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root/OpenMD/branches/development/src/parallel/ForceMatrixDecomposition.cpp

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs.
Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 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	<
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	<
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_.resize(nGroupsInRow_);
199		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 141 | Line 216 | namespace OpenMD {
216		}
217		}
218
219	<	skipsForRowAtom.clear();
220	<	skipsForRowAtom.resize(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.resize(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_.resize(nGroups_);
294		for (int i = 0; i < nGroups_; i++) {
#	Line 186 | Line 297 | namespace OpenMD {
297		int aid = AtomLocalToGlobal[j];
298		if (globalGroupMembership[aid] == gid) {
299		groupList_[i].push_back(j);
189	–
300		}
301		}
302		}
303
194	–	skipsForLocalAtom.clear();
195	–	skipsForLocalAtom.resize(nLocal_);
304
305	<	for (int i = 0; i < nLocal_; i++) {
198	<	int iglob = AtomLocalToGlobal[i];
199	<	for (int j = 0; j < nLocal_; j++) {
200	<	int jglob = AtomLocalToGlobal[j];
201	<	if (excludes.hasPair(iglob, jglob))
202	<	skipsForLocalAtom[i].push_back(j);
203	<	}
204	<	}
205	<	toposForLocalAtom.clear();
206	<	toposForLocalAtom.resize(nLocal_);
207	<	for (int i = 0; i < nLocal_; i++) {
208	<	int iglob = AtomLocalToGlobal[i];
209	<	int nTopos = 0;
210	<	for (int j = 0; j < nLocal_; j++) {
211	<	int jglob = AtomLocalToGlobal[j];
212	<	if (oneTwo.hasPair(iglob, jglob)) {
213	<	toposForLocalAtom[i].push_back(j);
214	<	topoDistLocal[i][nTopos] = 1;
215	<	nTopos++;
216	<	}
217	<	if (oneThree.hasPair(iglob, jglob)) {
218	<	toposForLocalAtom[i].push_back(j);
219	<	topoDistLocal[i][nTopos] = 2;
220	<	nTopos++;
221	<	}
222	<	if (oneFour.hasPair(iglob, jglob)) {
223	<	toposForLocalAtom[i].push_back(j);
224	<	topoDistLocal[i][nTopos] = 3;
225	<	nTopos++;
226	<	}
227	<	}
228	<	}
305	>	createGtypeCutoffMap();
306
307		}
308
309		void ForceMatrixDecomposition::createGtypeCutoffMap() {
310	<
310	>
311		RealType tol = 1e-6;
312	<	RealType rc;
312	>	largestRcut_ = 0.0;
313		int atid;
314		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315	<	vector<RealType> atypeCutoff;
316	<	atypeCutoff.resize( atypes.size() );
317	<
318	<	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
319	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
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	<	atypeCutoff[atid] = rc;
321	>	if (userChoseCutoff_)
322	>	atypeCutoff[atid] = userCutoff_;
323	>	else
324	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
325		}
326	<
326	>
327		vector<RealType> gTypeCutoffs;
248	–
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();
#	Line 275 | Line 355 | namespace OpenMD {
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();
#	Line 298 | Line 379 | namespace OpenMD {
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 = identsLocal[atom1];
392	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
391	>	atid = idents[atom1];
392	>	if (atypeCutoff[atid] > groupCutoff[cg1])
393		groupCutoff[cg1] = atypeCutoff[atid];
311	–	}
394		}
395	<
395	>
396		bool gTypeFound = false;
397	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
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) {
403	>	if (!gTypeFound) {
404		gTypeCutoffs.push_back( groupCutoff[cg1] );
405		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
406		}
#	Line 327 | Line 409 | namespace OpenMD {
409
410		// Now we find the maximum group cutoff value present in the simulation
411
412	<	vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
413	<	RealType groupMax = *groupMaxLoc;
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, MPI::MAX);
416	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
417	>	MPI::MAX);
418		#endif
419
420		RealType tradRcut = groupMax;
421
422	<	for (int i = 0; i < gTypeCutoffs.size();  i++) {
423	<	for (int j = 0; j < gTypeCutoffs.size();  j++) {
341	<
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();
441	>	simError();
442	>	break;
443		}
444
445		pair<int,int> key = make_pair(i,j);
446		gTypeCutoffMap[key].first = thisRcut;
361	–
447		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
363	–
448		gTypeCutoffMap[key].second = thisRcut*thisRcut;
365	–
449		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
367	–
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 does not match computed group Cutoff\n");
456	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
457		painCave.severity = OPENMD_ERROR;
458		painCave.isFatal = 1;
459		simError();
#	Line 381 | Line 463 | namespace OpenMD {
463		}
464		}
465
384	–
466		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467	<	int i, j;
387	<
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
395	<
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
402	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403	–	longRangePot_[j] = 0.0;
404	–	}
405	–
492		#ifdef IS_MPI
493		if (storageLayout_ & DataStorage::dslForce) {
494		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 418 | 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));
422	–
423	–	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 433 | 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 444 | 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	>	#endif
