	>	cellList_.resize(nCtot);
1010		#endif
1011
1012	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1013	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
859	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
860	<	Vector3i m1v(m1x, m1y, m1z);
861	<	int m1 = Vlinear(m1v, nCells_);
1012	>	if (!doAllPairs) {
1013	>	#ifdef IS_MPI
1014
1015	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1016	<	os != cellOffsets_.end(); ++os) {
1017	<
1018	<	Vector3i m2v = m1v + (*os);
1019	<
1020	<	if (m2v.x() >= nCells_.x()) {
1021	<	m2v.x() = 0;
1022	<	} else if (m2v.x() < 0) {
1023	<	m2v.x() = nCells_.x() - 1;
1024	<	}
1025	<
1026	<	if (m2v.y() >= nCells_.y()) {
1027	<	m2v.y() = 0;
1028	<	} else if (m2v.y() < 0) {
1029	<	m2v.y() = nCells_.y() - 1;
1030	<	}
1031	<
1032	<	if (m2v.z() >= nCells_.z()) {
1033	<	m2v.z() = 0;
1034	<	} else if (m2v.z() < 0) {
1035	<	m2v.z() = nCells_.z() - 1;
1036	<	}
1037	<
1038	<	int m2 = Vlinear (m2v, nCells_);
1015	>	for (int i = 0; i < nGroupsInRow_; i++) {
1016	>	rs = cgRowData.position[i];
1017	>
1018	>	// scaled positions relative to the box vectors
1019	>	scaled = invHmat * rs;
1020	>
1021	>	// wrap the vector back into the unit box by subtracting integer box
1022	>	// numbers
1023	>	for (int j = 0; j < 3; j++) {
1024	>	scaled[j] -= roundMe(scaled[j]);
1025	>	scaled[j] += 0.5;
1026	>	}
1027	>
1028	>	// find xyz-indices of cell that cutoffGroup is in.
1029	>	whichCell.x() = nCells_.x() * scaled.x();
1030	>	whichCell.y() = nCells_.y() * scaled.y();
1031	>	whichCell.z() = nCells_.z() * scaled.z();
1032	>
1033	>	// find single index of this cell:
1034	>	cellIndex = Vlinear(whichCell, nCells_);
1035	>
1036	>	// add this cutoff group to the list of groups in this cell;
1037	>	cellListRow_[cellIndex].push_back(i);
1038	>	}
1039	>
1040	>	for (int i = 0; i < nGroupsInCol_; i++) {
1041	>	rs = cgColData.position[i];
1042	>
1043	>	// scaled positions relative to the box vectors
1044	>	scaled = invHmat * rs;
1045	>
1046	>	// wrap the vector back into the unit box by subtracting integer box
1047	>	// numbers
1048	>	for (int j = 0; j < 3; j++) {
1049	>	scaled[j] -= roundMe(scaled[j]);
1050	>	scaled[j] += 0.5;
1051	>	}
1052	>
1053	>	// find xyz-indices of cell that cutoffGroup is in.
1054	>	whichCell.x() = nCells_.x() * scaled.x();
1055	>	whichCell.y() = nCells_.y() * scaled.y();
1056	>	whichCell.z() = nCells_.z() * scaled.z();
1057	>
1058	>	// find single index of this cell:
1059	>	cellIndex = Vlinear(whichCell, nCells_);
1060	>
1061	>	// add this cutoff group to the list of groups in this cell;
1062	>	cellListCol_[cellIndex].push_back(i);
1063	>	}
1064	>	#else
1065	>	for (int i = 0; i < nGroups_; i++) {
1066	>	rs = snap_->cgData.position[i];
1067	>
1068	>	// scaled positions relative to the box vectors
1069	>	scaled = invHmat * rs;
1070	>
1071	>	// wrap the vector back into the unit box by subtracting integer box
1072	>	// numbers
1073	>	for (int j = 0; j < 3; j++) {
1074	>	scaled[j] -= roundMe(scaled[j]);
1075	>	scaled[j] += 0.5;
1076	>	}
1077	>
1078	>	// find xyz-indices of cell that cutoffGroup is in.
