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root/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 1756 by gezelter, Mon Jun 18 18:23:20 2012 UTC

#	Line 36 | Line 36
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
#	Line 47 | Line 48 | namespace OpenMD {
48		using namespace std;
49		namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	+
53	+	// In a parallel computation, row and colum scans must visit all
54	+	// surrounding cells (not just the 14 upper triangular blocks that
55	+	// are used when the processor can see all pairs)
56	+	#ifdef IS_MPI
57	+	cellOffsets_.clear();
58	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
66	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	+	#endif
86	+	}
87	+
88	+
89		/**
90		* distributeInitialData is essentially a copy of the older fortran
91		* SimulationSetup
92		*/
54	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96		ff_ = info_->getForceField();
97		nLocal_ = snap_->getNumberOfAtoms();
98	<	nGroups_ = snap_->getNumberOfCutoffGroups();
99	<
98	>
99	>	nGroups_ = info_->getNLocalCutoffGroups();
100		// gather the information for atomtype IDs (atids):
101	<	identsLocal = info_->getIdentArray();
101	>	idents = info_->getIdentArray();
102		AtomLocalToGlobal = info_->getGlobalAtomIndices();
103		cgLocalToGlobal = info_->getGlobalGroupIndices();
104		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();
105
106	+	massFactors = info_->getMassFactors();
107	+
108	+	PairList* excludes = info_->getExcludedInteractions();
109	+	PairList* oneTwo = info_->getOneTwoInteractions();
110	+	PairList* oneThree = info_->getOneThreeInteractions();
111	+	PairList* oneFour = info_->getOneFourInteractions();
112	+
113	+	if (needVelocities_)
114	+	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
115	+	DataStorage::dslVelocity);
116	+	else
117	+	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118	+
119		#ifdef IS_MPI
120
121	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
122	<	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_);
121	>	MPI::Intracomm row = rowComm.getComm();
122	>	MPI::Intracomm col = colComm.getComm();
123
124	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
125	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
126	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
127	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
128	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
124	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
125	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
126	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
127	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
128	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
129
130	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
131	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
132	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
133	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
130	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
131	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
132	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
133	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
134	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
135
136	<	nAtomsInRow_ = AtomCommIntRow->getSize();
137	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
138	<	nGroupsInRow_ = cgCommIntRow->getSize();
139	<	nGroupsInCol_ = cgCommIntColumn->getSize();
136	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
137	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
138	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
139	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
140
141	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
142	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
143	+	nGroupsInRow_ = cgPlanIntRow->getSize();
144	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
145	+
146		// Modify the data storage objects with the correct layouts and sizes:
147		atomRowData.resize(nAtomsInRow_);
148		atomRowData.setStorageLayout(storageLayout_);
#	Line 102 | Line 151 | namespace OpenMD {
151		cgRowData.resize(nGroupsInRow_);
152		cgRowData.setStorageLayout(DataStorage::dslPosition);
153		cgColData.resize(nGroupsInCol_);
154	<	cgColData.setStorageLayout(DataStorage::dslPosition);
155	<
156	<	identsRow.reserve(nAtomsInRow_);
157	<	identsCol.reserve(nAtomsInCol_);
154	>	if (needVelocities_)
155	>	// we only need column velocities if we need them.
156	>	cgColData.setStorageLayout(DataStorage::dslPosition |
157	>	DataStorage::dslVelocity);
158	>	else
159	>	cgColData.setStorageLayout(DataStorage::dslPosition);
160	>
161	>	identsRow.resize(nAtomsInRow_);
162	>	identsCol.resize(nAtomsInCol_);
163
164	<	AtomCommIntRow->gather(identsLocal, identsRow);
165	<	AtomCommIntColumn->gather(identsLocal, identsCol);
164	>	AtomPlanIntRow->gather(idents, identsRow);
165	>	AtomPlanIntColumn->gather(idents, identsCol);
166
167	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
168	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
169	<
116	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
117	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
167	>	// allocate memory for the parallel objects
168	>	atypesRow.resize(nAtomsInRow_);
169	>	atypesCol.resize(nAtomsInCol_);
170
171	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
172	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
171	>	for (int i = 0; i < nAtomsInRow_; i++)
172	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
173	>	for (int i = 0; i < nAtomsInCol_; i++)
174	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
175
176	+	pot_row.resize(nAtomsInRow_);
177	+	pot_col.resize(nAtomsInCol_);
178	+
179	+	AtomRowToGlobal.resize(nAtomsInRow_);
180	+	AtomColToGlobal.resize(nAtomsInCol_);