563	>	// even in parallel, we need to zero out the local arrays:
564	>
565		if (storageLayout_ & DataStorage::dslParticlePot) {
566		fill(snap_->atomData.particlePot.begin(),
567		snap_->atomData.particlePot.end(), 0.0);
#	Line 455 | Line 571 | namespace OpenMD {
571		fill(snap_->atomData.density.begin(),
572		snap_->atomData.density.end(), 0.0);
573		}
574	+
575		if (storageLayout_ & DataStorage::dslFunctional) {
576		fill(snap_->atomData.functional.begin(),
577		snap_->atomData.functional.end(), 0.0);
578		}
579	+
580		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
581		fill(snap_->atomData.functionalDerivative.begin(),
582		snap_->atomData.functionalDerivative.end(), 0.0);
583		}
584	<	#endif
585	<
584	>
585	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
586	>	fill(snap_->atomData.skippedCharge.begin(),
587	>	snap_->atomData.skippedCharge.end(), 0.0);
588	>	}
589	>
590	>	if (storageLayout_ & DataStorage::dslElectricField) {
591	>	fill(snap_->atomData.electricField.begin(),
592	>	snap_->atomData.electricField.end(), V3Zero);
593	>	}
594		}
595
596
#	Line 474 | Line 600 | namespace OpenMD {
600		#ifdef IS_MPI
601
602		// gather up the atomic positions
603	<	AtomCommVectorRow->gather(snap_->atomData.position,
603	>	AtomPlanVectorRow->gather(snap_->atomData.position,
604		atomRowData.position);
605	<	AtomCommVectorColumn->gather(snap_->atomData.position,
605	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
606		atomColData.position);
607
608		// gather up the cutoff group positions
609	<	cgCommVectorRow->gather(snap_->cgData.position,
609	>
610	>	cgPlanVectorRow->gather(snap_->cgData.position,
611		cgRowData.position);
612	<	cgCommVectorColumn->gather(snap_->cgData.position,
612	>
613	>	cgPlanVectorColumn->gather(snap_->cgData.position,
614		cgColData.position);
615	+
616	+
617	+
618	+	if (needVelocities_) {
619	+	// gather up the atomic velocities
620	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
621	+	atomColData.velocity);
622	+
623	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
624	+	cgColData.velocity);
625	+	}
626	+
627
628		// if needed, gather the atomic rotation matrices
629		if (storageLayout_ & DataStorage::dslAmat) {
630	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
630	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
631		atomRowData.aMat);
632	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
632	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
633		atomColData.aMat);
634		}
635	<
636	<	// if needed, gather the atomic eletrostatic frames
637	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
638	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
639	<	atomRowData.electroFrame);
640	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
641	<	atomColData.electroFrame);
635	>
636	>	// if needed, gather the atomic eletrostatic information
637	>	if (storageLayout_ & DataStorage::dslDipole) {
638	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
639	>	atomRowData.dipole);
640	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
641	>	atomColData.dipole);
642		}
643	+
644	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
645	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
646	+	atomRowData.quadrupole);
647	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
648	+	atomColData.quadrupole);
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 513 | 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,
690	+	field_tmp);
691	+	for (int i = 0; i < n; i++)
692	+	snap_->atomData.electricField[i] += field_tmp[i];
693		}
694		#endif
695		}
#	Line 534 | Line 703 | namespace OpenMD {
703		storageLayout_ = sman_->getStorageLayout();
704		#ifdef IS_MPI
705		if (storageLayout_ & DataStorage::dslFunctional) {
706	<	AtomCommRealRow->gather(snap_->atomData.functional,
706	>	AtomPlanRealRow->gather(snap_->atomData.functional,
707		atomRowData.functional);
708	<	AtomCommRealColumn->gather(snap_->atomData.functional,
708	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
709		atomColData.functional);
710		}
711
712		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
713	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
713	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
714		atomRowData.functionalDerivative);
715	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
715	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
716		atomColData.functionalDerivative);
717		}
718		#endif
#	Line 557 | Line 726 | namespace OpenMD {
726		int n = snap_->atomData.force.size();
727		vector<Vector3d> frc_tmp(n, V3Zero);
728
729	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
729	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
730		for (int i = 0; i < n; i++) {
731		snap_->atomData.force[i] += frc_tmp[i];
732		frc_tmp[i] = 0.0;
733		}
734
735	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
736	<	for (int i = 0; i < n; i++)
735	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
736	>	for (int i = 0; i < n; i++) {
737		snap_->atomData.force[i] += frc_tmp[i];
738	<
739	<
738	>	}
739	>
740		if (storageLayout_ & DataStorage::dslTorque) {
741
742	<	int nt = snap_->atomData.force.size();
742	>	int nt = snap_->atomData.torque.size();
743		vector<Vector3d> trq_tmp(nt, V3Zero);
744
745	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
746	<	for (int i = 0; i < n; i++) {
745	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
746	>	for (int i = 0; i < nt; i++) {
747		snap_->atomData.torque[i] += trq_tmp[i];
