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

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1551 by gezelter, Thu Apr 28 18:38:21 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1893 by gezelter, Wed Jun 19 17:19:07 2013 UTC

#	Line 35 | Line 35
35		*
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).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
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	<	#ifdef IS_MPI
97	<	int nLocal = snap_->getNumberOfAtoms();
98	<	int nGroups = snap_->getNumberOfCutoffGroups();
96	>	ff_ = info_->getForceField();
97	>	nLocal_ = snap_->getNumberOfAtoms();
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	<	AtomCommIntRow = new Communicator<Row,int>(nLocal);
114	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
115	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
116	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
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	>	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	<	int nAtomsInRow = AtomCommIntRow->getSize();
137	<	int nAtomsInCol = AtomCommIntColumn->getSize();
138	<	int nGroupsInRow = cgCommIntRow->getSize();
139	<	int 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);
147	>	atomRowData.resize(nAtomsInRow_);
148		atomRowData.setStorageLayout(storageLayout_);
149	<	atomColData.resize(nAtomsInCol);
149	>	atomColData.resize(nAtomsInCol_);
150		atomColData.setStorageLayout(storageLayout_);
151	<	cgRowData.resize(nGroupsInRow);
151	>	cgRowData.resize(nGroupsInRow_);
152		cgRowData.setStorageLayout(DataStorage::dslPosition);
153	<	cgColData.resize(nGroupsInCol);
154	<	cgColData.setStorageLayout(DataStorage::dslPosition);
153	>	cgColData.resize(nGroupsInCol_);
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	<
99	<	// gather the information for atomtype IDs (atids):
100	<	vector<int> identsLocal = info_->getIdentArray();
101	<	identsRow.reserve(nAtomsInRow);
102	<	identsCol.reserve(nAtomsInCol);
103	<
104	<	AtomCommIntRow->gather(identsLocal, identsRow);
105	<	AtomCommIntColumn->gather(identsLocal, identsCol);
106	<
107	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
108	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
109	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
110	<
111	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
112	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
113	<	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	+	#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);
568	+	}
569	+
570	+	if (storageLayout_ & DataStorage::dslDensity) {
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	+
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	+
597		void ForceMatrixDecomposition::distributeData()  {
598		snap_ = sman_->getCurrentSnapshot();
599		storageLayout_ = sman_->getStorageLayout();
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
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 162 | 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	+	// this isn't necessary if we don't have polarizable atoms, but
683	+	// we'll leave it here for now.
684	+	if (storageLayout_ & DataStorage::dslElectricField) {
685	+
686	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
687	+	snap_->atomData.electricField);
688	+
689	+	int n = snap_->atomData.electricField.size();
690	+	vector<Vector3d> field_tmp(n, V3Zero);
691	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
692	+	field_tmp);
693	+	for (int i = 0; i < n; i++)
694	+	snap_->atomData.electricField[i] += field_tmp[i];
695	+	}
696		#endif
697		}
698	<
698	>
699	>	/*
700	>	* redistributes information obtained during the pre-pair loop out to
701	>	* row and column-indexed data structures
702	>	*/
703		void ForceMatrixDecomposition::distributeIntermediateData() {
704		snap_ = sman_->getCurrentSnapshot();
705		storageLayout_ = sman_->getStorageLayout();
706		#ifdef IS_MPI
707		if (storageLayout_ & DataStorage::dslFunctional) {
708	<	AtomCommRealRow->gather(snap_->atomData.functional,
708	>	AtomPlanRealRow->gather(snap_->atomData.functional,
709		atomRowData.functional);
710	<	AtomCommRealColumn->gather(snap_->atomData.functional,
710	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
711		atomColData.functional);
712		}
713
714		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
715	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
715	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
716		atomRowData.functionalDerivative);
717	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
717	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
718		atomColData.functionalDerivative);
719		}
720		#endif
#	Line 202 | Line 728 | namespace OpenMD {
728		int n = snap_->atomData.force.size();
729		vector<Vector3d> frc_tmp(n, V3Zero);
730
731	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
731	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
732		for (int i = 0; i < n; i++) {
733		snap_->atomData.force[i] += frc_tmp[i];
734		frc_tmp[i] = 0.0;
735		}
736
