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root/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 1760 by gezelter, Thu Jun 21 19:26:46 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	+	expot_row.resize(nAtomsInRow_);
180	+	expot_col.resize(nAtomsInCol_);
181	+
182	+	AtomRowToGlobal.resize(nAtomsInRow_);
183	+	AtomColToGlobal.resize(nAtomsInCol_);
184	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
185	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
186	+
187	+	cgRowToGlobal.resize(nGroupsInRow_);
188	+	cgColToGlobal.resize(nGroupsInCol_);
189	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
190	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
191	+
192	+	massFactorsRow.resize(nAtomsInRow_);
193	+	massFactorsCol.resize(nAtomsInCol_);
194	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
195	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
196	+
197		groupListRow_.clear();
198	<	groupListRow_.reserve(nGroupsInRow_);
198	>	groupListRow_.resize(nGroupsInRow_);
199		for (int i = 0; i < nGroupsInRow_; i++) {
200		int gid = cgRowToGlobal[i];
201		for (int j = 0; j < nAtomsInRow_; j++) {
#	Line 131 | Line 206 | namespace OpenMD {
206		}
207
208		groupListCol_.clear();
209	<	groupListCol_.reserve(nGroupsInCol_);
209	>	groupListCol_.resize(nGroupsInCol_);
210		for (int i = 0; i < nGroupsInCol_; i++) {
211		int gid = cgColToGlobal[i];
212		for (int j = 0; j < nAtomsInCol_; j++) {
#	Line 141 | Line 216 | namespace OpenMD {
216		}
217		}
218
219	<	skipsForRowAtom.clear();
220	<	skipsForRowAtom.reserve(nAtomsInRow_);
219	>	excludesForAtom.clear();
220	>	excludesForAtom.resize(nAtomsInRow_);
221	>	toposForAtom.clear();
222	>	toposForAtom.resize(nAtomsInRow_);
223	>	topoDist.clear();
224	>	topoDist.resize(nAtomsInRow_);
225		for (int i = 0; i < nAtomsInRow_; i++) {
226		int iglob = AtomRowToGlobal[i];
227	+
228		for (int j = 0; j < nAtomsInCol_; j++) {
229	<	int jglob = AtomColToGlobal[j];
230	<	if (excludes.hasPair(iglob, jglob))
231	<	skipsForRowAtom[i].push_back(j);
229	>	int jglob = AtomColToGlobal[j];
230	>
231	>	if (excludes->hasPair(iglob, jglob))
232	>	excludesForAtom[i].push_back(j);
233	>
234	>	if (oneTwo->hasPair(iglob, jglob)) {
235	>	toposForAtom[i].push_back(j);
236	>	topoDist[i].push_back(1);
237	>	} else {
238	>	if (oneThree->hasPair(iglob, jglob)) {
239	>	toposForAtom[i].push_back(j);
240	>	topoDist[i].push_back(2);
241	>	} else {
242	>	if (oneFour->hasPair(iglob, jglob)) {
243	>	toposForAtom[i].push_back(j);
244	>	topoDist[i].push_back(3);
245	>	}
246	>	}
247	>	}
248		}
249		}
250
251	<	toposForRowAtom.clear();
252	<	toposForRowAtom.reserve(nAtomsInRow_);
253	<	for (int i = 0; i < nAtomsInRow_; i++) {
254	<	int iglob = AtomRowToGlobal[i];
255	<	int nTopos = 0;
256	<	for (int j = 0; j < nAtomsInCol_; j++) {
257	<	int jglob = AtomColToGlobal[j];
258	<	if (oneTwo.hasPair(iglob, jglob)) {
259	<	toposForRowAtom[i].push_back(j);
260	<	topoDistRow[i][nTopos] = 1;
261	<	nTopos++;
251	>	#else
252	>	excludesForAtom.clear();
253	>	excludesForAtom.resize(nLocal_);
254	>	toposForAtom.clear();
255	>	toposForAtom.resize(nLocal_);
256	>	topoDist.clear();
257	>	topoDist.resize(nLocal_);
258	>
259	>	for (int i = 0; i < nLocal_; i++) {
260	>	int iglob = AtomLocalToGlobal[i];
261	>
262	>	for (int j = 0; j < nLocal_; j++) {
263	>	int jglob = AtomLocalToGlobal[j];
264	>
265	>	if (excludes->hasPair(iglob, jglob))
266	>	excludesForAtom[i].push_back(j);
267	>
268	>	if (oneTwo->hasPair(iglob, jglob)) {
269	>	toposForAtom[i].push_back(j);
270	>	topoDist[i].push_back(1);
271	>	} else {
272	>	if (oneThree->hasPair(iglob, jglob)) {
273	>	toposForAtom[i].push_back(j);
274	>	topoDist[i].push_back(2);
275	>	} else {
276	>	if (oneFour->hasPair(iglob, jglob)) {
277	>	toposForAtom[i].push_back(j);
278	>	topoDist[i].push_back(3);
279	>	}
280	>	}
281		}
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	–	}
282		}
283		}
179	–
284		#endif
285
286	+	// allocate memory for the parallel objects
287	+	atypesLocal.resize(nLocal_);
288	+
289	+	for (int i = 0; i < nLocal_; i++)
290	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
291	+
292		groupList_.clear();
293	<	groupList_.reserve(nGroups_);
293	>	groupList_.resize(nGroups_);
294		for (int i = 0; i < nGroups_; i++) {
295		int gid = cgLocalToGlobal[i];
296		for (int j = 0; j < nLocal_; j++) {
297		int aid = AtomLocalToGlobal[j];
298	<	if (globalGroupMembership[aid] == gid)
298	>	if (globalGroupMembership[aid] == gid) {
299		groupList_[i].push_back(j);
300	+	}
301		}
302		}
303
193	–	skipsForLocalAtom.clear();
194	–	skipsForLocalAtom.reserve(nLocal_);
304
305	<	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	<	}
305	>	createGtypeCutoffMap();
306
307	<	toposForLocalAtom.clear();
308	<	toposForLocalAtom.reserve(nLocal_);
309	<	for (int i = 0; i < nLocal_; i++) {
310	<	int iglob = AtomLocalToGlobal[i];
311	<	int nTopos = 0;
312	<	for (int j = 0; j < nLocal_; j++) {
313	<	int jglob = AtomLocalToGlobal[j];
314	<	if (oneTwo.hasPair(iglob, jglob)) {
315	<	toposForLocalAtom[i].push_back(j);
316	<	topoDistLocal[i][nTopos] = 1;
317	<	nTopos++;
307	>	}
308	>
309	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
310	>
311	>	RealType tol = 1e-6;
312	>	largestRcut_ = 0.0;
313	>	RealType rc;
314	>	int atid;
315	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
316	>
317	>	map<int, RealType> atypeCutoff;
318	>
319	>	for (set<AtomType*>::iterator at = atypes.begin();
320	>	at != atypes.end(); ++at){
321	>	atid = (*at)->getIdent();
322	>	if (userChoseCutoff_)
323	>	atypeCutoff[atid] = userCutoff_;
324	>	else
325	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
326	>	}
327	>
328	>	vector<RealType> gTypeCutoffs;
329	>	// first we do a single loop over the cutoff groups to find the
330	>	// largest cutoff for any atypes present in this group.