748		trq_tmp[i] = 0.0;
749		}
750
751	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
752	<	for (int i = 0; i < n; i++)
751	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
752	>	for (int i = 0; i < nt; i++)
753		snap_->atomData.torque[i] += trq_tmp[i];
754		}
755	+
756	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
757	+
758	+	int ns = snap_->atomData.skippedCharge.size();
759	+	vector<RealType> skch_tmp(ns, 0.0);
760	+
761	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
762	+	for (int i = 0; i < ns; i++) {
763	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
764	+	skch_tmp[i] = 0.0;
765	+	}
766	+
767	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
768	+	for (int i = 0; i < ns; i++)
769	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
770	+
771	+	}
772
773	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
774	+
775	+	int nq = snap_->atomData.flucQFrc.size();
776	+	vector<RealType> fqfrc_tmp(nq, 0.0);
777	+
778	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
779	+	for (int i = 0; i < nq; i++) {
780	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
781	+	fqfrc_tmp[i] = 0.0;
782	+	}
783	+
784	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
785	+	for (int i = 0; i < nq; i++)
786	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
787	+
788	+	}
789	+
790		nLocal_ = snap_->getNumberOfAtoms();
791
792		vector<potVec> pot_temp(nLocal_,
793		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
794	+	vector<potVec> expot_temp(nLocal_,
795	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
796
797		// scatter/gather pot_row into the members of my column
798
799	<	AtomCommPotRow->scatter(pot_row, pot_temp);
799	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
800	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
801
802	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
803	<	pot_local += pot_temp[ii];
804	<
802	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
803	>	pairwisePot += pot_temp[ii];
804	>
805	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
806	>	excludedPot += expot_temp[ii];
807	>
808	>	if (storageLayout_ & DataStorage::dslParticlePot) {
809	>	// This is the pairwise contribution to the particle pot.  The
810	>	// embedding contribution is added in each of the low level
811	>	// non-bonded routines.  In single processor, this is done in
812	>	// unpackInteractionData, not in collectData.
813	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
814	>	for (int i = 0; i < nLocal_; i++) {
815	>	// factor of two is because the total potential terms are divided
816	>	// by 2 in parallel due to row/ column scatter
817	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
818	>	}
819	>	}
820	>	}
821	>
822		fill(pot_temp.begin(), pot_temp.end(),
823		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
824	+	fill(expot_temp.begin(), expot_temp.end(),
825	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
826
827	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
827	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
828	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
829
830		for (int ii = 0;  ii < pot_temp.size(); ii++ )
831	<	pot_local += pot_temp[ii];
831	>	pairwisePot += pot_temp[ii];
832	>
833	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
834	>	excludedPot += expot_temp[ii];
835	>
836	>	if (storageLayout_ & DataStorage::dslParticlePot) {
837	>	// This is the pairwise contribution to the particle pot.  The
838	>	// embedding contribution is added in each of the low level
839	>	// non-bonded routines.  In single processor, this is done in
840	>	// unpackInteractionData, not in collectData.
841	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
842	>	for (int i = 0; i < nLocal_; i++) {
843	>	// factor of two is because the total potential terms are divided
844	>	// by 2 in parallel due to row/ column scatter
845	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
846	>	}
847	>	}
848	>	}
849
850	+	if (storageLayout_ & DataStorage::dslParticlePot) {
851	+	int npp = snap_->atomData.particlePot.size();
852	+	vector<RealType> ppot_temp(npp, 0.0);
853	+
854	+	// This is the direct or embedding contribution to the particle
855	+	// pot.
856	+
857	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
858	+	for (int i = 0; i < npp; i++) {
859	+	snap_->atomData.particlePot[i] += ppot_temp[i];
860	+	}
861	+
862	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
863	+
864	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
865	+	for (int i = 0; i < npp; i++) {
866	+	snap_->atomData.particlePot[i] += ppot_temp[i];
867	+	}
868	+	}
869	+
870	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
871	+	RealType ploc1 = pairwisePot[ii];
872	+	RealType ploc2 = 0.0;
873	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
874	+	pairwisePot[ii] = ploc2;
875	+	}
876	+
877	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
878	+	RealType ploc1 = excludedPot[ii];
879	+	RealType ploc2 = 0.0;
880	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
881	+	excludedPot[ii] = ploc2;
882	+	}
883	+
884	+	// Here be dragons.
885	+	MPI::Intracomm col = colComm.getComm();
886	+
887	+	col.Allreduce(MPI::IN_PLACE,
888	+	&snap_->frameData.conductiveHeatFlux[0], 3,
889	+	MPI::REALTYPE, MPI::SUM);
890	+
891	+
892		#endif
893	+
894		}
895
896	+	/**
897	+	* Collects information obtained during the post-pair (and embedding
898	+	* functional) loops onto local data structures.