181	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
182	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
183	+
184	+	cgRowToGlobal.resize(nGroupsInRow_);
185	+	cgColToGlobal.resize(nGroupsInCol_);
186	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
187	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
188	+
189	+	massFactorsRow.resize(nAtomsInRow_);
190	+	massFactorsCol.resize(nAtomsInCol_);
191	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
192	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
193	+
194		groupListRow_.clear();
195	<	groupListRow_.reserve(nGroupsInRow_);
195	>	groupListRow_.resize(nGroupsInRow_);
196		for (int i = 0; i < nGroupsInRow_; i++) {
197		int gid = cgRowToGlobal[i];
198		for (int j = 0; j < nAtomsInRow_; j++) {
#	Line 131 | Line 203 | namespace OpenMD {
203		}
204
205		groupListCol_.clear();
206	<	groupListCol_.reserve(nGroupsInCol_);
206	>	groupListCol_.resize(nGroupsInCol_);
207		for (int i = 0; i < nGroupsInCol_; i++) {
208		int gid = cgColToGlobal[i];
209		for (int j = 0; j < nAtomsInCol_; j++) {
#	Line 141 | Line 213 | namespace OpenMD {
213		}
214		}
215
216	<	skipsForRowAtom.clear();
217	<	skipsForRowAtom.reserve(nAtomsInRow_);
216	>	excludesForAtom.clear();
217	>	excludesForAtom.resize(nAtomsInRow_);
218	>	toposForAtom.clear();
219	>	toposForAtom.resize(nAtomsInRow_);
220	>	topoDist.clear();
221	>	topoDist.resize(nAtomsInRow_);
222		for (int i = 0; i < nAtomsInRow_; i++) {
223		int iglob = AtomRowToGlobal[i];
224	+
225		for (int j = 0; j < nAtomsInCol_; j++) {
226	<	int jglob = AtomColToGlobal[j];
227	<	if (excludes.hasPair(iglob, jglob))
228	<	skipsForRowAtom[i].push_back(j);
226	>	int jglob = AtomColToGlobal[j];
227	>
228	>	if (excludes->hasPair(iglob, jglob))
229	>	excludesForAtom[i].push_back(j);
230	>
231	>	if (oneTwo->hasPair(iglob, jglob)) {
232	>	toposForAtom[i].push_back(j);
233	>	topoDist[i].push_back(1);
234	>	} else {
235	>	if (oneThree->hasPair(iglob, jglob)) {
236	>	toposForAtom[i].push_back(j);
237	>	topoDist[i].push_back(2);
238	>	} else {
239	>	if (oneFour->hasPair(iglob, jglob)) {
240	>	toposForAtom[i].push_back(j);
241	>	topoDist[i].push_back(3);
242	>	}
243	>	}
244	>	}
245		}
246		}
247
248	<	toposForRowAtom.clear();
249	<	toposForRowAtom.reserve(nAtomsInRow_);
250	<	for (int i = 0; i < nAtomsInRow_; i++) {
251	<	int iglob = AtomRowToGlobal[i];
252	<	int nTopos = 0;
253	<	for (int j = 0; j < nAtomsInCol_; j++) {
254	<	int jglob = AtomColToGlobal[j];
255	<	if (oneTwo.hasPair(iglob, jglob)) {
256	<	toposForRowAtom[i].push_back(j);
257	<	topoDistRow[i][nTopos] = 1;
258	<	nTopos++;
248	>	#else
249	>	excludesForAtom.clear();
250	>	excludesForAtom.resize(nLocal_);
251	>	toposForAtom.clear();
252	>	toposForAtom.resize(nLocal_);
253	>	topoDist.clear();
254	>	topoDist.resize(nLocal_);
255	>
256	>	for (int i = 0; i < nLocal_; i++) {
257	>	int iglob = AtomLocalToGlobal[i];
258	>
259	>	for (int j = 0; j < nLocal_; j++) {
260	>	int jglob = AtomLocalToGlobal[j];
261	>
262	>	if (excludes->hasPair(iglob, jglob))
263	>	excludesForAtom[i].push_back(j);
264	>
265	>	if (oneTwo->hasPair(iglob, jglob)) {
266	>	toposForAtom[i].push_back(j);
267	>	topoDist[i].push_back(1);
268	>	} else {
269	>	if (oneThree->hasPair(iglob, jglob)) {
270	>	toposForAtom[i].push_back(j);
271	>	topoDist[i].push_back(2);
272	>	} else {
273	>	if (oneFour->hasPair(iglob, jglob)) {
274	>	toposForAtom[i].push_back(j);
275	>	topoDist[i].push_back(3);
276	>	}
277	>	}
278		}
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	–	}
279		}
280		}
179	–
281		#endif
282
283	+	// allocate memory for the parallel objects
284	+	atypesLocal.resize(nLocal_);
285	+
286	+	for (int i = 0; i < nLocal_; i++)
287	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
288	+
289		groupList_.clear();
290	<	groupList_.reserve(nGroups_);
290	>	groupList_.resize(nGroups_);
291		for (int i = 0; i < nGroups_; i++) {
292		int gid = cgLocalToGlobal[i];
293		for (int j = 0; j < nLocal_; j++) {
294		int aid = AtomLocalToGlobal[j];
295	<	if (globalGroupMembership[aid] == gid)
295	>	if (globalGroupMembership[aid] == gid) {
296		groupList_[i].push_back(j);
297	+	}
298		}
299		}
300
193	–	skipsForLocalAtom.clear();
194	–	skipsForLocalAtom.reserve(nLocal_);
301
302	<	for (int i = 0; i < nLocal_; i++) {
197	<	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	<	}
302	>	createGtypeCutoffMap();
303
205	–	toposForLocalAtom.clear();
206	–	toposForLocalAtom.reserve(nLocal_);
207	–	for (int i = 0; i < nLocal_; i++) {
208	–	int iglob = AtomLocalToGlobal[i];
209	–	int nTopos = 0;
210	–	for (int j = 0; j < nLocal_; j++) {
211	–	int jglob = AtomLocalToGlobal[j];
212	–	if (oneTwo.hasPair(iglob, jglob)) {
213	–	toposForLocalAtom[i].push_back(j);
214	–	topoDistLocal[i][nTopos] = 1;
215	–	nTopos++;
216	–	}
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	–	}
227	–	}
228	–	}
229	–
304		}
305
306		void ForceMatrixDecomposition::createGtypeCutoffMap() {
307	<
307	>
308		RealType tol = 1e-6;
309	+	largestRcut_ = 0.0;
310		RealType rc;
311		int atid;
312		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
313	<	vector<RealType> atypeCutoff;
314	<	atypeCutoff.reserve( atypes.size() );
315	<
316	<	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
317	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
313	>
314	>	map<int, RealType> atypeCutoff;
315	>
316	>	for (set<AtomType*>::iterator at = atypes.begin();
317	>	at != atypes.end(); ++at){
318		atid = (*at)->getIdent();
319	<	atypeCutoff[atid] = rc;
319	>	if (userChoseCutoff_)
320	>	atypeCutoff[atid] = userCutoff_;
321	>	else
322	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
323		}
324	<
324	>
325		vector<RealType> gTypeCutoffs;
248	–
326		// first we do a single loop over the cutoff groups to find the
327		// largest cutoff for any atypes present in this group.