331	>	#ifdef IS_MPI
332	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
333	>	groupRowToGtype.resize(nGroupsInRow_);
334	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
335	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
336	>	for (vector<int>::iterator ia = atomListRow.begin();
337	>	ia != atomListRow.end(); ++ia) {
338	>	int atom1 = (*ia);
339	>	atid = identsRow[atom1];
340	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
341	>	groupCutoffRow[cg1] = atypeCutoff[atid];
342		}
343	<	if (oneThree.hasPair(iglob, jglob)) {
344	<	toposForLocalAtom[i].push_back(j);
345	<	topoDistLocal[i][nTopos] = 2;
346	<	nTopos++;
347	<	}
348	<	if (oneFour.hasPair(iglob, jglob)) {
349	<	toposForLocalAtom[i].push_back(j);
350	<	topoDistLocal[i][nTopos] = 3;
351	<	nTopos++;
343	>	}
344	>
345	>	bool gTypeFound = false;
346	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
347	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
348	>	groupRowToGtype[cg1] = gt;
349	>	gTypeFound = true;
350	>	}
351	>	}
352	>	if (!gTypeFound) {
353	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
354	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
355	>	}
356	>
357	>	}
358	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
359	>	groupColToGtype.resize(nGroupsInCol_);
360	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
361	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
362	>	for (vector<int>::iterator jb = atomListCol.begin();
363	>	jb != atomListCol.end(); ++jb) {
364	>	int atom2 = (*jb);
365	>	atid = identsCol[atom2];
366	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
367	>	groupCutoffCol[cg2] = atypeCutoff[atid];
368		}
369	+	}
370	+	bool gTypeFound = false;
371	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
372	+	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
373	+	groupColToGtype[cg2] = gt;
374	+	gTypeFound = true;
375	+	}
376	+	}
377	+	if (!gTypeFound) {
378	+	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
379	+	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
380	+	}
381	+	}
382	+	#else
383	+
384	+	vector<RealType> groupCutoff(nGroups_, 0.0);
385	+	groupToGtype.resize(nGroups_);
386	+	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
387	+	groupCutoff[cg1] = 0.0;
388	+	vector<int> atomList = getAtomsInGroupRow(cg1);
389	+	for (vector<int>::iterator ia = atomList.begin();
390	+	ia != atomList.end(); ++ia) {
391	+	int atom1 = (*ia);
392	+	atid = idents[atom1];
393	+	if (atypeCutoff[atid] > groupCutoff[cg1])
394	+	groupCutoff[cg1] = atypeCutoff[atid];
395	+	}
396	+
397	+	bool gTypeFound = false;
398	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
399	+	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
400	+	groupToGtype[cg1] = gt;
401	+	gTypeFound = true;
402	+	}
403	+	}
404	+	if (!gTypeFound) {
405	+	gTypeCutoffs.push_back( groupCutoff[cg1] );
406	+	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
407		}
408		}
409	+	#endif
410	+
411	+	// Now we find the maximum group cutoff value present in the simulation
412	+
413	+	RealType groupMax = *max_element(gTypeCutoffs.begin(),
414	+	gTypeCutoffs.end());
415	+
416	+	#ifdef IS_MPI
417	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
418	+	MPI::MAX);
419	+	#endif
420	+
421	+	RealType tradRcut = groupMax;
422	+
423	+	for (int i = 0; i < gTypeCutoffs.size();  i++) {
424	+	for (int j = 0; j < gTypeCutoffs.size();  j++) {
425	+	RealType thisRcut;
426	+	switch(cutoffPolicy_) {
427	+	case TRADITIONAL:
428	+	thisRcut = tradRcut;
429	+	break;
430	+	case MIX:
431	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
432	+	break;
433	+	case MAX:
434	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
435	+	break;
436	+	default:
437	+	sprintf(painCave.errMsg,
438	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
439	+	"hit an unknown cutoff policy!\n");
440	+	painCave.severity = OPENMD_ERROR;
441	+	painCave.isFatal = 1;
442	+	simError();
443	+	break;
444	+	}
445	+
446	+	pair<int,int> key = make_pair(i,j);
447	+	gTypeCutoffMap[key].first = thisRcut;
448	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
449	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
450	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
451	+	// sanity check
452	+
453	+	if (userChoseCutoff_) {
454	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
455	+	sprintf(painCave.errMsg,
456	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
457	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
458	+	painCave.severity = OPENMD_ERROR;
459	+	painCave.isFatal = 1;
460	+	simError();
461	+	}
462	+	}
463	+	}
464	+	}
465		}
230	–
231	–	void ForceMatrixDecomposition::zeroWorkArrays() {
466
467	<	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
468	<	longRangePot_[j] = 0.0;
467	>	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
468	>	int i, j;
469	>	#ifdef IS_MPI
470	>	i = groupRowToGtype[cg1];
471	>	j = groupColToGtype[cg2];
472	>	#else
473	>	i = groupToGtype[cg1];
474	>	j = groupToGtype[cg2];
475	>	#endif
476	>	return gTypeCutoffMap[make_pair(i,j)];
477	>	}
478	>
479	>	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
480	>	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
481	>	if (toposForAtom[atom1][j] == atom2)
482	>	return topoDist[atom1][j];
483		}
484	+	return 0;
485	+	}
486
487	+	void ForceMatrixDecomposition::zeroWorkArrays() {
488	+	pairwisePot = 0.0;
489	+	embeddingPot = 0.0;
490	+	excludedPot = 0.0;
491	+
492		#ifdef IS_MPI
493		if (storageLayout_ & DataStorage::dslForce) {
494		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 249 | Line 504 | namespace OpenMD {
504		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
505
506		fill(pot_col.begin(), pot_col.end(),
507	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
508	+
509	+	fill(expot_row.begin(), expot_row.end(),
510		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
253	–
254	–	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
511
512	+	fill(expot_col.begin(), expot_col.end(),
513	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
514	+
515		if (storageLayout_ & DataStorage::dslParticlePot) {
