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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1567 by gezelter, Tue May 24 21:24:45 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1793 by gezelter, Fri Aug 31 21:16:10 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"
44		#include "nonbonded/NonBondedInteraction.hpp"
45		#include "brains/SnapshotManager.hpp"
46	+	#include "brains/PairList.hpp"
47
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		*/
53	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96	+	ff_ = info_->getForceField();
97		nLocal_ = snap_->getNumberOfAtoms();
98	<	nGroups_ = snap_->getNumberOfCutoffGroups();
98	>
99	>	nGroups_ = info_->getNLocalCutoffGroups();
100	>	// gather the information for atomtype IDs (atids):
101	>	idents = info_->getIdentArray();
102	>	AtomLocalToGlobal = info_->getGlobalAtomIndices();
103	>	cgLocalToGlobal = info_->getGlobalGroupIndices();
104	>	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
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_);
64	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
65	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(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_);
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 87 | Line 151 | namespace OpenMD {
151		cgRowData.resize(nGroupsInRow_);
152		cgRowData.setStorageLayout(DataStorage::dslPosition);
153		cgColData.resize(nGroupsInCol_);
154	<	cgColData.setStorageLayout(DataStorage::dslPosition);
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	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
165	<	vector<RealType> (nAtomsInRow_, 0.0));
166	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
167	<	vector<RealType> (nAtomsInCol_, 0.0));
164	>	AtomPlanIntRow->gather(idents, identsRow);
165	>	AtomPlanIntColumn->gather(idents, identsCol);
166	>
167	>	// allocate memory for the parallel objects
168	>	atypesRow.resize(nAtomsInRow_);
169	>	atypesCol.resize(nAtomsInCol_);
170
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	<	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
177	<
100	<	// gather the information for atomtype IDs (atids):
101	<	vector<int> identsLocal = info_->getIdentArray();
102	<	identsRow.reserve(nAtomsInRow_);
103	<	identsCol.reserve(nAtomsInCol_);
104	<
105	<	AtomCommIntRow->gather(identsLocal, identsRow);
106	<	AtomCommIntColumn->gather(identsLocal, identsCol);
107	<
108	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
109	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
110	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
111	<
112	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
113	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
114	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
176	>	pot_row.resize(nAtomsInRow_);
177	>	pot_col.resize(nAtomsInCol_);
178
179	<	// still need:
180	<	// topoDist
181	<	// exclude
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_.resize(nGroupsInRow_);
199	>	for (int i = 0; i < nGroupsInRow_; i++) {
200	>	int gid = cgRowToGlobal[i];
201	>	for (int j = 0; j < nAtomsInRow_; j++) {
202	>	int aid = AtomRowToGlobal[j];
203	>	if (globalGroupMembership[aid] == gid)
204	>	groupListRow_[i].push_back(j);
205	>	}
206	>	}
207	>
208	>	groupListCol_.clear();
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++) {
213	>	int aid = AtomColToGlobal[j];
214	>	if (globalGroupMembership[aid] == gid)
215	>	groupListCol_[i].push_back(j);
216	>	}
217	>	}
218	>
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	>
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	>	#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	>	}
282	>	}
283	>	}
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_.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) {
299	>	groupList_[i].push_back(j);
300	>	}
301	>	}
302	>	}
303	>
304	>
305	>	createGtypeCutoffMap();
306	>
307	>	}
308	>
309	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
310	>
311	>	RealType tol = 1e-6;
312	>	largestRcut_ = 0.0;
313	>	int atid;
314	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315	>
316	>	map<int, RealType> atypeCutoff;
317	>
318	>	for (set<AtomType*>::iterator at = atypes.begin();
319	>	at != atypes.end(); ++at){
320	>	atid = (*at)->getIdent();
321	>	if (userChoseCutoff_)
322	>	atypeCutoff[atid] = userCutoff_;
323	>	else
324	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
325	>	}
326	>
327	>	vector<RealType> gTypeCutoffs;
328	>	// first we do a single loop over the cutoff groups to find the
329	>	// largest cutoff for any atypes present in this group.