328		#ifdef IS_MPI
329		vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
330	+	groupRowToGtype.resize(nGroupsInRow_);
331		for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
332		vector<int> atomListRow = getAtomsInGroupRow(cg1);
333		for (vector<int>::iterator ia = atomListRow.begin();
#	Line 275 | Line 353 | namespace OpenMD {
353
354		}
355		vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
356	+	groupColToGtype.resize(nGroupsInCol_);
357		for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
358		vector<int> atomListCol = getAtomsInGroupColumn(cg2);
359		for (vector<int>::iterator jb = atomListCol.begin();
#	Line 298 | Line 377 | namespace OpenMD {
377		}
378		}
379		#else
380	+
381		vector<RealType> groupCutoff(nGroups_, 0.0);
382	+	groupToGtype.resize(nGroups_);
383		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
384		groupCutoff[cg1] = 0.0;
385		vector<int> atomList = getAtomsInGroupRow(cg1);
386		for (vector<int>::iterator ia = atomList.begin();
387		ia != atomList.end(); ++ia) {
388		int atom1 = (*ia);
389	<	atid = identsLocal[atom1];
390	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
389	>	atid = idents[atom1];
390	>	if (atypeCutoff[atid] > groupCutoff[cg1])
391		groupCutoff[cg1] = atypeCutoff[atid];
311	–	}
392		}
393	<
393	>
394		bool gTypeFound = false;
395		for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
396		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
#	Line 318 | Line 398 | namespace OpenMD {
398		gTypeFound = true;
399		}
400		}
401	<	if (!gTypeFound) {
401	>	if (!gTypeFound) {
402		gTypeCutoffs.push_back( groupCutoff[cg1] );
403		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
404		}
#	Line 327 | Line 407 | namespace OpenMD {
407
408		// Now we find the maximum group cutoff value present in the simulation
409
410	<	vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
411	<	RealType groupMax = *groupMaxLoc;
410	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
411	>	gTypeCutoffs.end());
412
413		#ifdef IS_MPI
414	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
414	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
415	>	MPI::MAX);
416		#endif
417
418		RealType tradRcut = groupMax;
419
420		for (int i = 0; i < gTypeCutoffs.size();  i++) {
421	<	for (int j = 0; j < gTypeCutoffs.size();  j++) {
341	<
421	>	for (int j = 0; j < gTypeCutoffs.size();  j++) {
422		RealType thisRcut;
423		switch(cutoffPolicy_) {
424		case TRADITIONAL:
425		thisRcut = tradRcut;
426	+	break;
427		case MIX:
428		thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
429	+	break;
430		case MAX:
431		thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
432	+	break;
433		default:
434		sprintf(painCave.errMsg,
435		"ForceMatrixDecomposition::createGtypeCutoffMap "
436		"hit an unknown cutoff policy!\n");
437		painCave.severity = OPENMD_ERROR;
438		painCave.isFatal = 1;
439	<	simError();
439	>	simError();
440	>	break;
441		}
442
443		pair<int,int> key = make_pair(i,j);
444		gTypeCutoffMap[key].first = thisRcut;
361	–
445		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
363	–
446		gTypeCutoffMap[key].second = thisRcut*thisRcut;
365	–
447		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
367	–
448		// sanity check
449
450		if (userChoseCutoff_) {
451		if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
452		sprintf(painCave.errMsg,
453		"ForceMatrixDecomposition::createGtypeCutoffMap "
454	<	"user-specified rCut does not match computed group Cutoff\n");
454	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
455		painCave.severity = OPENMD_ERROR;
456		painCave.isFatal = 1;
457		simError();
#	Line 381 | Line 461 | namespace OpenMD {
461		}
462		}
463
384	–
464		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
465	<	int i, j;
387	<
465	>	int i, j;
466		#ifdef IS_MPI
467		i = groupRowToGtype[cg1];
468		j = groupColToGtype[cg2];
469		#else
470		i = groupToGtype[cg1];
471		j = groupToGtype[cg2];
472	<	#endif
395	<
472	>	#endif
473		return gTypeCutoffMap[make_pair(i,j)];
474		}
475
476	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
477	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
478	+	if (toposForAtom[atom1][j] == atom2)
479	+	return topoDist[atom1][j];
480	+	}
481	+	return 0;
482	+	}
483
484		void ForceMatrixDecomposition::zeroWorkArrays() {
485	+	pairwisePot = 0.0;
486	+	embeddingPot = 0.0;
487
402	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403	–	longRangePot_[j] = 0.0;
404	–	}
405	–
488		#ifdef IS_MPI
489		if (storageLayout_ & DataStorage::dslForce) {
490		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 418 | Line 500 | namespace OpenMD {
500		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
501
502		fill(pot_col.begin(), pot_col.end(),
503	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422	<
423	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
503	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
504
505		if (storageLayout_ & DataStorage::dslParticlePot) {
506	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
507	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
506	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
507	>	0.0);
508	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
509	>	0.0);
510		}
511
512		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 433 | Line 515 | namespace OpenMD {
515		}
516
517		if (storageLayout_ & DataStorage::dslFunctional) {
518	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
519	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
518	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
519	>	0.0);
520	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
521	>	0.0);
522		}
523
524		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 444 | Line 528 | namespace OpenMD {
528		atomColData.functionalDerivative.end(), 0.0);
529		}
530
531	<	#else
532	<
531	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
532	>	fill(atomRowData.skippedCharge.begin(),
533	>	atomRowData.skippedCharge.end(), 0.0);
534	>	fill(atomColData.skippedCharge.begin(),
535	>	atomColData.skippedCharge.end(), 0.0);
536	>	}
537	>
538	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
539	>	fill(atomRowData.flucQFrc.begin(),
540	>	atomRowData.flucQFrc.end(), 0.0);
541	>	fill(atomColData.flucQFrc.begin(),
542	>	atomColData.flucQFrc.end(), 0.0);
543	>	}
544	>
545	>	if (storageLayout_ & DataStorage::dslElectricField) {
546	>	fill(atomRowData.electricField.begin(),
547	>	atomRowData.electricField.end(), V3Zero);
548	>	fill(atomColData.electricField.begin(),
549	>	atomColData.electricField.end(), V3Zero);
550	>	}
551	>
552	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
553	>	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
554	>	0.0);
555	>	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
556	>	0.0);
557	>	}
558	>
559	>	#endif
560	>	// even in parallel, we need to zero out the local arrays:
561	>
562		if (storageLayout_ & DataStorage::dslParticlePot) {
563		fill(snap_->atomData.particlePot.begin(),
564		snap_->atomData.particlePot.end(), 0.0);
#	Line 455 | Line 568 | namespace OpenMD {
568		fill(snap_->atomData.density.begin(),
569		snap_->atomData.density.end(), 0.0);
570		}
571	+
572		if (storageLayout_ & DataStorage::dslFunctional) {
573		fill(snap_->atomData.functional.begin(),
574		snap_->atomData.functional.end(), 0.0);
575		}
576	+
577		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
578		fill(snap_->atomData.functionalDerivative.begin(),
579		snap_->atomData.functionalDerivative.end(), 0.0);
580		}