516	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
517	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
516	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
517	>	0.0);
518	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
519	>	0.0);
520		}
521
522		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 264 | Line 525 | namespace OpenMD {
525		}
526
527		if (storageLayout_ & DataStorage::dslFunctional) {
528	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
529	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
528	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
529	>	0.0);
530	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
531	>	0.0);
532		}
533
534		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 275 | Line 538 | namespace OpenMD {
538		atomColData.functionalDerivative.end(), 0.0);
539		}
540
541	<	#else
542	<
541	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
542	>	fill(atomRowData.skippedCharge.begin(),
543	>	atomRowData.skippedCharge.end(), 0.0);
544	>	fill(atomColData.skippedCharge.begin(),
545	>	atomColData.skippedCharge.end(), 0.0);
546	>	}
547	>
548	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
549	>	fill(atomRowData.flucQFrc.begin(),
550	>	atomRowData.flucQFrc.end(), 0.0);
551	>	fill(atomColData.flucQFrc.begin(),
552	>	atomColData.flucQFrc.end(), 0.0);
553	>	}
554	>
555	>	if (storageLayout_ & DataStorage::dslElectricField) {
556	>	fill(atomRowData.electricField.begin(),
557	>	atomRowData.electricField.end(), V3Zero);
558	>	fill(atomColData.electricField.begin(),
559	>	atomColData.electricField.end(), V3Zero);
560	>	}
561	>
562	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
563	>	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
564	>	0.0);
565	>	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
566	>	0.0);
567	>	}
568	>
569	>	#endif
570	>	// even in parallel, we need to zero out the local arrays:
571	>
572		if (storageLayout_ & DataStorage::dslParticlePot) {
573		fill(snap_->atomData.particlePot.begin(),
574		snap_->atomData.particlePot.end(), 0.0);
#	Line 286 | Line 578 | namespace OpenMD {
578		fill(snap_->atomData.density.begin(),
579		snap_->atomData.density.end(), 0.0);
580		}
581	+
582		if (storageLayout_ & DataStorage::dslFunctional) {
583		fill(snap_->atomData.functional.begin(),
584		snap_->atomData.functional.end(), 0.0);
585		}
586	+
587		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
588		fill(snap_->atomData.functionalDerivative.begin(),
589		snap_->atomData.functionalDerivative.end(), 0.0);
590		}
591	<	#endif
592	<
591	>
592	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
593	>	fill(snap_->atomData.skippedCharge.begin(),
594	>	snap_->atomData.skippedCharge.end(), 0.0);
595	>	}
596	>
597	>	if (storageLayout_ & DataStorage::dslElectricField) {
598	>	fill(snap_->atomData.electricField.begin(),
599	>	snap_->atomData.electricField.end(), V3Zero);
600	>	}
601		}
602
603
#	Line 305 | Line 607 | namespace OpenMD {
607		#ifdef IS_MPI
608
609		// gather up the atomic positions
610	<	AtomCommVectorRow->gather(snap_->atomData.position,
610	>	AtomPlanVectorRow->gather(snap_->atomData.position,
611		atomRowData.position);
612	<	AtomCommVectorColumn->gather(snap_->atomData.position,
612	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
613		atomColData.position);
614
615		// gather up the cutoff group positions
616	<	cgCommVectorRow->gather(snap_->cgData.position,
616	>
617	>	cgPlanVectorRow->gather(snap_->cgData.position,
618		cgRowData.position);
619	<	cgCommVectorColumn->gather(snap_->cgData.position,
619	>
620	>	cgPlanVectorColumn->gather(snap_->cgData.position,
621		cgColData.position);
622	+
623	+
624	+
625	+	if (needVelocities_) {
626	+	// gather up the atomic velocities
627	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
628	+	atomColData.velocity);
629	+
630	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
631	+	cgColData.velocity);
632	+	}
633	+
634
635		// if needed, gather the atomic rotation matrices
636		if (storageLayout_ & DataStorage::dslAmat) {
637	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
637	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
638		atomRowData.aMat);
639	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
639	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
640		atomColData.aMat);
641		}
642
643		// if needed, gather the atomic eletrostatic frames
644		if (storageLayout_ & DataStorage::dslElectroFrame) {
645	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
645	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
646		atomRowData.electroFrame);
647	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
647	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
648		atomColData.electroFrame);
649		}
650	+
651	+	// if needed, gather the atomic fluctuating charge values
652	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
653	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
654	+	atomRowData.flucQPos);
655	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
656	+	atomColData.flucQPos);
657	+	}
658	+
659		#endif
660		}
661
#	Line 344 | Line 669 | namespace OpenMD {
669
670		if (storageLayout_ & DataStorage::dslDensity) {
671
672	<	AtomCommRealRow->scatter(atomRowData.density,
672	>	AtomPlanRealRow->scatter(atomRowData.density,
673		snap_->atomData.density);
674
675		int n = snap_->atomData.density.size();
676		vector<RealType> rho_tmp(n, 0.0);
677	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
677	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
678		for (int i = 0; i < n; i++)
679		snap_->atomData.density[i] += rho_tmp[i];
680		}
681	+
682	+	if (storageLayout_ & DataStorage::dslElectricField) {
683	+
684	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
685	+	snap_->atomData.electricField);
686	+
687	+	int n = snap_->atomData.electricField.size();
688	+	vector<Vector3d> field_tmp(n, V3Zero);
689	+	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
690	+	for (int i = 0; i < n; i++)
691	+	snap_->atomData.electricField[i] += field_tmp[i];
692	+	}
693		#endif
694		}
695