330	>	#ifdef IS_MPI
331	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
332	>	groupRowToGtype.resize(nGroupsInRow_);
333	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
334	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
335	>	for (vector<int>::iterator ia = atomListRow.begin();
336	>	ia != atomListRow.end(); ++ia) {
337	>	int atom1 = (*ia);
338	>	atid = identsRow[atom1];
339	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
340	>	groupCutoffRow[cg1] = atypeCutoff[atid];
341	>	}
342	>	}
343	>
344	>	bool gTypeFound = false;
345	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
346	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
347	>	groupRowToGtype[cg1] = gt;
348	>	gTypeFound = true;
349	>	}
350	>	}
351	>	if (!gTypeFound) {
352	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
353	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
354	>	}
355	>
356	>	}
357	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
358	>	groupColToGtype.resize(nGroupsInCol_);
359	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
360	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
361	>	for (vector<int>::iterator jb = atomListCol.begin();
362	>	jb != atomListCol.end(); ++jb) {
363	>	int atom2 = (*jb);
364	>	atid = identsCol[atom2];
365	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
366	>	groupCutoffCol[cg2] = atypeCutoff[atid];
367	>	}
368	>	}
369	>	bool gTypeFound = false;
370	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
371	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
372	>	groupColToGtype[cg2] = gt;
373	>	gTypeFound = true;
374	>	}
375	>	}
376	>	if (!gTypeFound) {
377	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
378	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
379	>	}
380	>	}
381	>	#else
382	>
383	>	vector<RealType> groupCutoff(nGroups_, 0.0);
384	>	groupToGtype.resize(nGroups_);
385	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
386	>	groupCutoff[cg1] = 0.0;
387	>	vector<int> atomList = getAtomsInGroupRow(cg1);
388	>	for (vector<int>::iterator ia = atomList.begin();
389	>	ia != atomList.end(); ++ia) {
390	>	int atom1 = (*ia);
391	>	atid = idents[atom1];
392	>	if (atypeCutoff[atid] > groupCutoff[cg1])
393	>	groupCutoff[cg1] = atypeCutoff[atid];
394	>	}
395	>
396	>	bool gTypeFound = false;
397	>	for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
398	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
399	>	groupToGtype[cg1] = gt;
400	>	gTypeFound = true;
401	>	}
402	>	}
403	>	if (!gTypeFound) {
404	>	gTypeCutoffs.push_back( groupCutoff[cg1] );
405	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
406	>	}
407	>	}
408	>	#endif
409	>
410	>	// Now we find the maximum group cutoff value present in the simulation
411	>
412	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
413	>	gTypeCutoffs.end());
414	>
415	>	#ifdef IS_MPI
416	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
417	>	MPI::MAX);
418		#endif
419	+
420	+	RealType tradRcut = groupMax;
421	+
422	+	for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
423	+	for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {
424	+	RealType thisRcut;
425	+	switch(cutoffPolicy_) {
426	+	case TRADITIONAL:
427	+	thisRcut = tradRcut;
428	+	break;
429	+	case MIX:
430	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
431	+	break;
432	+	case MAX:
433	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
434	+	break;
435	+	default:
436	+	sprintf(painCave.errMsg,
437	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
438	+	"hit an unknown cutoff policy!\n");
439	+	painCave.severity = OPENMD_ERROR;
440	+	painCave.isFatal = 1;
441	+	simError();
442	+	break;
443	+	}
444	+
445	+	pair<int,int> key = make_pair(i,j);
446	+	gTypeCutoffMap[key].first = thisRcut;
447	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
448	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
449	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
450	+	// sanity check
451	+
452	+	if (userChoseCutoff_) {
453	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
454	+	sprintf(painCave.errMsg,
455	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
456	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
457	+	painCave.severity = OPENMD_ERROR;
458	+	painCave.isFatal = 1;
459	+	simError();
460	+	}
461	+	}
462	+	}
463	+	}
464		}
465	+
466	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467	+	int i, j;
468	+	#ifdef IS_MPI
469	+	i = groupRowToGtype[cg1];
470	+	j = groupColToGtype[cg2];
471	+	#else
472	+	i = groupToGtype[cg1];
473	+	j = groupToGtype[cg2];
474	+	#endif
475	+	return gTypeCutoffMap[make_pair(i,j)];
476	+	}
477	+
478	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
479	+	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
480	+	if (toposForAtom[atom1][j] == atom2)
481	+	return topoDist[atom1][j];
482	+	}
483	+	return 0;
484	+	}
485	+
486	+	void ForceMatrixDecomposition::zeroWorkArrays() {
487	+	pairwisePot = 0.0;
488	+	embeddingPot = 0.0;
489	+	excludedPot = 0.0;
490	+	excludedSelfPot = 0.0;
491	+
492	+	#ifdef IS_MPI
493	+	if (storageLayout_ & DataStorage::dslForce) {
494	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
495	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
496	+	}
497	+
498	+	if (storageLayout_ & DataStorage::dslTorque) {
499	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
500	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
501	+	}
502
503	+	fill(pot_row.begin(), pot_row.end(),
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));
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(),
517	+	0.0);
518	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
519	+	0.0);
520	+	}
521	+
522	+	if (storageLayout_ & DataStorage::dslDensity) {
523	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
524	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
525	+	}
526	+
527	+	if (storageLayout_ & DataStorage::dslFunctional) {
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) {
535	+	fill(atomRowData.functionalDerivative.begin(),
536	+	atomRowData.functionalDerivative.end(), 0.0);
537	+	fill(atomColData.functionalDerivative.begin(),
538	+	atomColData.functionalDerivative.end(), 0.0);
539	+	}
540	+
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);
575	+	}
576	+
577	+	if (storageLayout_ & DataStorage::dslDensity) {
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	+
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	+
604		void ForceMatrixDecomposition::distributeData()  {
605		snap_ = sman_->getCurrentSnapshot();
606		storageLayout_ = sman_->getStorageLayout();
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
662	+	/* collects information obtained during the pre-pair loop onto local
663	+	* data structures.