581	<	#endif
582	<
581	>
582	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
583	>	fill(snap_->atomData.skippedCharge.begin(),
584	>	snap_->atomData.skippedCharge.end(), 0.0);
585	>	}
586	>
587	>	if (storageLayout_ & DataStorage::dslElectricField) {
588	>	fill(snap_->atomData.electricField.begin(),
589	>	snap_->atomData.electricField.end(), V3Zero);
590	>	}
591		}
592
593
#	Line 474 | Line 597 | namespace OpenMD {
597		#ifdef IS_MPI
598
599		// gather up the atomic positions
600	<	AtomCommVectorRow->gather(snap_->atomData.position,
600	>	AtomPlanVectorRow->gather(snap_->atomData.position,
601		atomRowData.position);
602	<	AtomCommVectorColumn->gather(snap_->atomData.position,
602	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
603		atomColData.position);
604
605		// gather up the cutoff group positions
606	<	cgCommVectorRow->gather(snap_->cgData.position,
606	>
607	>	cgPlanVectorRow->gather(snap_->cgData.position,
608		cgRowData.position);
609	<	cgCommVectorColumn->gather(snap_->cgData.position,
609	>
610	>	cgPlanVectorColumn->gather(snap_->cgData.position,
611		cgColData.position);
612	+
613	+
614	+
615	+	if (needVelocities_) {
616	+	// gather up the atomic velocities
617	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
618	+	atomColData.velocity);
619	+
620	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
621	+	cgColData.velocity);
622	+	}
623	+
624
625		// if needed, gather the atomic rotation matrices
626		if (storageLayout_ & DataStorage::dslAmat) {
627	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
627	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
628		atomRowData.aMat);
629	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
629	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
630		atomColData.aMat);
631		}
632
633		// if needed, gather the atomic eletrostatic frames
634		if (storageLayout_ & DataStorage::dslElectroFrame) {
635	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
635	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
636		atomRowData.electroFrame);
637	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
637	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
638		atomColData.electroFrame);
639	+	}
640	+
641	+	// if needed, gather the atomic fluctuating charge values
642	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
643	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
644	+	atomRowData.flucQPos);
645	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
646	+	atomColData.flucQPos);
647		}
648	+
649		#endif
650		}
651
#	Line 513 | Line 659 | namespace OpenMD {
659
660		if (storageLayout_ & DataStorage::dslDensity) {
661
662	<	AtomCommRealRow->scatter(atomRowData.density,
662	>	AtomPlanRealRow->scatter(atomRowData.density,
663		snap_->atomData.density);
664
665		int n = snap_->atomData.density.size();
666		vector<RealType> rho_tmp(n, 0.0);
667	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
667	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
668		for (int i = 0; i < n; i++)
669		snap_->atomData.density[i] += rho_tmp[i];
670		}
671	+
672	+	if (storageLayout_ & DataStorage::dslElectricField) {
673	+
674	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
675	+	snap_->atomData.electricField);
676	+
677	+	int n = snap_->atomData.electricField.size();
678	+	vector<Vector3d> field_tmp(n, V3Zero);
679	+	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
680	+	for (int i = 0; i < n; i++)
681	+	snap_->atomData.electricField[i] += field_tmp[i];
682	+	}
683		#endif
684		}
685
#	Line 534 | Line 692 | namespace OpenMD {
692		storageLayout_ = sman_->getStorageLayout();
693		#ifdef IS_MPI
694		if (storageLayout_ & DataStorage::dslFunctional) {
695	<	AtomCommRealRow->gather(snap_->atomData.functional,
695	>	AtomPlanRealRow->gather(snap_->atomData.functional,
696		atomRowData.functional);
697	<	AtomCommRealColumn->gather(snap_->atomData.functional,
697	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
698		atomColData.functional);
699		}
700
701		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
702	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
702	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
703		atomRowData.functionalDerivative);
704	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
704	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
705		atomColData.functionalDerivative);
706		}
707		#endif
#	Line 557 | Line 715 | namespace OpenMD {
715		int n = snap_->atomData.force.size();
716		vector<Vector3d> frc_tmp(n, V3Zero);
717
718	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
718	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
719		for (int i = 0; i < n; i++) {
720		snap_->atomData.force[i] += frc_tmp[i];
721		frc_tmp[i] = 0.0;
722		}
723
724	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
725	<	for (int i = 0; i < n; i++)
724	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
725	>	for (int i = 0; i < n; i++) {
726		snap_->atomData.force[i] += frc_tmp[i];
727	<
728	<
727	>	}
728	>
729		if (storageLayout_ & DataStorage::dslTorque) {
730
731	<	int nt = snap_->atomData.force.size();
731	>	int nt = snap_->atomData.torque.size();
732		vector<Vector3d> trq_tmp(nt, V3Zero);
733
734	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
735	<	for (int i = 0; i < n; i++) {
734	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
735	>	for (int i = 0; i < nt; i++) {
736		snap_->atomData.torque[i] += trq_tmp[i];
737		trq_tmp[i] = 0.0;
738		}
739
740	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
741	<	for (int i = 0; i < n; i++)
740	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
741	>	for (int i = 0; i < nt; i++)
742		snap_->atomData.torque[i] += trq_tmp[i];
743		}
744	+
745	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
746	+
747	+	int ns = snap_->atomData.skippedCharge.size();
748	+	vector<RealType> skch_tmp(ns, 0.0);
749	+
750	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
751	+	for (int i = 0; i < ns; i++) {
752	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
753	+	skch_tmp[i] = 0.0;
754	+	}
755	+
756	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
757	+	for (int i = 0; i < ns; i++)
758	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
759	+
760	+	}
761
762	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
763	+
764	+	int nq = snap_->atomData.flucQFrc.size();
765	+	vector<RealType> fqfrc_tmp(nq, 0.0);
766	+
767	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
768	+	for (int i = 0; i < nq; i++) {
769	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
770	+	fqfrc_tmp[i] = 0.0;
771	+	}
772	+
773	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
774	+	for (int i = 0; i < nq; i++)
775	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
776	+
777	+	}
778	+
779		nLocal_ = snap_->getNumberOfAtoms();
780
781		vector<potVec> pot_temp(nLocal_,
#	Line 591 | Line 783 | namespace OpenMD {
783
784		// scatter/gather pot_row into the members of my column
785
786	<	AtomCommPotRow->scatter(pot_row, pot_temp);
786	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
787
788		for (int ii = 0;  ii < pot_temp.size(); ii++ )
789	<	pot_local += pot_temp[ii];
790	<
789	>	pairwisePot += pot_temp[ii];
790	>
791	>	if (storageLayout_ & DataStorage::dslParticlePot) {
792	>	// This is the pairwise contribution to the particle pot.  The
793	>	// embedding contribution is added in each of the low level
794	>	// non-bonded routines.  In single processor, this is done in
795	>	// unpackInteractionData, not in collectData.