899	+	*/
900	+	void ForceMatrixDecomposition::collectSelfData() {
901	+	snap_ = sman_->getCurrentSnapshot();
902	+	storageLayout_ = sman_->getStorageLayout();
903	+
904	+	#ifdef IS_MPI
905	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
906	+	RealType ploc1 = embeddingPot[ii];
907	+	RealType ploc2 = 0.0;
908	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
909	+	embeddingPot[ii] = ploc2;
910	+	}
911	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
912	+	RealType ploc1 = excludedSelfPot[ii];
913	+	RealType ploc2 = 0.0;
914	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
915	+	excludedSelfPot[ii] = ploc2;
916	+	}
917	+	#endif
918	+
919	+	}
920	+
921	+
922	+
923		int ForceMatrixDecomposition::getNAtomsInRow() {
924		#ifdef IS_MPI
925		return nAtomsInRow_;
#	Line 647 | Line 960 | namespace OpenMD {
960		return d;
961		}
962
963	+	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
964	+	#ifdef IS_MPI
965	+	return cgColData.velocity[cg2];
966	+	#else
967	+	return snap_->cgData.velocity[cg2];
968	+	#endif
969	+	}
970
971	+	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
972	+	#ifdef IS_MPI
973	+	return atomColData.velocity[atom2];
974	+	#else
975	+	return snap_->atomData.velocity[atom2];
976	+	#endif
977	+	}
978	+
979	+
980		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
981
982		Vector3d d;
#	Line 679 | Line 1008 | namespace OpenMD {
1008		#ifdef IS_MPI
1009		return massFactorsRow[atom1];
1010		#else
1011	<	return massFactorsLocal[atom1];
1011	>	return massFactors[atom1];
1012		#endif
1013		}
1014
#	Line 687 | Line 1016 | namespace OpenMD {
1016		#ifdef IS_MPI
1017		return massFactorsCol[atom2];
1018		#else
1019	<	return massFactorsLocal[atom2];
1019	>	return massFactors[atom2];
1020		#endif
1021
1022		}
#	Line 705 | Line 1034 | namespace OpenMD {
1034		return d;
1035		}
1036
1037	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
1038	<	#ifdef IS_MPI
710	<	return skipsForRowAtom[atom1];
711	<	#else
712	<	return skipsForLocalAtom[atom1];
713	<	#endif
1037	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1038	>	return excludesForAtom[atom1];
1039		}
1040
1041		/**
1042	<	* There are a number of reasons to skip a pair or a
718	<	* particle. Mostly we do this to exclude atoms who are involved in
719	<	* short range interactions (bonds, bends, torsions), but we also
720	<	* need to exclude some overcounted interactions that result from
1042	>	* We need to exclude some overcounted interactions that result from
1043		* the parallel decomposition.
1044		*/
1045	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1045	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1046		int unique_id_1, unique_id_2;
1047	<
1047	>
1048		#ifdef IS_MPI
1049		// in MPI, we have to look up the unique IDs for each atom
1050		unique_id_1 = AtomRowToGlobal[atom1];
1051		unique_id_2 = AtomColToGlobal[atom2];
1052	+	// group1 = cgRowToGlobal[cg1];
1053	+	// group2 = cgColToGlobal[cg2];
1054	+	#else
1055	+	unique_id_1 = AtomLocalToGlobal[atom1];
1056	+	unique_id_2 = AtomLocalToGlobal[atom2];
1057	+	int group1 = cgLocalToGlobal[cg1];
1058	+	int group2 = cgLocalToGlobal[cg2];
1059	+	#endif
1060
731	–	// this situation should only arise in MPI simulations
1061		if (unique_id_1 == unique_id_2) return true;
1062	<
1062	>
1063	>	#ifdef IS_MPI
1064		// this prevents us from doing the pair on multiple processors
1065		if (unique_id_1 < unique_id_2) {
1066		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1067		} else {
1068	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1068	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1069		}
1070	<	#else
1071	<	// in the normal loop, the atom numbers are unique
1072	<	unique_id_1 = atom1;
1073	<	unique_id_2 = atom2;
1070	>	#endif
1071	>
1072	>	#ifndef IS_MPI
1073	>	if (group1 == group2) {
1074	>	if (unique_id_1 < unique_id_2) return true;
1075	>	}
1076		#endif
1077
1078	<	#ifdef IS_MPI
747	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748	<	i != skipsForRowAtom[atom1].end(); ++i) {
749	<	if ( (*i) == unique_id_2 ) return true;
750	<	}
751	<	#else
752	<	for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
753	<	i != skipsForLocalAtom[atom1].end(); ++i) {
754	<	if ( (*i) == unique_id_2 ) return true;
755	<	}
756	<	#endif
1078	>	return false;
1079		}
1080
1081	<	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
1081	>	/**
1082	>	* We need to handle the interactions for atoms who are involved in
1083	>	* the same rigid body as well as some short range interactions
1084	>	* (bonds, bends, torsions) differently from other interactions.
1085	>	* We'll still visit the pairwise routines, but with a flag that
1086	>	* tells those routines to exclude the pair from direct long range
1087	>	* interactions.  Some indirect interactions (notably reaction
1088	>	* field) must still be handled for these pairs.