664	+	*/
665		void ForceMatrixDecomposition::collectIntermediateData() {
666		snap_ = sman_->getCurrentSnapshot();
667		storageLayout_ = sman_->getStorageLayout();
#	Line 163 | 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	<	std::vector<RealType> rho_tmp(n, 0.0);
677	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
676	>	vector<RealType> rho_tmp(n, 0.0);
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	<
695	>
696	>	/*
697	>	* redistributes information obtained during the pre-pair loop out to
698	>	* row and column-indexed data structures
699	>	*/
700		void ForceMatrixDecomposition::distributeIntermediateData() {
701		snap_ = sman_->getCurrentSnapshot();
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 203 | 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<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
792	<	vector<RealType> (nLocal_, 0.0));
793	<
794	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
795	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
796	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
797	<	pot_local[i] += pot_temp[i][ii];
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	>	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	>	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	>	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	>	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	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
911	+	RealType ploc1 = excludedSelfPot[ii];
912	+	RealType ploc2 = 0.0;
913	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
914	+	excludedSelfPot[ii] = ploc2;
915	+	}
916	+	#endif
917	+
918	+	}
919	+
920	+
921	+
922	+	int ForceMatrixDecomposition::getNAtomsInRow() {
923	+	#ifdef IS_MPI
924	+	return nAtomsInRow_;
925	+	#else
926	+	return nLocal_;
927	+	#endif
928	+	}
929	+
930	+	/**
931	+	* returns the list of atoms belonging to this group.
932	+	*/
933	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
934	+	#ifdef IS_MPI
935	+	return groupListRow_[cg1];
936	+	#else
937	+	return groupList_[cg1];
938	+	#endif
939	+	}
940	+
941	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
942	+	#ifdef IS_MPI
943	+	return groupListCol_[cg2];
944	+	#else
945	+	return groupList_[cg2];
946	+	#endif
947	+	}
948
949		Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
950		Vector3d d;
#	Line 258 | Line 959 | namespace OpenMD {
959		return d;
960		}
961
962	+	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
963	+	#ifdef IS_MPI
964	+	return cgColData.velocity[cg2];
965	+	#else
966	+	return snap_->cgData.velocity[cg2];
967	+	#endif
968	+	}
969
970	+	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
971	+	#ifdef IS_MPI
972	+	return atomColData.velocity[atom2];
973	+	#else
974	+	return snap_->atomData.velocity[atom2];
975	+	#endif
976	+	}
977	+
978	+
979		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
980
981		Vector3d d;
#	Line 285 | Line 1002 | namespace OpenMD {
1002		snap_->wrapVector(d);
1003		return d;
1004		}
1005	+
1006	+	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1007	+	#ifdef IS_MPI
1008	+	return massFactorsRow[atom1];
1009	+	#else
1010	+	return massFactors[atom1];
1011	+	#endif
1012	+	}
1013	+
1014	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1015	+	#ifdef IS_MPI
1016	+	return massFactorsCol[atom2];
1017	+	#else
1018	+	return massFactors[atom2];
1019	+	#endif
1020	+
1021	+	}
1022
1023		Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
1024		Vector3d d;
#	Line 299 | Line 1033 | namespace OpenMD {
1033		return d;
1034		}
1035
1036	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1037	+	return excludesForAtom[atom1];
1038	+	}
1039	+
1040	+	/**
1041	+	* We need to exclude some overcounted interactions that result from
1042	+	* the parallel decomposition.