737	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
738	<	for (int i = 0; i < n; i++)
737	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
738	>	for (int i = 0; i < n; i++) {
739		snap_->atomData.force[i] += frc_tmp[i];
740	<
741	<
740	>	}
741	>
742		if (storageLayout_ & DataStorage::dslTorque) {
743
744	<	int nt = snap_->atomData.force.size();
744	>	int nt = snap_->atomData.torque.size();
745		vector<Vector3d> trq_tmp(nt, V3Zero);
746
747	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
748	<	for (int i = 0; i < n; i++) {
747	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
748	>	for (int i = 0; i < nt; i++) {
749		snap_->atomData.torque[i] += trq_tmp[i];
750		trq_tmp[i] = 0.0;
751		}
752
753	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
754	<	for (int i = 0; i < n; i++)
753	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
754	>	for (int i = 0; i < nt; i++)
755		snap_->atomData.torque[i] += trq_tmp[i];
756		}
231	–
232	–	int nLocal = snap_->getNumberOfAtoms();
757
758	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
759	<	vector<RealType> (nLocal, 0.0));
758	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
759	>
760	>	int ns = snap_->atomData.skippedCharge.size();
761	>	vector<RealType> skch_tmp(ns, 0.0);
762	>
763	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
764	>	for (int i = 0; i < ns; i++) {
765	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
766	>	skch_tmp[i] = 0.0;
767	>	}
768	>
769	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
770	>	for (int i = 0; i < ns; i++)
771	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
772	>
773	>	}
774
775	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
776	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
777	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
778	<	pot_local[i] += pot_temp[i][ii];
775	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
776	>
777	>	int nq = snap_->atomData.flucQFrc.size();
778	>	vector<RealType> fqfrc_tmp(nq, 0.0);
779	>
780	>	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
781	>	for (int i = 0; i < nq; i++) {
782	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
783	>	fqfrc_tmp[i] = 0.0;
784		}
785	+
786	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
787	+	for (int i = 0; i < nq; i++)
788	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
789	+
790		}
791	+
792	+	if (storageLayout_ & DataStorage::dslElectricField) {
793	+
794	+	int nef = snap_->atomData.electricField.size();
795	+	vector<Vector3d> efield_tmp(nef, V3Zero);
796	+
797	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
798	+	for (int i = 0; i < nef; i++) {
799	+	snap_->atomData.electricField[i] += efield_tmp[i];
800	+	efield_tmp[i] = 0.0;
801	+	}
802	+
803	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
804	+	for (int i = 0; i < nef; i++)
805	+	snap_->atomData.electricField[i] += efield_tmp[i];
806	+	}
807	+
808	+
809	+	nLocal_ = snap_->getNumberOfAtoms();
810	+
811	+	vector<potVec> pot_temp(nLocal_,
812	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
813	+	vector<potVec> expot_temp(nLocal_,
814	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
815	+
816	+	// scatter/gather pot_row into the members of my column
817	+
818	+	AtomPlanPotRow->scatter(pot_row, pot_temp);
819	+	AtomPlanPotRow->scatter(expot_row, expot_temp);
820	+
821	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
822	+	pairwisePot += pot_temp[ii];
823	+
824	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
825	+	excludedPot += expot_temp[ii];
826	+
827	+	if (storageLayout_ & DataStorage::dslParticlePot) {
828	+	// This is the pairwise contribution to the particle pot.  The
829	+	// embedding contribution is added in each of the low level
830	+	// non-bonded routines.  In single processor, this is done in
831	+	// unpackInteractionData, not in collectData.
832	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
833	+	for (int i = 0; i < nLocal_; i++) {
834	+	// factor of two is because the total potential terms are divided
835	+	// by 2 in parallel due to row/ column scatter
836	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
837	+	}
838	+	}
839	+	}
840	+
841	+	fill(pot_temp.begin(), pot_temp.end(),
842	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
843	+	fill(expot_temp.begin(), expot_temp.end(),
844	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
845	+
846	+	AtomPlanPotColumn->scatter(pot_col, pot_temp);
847	+	AtomPlanPotColumn->scatter(expot_col, expot_temp);
848	+
849	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
850	+	pairwisePot += pot_temp[ii];
851	+
852	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
853	+	excludedPot += expot_temp[ii];
854	+
855	+	if (storageLayout_ & DataStorage::dslParticlePot) {
856	+	// This is the pairwise contribution to the particle pot.  The
857	+	// embedding contribution is added in each of the low level
858	+	// non-bonded routines.  In single processor, this is done in
859	+	// unpackInteractionData, not in collectData.