#	Line 365 | Line 702 | namespace OpenMD {
702		storageLayout_ = sman_->getStorageLayout();
703		#ifdef IS_MPI
704		if (storageLayout_ & DataStorage::dslFunctional) {
705	<	AtomCommRealRow->gather(snap_->atomData.functional,
705	>	AtomPlanRealRow->gather(snap_->atomData.functional,
706		atomRowData.functional);
707	<	AtomCommRealColumn->gather(snap_->atomData.functional,
707	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
708		atomColData.functional);
709		}
710
711		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
712	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
712	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
713		atomRowData.functionalDerivative);
714	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
714	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
715		atomColData.functionalDerivative);
716		}
717		#endif
#	Line 388 | Line 725 | namespace OpenMD {
725		int n = snap_->atomData.force.size();
726		vector<Vector3d> frc_tmp(n, V3Zero);
727
728	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
728	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
729		for (int i = 0; i < n; i++) {
730		snap_->atomData.force[i] += frc_tmp[i];
731		frc_tmp[i] = 0.0;
732		}
733
734	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
735	<	for (int i = 0; i < n; i++)
734	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
735	>	for (int i = 0; i < n; i++) {
736		snap_->atomData.force[i] += frc_tmp[i];
737	<
738	<
737	>	}
738	>
739		if (storageLayout_ & DataStorage::dslTorque) {
740
741	<	int nt = snap_->atomData.force.size();
741	>	int nt = snap_->atomData.torque.size();
742		vector<Vector3d> trq_tmp(nt, V3Zero);
743
744	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
745	<	for (int i = 0; i < n; i++) {
744	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
745	>	for (int i = 0; i < nt; i++) {
746		snap_->atomData.torque[i] += trq_tmp[i];
747		trq_tmp[i] = 0.0;
748		}
749
750	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
751	<	for (int i = 0; i < n; i++)
750	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
751	>	for (int i = 0; i < nt; i++)
752		snap_->atomData.torque[i] += trq_tmp[i];
753		}
754	+
755	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
756	+
757	+	int ns = snap_->atomData.skippedCharge.size();
758	+	vector<RealType> skch_tmp(ns, 0.0);
759	+
760	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
761	+	for (int i = 0; i < ns; i++) {
762	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
763	+	skch_tmp[i] = 0.0;
764	+	}
765	+
766	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
767	+	for (int i = 0; i < ns; i++)
768	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
769	+
770	+	}
771
772	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
773	+
774	+	int nq = snap_->atomData.flucQFrc.size();
775	+	vector<RealType> fqfrc_tmp(nq, 0.0);
776	+
777	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
778	+	for (int i = 0; i < nq; i++) {
779	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
780	+	fqfrc_tmp[i] = 0.0;
781	+	}
782	+
783	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
784	+	for (int i = 0; i < nq; i++)
785	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
786	+
787	+	}
788	+
789		nLocal_ = snap_->getNumberOfAtoms();
790
791		vector<potVec> pot_temp(nLocal_,
792		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
793	+	vector<potVec> expot_temp(nLocal_,
794	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
795
796		// scatter/gather pot_row into the members of my column
797
798	<	AtomCommPotRow->scatter(pot_row, pot_temp);
798	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
799	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
800
801	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
802	<	pot_local += pot_temp[ii];
803	<
801	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
802	>	pairwisePot += pot_temp[ii];
803	>
804	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
805	>	excludedPot += expot_temp[ii];
806	>
807	>	if (storageLayout_ & DataStorage::dslParticlePot) {
808	>	// This is the pairwise contribution to the particle pot.  The
809	>	// embedding contribution is added in each of the low level
810	>	// non-bonded routines.  In single processor, this is done in
811	>	// unpackInteractionData, not in collectData.
812	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
813	>	for (int i = 0; i < nLocal_; i++) {
814	>	// factor of two is because the total potential terms are divided
815	>	// by 2 in parallel due to row/ column scatter
816	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
817	>	}
818	>	}
819	>	}
820	>
821		fill(pot_temp.begin(), pot_temp.end(),
822		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
823	+	fill(expot_temp.begin(), expot_temp.end(),
824	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
825
826	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
826	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
827	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
828
829		for (int ii = 0;  ii < pot_temp.size(); ii++ )
830	<	pot_local += pot_temp[ii];
830	>	pairwisePot += pot_temp[ii];
831	>
832	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
833	>	excludedPot += expot_temp[ii];
834	>
835	>	if (storageLayout_ & DataStorage::dslParticlePot) {
836	>	// This is the pairwise contribution to the particle pot.  The
837	>	// embedding contribution is added in each of the low level
838	>	// non-bonded routines.  In single processor, this is done in
839	>	// unpackInteractionData, not in collectData.
840	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
841	>	for (int i = 0; i < nLocal_; i++) {
842	>	// factor of two is because the total potential terms are divided
843	>	// by 2 in parallel due to row/ column scatter
844	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
845	>	}
846	>	}
847	>	}
848
849	+	if (storageLayout_ & DataStorage::dslParticlePot) {
850	+	int npp = snap_->atomData.particlePot.size();
851	+	vector<RealType> ppot_temp(npp, 0.0);
852	+
853	+	// This is the direct or embedding contribution to the particle
854	+	// pot.