1043	+	*/
1044	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1045	+	int unique_id_1, unique_id_2, group1, group2;
1046	+
1047	+	#ifdef IS_MPI
1048	+	// in MPI, we have to look up the unique IDs for each atom
1049	+	unique_id_1 = AtomRowToGlobal[atom1];
1050	+	unique_id_2 = AtomColToGlobal[atom2];
1051	+	group1 = cgRowToGlobal[cg1];
1052	+	group2 = cgColToGlobal[cg2];
1053	+	#else
1054	+	unique_id_1 = AtomLocalToGlobal[atom1];
1055	+	unique_id_2 = AtomLocalToGlobal[atom2];
1056	+	group1 = cgLocalToGlobal[cg1];
1057	+	group2 = cgLocalToGlobal[cg2];
1058	+	#endif
1059	+
1060	+	if (unique_id_1 == unique_id_2) return true;
1061	+
1062	+	#ifdef IS_MPI
1063	+	// this prevents us from doing the pair on multiple processors
1064	+	if (unique_id_1 < unique_id_2) {
1065	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1066	+	} else {
1067	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1068	+	}
1069	+	#endif
1070	+
1071	+	#ifndef IS_MPI
1072	+	if (group1 == group2) {
1073	+	if (unique_id_1 < unique_id_2) return true;
1074	+	}
1075	+	#endif
1076	+
1077	+	return false;
1078	+	}
1079	+
1080	+	/**
1081	+	* We need to handle the interactions for atoms who are involved in
1082	+	* the same rigid body as well as some short range interactions
1083	+	* (bonds, bends, torsions) differently from other interactions.
1084	+	* We'll still visit the pairwise routines, but with a flag that
1085	+	* tells those routines to exclude the pair from direct long range
1086	+	* interactions.  Some indirect interactions (notably reaction
1087	+	* field) must still be handled for these pairs.
1088	+	*/
1089	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1090	+
1091	+	// excludesForAtom was constructed to use row/column indices in the MPI
1092	+	// version, and to use local IDs in the non-MPI version:
1093	+
1094	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1095	+	i != excludesForAtom[atom1].end(); ++i) {
1096	+	if ( (*i) == atom2 ) return true;
1097	+	}
1098	+
1099	+	return false;
1100	+	}
1101	+
1102	+
1103		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1104		#ifdef IS_MPI
1105		atomRowData.force[atom1] += fg;
#	Line 316 | Line 1117 | namespace OpenMD {
1117		}
1118
1119		// filling interaction blocks with pointers
1120	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1121	<	InteractionData idat;
1120	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1121	>	int atom1, int atom2) {
1122
1123	+	idat.excluded = excludeAtomPair(atom1, atom2);
1124	+
1125		#ifdef IS_MPI
1126	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1127	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1128	+	//                         ff_->getAtomType(identsCol[atom2]) );
1129	+
1130		if (storageLayout_ & DataStorage::dslAmat) {
1131		idat.A1 = &(atomRowData.aMat[atom1]);
1132		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 340 | Line 1147 | namespace OpenMD {
1147		idat.rho2 = &(atomColData.density[atom2]);
1148		}
1149
1150	+	if (storageLayout_ & DataStorage::dslFunctional) {
1151	+	idat.frho1 = &(atomRowData.functional[atom1]);
1152	+	idat.frho2 = &(atomColData.functional[atom2]);
1153	+	}
1154	+
1155		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1156		idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1157		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1158		}
1159	+
1160	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1161	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1162	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1163	+	}
1164	+
1165	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1166	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1167	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1168	+	}
1169	+
1170	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1171	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1172	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1173	+	}
1174	+
1175		#else
1176	+
1177	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1178	+
1179		if (storageLayout_ & DataStorage::dslAmat) {
1180		idat.A1 = &(snap_->atomData.aMat[atom1]);
1181		idat.A2 = &(snap_->atomData.aMat[atom2]);
#	Line 360 | Line 1191 | namespace OpenMD {
1191		idat.t2 = &(snap_->atomData.torque[atom2]);
1192		}
1193
1194	<	if (storageLayout_ & DataStorage::dslDensity) {
1194	>	if (storageLayout_ & DataStorage::dslDensity) {
1195		idat.rho1 = &(snap_->atomData.density[atom1]);
1196		idat.rho2 = &(snap_->atomData.density[atom2]);
1197		}
1198
1199	+	if (storageLayout_ & DataStorage::dslFunctional) {
1200	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1201	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1202	+	}
1203	+
1204		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1205		idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1206		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1207		}
372	–	#endif
373	–	return idat;
374	–	}
1208
1209	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1209	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1210	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1211	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1212	>	}
1213
1214	<	InteractionData idat;
1215	<	#ifdef IS_MPI
1216	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
381	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
382	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1214	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1215	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1216	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1217		}
1218	<	if (storageLayout_ & DataStorage::dslTorque) {
1219	<	idat.t1 = &(atomRowData.torque[atom1]);
1220	<	idat.t2 = &(atomColData.torque[atom2]);