796	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
797	>	for (int i = 0; i < nLocal_; i++) {
798	>	// factor of two is because the total potential terms are divided
799	>	// by 2 in parallel due to row/ column scatter
800	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
801	>	}
802	>	}
803	>	}
804	>
805		fill(pot_temp.begin(), pot_temp.end(),
806		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
807
808	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
808	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
809
810		for (int ii = 0;  ii < pot_temp.size(); ii++ )
811	<	pot_local += pot_temp[ii];
811	>	pairwisePot += pot_temp[ii];
812	>
813	>	if (storageLayout_ & DataStorage::dslParticlePot) {
814	>	// This is the pairwise contribution to the particle pot.  The
815	>	// embedding contribution is added in each of the low level
816	>	// non-bonded routines.  In single processor, this is done in
817	>	// unpackInteractionData, not in collectData.
818	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
819	>	for (int i = 0; i < nLocal_; i++) {
820	>	// factor of two is because the total potential terms are divided
821	>	// by 2 in parallel due to row/ column scatter
822	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
823	>	}
824	>	}
825	>	}
826
827	+	if (storageLayout_ & DataStorage::dslParticlePot) {
828	+	int npp = snap_->atomData.particlePot.size();
829	+	vector<RealType> ppot_temp(npp, 0.0);
830	+
831	+	// This is the direct or embedding contribution to the particle
832	+	// pot.
833	+
834	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
835	+	for (int i = 0; i < npp; i++) {
836	+	snap_->atomData.particlePot[i] += ppot_temp[i];
837	+	}
838	+
839	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
840	+
841	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
842	+	for (int i = 0; i < npp; i++) {
843	+	snap_->atomData.particlePot[i] += ppot_temp[i];
844	+	}
845	+	}
846	+
847	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
848	+	RealType ploc1 = pairwisePot[ii];
849	+	RealType ploc2 = 0.0;
850	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
851	+	pairwisePot[ii] = ploc2;
852	+	}
853	+
854	+	// Here be dragons.
855	+	MPI::Intracomm col = colComm.getComm();
856	+
857	+	col.Allreduce(MPI::IN_PLACE,
858	+	&snap_->frameData.conductiveHeatFlux[0], 3,
859	+	MPI::REALTYPE, MPI::SUM);
860	+
861	+
862		#endif
863	+
864		}
865
866	+	/**
867	+	* Collects information obtained during the post-pair (and embedding
868	+	* functional) loops onto local data structures.
869	+	*/
870	+	void ForceMatrixDecomposition::collectSelfData() {
871	+	snap_ = sman_->getCurrentSnapshot();
872	+	storageLayout_ = sman_->getStorageLayout();
873	+
874	+	#ifdef IS_MPI
875	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
876	+	RealType ploc1 = embeddingPot[ii];
877	+	RealType ploc2 = 0.0;
878	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
879	+	embeddingPot[ii] = ploc2;
880	+	}
881	+	#endif
882	+
883	+	}
884	+
885	+
886	+
887		int ForceMatrixDecomposition::getNAtomsInRow() {
888		#ifdef IS_MPI
889		return nAtomsInRow_;
#	Line 647 | Line 924 | namespace OpenMD {
924		return d;
925		}
926
927	+	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
928	+	#ifdef IS_MPI
929	+	return cgColData.velocity[cg2];
930	+	#else
931	+	return snap_->cgData.velocity[cg2];
932	+	#endif
933	+	}
934
935	+	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
936	+	#ifdef IS_MPI
937	+	return atomColData.velocity[atom2];
938	+	#else
939	+	return snap_->atomData.velocity[atom2];
940	+	#endif
941	+	}
942	+
943	+
944		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
945
946		Vector3d d;
#	Line 679 | Line 972 | namespace OpenMD {
972		#ifdef IS_MPI
973		return massFactorsRow[atom1];
974		#else
975	<	return massFactorsLocal[atom1];
975	>	return massFactors[atom1];
976		#endif
977		}
978
#	Line 687 | Line 980 | namespace OpenMD {
980		#ifdef IS_MPI
981		return massFactorsCol[atom2];
982		#else
983	<	return massFactorsLocal[atom2];
983	>	return massFactors[atom2];
984		#endif
985
986		}
#	Line 705 | Line 998 | namespace OpenMD {
998		return d;
999		}
1000
1001	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
1002	<	#ifdef IS_MPI
710	<	return skipsForRowAtom[atom1];
711	<	#else
712	<	return skipsForLocalAtom[atom1];
713	<	#endif
1001	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1002	>	return excludesForAtom[atom1];
1003		}
1004
1005		/**
1006	<	* 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
1006	>	* We need to exclude some overcounted interactions that result from
1007		* the parallel decomposition.