855	+
856	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
857	+	for (int i = 0; i < npp; i++) {
858	+	snap_->atomData.particlePot[i] += ppot_temp[i];
859	+	}
860	+
861	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
862	+
863	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
864	+	for (int i = 0; i < npp; i++) {
865	+	snap_->atomData.particlePot[i] += ppot_temp[i];
866	+	}
867	+	}
868	+
869	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
870	+	RealType ploc1 = pairwisePot[ii];
871	+	RealType ploc2 = 0.0;
872	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
873	+	pairwisePot[ii] = ploc2;
874	+	}
875	+
876	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
877	+	RealType ploc1 = excludedPot[ii];
878	+	RealType ploc2 = 0.0;
879	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
880	+	excludedPot[ii] = ploc2;
881	+	}
882	+
883	+	// Here be dragons.
884	+	MPI::Intracomm col = colComm.getComm();
885	+
886	+	col.Allreduce(MPI::IN_PLACE,
887	+	&snap_->frameData.conductiveHeatFlux[0], 3,
888	+	MPI::REALTYPE, MPI::SUM);
889	+
890	+
891		#endif
892	+
893		}
894
895	+	/**
896	+	* Collects information obtained during the post-pair (and embedding
897	+	* functional) loops onto local data structures.
898	+	*/
899	+	void ForceMatrixDecomposition::collectSelfData() {
900	+	snap_ = sman_->getCurrentSnapshot();
901	+	storageLayout_ = sman_->getStorageLayout();
902	+
903	+	#ifdef IS_MPI
904	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
905	+	RealType ploc1 = embeddingPot[ii];
906	+	RealType ploc2 = 0.0;
907	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
908	+	embeddingPot[ii] = ploc2;
909	+	}
910	+	#endif
911	+
912	+	}
913	+
914	+
915	+
916		int ForceMatrixDecomposition::getNAtomsInRow() {
917		#ifdef IS_MPI
918		return nAtomsInRow_;
#	Line 478 | Line 953 | namespace OpenMD {
953		return d;
954		}
955
956	+	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
957	+	#ifdef IS_MPI
958	+	return cgColData.velocity[cg2];
959	+	#else
960	+	return snap_->cgData.velocity[cg2];
961	+	#endif
962	+	}
963
964	+	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
965	+	#ifdef IS_MPI
966	+	return atomColData.velocity[atom2];
967	+	#else
968	+	return snap_->atomData.velocity[atom2];
969	+	#endif
970	+	}
971	+
972	+
973		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
974
975		Vector3d d;
#	Line 510 | Line 1001 | namespace OpenMD {
1001		#ifdef IS_MPI
1002		return massFactorsRow[atom1];
1003		#else
1004	<	return massFactorsLocal[atom1];
1004	>	return massFactors[atom1];
1005		#endif
1006		}
1007
#	Line 518 | Line 1009 | namespace OpenMD {
1009		#ifdef IS_MPI
1010		return massFactorsCol[atom2];
1011		#else
1012	<	return massFactorsLocal[atom2];
1012	>	return massFactors[atom2];
1013		#endif
1014
1015		}
#	Line 536 | Line 1027 | namespace OpenMD {
1027		return d;
1028		}
1029
1030	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
1031	<	#ifdef IS_MPI
541	<	return skipsForRowAtom[atom1];
542	<	#else
543	<	return skipsForLocalAtom[atom1];
544	<	#endif
1030	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1031	>	return excludesForAtom[atom1];
1032		}
1033
1034		/**
1035	<	* 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
1035	>	* We need to exclude some overcounted interactions that result from
1036		* the parallel decomposition.
1037		*/
1038	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1039	<	int unique_id_1, unique_id_2;
1040	<
1038	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1039	>	int unique_id_1, unique_id_2, group1, group2;
1040	>
1041		#ifdef IS_MPI
1042		// in MPI, we have to look up the unique IDs for each atom
1043		unique_id_1 = AtomRowToGlobal[atom1];
1044		unique_id_2 = AtomColToGlobal[atom2];
1045	+	group1 = cgRowToGlobal[cg1];
1046	+	group2 = cgColToGlobal[cg2];
1047	+	#else
1048	+	unique_id_1 = AtomLocalToGlobal[atom1];
1049	+	unique_id_2 = AtomLocalToGlobal[atom2];
1050	+	group1 = cgLocalToGlobal[cg1];
1051	+	group2 = cgLocalToGlobal[cg2];
1052	+	#endif
1053
562	–	// this situation should only arise in MPI simulations
1054		if (unique_id_1 == unique_id_2) return true;
1055	<
1055	>
1056	>	#ifdef IS_MPI
1057		// this prevents us from doing the pair on multiple processors
1058		if (unique_id_1 < unique_id_2) {
1059		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1060		} else {
1061	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1061	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1062		}
1063	<	#else
1064	<	// in the normal loop, the atom numbers are unique
1065	<	unique_id_1 = atom1;
1066	<	unique_id_2 = atom2;
1067	<	#endif
1068	<
577	<	#ifdef IS_MPI
578	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
579	<	i != skipsForRowAtom[atom1].end(); ++i) {
580	<	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	<	}
1063	>	#endif
1064	>
1065	>	#ifndef IS_MPI
1066	>	if (group1 == group2) {
1067	>	if (unique_id_1 < unique_id_2) return true;
1068	>	}
1069		#endif
1070	+
1071	+	return false;
1072		}
1073
1074	<	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
1074	>	/**
1075	>	* We need to handle the interactions for atoms who are involved in
1076	>	* the same rigid body as well as some short range interactions
1077	>	* (bonds, bends, torsions) differently from other interactions.
1078	>	* We'll still visit the pairwise routines, but with a flag that
1079	>	* tells those routines to exclude the pair from direct long range
1080	>	* interactions.  Some indirect interactions (notably reaction
1081	>	* field) must still be handled for these pairs.