1218	>
1219	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1220	>	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1221	>	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1222		}
1223	<	if (storageLayout_ & DataStorage::dslForce) {
389	<	idat.t1 = &(atomRowData.force[atom1]);
390	<	idat.t2 = &(atomColData.force[atom2]);
391	<	}
392	<	#else
393	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
394	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
395	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
396	<	}
397	<	if (storageLayout_ & DataStorage::dslTorque) {
398	<	idat.t1 = &(snap_->atomData.torque[atom1]);
399	<	idat.t2 = &(snap_->atomData.torque[atom2]);
400	<	}
401	<	if (storageLayout_ & DataStorage::dslForce) {
402	<	idat.t1 = &(snap_->atomData.force[atom1]);
403	<	idat.t2 = &(snap_->atomData.force[atom2]);
404	<	}
1223	>
1224		#endif
406	–
1225		}
1226
1227	<	SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
1228	<	SelfData sdat;
1229	<	// Still Missing atype, skippedCharge, potVec pot,
1230	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1231	<	sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
1227	>
1228	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1229	>	#ifdef IS_MPI
1230	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1231	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1232	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1233	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1234	>
1235	>	atomRowData.force[atom1] += *(idat.f1);
1236	>	atomColData.force[atom2] -= *(idat.f1);
1237	>
1238	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1239	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1240	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1241		}
1242	<
1243	<	if (storageLayout_ & DataStorage::dslTorque) {
1244	<	sdat.t = &(snap_->atomData.torque[atom1]);
1242	>
1243	>	if (storageLayout_ & DataStorage::dslElectricField) {
1244	>	atomRowData.electricField[atom1] += *(idat.eField1);
1245	>	atomColData.electricField[atom2] += *(idat.eField2);
1246		}
1247	<
1248	<	if (storageLayout_ & DataStorage::dslDensity) {
1249	<	sdat.rho = &(snap_->atomData.density[atom1]);
1247	>
1248	>	#else
1249	>	pairwisePot += *(idat.pot);
1250	>	excludedPot += *(idat.excludedPot);
1251	>
1252	>	snap_->atomData.force[atom1] += *(idat.f1);
1253	>	snap_->atomData.force[atom2] -= *(idat.f1);
1254	>
1255	>	if (idat.doParticlePot) {
1256	>	// This is the pairwise contribution to the particle pot.  The
1257	>	// embedding contribution is added in each of the low level
1258	>	// non-bonded routines.  In parallel, this calculation is done
1259	>	// in collectData, not in unpackInteractionData.
1260	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1261	>	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1262		}
1263
1264	<	if (storageLayout_ & DataStorage::dslFunctional) {
1265	<	sdat.frho = &(snap_->atomData.functional[atom1]);
1264	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1265	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1266	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1267		}
1268	<
1269	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1270	<	sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
1268	>
1269	>	if (storageLayout_ & DataStorage::dslElectricField) {
1270	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1271	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1272		}
1273
1274	<	return sdat;
1274	>	#endif
1275	>
1276		}
1277
435	–
436	–
1278		/*
1279		* buildNeighborList
1280		*
#	Line 443 | Line 1284 | namespace OpenMD {
1284		vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1285
1286		vector<pair<int, int> > neighborList;
1287	+	groupCutoffs cuts;
1288	+	bool doAllPairs = false;
1289	+
1290		#ifdef IS_MPI
1291	<	CellListRow.clear();
1292	<	CellListCol.clear();
1291	>	cellListRow_.clear();
1292	>	cellListCol_.clear();
1293		#else
1294	<	CellList.clear();
1294	>	cellList_.clear();
1295		#endif
1296
1297	<	// dangerous to not do error checking.
454	<	RealType skinThickness_ = info_->getSimParams()->getSkinThickness();
455	<	RealType rCut_;
456	<
457	<	RealType rList_ = (rCut_ + skinThickness_);
458	<	RealType rl2 = rList_ * rList_;
1297	>	RealType rList_ = (largestRcut_ + skinThickness_);
1298		Snapshot* snap_ = sman_->getCurrentSnapshot();
1299		Mat3x3d Hmat = snap_->getHmat();
1300		Vector3d Hx = Hmat.getColumn(0);
1301		Vector3d Hy = Hmat.getColumn(1);
1302		Vector3d Hz = Hmat.getColumn(2);
464	–	Vector3i nCells;
1303
1304	<	nCells.x() = (int) ( Hx.length() )/ rList_;
1305	<	nCells.y() = (int) ( Hy.length() )/ rList_;
1306	<	nCells.z() = (int) ( Hz.length() )/ rList_;
1304	>	nCells_.x() = (int) ( Hx.length() )/ rList_;
1305	>	nCells_.y() = (int) ( Hy.length() )/ rList_;
1306	>	nCells_.z() = (int) ( Hz.length() )/ rList_;
1307
1308	+	// handle small boxes where the cell offsets can end up repeating cells
1309	+
1310	+	if (nCells_.x() < 3) doAllPairs = true;
1311	+	if (nCells_.y() < 3) doAllPairs = true;
1312	+	if (nCells_.z() < 3) doAllPairs = true;
1313	+
1314		Mat3x3d invHmat = snap_->getInvHmat();
1315		Vector3d rs, scaled, dr;
1316		Vector3i whichCell;
1317		int cellIndex;
1318	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1319
1320		#ifdef IS_MPI
1321	<	for (int i = 0; i < nGroupsInRow_; i++) {
1322	<	rs = cgRowData.position[i];
1323	<	// scaled positions relative to the box vectors
1324	<	scaled = invHmat * rs;
1325	<	// wrap the vector back into the unit box by subtracting integer box
481	<	// numbers
482	<	for (int j = 0; j < 3; j++)
483	<	scaled[j] -= roundMe(scaled[j]);
484	<
485	<	// find xyz-indices of cell that cutoffGroup is in.