860	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
861	+	for (int i = 0; i < nLocal_; i++) {
862	+	// factor of two is because the total potential terms are divided
863	+	// by 2 in parallel due to row/ column scatter
864	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
865	+	}
866	+	}
867	+	}
868	+
869	+	if (storageLayout_ & DataStorage::dslParticlePot) {
870	+	int npp = snap_->atomData.particlePot.size();
871	+	vector<RealType> ppot_temp(npp, 0.0);
872	+
873	+	// This is the direct or embedding contribution to the particle
874	+	// pot.
875	+
876	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
877	+	for (int i = 0; i < npp; i++) {
878	+	snap_->atomData.particlePot[i] += ppot_temp[i];
879	+	}
880	+
881	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
882	+
883	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
884	+	for (int i = 0; i < npp; i++) {
885	+	snap_->atomData.particlePot[i] += ppot_temp[i];
886	+	}
887	+	}
888	+
889	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
890	+	RealType ploc1 = pairwisePot[ii];
891	+	RealType ploc2 = 0.0;
892	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
893	+	pairwisePot[ii] = ploc2;
894	+	}
895	+
896	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
897	+	RealType ploc1 = excludedPot[ii];
898	+	RealType ploc2 = 0.0;
899	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
900	+	excludedPot[ii] = ploc2;
901	+	}
902	+
903	+	// Here be dragons.
904	+	MPI::Intracomm col = colComm.getComm();
905	+
906	+	col.Allreduce(MPI::IN_PLACE,
907	+	&snap_->frameData.conductiveHeatFlux[0], 3,
908	+	MPI::REALTYPE, MPI::SUM);
909	+
910	+
911		#endif
912	+
913		}
914
915	+	/**
916	+	* Collects information obtained during the post-pair (and embedding
917	+	* functional) loops onto local data structures.
918	+	*/
919	+	void ForceMatrixDecomposition::collectSelfData() {
920	+	snap_ = sman_->getCurrentSnapshot();
921	+	storageLayout_ = sman_->getStorageLayout();
922	+
923	+	#ifdef IS_MPI
924	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
925	+	RealType ploc1 = embeddingPot[ii];
926	+	RealType ploc2 = 0.0;
927	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
928	+	embeddingPot[ii] = ploc2;
929	+	}
930	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
931	+	RealType ploc1 = excludedSelfPot[ii];
932	+	RealType ploc2 = 0.0;
933	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
934	+	excludedSelfPot[ii] = ploc2;
935	+	}
936	+	#endif
937	+
938	+	}
939	+
940	+
941	+
942	+	int& ForceMatrixDecomposition::getNAtomsInRow() {
943	+	#ifdef IS_MPI
944	+	return nAtomsInRow_;
945	+	#else
946	+	return nLocal_;
947	+	#endif
948	+	}
949	+
950	+	/**
951	+	* returns the list of atoms belonging to this group.
952	+	*/
953	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
954	+	#ifdef IS_MPI
955	+	return groupListRow_[cg1];
956	+	#else
957	+	return groupList_[cg1];
958	+	#endif
959	+	}
960	+
961	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
962	+	#ifdef IS_MPI
963	+	return groupListCol_[cg2];
964	+	#else
965	+	return groupList_[cg2];
966	+	#endif
967	+	}
968
969		Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
970		Vector3d d;
#	Line 253 | Line 975 | namespace OpenMD {
975		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
976		#endif
977
978	<	snap_->wrapVector(d);
978	>	if (usePeriodicBoundaryConditions_) {
979	>	snap_->wrapVector(d);
980	>	}
981		return d;
982		}
983
984	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
985	+	#ifdef IS_MPI
986	+	return cgColData.velocity[cg2];
987	+	#else
988	+	return snap_->cgData.velocity[cg2];
989	+	#endif
990	+	}
991
992	+	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
993	+	#ifdef IS_MPI
994	+	return atomColData.velocity[atom2];
995	+	#else
996	+	return snap_->atomData.velocity[atom2];
997	+	#endif
998	+	}
999	+
1000	+
1001		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
1002
1003		Vector3d d;
#	Line 267 | Line 1007 | namespace OpenMD {
1007		#else
1008		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1009		#endif
1010	<
1011	<	snap_->wrapVector(d);
1010	>	if (usePeriodicBoundaryConditions_) {
1011	>	snap_->wrapVector(d);
1012	>	}
1013		return d;
1014		}
1015
#	Line 280 | Line 1021 | namespace OpenMD {
1021		#else
1022		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1023		#endif
1024	<
1025	<	snap_->wrapVector(d);
1024	>	if (usePeriodicBoundaryConditions_) {
1025	>	snap_->wrapVector(d);
1026	>	}
1027		return d;
1028		}
1029	+
1030	+	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1031	+	#ifdef IS_MPI
1032	+	return massFactorsRow[atom1];
1033	+	#else
1034	+	return massFactors[atom1];
1035	+	#endif
1036	+	}
1037	+
1038	+	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1039	+	#ifdef IS_MPI
1040	+	return massFactorsCol[atom2];
1041	+	#else
1042	+	return massFactors[atom2];
1043	+	#endif
1044	+
1045	+	}
1046
1047		Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
1048		Vector3d d;
#	Line 293 | Line 1052 | namespace OpenMD {
1052		#else
1053		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1054		#endif
1055	<
1056	<	snap_->wrapVector(d);
1055	>	if (usePeriodicBoundaryConditions_) {
1056	>	snap_->wrapVector(d);
1057	>	}
1058		return d;
1059		}
1060
1061	+	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1062	+	return excludesForAtom[atom1];
1063	+	}
1064	+
1065	+	/**
1066	+	* We need to exclude some overcounted interactions that result from
1067	+	* the parallel decomposition.