1082	>	*/
1083	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1084	>
1085	>	// excludesForAtom was constructed to use row/column indices in the MPI
1086	>	// version, and to use local IDs in the non-MPI version:
1087
1088	<	#ifdef IS_MPI
1089	<	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
1090	<	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
1088	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1089	>	i != excludesForAtom[atom1].end(); ++i) {
1090	>	if ( (*i) == atom2 ) return true;
1091		}
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
1092
1093	<	// zero is default for unconnected (i.e. normal) pair interactions
603	<	return 0;
1093	>	return false;
1094		}
1095
1096	+
1097		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1098		#ifdef IS_MPI
1099		atomRowData.force[atom1] += fg;
#	Line 620 | Line 1111 | namespace OpenMD {
1111		}
1112
1113		// filling interaction blocks with pointers
1114	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1115	<	InteractionData idat;
1114	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1115	>	int atom1, int atom2) {
1116
1117	+	idat.excluded = excludeAtomPair(atom1, atom2);
1118	+
1119		#ifdef IS_MPI
1120	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1121	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1122	+	//                         ff_->getAtomType(identsCol[atom2]) );
1123
628	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
629	–	ff_->getAtomType(identsCol[atom2]) );
630	–
631	–
1124		if (storageLayout_ & DataStorage::dslAmat) {
1125		idat.A1 = &(atomRowData.aMat[atom1]);
1126		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 664 | Line 1156 | namespace OpenMD {
1156		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1157		}
1158
1159	<	#else
1159	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1160	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1161	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1162	>	}
1163
1164	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
1165	<	ff_->getAtomType(identsLocal[atom2]) );
1164	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1165	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1166	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1167	>	}
1168
1169	+	#else
1170	+
1171	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1172	+
1173		if (storageLayout_ & DataStorage::dslAmat) {
1174		idat.A1 = &(snap_->atomData.aMat[atom1]);
1175		idat.A2 = &(snap_->atomData.aMat[atom2]);
#	Line 684 | Line 1185 | namespace OpenMD {
1185		idat.t2 = &(snap_->atomData.torque[atom2]);
1186		}
1187
1188	<	if (storageLayout_ & DataStorage::dslDensity) {
1188	>	if (storageLayout_ & DataStorage::dslDensity) {
1189		idat.rho1 = &(snap_->atomData.density[atom1]);
1190		idat.rho2 = &(snap_->atomData.density[atom2]);
1191		}
#	Line 704 | Line 1205 | namespace OpenMD {
1205		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1206		}
1207
1208	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1209	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1210	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1211	+	}
1212	+
1213	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1214	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1215	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1216	+	}
1217	+
1218		#endif
708	–	return idat;
1219		}
1220
1221
1222	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
1222	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1223		#ifdef IS_MPI
1224	<	pot_row[atom1] += 0.5 *  *(idat.pot);
1225	<	pot_col[atom2] += 0.5 *  *(idat.pot);
1224	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1225	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1226	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1227	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1228
1229		atomRowData.force[atom1] += *(idat.f1);
1230		atomColData.force[atom2] -= *(idat.f1);
719	–	#else
720	–	longRangePot_ += *(idat.pot);
721	–
722	–	snap_->atomData.force[atom1] += *(idat.f1);
723	–	snap_->atomData.force[atom2] -= *(idat.f1);
724	–	#endif
1231
1232	<	}
1232	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1233	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1234	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1235	>	}
1236
1237	+	if (storageLayout_ & DataStorage::dslElectricField) {
1238	+	atomRowData.electricField[atom1] += *(idat.eField1);
1239	+	atomColData.electricField[atom2] += *(idat.eField2);
1240	+	}
1241
1242	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1242	>	#else
1243	>	pairwisePot += *(idat.pot);
1244	>	excludedPot += *(idat.excludedPot);
1245
1246	<	InteractionData idat;
1247	<	#ifdef IS_MPI
733	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
734	<	ff_->getAtomType(identsCol[atom2]) );
1246	>	snap_->atomData.force[atom1] += *(idat.f1);
1247	>	snap_->atomData.force[atom2] -= *(idat.f1);
1248
1249	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1250	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1251	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1249	>	if (idat.doParticlePot) {
1250	>	// This is the pairwise contribution to the particle pot.  The
1251	>	// embedding contribution is added in each of the low level
1252	>	// non-bonded routines.  In parallel, this calculation is done
1253	>	// in collectData, not in unpackInteractionData.
1254	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1255	>	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1256		}
1257	<	if (storageLayout_ & DataStorage::dslTorque) {
1258	<	idat.t1 = &(atomRowData.torque[atom1]);
1259	<	idat.t2 = &(atomColData.torque[atom2]);
1257	>
1258	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1259	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1260	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1261		}
744	–	#else
745	–	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
746	–	ff_->getAtomType(identsLocal[atom2]) );
1262
1263	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1264	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1265	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1263	>	if (storageLayout_ & DataStorage::dslElectricField) {
1264	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1265	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1266		}
1267	<	if (storageLayout_ & DataStorage::dslTorque) {
1268	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1269	<	idat.t2 = &(snap_->atomData.torque[atom2]);
755	<	}
756	<	#endif
1267	>
1268	>	#endif
1269	>
1270		}
1271
1272		/*
#	Line 765 | Line 1278 | namespace OpenMD {
1278		vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1279
1280		vector<pair<int, int> > neighborList;
1281	+	groupCutoffs cuts;
1282	+	bool doAllPairs = false;
1283	+
1284		#ifdef IS_MPI
1285		cellListRow_.clear();
1286		cellListCol_.clear();
#	Line 772 | Line 1288 | namespace OpenMD {
1288		cellList_.clear();
1289		#endif
1290
1291	<	// dangerous to not do error checking.