1079	>	whichCell.x() = nCells_.x() * scaled.x();
1080	>	whichCell.y() = nCells_.y() * scaled.y();
1081	>	whichCell.z() = nCells_.z() * scaled.z();
1082	>
1083	>	// find single index of this cell:
1084	>	cellIndex = Vlinear(whichCell, nCells_);
1085	>
1086	>	// add this cutoff group to the list of groups in this cell;
1087	>	cellList_[cellIndex].push_back(i);
1088	>	}
1089	>	#endif
1090
1091	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1092	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1093	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1094	+	Vector3i m1v(m1x, m1y, m1z);
1095	+	int m1 = Vlinear(m1v, nCells_);
1096	+
1097	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1098	+	os != cellOffsets_.end(); ++os) {
1099	+
1100	+	Vector3i m2v = m1v + (*os);
1101	+
1102	+	if (m2v.x() >= nCells_.x()) {
1103	+	m2v.x() = 0;
1104	+	} else if (m2v.x() < 0) {
1105	+	m2v.x() = nCells_.x() - 1;
1106	+	}
1107	+
1108	+	if (m2v.y() >= nCells_.y()) {
1109	+	m2v.y() = 0;
1110	+	} else if (m2v.y() < 0) {
1111	+	m2v.y() = nCells_.y() - 1;
1112	+	}
1113	+
1114	+	if (m2v.z() >= nCells_.z()) {
1115	+	m2v.z() = 0;
1116	+	} else if (m2v.z() < 0) {
1117	+	m2v.z() = nCells_.z() - 1;
1118	+	}
1119	+
1120	+	int m2 = Vlinear (m2v, nCells_);
1121	+
1122		#ifdef IS_MPI
1123	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1124	<	j1 != cellListRow_[m1].end(); ++j1) {
1125	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1126	<	j2 != cellListCol_[m2].end(); ++j2) {
1127	<
1128	<	// Always do this if we're in different cells or if
1129	<	// we're in the same cell and the global index of the
1130	<	// j2 cutoff group is less than the j1 cutoff group
1131	<
1132	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1133	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1134	<	snap_->wrapVector(dr);
1135	<	if (dr.lengthSquare() < rl2) {
1136	<	neighborList.push_back(make_pair((j1), (j2)));
1123	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1124	>	j1 != cellListRow_[m1].end(); ++j1) {
1125	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1126	>	j2 != cellListCol_[m2].end(); ++j2) {
1127	>
1128	>	// Always do this if we're in different cells or if
1129	>	// we're in the same cell and the global index of the
1130	>	// j2 cutoff group is less than the j1 cutoff group
1131	>
1132	>	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1133	>	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1134	>	snap_->wrapVector(dr);
1135	>	cuts = getGroupCutoffs( (j1), (j2) );
1136	>	if (dr.lengthSquare() < cuts.third) {
1137	>	neighborList.push_back(make_pair((j1), (j2)));
1138	>	}
1139		}
1140		}
1141		}
906	–	}
1142		#else
1143	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1144	<	j1 != cellList_[m1].end(); ++j1) {
1145	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1146	<	j2 != cellList_[m2].end(); ++j2) {
1147	<
1148	<	// Always do this if we're in different cells or if
1149	<	// we're in the same cell and the global index of the
1150	<	// j2 cutoff group is less than the j1 cutoff group
1151	<
1152	<	if (m2 != m1 \|\| (j2) < (j1)) {
1153	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1154	<	snap_->wrapVector(dr);
1155	<	if (dr.lengthSquare() < rl2) {
1156	<	neighborList.push_back(make_pair((j1), (j2)));
1143	>
1144	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1145	>	j1 != cellList_[m1].end(); ++j1) {
1146	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1147	>	j2 != cellList_[m2].end(); ++j2) {
1148	>
1149	>	// Always do this if we're in different cells or if
1150	>	// we're in the same cell and the global index of the
1151	>	// j2 cutoff group is less than the j1 cutoff group
1152	>
1153	>	if (m2 != m1 \|\| (j2) < (j1)) {
1154	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1155	>	snap_->wrapVector(dr);
1156	>	cuts = getGroupCutoffs( (j1), (j2) );
1157	>	if (dr.lengthSquare() < cuts.third) {
1158	>	neighborList.push_back(make_pair((j1), (j2)));
1159	>	}
1160		}
1161		}
1162		}
925	–	}
1163		#endif
1164	+	}
1165		}
1166		}
1167		}
1168	+	} else {
1169	+	// branch to do all cutoff group pairs
1170	+	#ifdef IS_MPI
1171	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1172	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1173	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1174	+	snap_->wrapVector(dr);
1175	+	cuts = getGroupCutoffs( j1, j2 );
1176	+	if (dr.lengthSquare() < cuts.third) {
1177	+	neighborList.push_back(make_pair(j1, j2));
1178	+	}
1179	+	}
1180	+	}
1181	+	#else
1182	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1183	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1184	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1185	+	snap_->wrapVector(dr);
1186	+	cuts = getGroupCutoffs( j1, j2 );
1187	+	if (dr.lengthSquare() < cuts.third) {
1188	+	neighborList.push_back(make_pair(j1, j2));
1189	+	}
1190	+	}
1191	+	}
1192	+	#endif
1193		}
1194	<
1194	>
1195		// save the local cutoff group positions for the check that is
1196		// done on each loop:
1197		saved_CG_positions_.clear();
1198		for (int i = 0; i < nGroups_; i++)
1199		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1200	<
1200	>
1201		return neighborList;
1202		}
1203		} //end namespace OpenMD

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs. Revision 1591 by gezelter, Tue Jul 12 15:25:07 2011 UTC

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1591 by gezelter, Tue Jul 12 15:25:07 2011 UTC