486	<	whichCell.x() = nCells.x() * scaled.x();
487	<	whichCell.y() = nCells.y() * scaled.y();
488	<	whichCell.z() = nCells.z() * scaled.z();
1321	>	cellListRow_.resize(nCtot);
1322	>	cellListCol_.resize(nCtot);
1323	>	#else
1324	>	cellList_.resize(nCtot);
1325	>	#endif
1326
1327	<	// find single index of this cell:
1328	<	cellIndex = Vlinear(whichCell, nCells);
492	<	// add this cutoff group to the list of groups in this cell;
493	<	CellListRow[cellIndex].push_back(i);
494	<	}
1327	>	if (!doAllPairs) {
1328	>	#ifdef IS_MPI
1329
1330	<	for (int i = 0; i < nGroupsInCol_; i++) {
1331	<	rs = cgColData.position[i];
1332	<	// scaled positions relative to the box vectors
1333	<	scaled = invHmat * rs;
1334	<	// wrap the vector back into the unit box by subtracting integer box
1335	<	// numbers
1336	<	for (int j = 0; j < 3; j++)
1337	<	scaled[j] -= roundMe(scaled[j]);
1338	<
1339	<	// find xyz-indices of cell that cutoffGroup is in.
1340	<	whichCell.x() = nCells.x() * scaled.x();
1341	<	whichCell.y() = nCells.y() * scaled.y();
1342	<	whichCell.z() = nCells.z() * scaled.z();
1343	<
1344	<	// find single index of this cell:
1345	<	cellIndex = Vlinear(whichCell, nCells);
1346	<	// add this cutoff group to the list of groups in this cell;
1347	<	CellListCol[cellIndex].push_back(i);
1348	<	}
1330	>	for (int i = 0; i < nGroupsInRow_; i++) {
1331	>	rs = cgRowData.position[i];
1332	>
1333	>	// scaled positions relative to the box vectors
1334	>	scaled = invHmat * rs;
1335	>
1336	>	// wrap the vector back into the unit box by subtracting integer box
1337	>	// numbers
1338	>	for (int j = 0; j < 3; j++) {
1339	>	scaled[j] -= roundMe(scaled[j]);
1340	>	scaled[j] += 0.5;
1341	>	// Handle the special case when an object is exactly on the
1342	>	// boundary (a scaled coordinate of 1.0 is the same as
1343	>	// scaled coordinate of 0.0)
1344	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1345	>	}
1346	>
1347	>	// find xyz-indices of cell that cutoffGroup is in.
1348	>	whichCell.x() = nCells_.x() * scaled.x();
1349	>	whichCell.y() = nCells_.y() * scaled.y();
1350	>	whichCell.z() = nCells_.z() * scaled.z();
1351	>
1352	>	// find single index of this cell:
1353	>	cellIndex = Vlinear(whichCell, nCells_);
1354	>
1355	>	// add this cutoff group to the list of groups in this cell;
1356	>	cellListRow_[cellIndex].push_back(i);
1357	>	}
1358	>	for (int i = 0; i < nGroupsInCol_; i++) {
1359	>	rs = cgColData.position[i];
1360	>
1361	>	// scaled positions relative to the box vectors
1362	>	scaled = invHmat * rs;
1363	>
1364	>	// wrap the vector back into the unit box by subtracting integer box
1365	>	// numbers
1366	>	for (int j = 0; j < 3; j++) {
1367	>	scaled[j] -= roundMe(scaled[j]);
1368	>	scaled[j] += 0.5;
1369	>	// Handle the special case when an object is exactly on the
1370	>	// boundary (a scaled coordinate of 1.0 is the same as
1371	>	// scaled coordinate of 0.0)
1372	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1373	>	}
1374	>
1375	>	// find xyz-indices of cell that cutoffGroup is in.