776	<	RealType rCut_;
777	<
778	<	RealType rList_ = (rCut_ + skinThickness_);
1291	>	RealType rList_ = (largestRcut_ + skinThickness_);
1292		RealType rl2 = rList_ * rList_;
1293		Snapshot* snap_ = sman_->getCurrentSnapshot();
1294		Mat3x3d Hmat = snap_->getHmat();
#	Line 787 | Line 1300 | namespace OpenMD {
1300		nCells_.y() = (int) ( Hy.length() )/ rList_;
1301		nCells_.z() = (int) ( Hz.length() )/ rList_;
1302
1303	+	// handle small boxes where the cell offsets can end up repeating cells
1304	+
1305	+	if (nCells_.x() < 3) doAllPairs = true;
1306	+	if (nCells_.y() < 3) doAllPairs = true;
1307	+	if (nCells_.z() < 3) doAllPairs = true;
1308	+
1309		Mat3x3d invHmat = snap_->getInvHmat();
1310		Vector3d rs, scaled, dr;
1311		Vector3i whichCell;
1312		int cellIndex;
1313	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1314
1315		#ifdef IS_MPI
1316	<	for (int i = 0; i < nGroupsInRow_; i++) {
1317	<	rs = cgRowData.position[i];
1318	<	// scaled positions relative to the box vectors
1319	<	scaled = invHmat * rs;
1320	<	// 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();
1316	>	cellListRow_.resize(nCtot);
1317	>	cellListCol_.resize(nCtot);
1318	>	#else
1319	>	cellList_.resize(nCtot);
1320	>	#endif
1321
1322	<	// find single index of this cell:
1323	<	cellIndex = Vlinear(whichCell, nCells_);
812	<	// add this cutoff group to the list of groups in this cell;
813	<	cellListRow_[cellIndex].push_back(i);
814	<	}
1322	>	if (!doAllPairs) {
1323	>	#ifdef IS_MPI
1324
1325	<	for (int i = 0; i < nGroupsInCol_; i++) {
1326	<	rs = cgColData.position[i];
1327	<	// scaled positions relative to the box vectors
1328	<	scaled = invHmat * rs;
1329	<	// wrap the vector back into the unit box by subtracting integer box
1330	<	// numbers
1331	<	for (int j = 0; j < 3; j++)
1332	<	scaled[j] -= roundMe(scaled[j]);
1333	<
1334	<	// find xyz-indices of cell that cutoffGroup is in.
1335	<	whichCell.x() = nCells_.x() * scaled.x();
1336	<	whichCell.y() = nCells_.y() * scaled.y();
1337	<	whichCell.z() = nCells_.z() * scaled.z();
1338	<
1339	<	// find single index of this cell:
1340	<	cellIndex = Vlinear(whichCell, nCells_);
1341	<	// add this cutoff group to the list of groups in this cell;
1342	<	cellListCol_[cellIndex].push_back(i);
1343	<	}
1325	>	for (int i = 0; i < nGroupsInRow_; i++) {
1326	>	rs = cgRowData.position[i];
1327	>
1328	>	// scaled positions relative to the box vectors
1329	>	scaled = invHmat * rs;
1330	>
1331	>	// wrap the vector back into the unit box by subtracting integer box
1332	>	// numbers
1333	>	for (int j = 0; j < 3; j++) {
1334	>	scaled[j] -= roundMe(scaled[j]);
1335	>	scaled[j] += 0.5;
1336	>	}
1337	>
1338	>	// find xyz-indices of cell that cutoffGroup is in.
1339	>	whichCell.x() = nCells_.x() * scaled.x();
1340	>	whichCell.y() = nCells_.y() * scaled.y();
1341	>	whichCell.z() = nCells_.z() * scaled.z();
1342	>
1343	>	// find single index of this cell:
1344	>	cellIndex = Vlinear(whichCell, nCells_);
1345	>
1346	>	// add this cutoff group to the list of groups in this cell;
1347	>	cellListRow_[cellIndex].push_back(i);
1348	>	}
1349	>	for (int i = 0; i < nGroupsInCol_; i++) {
1350	>	rs = cgColData.position[i];
1351	>
1352	>	// scaled positions relative to the box vectors
1353	>	scaled = invHmat * rs;
1354	>
1355	>	// wrap the vector back into the unit box by subtracting integer box
1356	>	// numbers
1357	>	for (int j = 0; j < 3; j++) {
1358	>	scaled[j] -= roundMe(scaled[j]);
1359	>	scaled[j] += 0.5;
1360	>	}
1361	>
1362	>	// find xyz-indices of cell that cutoffGroup is in.
1363	>	whichCell.x() = nCells_.x() * scaled.x();
1364	>	whichCell.y() = nCells_.y() * scaled.y();
1365	>	whichCell.z() = nCells_.z() * scaled.z();
1366	>
1367	>	// find single index of this cell:
1368	>	cellIndex = Vlinear(whichCell, nCells_);
1369	>
1370	>	// add this cutoff group to the list of groups in this cell;
1371	>	cellListCol_[cellIndex].push_back(i);
1372	>	}
1373	>
1374		#else
1375	<	for (int i = 0; i < nGroups_; i++) {
1376	<	rs = snap_->cgData.position[i];
1377	<	// scaled positions relative to the box vectors
1378	<	scaled = invHmat * rs;
1379	<	// wrap the vector back into the unit box by subtracting integer box
1380	<	// numbers
1381	<	for (int j = 0; j < 3; j++)
1382	<	scaled[j] -= roundMe(scaled[j]);
1375	>	for (int i = 0; i < nGroups_; i++) {
1376	>	rs = snap_->cgData.position[i];
1377	>
1378	>	// scaled positions relative to the box vectors
1379	>	scaled = invHmat * rs;
1380	>
1381	>	// wrap the vector back into the unit box by subtracting integer box
1382	>	// numbers
1383	>	for (int j = 0; j < 3; j++) {
1384	>	scaled[j] -= roundMe(scaled[j]);
1385	>	scaled[j] += 0.5;
1386	>	}
1387	>
1388	>	// find xyz-indices of cell that cutoffGroup is in.