1089	>	*/
1090	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1091	>
1092	>	// excludesForAtom was constructed to use row/column indices in the MPI
1093	>	// version, and to use local IDs in the non-MPI version:
1094
1095	<	#ifdef IS_MPI
1096	<	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
1097	<	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
1095	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1096	>	i != excludesForAtom[atom1].end(); ++i) {
1097	>	if ( (*i) == atom2 ) return true;
1098		}
765	–	#else
766	–	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
767	–	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
768	–	}
769	–	#endif
1099
1100	<	// zero is default for unconnected (i.e. normal) pair interactions
772	<	return 0;
1100	>	return false;
1101		}
1102
1103	+
1104		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1105		#ifdef IS_MPI
1106		atomRowData.force[atom1] += fg;
#	Line 789 | Line 1118 | namespace OpenMD {
1118		}
1119
1120		// filling interaction blocks with pointers
1121	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1122	<	InteractionData idat;
1121	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1122	>	int atom1, int atom2) {
1123
1124	+	idat.excluded = excludeAtomPair(atom1, atom2);
1125	+
1126		#ifdef IS_MPI
1127	<
1128	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1129	<	ff_->getAtomType(identsCol[atom2]) );
799	<
1127	>	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1128	>	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1129	>	//                         ff_->getAtomType(identsCol[atom2]) );
1130
1131		if (storageLayout_ & DataStorage::dslAmat) {
1132		idat.A1 = &(atomRowData.aMat[atom1]);
1133		idat.A2 = &(atomColData.aMat[atom2]);
1134		}
1135
806	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
807	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
808	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
809	–	}
810	–
1136		if (storageLayout_ & DataStorage::dslTorque) {
1137		idat.t1 = &(atomRowData.torque[atom1]);
1138		idat.t2 = &(atomColData.torque[atom2]);
1139		}
1140
1141	+	if (storageLayout_ & DataStorage::dslDipole) {
1142	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1143	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1144	+	}
1145	+
1146	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1147	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1148	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1149	+	}
1150	+
1151		if (storageLayout_ & DataStorage::dslDensity) {
1152		idat.rho1 = &(atomRowData.density[atom1]);
1153		idat.rho2 = &(atomColData.density[atom2]);
#	Line 833 | Line 1168 | namespace OpenMD {
1168		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1169		}
1170
1171	<	#else
1171	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1172	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1173	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1174	>	}
1175
1176	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
1177	<	ff_->getAtomType(identsLocal[atom2]) );
1176	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1177	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1178	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1179	>	}
1180
1181	+	#else
1182	+
1183	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1184	+
1185		if (storageLayout_ & DataStorage::dslAmat) {
1186		idat.A1 = &(snap_->atomData.aMat[atom1]);
1187		idat.A2 = &(snap_->atomData.aMat[atom2]);
1188		}
1189
1190	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
847	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
848	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
849	<	}
1190	>	RealType ct = dot(idat.A1->getColumn(2), idat.A2->getColumn(2));
1191
1192		if (storageLayout_ & DataStorage::dslTorque) {
1193		idat.t1 = &(snap_->atomData.torque[atom1]);
1194		idat.t2 = &(snap_->atomData.torque[atom2]);
1195		}
1196
1197	<	if (storageLayout_ & DataStorage::dslDensity) {
1197	>	if (storageLayout_ & DataStorage::dslDipole) {
1198	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1199	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1200	>	}
1201	>
1202	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1203	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1204	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1205	>	}
1206	>
1207	>	if (storageLayout_ & DataStorage::dslDensity) {
1208		idat.rho1 = &(snap_->atomData.density[atom1]);
1209		idat.rho2 = &(snap_->atomData.density[atom2]);
1210		}
#	Line 873 | Line 1224 | namespace OpenMD {
1224		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1225		}
1226
1227	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1228	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1229	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1230	+	}
1231	+
1232	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1233	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1234	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1235	+	}
1236	+
1237		#endif
877	–	return idat;
1238		}
1239
1240
1241	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
1241	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1242		#ifdef IS_MPI
1243	<	pot_row[atom1] += 0.5 *  *(idat.pot);
1244	<	pot_col[atom2] += 0.5 *  *(idat.pot);
1243	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1244	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1245	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1246	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1247
1248		atomRowData.force[atom1] += *(idat.f1);
1249		atomColData.force[atom2] -= *(idat.f1);
888	–	#else
889	–	longRangePot_ += *(idat.pot);
890	–
891	–	snap_->atomData.force[atom1] += *(idat.f1);
892	–	snap_->atomData.force[atom2] -= *(idat.f1);
893	–	#endif
1250
1251	<	}
1251	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1252	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1253	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1254	>	}
1255
1256	+	if (storageLayout_ & DataStorage::dslElectricField) {
1257	+	atomRowData.electricField[atom1] += *(idat.eField1);
1258	+	atomColData.electricField[atom2] += *(idat.eField2);
1259	+	}
1260
1261	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1261	>	#else
1262	>	pairwisePot += *(idat.pot);
1263	>	excludedPot += *(idat.excludedPot);
1264
1265	<	InteractionData idat;
1266	<	#ifdef IS_MPI
902	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
903	<	ff_->getAtomType(identsCol[atom2]) );
1265	>	snap_->atomData.force[atom1] += *(idat.f1);
1266	>	snap_->atomData.force[atom2] -= *(idat.f1);
1267
1268	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1269	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1270	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1268	>	if (idat.doParticlePot) {
1269	>	// This is the pairwise contribution to the particle pot.  The
1270	>	// embedding contribution is added in each of the low level
1271	>	// non-bonded routines.  In parallel, this calculation is done
1272	>	// in collectData, not in unpackInteractionData.