1376	>	whichCell.x() = nCells_.x() * scaled.x();
1377	>	whichCell.y() = nCells_.y() * scaled.y();
1378	>	whichCell.z() = nCells_.z() * scaled.z();
1379	>
1380	>	// find single index of this cell:
1381	>	cellIndex = Vlinear(whichCell, nCells_);
1382	>
1383	>	// add this cutoff group to the list of groups in this cell;
1384	>	cellListCol_[cellIndex].push_back(i);
1385	>	}
1386	>
1387		#else
1388	<	for (int i = 0; i < nGroups_; i++) {
1389	<	rs = snap_->cgData.position[i];
1390	<	// scaled positions relative to the box vectors
1391	<	scaled = invHmat * rs;
1392	<	// wrap the vector back into the unit box by subtracting integer box
1393	<	// numbers
1394	<	for (int j = 0; j < 3; j++)
1395	<	scaled[j] -= roundMe(scaled[j]);
1388	>	for (int i = 0; i < nGroups_; i++) {
1389	>	rs = snap_->cgData.position[i];
1390	>
1391	>	// scaled positions relative to the box vectors
1392	>	scaled = invHmat * rs;
1393	>
1394	>	// wrap the vector back into the unit box by subtracting integer box
1395	>	// numbers
1396	>	for (int j = 0; j < 3; j++) {
1397	>	scaled[j] -= roundMe(scaled[j]);
1398	>	scaled[j] += 0.5;
1399	>	// Handle the special case when an object is exactly on the
1400	>	// boundary (a scaled coordinate of 1.0 is the same as
1401	>	// scaled coordinate of 0.0)
1402	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1403	>	}
1404	>
1405	>	// find xyz-indices of cell that cutoffGroup is in.
1406	>	whichCell.x() = nCells_.x() * scaled.x();
1407	>	whichCell.y() = nCells_.y() * scaled.y();
1408	>	whichCell.z() = nCells_.z() * scaled.z();
1409	>
1410	>	// find single index of this cell:
1411	>	cellIndex = Vlinear(whichCell, nCells_);
1412	>
1413	>	// add this cutoff group to the list of groups in this cell;
1414	>	cellList_[cellIndex].push_back(i);
1415	>	}
1416
525	–	// find xyz-indices of cell that cutoffGroup is in.
526	–	whichCell.x() = nCells.x() * scaled.x();
527	–	whichCell.y() = nCells.y() * scaled.y();
528	–	whichCell.z() = nCells.z() * scaled.z();
529	–
530	–	// find single index of this cell:
531	–	cellIndex = Vlinear(whichCell, nCells);
532	–	// add this cutoff group to the list of groups in this cell;
533	–	CellList[cellIndex].push_back(i);
534	–	}
1417		#endif
1418
1419	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1420	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1421	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1422	+	Vector3i m1v(m1x, m1y, m1z);
1423	+	int m1 = Vlinear(m1v, nCells_);
1424	+
1425	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1426	+	os != cellOffsets_.end(); ++os) {
1427	+
1428	+	Vector3i m2v = m1v + (*os);
1429	+
1430
1431	+	if (m2v.x() >= nCells_.x()) {
1432	+	m2v.x() = 0;
1433	+	} else if (m2v.x() < 0) {
1434	+	m2v.x() = nCells_.x() - 1;
1435	+	}
1436	+
1437	+	if (m2v.y() >= nCells_.y()) {
1438	+	m2v.y() = 0;
1439	+	} else if (m2v.y() < 0) {
1440	+	m2v.y() = nCells_.y() - 1;
1441	+	}
1442	+
1443	+	if (m2v.z() >= nCells_.z()) {
1444	+	m2v.z() = 0;
1445	+	} else if (m2v.z() < 0) {
1446	+	m2v.z() = nCells_.z() - 1;
1447	+	}
1448
1449	<	for (int m1z = 0; m1z < nCells.z(); m1z++) {
1450	<	for (int m1y = 0; m1y < nCells.y(); m1y++) {
541	<	for (int m1x = 0; m1x < nCells.x(); m1x++) {
542	<	Vector3i m1v(m1x, m1y, m1z);
543	<	int m1 = Vlinear(m1v, nCells);
544	<	for (int offset = 0; offset < nOffset_; offset++) {
545	<	Vector3i m2v = m1v + cellOffsets_[offset];
546	<
547	<	if (m2v.x() >= nCells.x()) {
548	<	m2v.x() = 0;
549	<	} else if (m2v.x() < 0) {
550	<	m2v.x() = nCells.x() - 1;
551	<	}
552	<
553	<	if (m2v.y() >= nCells.y()) {
554	<	m2v.y() = 0;
555	<	} else if (m2v.y() < 0) {
556	<	m2v.y() = nCells.y() - 1;
557	<	}
558	<
559	<	if (m2v.z() >= nCells.z()) {
560	<	m2v.z() = 0;
561	<	} else if (m2v.z() < 0) {
562	<	m2v.z() = nCells.z() - 1;
563	<	}
564	<
565	<	int m2 = Vlinear (m2v, nCells);
566	<
1449	>	int m2 = Vlinear (m2v, nCells_);
1450	>
1451		#ifdef IS_MPI
1452	<	for (vector<int>::iterator j1 = CellListRow[m1].begin();
1453	<	j1 != CellListRow[m1].end(); ++j1) {
1454	<	for (vector<int>::iterator j2 = CellListCol[m2].begin();
1455	<	j2 != CellListCol[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
576	<
577	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1452	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1453	>	j1 != cellListRow_[m1].end(); ++j1) {
1454	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1455	>	j2 != cellListCol_[m2].end(); ++j2) {
1456	>
1457	>	// In parallel, we need to visit *all* pairs of row
1458	>	// & column indicies and will divide labor in the
1459	>	// force evaluation later.