1389	>	whichCell.x() = nCells_.x() * scaled.x();
1390	>	whichCell.y() = nCells_.y() * scaled.y();
1391	>	whichCell.z() = nCells_.z() * scaled.z();
1392	>
1393	>	// find single index of this cell:
1394	>	cellIndex = Vlinear(whichCell, nCells_);
1395	>
1396	>	// add this cutoff group to the list of groups in this cell;
1397	>	cellList_[cellIndex].push_back(i);
1398	>	}
1399
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	–	}
1400		#endif
1401
1402	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1403	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1404	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1405	<	Vector3i m1v(m1x, m1y, m1z);
1406	<	int m1 = Vlinear(m1v, nCells_);
862	<
863	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
864	<	os != cellOffsets_.end(); ++os) {
1402	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1403	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1404	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1405	>	Vector3i m1v(m1x, m1y, m1z);
1406	>	int m1 = Vlinear(m1v, nCells_);
1407
1408	<	Vector3i m2v = m1v + (*os);
1409	<
1410	<	if (m2v.x() >= nCells_.x()) {
1411	<	m2v.x() = 0;
1412	<	} else if (m2v.x() < 0) {
871	<	m2v.x() = nCells_.x() - 1;
872	<	}
873	<
874	<	if (m2v.y() >= nCells_.y()) {
875	<	m2v.y() = 0;
876	<	} else if (m2v.y() < 0) {
877	<	m2v.y() = nCells_.y() - 1;
878	<	}
879	<
880	<	if (m2v.z() >= nCells_.z()) {
881	<	m2v.z() = 0;
882	<	} else if (m2v.z() < 0) {
883	<	m2v.z() = nCells_.z() - 1;
884	<	}
885	<
886	<	int m2 = Vlinear (m2v, nCells_);
1408	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1409	>	os != cellOffsets_.end(); ++os) {
1410	>
1411	>	Vector3i m2v = m1v + (*os);
1412	>
1413
1414	<	#ifdef IS_MPI
1415	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1416	<	j1 != cellListRow_[m1].end(); ++j1) {
1417	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1418	<	j2 != cellListCol_[m2].end(); ++j2) {
1419	<
1420	<	// Always do this if we're in different cells or if
1421	<	// we're in the same cell and the global index of the
1422	<	// j2 cutoff group is less than the j1 cutoff group
1414	>	if (m2v.x() >= nCells_.x()) {
1415	>	m2v.x() = 0;
1416	>	} else if (m2v.x() < 0) {
1417	>	m2v.x() = nCells_.x() - 1;
1418	>	}
1419	>
1420	>	if (m2v.y() >= nCells_.y()) {
1421	>	m2v.y() = 0;
1422	>	} else if (m2v.y() < 0) {
1423	>	m2v.y() = nCells_.y() - 1;
1424	>	}
1425	>
1426	>	if (m2v.z() >= nCells_.z()) {
1427	>	m2v.z() = 0;
1428	>	} else if (m2v.z() < 0) {
1429	>	m2v.z() = nCells_.z() - 1;
1430	>	}
1431
1432	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1432	>	int m2 = Vlinear (m2v, nCells_);
1433	>
1434	>	#ifdef IS_MPI
1435	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1436	>	j1 != cellListRow_[m1].end(); ++j1) {
1437	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1438	>	j2 != cellListCol_[m2].end(); ++j2) {
1439	>
1440	>	// In parallel, we need to visit *all* pairs of row
1441	>	// & column indicies and will divide labor in the
1442	>	// force evaluation later.
1443		dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1444		snap_->wrapVector(dr);
1445	<	if (dr.lengthSquare() < rl2) {
1445	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1446	>	if (dr.lengthSquare() < cuts.third) {
1447		neighborList.push_back(make_pair((*j1), (*j2)));
1448	<	}
1448	>	}
1449		}
1450		}
906	–	}
1451		#else
1452	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1453	<	j1 != cellList_[m1].end(); ++j1) {
1454	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1455	<	j2 != cellList_[m2].end(); ++j2) {
1456	<
1457	<	// Always do this if we're in different cells or if
1458	<	// we're in the same cell and the global index of the
1459	<	// j2 cutoff group is less than the j1 cutoff group
1452	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1453	>	j1 != cellList_[m1].end(); ++j1) {
1454	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1455	>	j2 != cellList_[m2].end(); ++j2) {
1456	>
1457	>	// Always do this if we're in different cells or if
1458	>	// we're in the same cell and the global index of
1459	>	// the j2 cutoff group is greater than or equal to
1460	>	// the j1 cutoff group.  Note that Rappaport's code
1461	>	// has a "less than" conditional here, but that
1462	>	// deals with atom-by-atom computation.  OpenMD
1463	>	// allows atoms within a single cutoff group to
1464	>	// interact with each other.
1465
1466	<	if (m2 != m1 || (*j2) < (*j1)) {
1467	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1468	<	snap_->wrapVector(dr);
1469	<	if (dr.lengthSquare() < rl2) {
1470	<	neighborList.push_back(make_pair((*j1), (*j2)));
1466	>
1467	>
1468	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1469	>
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		}
925	–	}
1479		#endif
1480	+	}
1481		}
1482		}
1483		}
1484	+	} else {
1485	+	// branch to do all cutoff group pairs
1486	+	#ifdef IS_MPI
1487	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1488	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1489	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1490	+	snap_->wrapVector(dr);
1491	+	cuts = getGroupCutoffs( j1, j2 );
1492	+	if (dr.lengthSquare() < cuts.third) {
1493	+	neighborList.push_back(make_pair(j1, j2));
1494	+	}
1495	+	}
1496	+	}
1497	+	#else
1498	+	// include all groups here.
1499	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1500	+	// include self group interactions j2 == j1
1501	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1502	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1503	+	snap_->wrapVector(dr);
1504	+	cuts = getGroupCutoffs( j1, j2 );
1505	+	if (dr.lengthSquare() < cuts.third) {
1506	+	neighborList.push_back(make_pair(j1, j2));
1507	+	}
1508	+	}
1509	+	}
1510	+	#endif
1511		}
1512	<
1512	>
1513		// save the local cutoff group positions for the check that is
1514		// done on each loop:
1515		saved_CG_positions_.clear();
1516		for (int i = 0; i < nGroups_; i++)
1517		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1518	<
1518	>
1519		return neighborList;
1520		}
1521		} //end namespace OpenMD

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