1008		*/
1009	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1010	<	int unique_id_1, unique_id_2;
1011	<
1009	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1010	>	int unique_id_1, unique_id_2, group1, group2;
1011	>
1012		#ifdef IS_MPI
1013		// in MPI, we have to look up the unique IDs for each atom
1014		unique_id_1 = AtomRowToGlobal[atom1];
1015		unique_id_2 = AtomColToGlobal[atom2];
1016	+	group1 = cgRowToGlobal[cg1];
1017	+	group2 = cgColToGlobal[cg2];
1018	+	#else
1019	+	unique_id_1 = AtomLocalToGlobal[atom1];
1020	+	unique_id_2 = AtomLocalToGlobal[atom2];
1021	+	group1 = cgLocalToGlobal[cg1];
1022	+	group2 = cgLocalToGlobal[cg2];
1023	+	#endif
1024
731	–	// this situation should only arise in MPI simulations
1025		if (unique_id_1 == unique_id_2) return true;
1026	<
1026	>
1027	>	#ifdef IS_MPI
1028		// this prevents us from doing the pair on multiple processors
1029		if (unique_id_1 < unique_id_2) {
1030		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1031		} else {
1032	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1032	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1033		}
1034	<	#else
1035	<	// in the normal loop, the atom numbers are unique
1036	<	unique_id_1 = atom1;
1037	<	unique_id_2 = atom2;
1034	>	#endif
1035	>
1036	>	#ifndef IS_MPI
1037	>	if (group1 == group2) {
1038	>	if (unique_id_1 < unique_id_2) return true;
1039	>	}
1040		#endif
1041
1042	<	#ifdef IS_MPI
747	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748	<	i != skipsForRowAtom[atom1].end(); ++i) {
749	<	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
1042	>	return false;
1043		}
1044
1045	<	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
1045	>	/**
1046	>	* We need to handle the interactions for atoms who are involved in
1047	>	* the same rigid body as well as some short range interactions
1048	>	* (bonds, bends, torsions) differently from other interactions.
1049	>	* We'll still visit the pairwise routines, but with a flag that
1050	>	* tells those routines to exclude the pair from direct long range
1051	>	* interactions.  Some indirect interactions (notably reaction
1052	>	* field) must still be handled for these pairs.
1053	>	*/
1054	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1055	>
1056	>	// excludesForAtom was constructed to use row/column indices in the MPI
1057	>	// version, and to use local IDs in the non-MPI version:
1058
1059	<	#ifdef IS_MPI
1060	<	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
1061	<	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];
1059	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1060	>	i != excludesForAtom[atom1].end(); ++i) {
1061	>	if ( (*i) == atom2 ) return true;
1062		}
769	–	#endif
1063
1064	<	// zero is default for unconnected (i.e. normal) pair interactions
772	<	return 0;
1064	>	return false;
1065		}
1066
1067	+
1068		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1069		#ifdef IS_MPI
1070		atomRowData.force[atom1] += fg;
#	Line 789 | Line 1082 | namespace OpenMD {
1082		}
1083
1084		// filling interaction blocks with pointers
1085	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1086	<	InteractionData idat;
1085	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1086	>	int atom1, int atom2) {
1087
1088	+	idat.excluded = excludeAtomPair(atom1, atom2);
1089	+
1090		#ifdef IS_MPI
1091	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1092	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1093	+	//                         ff_->getAtomType(identsCol[atom2]) );
1094
797	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
798	–	ff_->getAtomType(identsCol[atom2]) );
799	–
800	–
1095		if (storageLayout_ & DataStorage::dslAmat) {
1096		idat.A1 = &(atomRowData.aMat[atom1]);
1097		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 833 | Line 1127 | namespace OpenMD {
1127		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1128		}
1129
1130	<	#else
1130	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1131	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1132	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1133	>	}
1134
1135	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
1136	<	ff_->getAtomType(identsLocal[atom2]) );
1135	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1136	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1137	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1138	>	}
1139
1140	+	#else
1141	+
1142	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1143	+
1144		if (storageLayout_ & DataStorage::dslAmat) {
1145		idat.A1 = &(snap_->atomData.aMat[atom1]);
1146		idat.A2 = &(snap_->atomData.aMat[atom2]);
#	Line 853 | Line 1156 | namespace OpenMD {
1156		idat.t2 = &(snap_->atomData.torque[atom2]);
1157		}
1158
1159	<	if (storageLayout_ & DataStorage::dslDensity) {
1159	>	if (storageLayout_ & DataStorage::dslDensity) {
1160		idat.rho1 = &(snap_->atomData.density[atom1]);
1161		idat.rho2 = &(snap_->atomData.density[atom2]);
1162		}
#	Line 873 | Line 1176 | namespace OpenMD {
1176		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1177		}
1178
1179	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1180	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1181	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1182	+	}
1183	+
1184	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1185	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1186	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1187	+	}
1188	+
1189		#endif
877	–	return idat;
1190		}
1191
1192
1193	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
1193	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1194		#ifdef IS_MPI
1195	<	pot_row[atom1] += 0.5 *  *(idat.pot);
1196	<	pot_col[atom2] += 0.5 *  *(idat.pot);
1195	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1196	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1197
1198		atomRowData.force[atom1] += *(idat.f1);
1199		atomColData.force[atom2] -= *(idat.f1);
888	–	#else
889	–	longRangePot_ += *(idat.pot);
890	–
891	–	snap_->atomData.force[atom1] += *(idat.f1);
892	–	snap_->atomData.force[atom2] -= *(idat.f1);
893	–	#endif
1200
1201	<	}
1201	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1202	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1203	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1204	>	}
1205
1206	+	if (storageLayout_ & DataStorage::dslElectricField) {
1207	+	atomRowData.electricField[atom1] += *(idat.eField1);
1208	+	atomColData.electricField[atom2] += *(idat.eField2);
1209	+	}
1210
1211	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1211	>	#else
1212	>	pairwisePot += *(idat.pot);
1213
1214	<	InteractionData idat;
1215	<	#ifdef IS_MPI
902	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
903	<	ff_->getAtomType(identsCol[atom2]) );
1214	>	snap_->atomData.force[atom1] += *(idat.f1);
1215	>	snap_->atomData.force[atom2] -= *(idat.f1);
1216
1217	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1218	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1219	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1217	>	if (idat.doParticlePot) {
1218	>	// This is the pairwise contribution to the particle pot.  The
1219	>	// embedding contribution is added in each of the low level
1220	>	// non-bonded routines.  In parallel, this calculation is done
1221	>	// in collectData, not in unpackInteractionData.