1460		dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1461		snap_->wrapVector(dr);
1462	<	if (dr.lengthSquare() < rl2) {
1462	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1463	>	if (dr.lengthSquare() < cuts.third) {
1464		neighborList.push_back(make_pair((*j1), (*j2)));
1465	<	}
1465	>	}
1466		}
1467		}
585	–	}
1468		#else
1469	<	for (vector<int>::iterator j1 = CellList[m1].begin();
1470	<	j1 != CellList[m1].end(); ++j1) {
1471	<	for (vector<int>::iterator j2 = CellList[m2].begin();
1472	<	j2 != CellList[m2].end(); ++j2) {
1473	<
1474	<	// Always do this if we're in different cells or if
1475	<	// we're in the same cell and the global index of the
1476	<	// j2 cutoff group is less than the j1 cutoff group
1469	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1470	>	j1 != cellList_[m1].end(); ++j1) {
1471	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1472	>	j2 != cellList_[m2].end(); ++j2) {
1473	>
1474	>	// Always do this if we're in different cells or if
1475	>	// we're in the same cell and the global index of
1476	>	// the j2 cutoff group is greater than or equal to
1477	>	// the j1 cutoff group.  Note that Rappaport's code
1478	>	// has a "less than" conditional here, but that
1479	>	// deals with atom-by-atom computation.  OpenMD
1480	>	// allows atoms within a single cutoff group to
1481	>	// interact with each other.
1482
1483	<	if (m2 != m1 || (*j2) < (*j1)) {
1484	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1485	<	snap_->wrapVector(dr);
1486	<	if (dr.lengthSquare() < rl2) {
1487	<	neighborList.push_back(make_pair((*j1), (*j2)));
1483	>
1484	>
1485	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1486	>
1487	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1488	>	snap_->wrapVector(dr);
1489	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1490	>	if (dr.lengthSquare() < cuts.third) {
1491	>	neighborList.push_back(make_pair((*j1), (*j2)));
1492	>	}
1493		}
1494		}
1495		}
604	–	}
1496		#endif
1497	+	}
1498		}
1499		}
1500		}
1501	+	} else {
1502	+	// branch to do all cutoff group pairs
1503	+	#ifdef IS_MPI
1504	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1505	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1506	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1507	+	snap_->wrapVector(dr);
1508	+	cuts = getGroupCutoffs( j1, j2 );
1509	+	if (dr.lengthSquare() < cuts.third) {
1510	+	neighborList.push_back(make_pair(j1, j2));
1511	+	}
1512	+	}
1513	+	}
1514	+	#else
1515	+	// include all groups here.
1516	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1517	+	// include self group interactions j2 == j1
1518	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1519	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1520	+	snap_->wrapVector(dr);
1521	+	cuts = getGroupCutoffs( j1, j2 );
1522	+	if (dr.lengthSquare() < cuts.third) {
1523	+	neighborList.push_back(make_pair(j1, j2));
1524	+	}
1525	+	}
1526	+	}
1527	+	#endif
1528		}
1529	+
1530	+	// save the local cutoff group positions for the check that is
1531	+	// done on each loop:
1532	+	saved_CG_positions_.clear();
1533	+	for (int i = 0; i < nGroups_; i++)
1534	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1535	+
1536		return neighborList;
1537		}
1538		} //end namespace OpenMD

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