1273	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1274	>	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1275		}
1276	<	if (storageLayout_ & DataStorage::dslTorque) {
1277	<	idat.t1 = &(atomRowData.torque[atom1]);
1278	<	idat.t2 = &(atomColData.torque[atom2]);
1276	>
1277	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1278	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1279	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1280		}
913	–	#else
914	–	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
915	–	ff_->getAtomType(identsLocal[atom2]) );
1281
1282	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1283	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1284	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1282	>	if (storageLayout_ & DataStorage::dslElectricField) {
1283	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1284	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1285		}
1286	<	if (storageLayout_ & DataStorage::dslTorque) {
1287	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1288	<	idat.t2 = &(snap_->atomData.torque[atom2]);
924	<	}
925	<	#endif
1286	>
1287	>	#endif
1288	>
1289		}
1290
1291		/*
#	Line 935 | Line 1298 | namespace OpenMD {
1298
1299		vector<pair<int, int> > neighborList;
1300		groupCutoffs cuts;
1301	+	bool doAllPairs = false;
1302	+
1303		#ifdef IS_MPI
1304		cellListRow_.clear();
1305		cellListCol_.clear();
#	Line 943 | Line 1308 | namespace OpenMD {
1308		#endif
1309
1310		RealType rList_ = (largestRcut_ + skinThickness_);
946	–	RealType rl2 = rList_ * rList_;
1311		Snapshot* snap_ = sman_->getCurrentSnapshot();
1312		Mat3x3d Hmat = snap_->getHmat();
1313		Vector3d Hx = Hmat.getColumn(0);
#	Line 954 | Line 1318 | namespace OpenMD {
1318		nCells_.y() = (int) ( Hy.length() )/ rList_;
1319		nCells_.z() = (int) ( Hz.length() )/ rList_;
1320
1321	+	// handle small boxes where the cell offsets can end up repeating cells
1322	+
1323	+	if (nCells_.x() < 3) doAllPairs = true;
1324	+	if (nCells_.y() < 3) doAllPairs = true;
1325	+	if (nCells_.z() < 3) doAllPairs = true;
1326	+
1327		Mat3x3d invHmat = snap_->getInvHmat();
1328		Vector3d rs, scaled, dr;
1329		Vector3i whichCell;
1330		int cellIndex;
1331	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1332
1333		#ifdef IS_MPI
1334	<	for (int i = 0; i < nGroupsInRow_; i++) {
1335	<	rs = cgRowData.position[i];
1336	<	// scaled positions relative to the box vectors
1337	<	scaled = invHmat * rs;
1338	<	// wrap the vector back into the unit box by subtracting integer box
968	<	// numbers
969	<	for (int j = 0; j < 3; j++)
970	<	scaled[j] -= roundMe(scaled[j]);
971	<
972	<	// find xyz-indices of cell that cutoffGroup is in.
973	<	whichCell.x() = nCells_.x() * scaled.x();
974	<	whichCell.y() = nCells_.y() * scaled.y();
975	<	whichCell.z() = nCells_.z() * scaled.z();
1334	>	cellListRow_.resize(nCtot);
1335	>	cellListCol_.resize(nCtot);
1336	>	#else
1337	>	cellList_.resize(nCtot);
1338	>	#endif
1339
1340	<	// find single index of this cell:
1341	<	cellIndex = Vlinear(whichCell, nCells_);
979	<	// add this cutoff group to the list of groups in this cell;
980	<	cellListRow_[cellIndex].push_back(i);
981	<	}
1340	>	if (!doAllPairs) {
1341	>	#ifdef IS_MPI
1342
1343	<	for (int i = 0; i < nGroupsInCol_; i++) {
1344	<	rs = cgColData.position[i];
1345	<	// scaled positions relative to the box vectors
1346	<	scaled = invHmat * rs;
1347	<	// wrap the vector back into the unit box by subtracting integer box
1348	<	// numbers
1349	<	for (int j = 0; j < 3; j++)
1350	<	scaled[j] -= roundMe(scaled[j]);
1351	<
1352	<	// find xyz-indices of cell that cutoffGroup is in.
1353	<	whichCell.x() = nCells_.x() * scaled.x();
1354	<	whichCell.y() = nCells_.y() * scaled.y();
1355	<	whichCell.z() = nCells_.z() * scaled.z();
1356	<
1357	<	// find single index of this cell:
1358	<	cellIndex = Vlinear(whichCell, nCells_);
1359	<	// add this cutoff group to the list of groups in this cell;
1360	<	cellListCol_[cellIndex].push_back(i);
1361	<	}
1343	>	for (int i = 0; i < nGroupsInRow_; i++) {
1344	>	rs = cgRowData.position[i];
1345	>
1346	>	// scaled positions relative to the box vectors
1347	>	scaled = invHmat * rs;
1348	>
1349	>	// wrap the vector back into the unit box by subtracting integer box
1350	>	// numbers
1351	>	for (int j = 0; j < 3; j++) {
1352	>	scaled[j] -= roundMe(scaled[j]);
1353	>	scaled[j] += 0.5;
1354	>	// Handle the special case when an object is exactly on the
1355	>	// boundary (a scaled coordinate of 1.0 is the same as
1356	>	// scaled coordinate of 0.0)
1357	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1358	>	}
1359	>
1360	>	// find xyz-indices of cell that cutoffGroup is in.