1222	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1223	>	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1224		}
1225	<	if (storageLayout_ & DataStorage::dslTorque) {
1226	<	idat.t1 = &(atomRowData.torque[atom1]);
1227	<	idat.t2 = &(atomColData.torque[atom2]);
1225	>
1226	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1227	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1228	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1229		}
913	–	#else
914	–	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
915	–	ff_->getAtomType(identsLocal[atom2]) );
1230
1231	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1232	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1233	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1231	>	if (storageLayout_ & DataStorage::dslElectricField) {
1232	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1233	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1234		}
1235	<	if (storageLayout_ & DataStorage::dslTorque) {
1236	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1237	<	idat.t2 = &(snap_->atomData.torque[atom2]);
924	<	}
925	<	#endif
1235	>
1236	>	#endif
1237	>
1238		}
1239
1240		/*
#	Line 935 | Line 1247 | namespace OpenMD {
1247
1248		vector<pair<int, int> > neighborList;
1249		groupCutoffs cuts;
1250	+	bool doAllPairs = false;
1251	+
1252		#ifdef IS_MPI
1253		cellListRow_.clear();
1254		cellListCol_.clear();
#	Line 954 | Line 1268 | namespace OpenMD {
1268		nCells_.y() = (int) ( Hy.length() )/ rList_;
1269		nCells_.z() = (int) ( Hz.length() )/ rList_;
1270
1271	+	// handle small boxes where the cell offsets can end up repeating cells
1272	+
1273	+	if (nCells_.x() < 3) doAllPairs = true;
1274	+	if (nCells_.y() < 3) doAllPairs = true;
1275	+	if (nCells_.z() < 3) doAllPairs = true;
1276	+
1277		Mat3x3d invHmat = snap_->getInvHmat();
1278		Vector3d rs, scaled, dr;
1279		Vector3i whichCell;
1280		int cellIndex;
1281	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1282
1283		#ifdef IS_MPI
1284	<	for (int i = 0; i < nGroupsInRow_; i++) {
1285	<	rs = cgRowData.position[i];
1286	<	// scaled positions relative to the box vectors
1287	<	scaled = invHmat * rs;
1288	<	// 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();
1284	>	cellListRow_.resize(nCtot);
1285	>	cellListCol_.resize(nCtot);
1286	>	#else
1287	>	cellList_.resize(nCtot);
1288	>	#endif
1289
1290	<	// find single index of this cell:
1291	<	cellIndex = Vlinear(whichCell, nCells_);
979	<	// add this cutoff group to the list of groups in this cell;
980	<	cellListRow_[cellIndex].push_back(i);
981	<	}
1290	>	if (!doAllPairs) {
1291	>	#ifdef IS_MPI
1292
1293	<	for (int i = 0; i < nGroupsInCol_; i++) {
1294	<	rs = cgColData.position[i];
1295	<	// scaled positions relative to the box vectors
1296	<	scaled = invHmat * rs;
1297	<	// wrap the vector back into the unit box by subtracting integer box
1298	<	// numbers
1299	<	for (int j = 0; j < 3; j++)
1300	<	scaled[j] -= roundMe(scaled[j]);
1301	<
1302	<	// find xyz-indices of cell that cutoffGroup is in.
1303	<	whichCell.x() = nCells_.x() * scaled.x();
1304	<	whichCell.y() = nCells_.y() * scaled.y();
1305	<	whichCell.z() = nCells_.z() * scaled.z();
1306	<
1307	<	// find single index of this cell:
1308	<	cellIndex = Vlinear(whichCell, nCells_);
1309	<	// add this cutoff group to the list of groups in this cell;
1310	<	cellListCol_[cellIndex].push_back(i);
1311	<	}
1293	>	for (int i = 0; i < nGroupsInRow_; i++) {
1294	>	rs = cgRowData.position[i];
1295	>
1296	>	// scaled positions relative to the box vectors
1297	>	scaled = invHmat * rs;
1298	>
1299	>	// wrap the vector back into the unit box by subtracting integer box
1300	>	// numbers
1301	>	for (int j = 0; j < 3; j++) {
1302	>	scaled[j] -= roundMe(scaled[j]);
1303	>	scaled[j] += 0.5;
1304	>	}
1305	>
1306	>	// find xyz-indices of cell that cutoffGroup is in.
1307	>	whichCell.x() = nCells_.x() * scaled.x();
1308	>	whichCell.y() = nCells_.y() * scaled.y();
1309	>	whichCell.z() = nCells_.z() * scaled.z();
1310	>
1311	>	// find single index of this cell:
1312	>	cellIndex = Vlinear(whichCell, nCells_);
1313	>
1314	>	// add this cutoff group to the list of groups in this cell;
1315	>	cellListRow_[cellIndex].push_back(i);
1316	>	}
1317	>	for (int i = 0; i < nGroupsInCol_; i++) {
1318	>	rs = cgColData.position[i];
1319	>
1320	>	// scaled positions relative to the box vectors
1321	>	scaled = invHmat * rs;
1322	>
1323	>	// wrap the vector back into the unit box by subtracting integer box
1324	>	// numbers
1325	>	for (int j = 0; j < 3; j++) {
1326	>	scaled[j] -= roundMe(scaled[j]);
1327	>	scaled[j] += 0.5;
1328	>	}
1329	>
1330	>	// find xyz-indices of cell that cutoffGroup is in.
1331	>	whichCell.x() = nCells_.x() * scaled.x();
1332	>	whichCell.y() = nCells_.y() * scaled.y();
1333	>	whichCell.z() = nCells_.z() * scaled.z();
1334	>
1335	>	// find single index of this cell:
1336	>	cellIndex = Vlinear(whichCell, nCells_);
1337	>
1338	>	// add this cutoff group to the list of groups in this cell;
1339	>	cellListCol_[cellIndex].push_back(i);
1340	>	}
1341	>
1342		#else
1343	<	for (int i = 0; i < nGroups_; i++) {
1344	<	rs = snap_->cgData.position[i];
1345	<	// scaled positions relative to the box vectors
1346	<	scaled = invHmat * rs;
1347	<	// wrap the vector back into the unit box by subtracting integer box
1348	<	// numbers
1349	<	for (int j = 0; j < 3; j++)
1350	<	scaled[j] -= roundMe(scaled[j]);
1343	>	for (int i = 0; i < nGroups_; i++) {
1344	>	rs = snap_->cgData.position[i];
1345	>
1346	>	// scaled positions relative to the box vectors
1347	>	scaled = invHmat * rs;
1348	>
1349	>	// wrap the vector back into the unit box by subtracting integer box
1350	>	// numbers
1351	>	for (int j = 0; j < 3; j++) {
1352	>	scaled[j] -= roundMe(scaled[j]);
1353	>	scaled[j] += 0.5;
1354	>	}
1355	>
1356	>	// find xyz-indices of cell that cutoffGroup is in.