1068	+	*/
1069	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1070	+	int unique_id_1, unique_id_2;
1071	+
1072	+	#ifdef IS_MPI
1073	+	// in MPI, we have to look up the unique IDs for each atom
1074	+	unique_id_1 = AtomRowToGlobal[atom1];
1075	+	unique_id_2 = AtomColToGlobal[atom2];
1076	+	// group1 = cgRowToGlobal[cg1];
1077	+	// group2 = cgColToGlobal[cg2];
1078	+	#else
1079	+	unique_id_1 = AtomLocalToGlobal[atom1];
1080	+	unique_id_2 = AtomLocalToGlobal[atom2];
1081	+	int group1 = cgLocalToGlobal[cg1];
1082	+	int group2 = cgLocalToGlobal[cg2];
1083	+	#endif
1084	+
1085	+	if (unique_id_1 == unique_id_2) return true;
1086	+
1087	+	#ifdef IS_MPI
1088	+	// this prevents us from doing the pair on multiple processors
1089	+	if (unique_id_1 < unique_id_2) {
1090	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1091	+	} else {
1092	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1093	+	}
1094	+	#endif
1095	+
1096	+	#ifndef IS_MPI
1097	+	if (group1 == group2) {
1098	+	if (unique_id_1 < unique_id_2) return true;
1099	+	}
1100	+	#endif
1101	+
1102	+	return false;
1103	+	}
1104	+
1105	+	/**
1106	+	* We need to handle the interactions for atoms who are involved in
1107	+	* the same rigid body as well as some short range interactions
1108	+	* (bonds, bends, torsions) differently from other interactions.
1109	+	* We'll still visit the pairwise routines, but with a flag that
1110	+	* tells those routines to exclude the pair from direct long range
1111	+	* interactions.  Some indirect interactions (notably reaction
1112	+	* field) must still be handled for these pairs.
1113	+	*/
1114	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1115	+
1116	+	// excludesForAtom was constructed to use row/column indices in the MPI
1117	+	// version, and to use local IDs in the non-MPI version:
1118	+
1119	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1120	+	i != excludesForAtom[atom1].end(); ++i) {
1121	+	if ( (*i) == atom2 ) return true;
1122	+	}
1123	+
1124	+	return false;
1125	+	}
1126	+
1127	+
1128		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1129		#ifdef IS_MPI
1130		atomRowData.force[atom1] += fg;
#	Line 312 | Line 1139 | namespace OpenMD {
1139		#else
1140		snap_->atomData.force[atom2] += fg;
1141		#endif
315	–
1142		}
1143
1144		// filling interaction blocks with pointers
1145	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1145	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1146	>	int atom1, int atom2) {
1147
1148	<	InteractionData idat;
1148	>	idat.excluded = excludeAtomPair(atom1, atom2);
1149	>
1150		#ifdef IS_MPI
1151	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1152	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1153	+	//                         ff_->getAtomType(identsCol[atom2]) );
1154	+
1155		if (storageLayout_ & DataStorage::dslAmat) {
1156	<	idat.A1 = atomRowData.aMat[atom1];
1157	<	idat.A2 = atomColData.aMat[atom2];
1156	>	idat.A1 = &(atomRowData.aMat[atom1]);
1157	>	idat.A2 = &(atomColData.aMat[atom2]);
1158		}
1159	+
1160	+	if (storageLayout_ & DataStorage::dslTorque) {
1161	+	idat.t1 = &(atomRowData.torque[atom1]);
1162	+	idat.t2 = &(atomColData.torque[atom2]);
1163	+	}
1164
1165	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1166	<	idat.eFrame1 = atomRowData.electroFrame[atom1];
1167	<	idat.eFrame2 = atomColData.electroFrame[atom2];
1165	>	if (storageLayout_ & DataStorage::dslDipole) {
1166	>	idat.dipole1 = &(atomRowData.dipole[atom1]);
1167	>	idat.dipole2 = &(atomColData.dipole[atom2]);
1168		}
1169
1170	<	if (storageLayout_ & DataStorage::dslTorque) {
1171	<	idat.t1 = atomRowData.torque[atom1];
1172	<	idat.t2 = atomColData.torque[atom2];
1170	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1171	>	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1172	>	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1173		}
1174
1175		if (storageLayout_ & DataStorage::dslDensity) {
1176	<	idat.rho1 = atomRowData.density[atom1];
1177	<	idat.rho2 = atomColData.density[atom2];
1176	>	idat.rho1 = &(atomRowData.density[atom1]);
1177	>	idat.rho2 = &(atomColData.density[atom2]);
1178		}
1179
1180	+	if (storageLayout_ & DataStorage::dslFunctional) {
1181	+	idat.frho1 = &(atomRowData.functional[atom1]);
1182	+	idat.frho2 = &(atomColData.functional[atom2]);
1183	+	}
1184	+