1361	>	whichCell.x() = nCells_.x() * scaled.x();
1362	>	whichCell.y() = nCells_.y() * scaled.y();
1363	>	whichCell.z() = nCells_.z() * scaled.z();
1364	>
1365	>	// find single index of this cell:
1366	>	cellIndex = Vlinear(whichCell, nCells_);
1367	>
1368	>	// add this cutoff group to the list of groups in this cell;
1369	>	cellListRow_[cellIndex].push_back(i);
1370	>	}
1371	>	for (int i = 0; i < nGroupsInCol_; i++) {
1372	>	rs = cgColData.position[i];
1373	>
1374	>	// scaled positions relative to the box vectors
1375	>	scaled = invHmat * rs;
1376	>
1377	>	// wrap the vector back into the unit box by subtracting integer box
1378	>	// numbers
1379	>	for (int j = 0; j < 3; j++) {
1380	>	scaled[j] -= roundMe(scaled[j]);
1381	>	scaled[j] += 0.5;
1382	>	// Handle the special case when an object is exactly on the
1383	>	// boundary (a scaled coordinate of 1.0 is the same as
1384	>	// scaled coordinate of 0.0)
1385	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
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	>	cellListCol_[cellIndex].push_back(i);
1398	>	}
1399	>
1400		#else
1401	<	for (int i = 0; i < nGroups_; i++) {
1402	<	rs = snap_->cgData.position[i];
1403	<	// scaled positions relative to the box vectors
1404	<	scaled = invHmat * rs;
1405	<	// wrap the vector back into the unit box by subtracting integer box
1406	<	// numbers
1407	<	for (int j = 0; j < 3; j++)
1408	<	scaled[j] -= roundMe(scaled[j]);
1401	>	for (int i = 0; i < nGroups_; i++) {
1402	>	rs = snap_->cgData.position[i];
1403	>
1404	>	// scaled positions relative to the box vectors
1405	>	scaled = invHmat * rs;
1406	>
1407	>	// wrap the vector back into the unit box by subtracting integer box
1408	>	// numbers
1409	>	for (int j = 0; j < 3; j++) {
1410	>	scaled[j] -= roundMe(scaled[j]);
1411	>	scaled[j] += 0.5;
1412	>	// Handle the special case when an object is exactly on the
1413	>	// boundary (a scaled coordinate of 1.0 is the same as
1414	>	// scaled coordinate of 0.0)
1415	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1416	>	}
1417	>
1418	>	// find xyz-indices of cell that cutoffGroup is in.
1419	>	whichCell.x() = nCells_.x() * scaled.x();
1420	>	whichCell.y() = nCells_.y() * scaled.y();
1421	>	whichCell.z() = nCells_.z() * scaled.z();
1422	>
1423	>	// find single index of this cell:
1424	>	cellIndex = Vlinear(whichCell, nCells_);
1425	>
1426	>	// add this cutoff group to the list of groups in this cell;
1427	>	cellList_[cellIndex].push_back(i);
1428	>	}
1429
1012	–	// find xyz-indices of cell that cutoffGroup is in.