1357	>	whichCell.x() = nCells_.x() * scaled.x();
1358	>	whichCell.y() = nCells_.y() * scaled.y();
1359	>	whichCell.z() = nCells_.z() * scaled.z();
1360	>
1361	>	// find single index of this cell:
1362	>	cellIndex = Vlinear(whichCell, nCells_);
1363	>
1364	>	// add this cutoff group to the list of groups in this cell;
1365	>	cellList_[cellIndex].push_back(i);
1366	>	}
1367
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	–	}
1368		#endif
1369
1370	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1371	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1372	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1373	<	Vector3i m1v(m1x, m1y, m1z);
1374	<	int m1 = Vlinear(m1v, nCells_);
1029	<
1030	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1031	<	os != cellOffsets_.end(); ++os) {
1370	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1371	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1372	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1373	>	Vector3i m1v(m1x, m1y, m1z);
1374	>	int m1 = Vlinear(m1v, nCells_);
1375
1376	<	Vector3i m2v = m1v + (*os);
1377	<
1378	<	if (m2v.x() >= nCells_.x()) {
1379	<	m2v.x() = 0;
1380	<	} 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_);
1376	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1377	>	os != cellOffsets_.end(); ++os) {
1378	>
1379	>	Vector3i m2v = m1v + (*os);
1380	>
1381
1382	<	#ifdef IS_MPI
1383	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1384	<	j1 != cellListRow_[m1].end(); ++j1) {
1385	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1386	<	j2 != cellListCol_[m2].end(); ++j2) {
1387	<
1388	<	// Always do this if we're in different cells or if
1389	<	// we're in the same cell and the global index of the
1390	<	// j2 cutoff group is less than the j1 cutoff group
1382	>	if (m2v.x() >= nCells_.x()) {
1383	>	m2v.x() = 0;
1384	>	} else if (m2v.x() < 0) {
1385	>	m2v.x() = nCells_.x() - 1;
1386	>	}
1387	>
1388	>	if (m2v.y() >= nCells_.y()) {
1389	>	m2v.y() = 0;
1390	>	} else if (m2v.y() < 0) {
1391	>	m2v.y() = nCells_.y() - 1;
1392	>	}
1393	>
1394	>	if (m2v.z() >= nCells_.z()) {
1395	>	m2v.z() = 0;
1396	>	} else if (m2v.z() < 0) {
1397	>	m2v.z() = nCells_.z() - 1;
1398	>	}
1399
1400	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1400	>	int m2 = Vlinear (m2v, nCells_);
1401	>
1402	>	#ifdef IS_MPI
1403	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1404	>	j1 != cellListRow_[m1].end(); ++j1) {
1405	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1406	>	j2 != cellListCol_[m2].end(); ++j2) {
1407	>
1408	>	// In parallel, we need to visit *all* pairs of row
1409	>	// & column indicies and will divide labor in the
1410	>	// force evaluation later.
1411		dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1412		snap_->wrapVector(dr);
1413		cuts = getGroupCutoffs( (*j1), (*j2) );
1414		if (dr.lengthSquare() < cuts.third) {
1415		neighborList.push_back(make_pair((*j1), (*j2)));
1416	<	}
1416	>	}
1417		}
1418		}
1074	–	}
1419		#else
1420	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1421	<	j1 != cellList_[m1].end(); ++j1) {
1422	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1423	<	j2 != cellList_[m2].end(); ++j2) {
1424	<
1425	<	// Always do this if we're in different cells or if
1426	<	// we're in the same cell and the global index of the
1427	<	// j2 cutoff group is less than the j1 cutoff group
1420	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1421	>	j1 != cellList_[m1].end(); ++j1) {
1422	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1423	>	j2 != cellList_[m2].end(); ++j2) {
1424	>
1425	>	// Always do this if we're in different cells or if
1426	>	// we're in the same cell and the global index of
1427	>	// the j2 cutoff group is greater than or equal to
1428	>	// the j1 cutoff group.  Note that Rappaport's code
1429	>	// has a "less than" conditional here, but that
1430	>	// deals with atom-by-atom computation.  OpenMD
1431	>	// allows atoms within a single cutoff group to
1432	>	// interact with each other.
1433
1434	<	if (m2 != m1 || (*j2) < (*j1)) {
1435	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1436	<	snap_->wrapVector(dr);
1437	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1438	<	if (dr.lengthSquare() < cuts.third) {
1439	<	neighborList.push_back(make_pair((*j1), (*j2)));
1434	>
1435	>
1436	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1437	>
1438	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1439	>	snap_->wrapVector(dr);
1440	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1441	>	if (dr.lengthSquare() < cuts.third) {
1442	>	neighborList.push_back(make_pair((*j1), (*j2)));
1443	>	}
1444		}
1445		}
1446		}
1094	–	}
1447		#endif
1448	+	}
1449		}
1450		}
1451		}
1452	+	} else {
1453	+	// branch to do all cutoff group pairs
1454	+	#ifdef IS_MPI
1455	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1456	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1457	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1458	+	snap_->wrapVector(dr);
1459	+	cuts = getGroupCutoffs( j1, j2 );
1460	+	if (dr.lengthSquare() < cuts.third) {
1461	+	neighborList.push_back(make_pair(j1, j2));
1462	+	}
1463	+	}
1464	+	}
1465	+	#else
1466	+	// include all groups here.
1467	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1468	+	// include self group interactions j2 == j1
1469	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1470	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1471	+	snap_->wrapVector(dr);
1472	+	cuts = getGroupCutoffs( j1, j2 );
1473	+	if (dr.lengthSquare() < cuts.third) {
1474	+	neighborList.push_back(make_pair(j1, j2));
1475	+	}
1476	+	}
1477	+	}
1478	+	#endif
1479		}
1480	<
1480	>
1481		// save the local cutoff group positions for the check that is
1482		// done on each loop:
1483		saved_CG_positions_.clear();
1484		for (int i = 0; i < nGroups_; i++)
1485		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1486	<
1486	>
1487		return neighborList;
1488		}
1489		} //end namespace OpenMD

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