1185		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1186	<	idat.dfrho1 = atomRowData.functionalDerivative[atom1];
1187	<	idat.dfrho2 = atomColData.functionalDerivative[atom2];
1186	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1187	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1188		}
1189	<	#endif
1189	>
1190	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1191	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1192	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1193	>	}
1194	>
1195	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1196	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1197	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1198	>	}
1199	>
1200	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1201	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1202	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1203	>	}
1204	>
1205	>	#else
1206
1207	<	}
1208	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1209	<	}
1210	<	SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
1207	>	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1208	>
1209	>	if (storageLayout_ & DataStorage::dslAmat) {
1210	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1211	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1212	>	}
1213	>
1214	>	if (storageLayout_ & DataStorage::dslTorque) {
1215	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1216	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1217	>	}
1218	>
1219	>	if (storageLayout_ & DataStorage::dslDipole) {
1220	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1221	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1222	>	}
1223	>
1224	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1225	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1226	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1227	>	}
1228	>
1229	>	if (storageLayout_ & DataStorage::dslDensity) {
1230	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1231	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1232	>	}
1233	>
1234	>	if (storageLayout_ & DataStorage::dslFunctional) {
1235	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1236	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1237	>	}
1238	>
1239	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1240	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1241	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1242	>	}
1243	>
1244	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1245	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1246	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1247	>	}
1248	>
1249	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1250	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1251	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1252	>	}
1253	>
1254	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1255	>	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1256	>	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1257	>	}
1258	>
1259	>	#endif
1260		}
1261
1262
1263	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1264	+	#ifdef IS_MPI
1265	+	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1266	+	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1267	+	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1268	+	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1269	+
1270	+	atomRowData.force[atom1] += *(idat.f1);
1271	+	atomColData.force[atom2] -= *(idat.f1);
1272	+
1273	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1274	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1275	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1276	+	}
1277	+
1278	+	if (storageLayout_ & DataStorage::dslElectricField) {
1279	+	atomRowData.electricField[atom1] += *(idat.eField1);
1280	+	atomColData.electricField[atom2] += *(idat.eField2);
1281	+	}
1282	+
1283	+	#else
1284	+	pairwisePot += *(idat.pot);
1285	+	excludedPot += *(idat.excludedPot);
1286	+
1287	+	snap_->atomData.force[atom1] += *(idat.f1);
1288	+	snap_->atomData.force[atom2] -= *(idat.f1);
1289	+
1290	+	if (idat.doParticlePot) {
1291	+	// This is the pairwise contribution to the particle pot.  The
1292	+	// embedding contribution is added in each of the low level
1293	+	// non-bonded routines.  In parallel, this calculation is done
1294	+	// in collectData, not in unpackInteractionData.