1013	–	whichCell.x() = nCells_.x() * scaled.x();
1014	–	whichCell.y() = nCells_.y() * scaled.y();
1015	–	whichCell.z() = nCells_.z() * scaled.z();
1016	–
1017	–	// find single index of this cell:
1018	–	cellIndex = Vlinear(whichCell, nCells_);
1019	–	// add this cutoff group to the list of groups in this cell;
1020	–	cellList_[cellIndex].push_back(i);
1021	–	}
1430		#endif
1431
1432	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1433	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1434	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1435	<	Vector3i m1v(m1x, m1y, m1z);
1436	<	int m1 = Vlinear(m1v, nCells_);
1029	<
1030	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1031	<	os != cellOffsets_.end(); ++os) {
1432	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1433	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1434	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1435	>	Vector3i m1v(m1x, m1y, m1z);
1436	>	int m1 = Vlinear(m1v, nCells_);
1437
1438	<	Vector3i m2v = m1v + (*os);
1439	<
1440	<	if (m2v.x() >= nCells_.x()) {
1441	<	m2v.x() = 0;
1442	<	} else if (m2v.x() < 0) {
1038	<	m2v.x() = nCells_.x() - 1;
1039	<	}
1040	<
1041	<	if (m2v.y() >= nCells_.y()) {
1042	<	m2v.y() = 0;
1043	<	} else if (m2v.y() < 0) {
1044	<	m2v.y() = nCells_.y() - 1;
1045	<	}
1046	<
1047	<	if (m2v.z() >= nCells_.z()) {
1048	<	m2v.z() = 0;
1049	<	} else if (m2v.z() < 0) {
1050	<	m2v.z() = nCells_.z() - 1;
1051	<	}
1052	<
1053	<	int m2 = Vlinear (m2v, nCells_);
1438	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1439	>	os != cellOffsets_.end(); ++os) {
1440	>
1441	>	Vector3i m2v = m1v + (*os);
1442	>
1443
1444	<	#ifdef IS_MPI
1445	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1446	<	j1 != cellListRow_[m1].end(); ++j1) {
1447	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1448	<	j2 != cellListCol_[m2].end(); ++j2) {
1449	<
1450	<	// Always do this if we're in different cells or if
1451	<	// we're in the same cell and the global index of the
1452	<	// j2 cutoff group is less than the j1 cutoff group
1444	>	if (m2v.x() >= nCells_.x()) {
1445	>	m2v.x() = 0;
1446	>	} else if (m2v.x() < 0) {
1447	>	m2v.x() = nCells_.x() - 1;
1448	>	}
1449	>
1450	>	if (m2v.y() >= nCells_.y()) {
1451	>	m2v.y() = 0;
1452	>	} else if (m2v.y() < 0) {
1453	>	m2v.y() = nCells_.y() - 1;
1454	>	}
1455	>
1456	>	if (m2v.z() >= nCells_.z()) {
1457	>	m2v.z() = 0;
1458	>	} else if (m2v.z() < 0) {
1459	>	m2v.z() = nCells_.z() - 1;
1460	>	}
1461
1462	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1462	>	int m2 = Vlinear (m2v, nCells_);
1463	>
1464	>	#ifdef IS_MPI
1465	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1466	>	j1 != cellListRow_[m1].end(); ++j1) {
1467	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1468	>	j2 != cellListCol_[m2].end(); ++j2) {
1469	>
1470	>	// In parallel, we need to visit *all* pairs of row
1471	>	// & column indicies and will divide labor in the
1472	>	// force evaluation later.
1473		dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1474		snap_->wrapVector(dr);
1475		cuts = getGroupCutoffs( (*j1), (*j2) );
1476		if (dr.lengthSquare() < cuts.third) {
1477		neighborList.push_back(make_pair((*j1), (*j2)));
1478	<	}
1478	>	}
1479		}
1480		}
1074	–	}
1481		#else
1482	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1483	<	j1 != cellList_[m1].end(); ++j1) {
1484	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1485	<	j2 != cellList_[m2].end(); ++j2) {
1486	<
1487	<	// Always do this if we're in different cells or if
1488	<	// we're in the same cell and the global index of the
1489	<	// j2 cutoff group is less than the j1 cutoff group
1482	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1483	>	j1 != cellList_[m1].end(); ++j1) {
1484	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1485	>	j2 != cellList_[m2].end(); ++j2) {
1486	>
1487	>	// Always do this if we're in different cells or if
1488	>	// we're in the same cell and the global index of
1489	>	// the j2 cutoff group is greater than or equal to
1490	>	// the j1 cutoff group.  Note that Rappaport's code
1491	>	// has a "less than" conditional here, but that
1492	>	// deals with atom-by-atom computation.  OpenMD
1493	>	// allows atoms within a single cutoff group to
1494	>	// interact with each other.
1495
1496	<	if (m2 != m1 || (*j2) < (*j1)) {
1497	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1498	<	snap_->wrapVector(dr);
1499	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1500	<	if (dr.lengthSquare() < cuts.third) {
1501	<	neighborList.push_back(make_pair((*j1), (*j2)));
1496	>
1497	>
1498	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1499	>
1500	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1501	>	snap_->wrapVector(dr);
1502	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1503	>	if (dr.lengthSquare() < cuts.third) {
1504	>	neighborList.push_back(make_pair((*j1), (*j2)));
1505	>	}
1506		}
1507		}
1508		}
1094	–	}
1509		#endif
1510	+	}
1511		}
1512		}
1513		}
1514	+	} else {
1515	+	// branch to do all cutoff group pairs
1516	+	#ifdef IS_MPI
1517	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1518	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1519	+	dr = cgColData.position[j2] - cgRowData.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	+	#else
1528	+	// include all groups here.
1529	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1530	+	// include self group interactions j2 == j1
1531	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1532	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1533	+	snap_->wrapVector(dr);
1534	+	cuts = getGroupCutoffs( j1, j2 );
1535	+	if (dr.lengthSquare() < cuts.third) {
1536	+	neighborList.push_back(make_pair(j1, j2));
1537	+	}
1538	+	}
1539	+	}
1540	+	#endif
1541		}
1542	<
1542	>
1543		// save the local cutoff group positions for the check that is
1544		// done on each loop:
1545		saved_CG_positions_.clear();
1546		for (int i = 0; i < nGroups_; i++)
1547		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1548	<
1548	>
1549		return neighborList;
1550		}
1551		} //end namespace OpenMD

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