1295	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1296	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1297	+	}
1298	+
1299	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1300	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1301	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1302	+	}
1303	+
1304	+	if (storageLayout_ & DataStorage::dslElectricField) {
1305	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1306	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1307	+	}
1308	+
1309	+	#endif
1310	+
1311	+	}
1312	+
1313	+	/*
1314	+	* buildNeighborList
1315	+	*
1316	+	* first element of pair is row-indexed CutoffGroup
1317	+	* second element of pair is column-indexed CutoffGroup
1318	+	*/
1319	+	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1320	+
1321	+	vector<pair<int, int> > neighborList;
1322	+	groupCutoffs cuts;
1323	+	bool doAllPairs = false;
1324	+
1325	+	RealType rList_ = (largestRcut_ + skinThickness_);
1326	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1327	+	Mat3x3d box;
1328	+	Mat3x3d invBox;
1329	+
1330	+	Vector3d rs, scaled, dr;
1331	+	Vector3i whichCell;
1332	+	int cellIndex;
1333	+
1334	+	#ifdef IS_MPI
1335	+	cellListRow_.clear();
1336	+	cellListCol_.clear();
1337	+	#else
1338	+	cellList_.clear();
1339	+	#endif
1340	+
1341	+	if (!usePeriodicBoundaryConditions_) {
1342	+	box = snap_->getBoundingBox();
1343	+	invBox = snap_->getInvBoundingBox();
1344	+	} else {
1345	+	box = snap_->getHmat();
1346	+	invBox = snap_->getInvHmat();
1347	+	}
1348	+
1349	+	Vector3d boxX = box.getColumn(0);
1350	+	Vector3d boxY = box.getColumn(1);
1351	+	Vector3d boxZ = box.getColumn(2);
1352	+
1353	+	nCells_.x() = (int) ( boxX.length() )/ rList_;
1354	+	nCells_.y() = (int) ( boxY.length() )/ rList_;
1355	+	nCells_.z() = (int) ( boxZ.length() )/ rList_;
1356	+
1357	+	// handle small boxes where the cell offsets can end up repeating cells
1358	+
1359	+	if (nCells_.x() < 3) doAllPairs = true;
1360	+	if (nCells_.y() < 3) doAllPairs = true;
1361	+	if (nCells_.z() < 3) doAllPairs = true;
1362	+
1363	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1364	+
1365	+	#ifdef IS_MPI
1366	+	cellListRow_.resize(nCtot);
1367	+	cellListCol_.resize(nCtot);
1368	+	#else
1369	+	cellList_.resize(nCtot);
1370	+	#endif
1371	+
1372	+	if (!doAllPairs) {
1373	+	#ifdef IS_MPI
1374	+
1375	+	for (int i = 0; i < nGroupsInRow_; i++) {
1376	+	rs = cgRowData.position[i];
1377	+
1378	+	// scaled positions relative to the box vectors
1379	+	scaled = invBox * rs;
1380	+
1381	+	// wrap the vector back into the unit box by subtracting integer box
1382	+	// numbers
1383	+	for (int j = 0; j < 3; j++) {
1384	+	scaled[j] -= roundMe(scaled[j]);
1385	+	scaled[j] += 0.5;
1386	+	// Handle the special case when an object is exactly on the
1387	+	// boundary (a scaled coordinate of 1.0 is the same as
1388	+	// scaled coordinate of 0.0)
1389	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1390	+	}
1391	+
1392	+	// find xyz-indices of cell that cutoffGroup is in.
1393	+	whichCell.x() = nCells_.x() * scaled.x();
1394	+	whichCell.y() = nCells_.y() * scaled.y();
1395	+	whichCell.z() = nCells_.z() * scaled.z();
1396	+
1397	+	// find single index of this cell:
1398	+	cellIndex = Vlinear(whichCell, nCells_);
1399	+
1400	+	// add this cutoff group to the list of groups in this cell;
1401	+	cellListRow_[cellIndex].push_back(i);
1402	+	}
1403	+	for (int i = 0; i < nGroupsInCol_; i++) {
1404	+	rs = cgColData.position[i];
1405	+
1406	+	// scaled positions relative to the box vectors
1407	+	scaled = invBox * rs;
1408	+
1409	+	// wrap the vector back into the unit box by subtracting integer box
1410	+	// numbers
1411	+	for (int j = 0; j < 3; j++) {
1412	+	scaled[j] -= roundMe(scaled[j]);
1413	+	scaled[j] += 0.5;
1414	+	// Handle the special case when an object is exactly on the
1415	+	// boundary (a scaled coordinate of 1.0 is the same as
1416	+	// scaled coordinate of 0.0)
1417	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1418	+	}
1419	+
1420	+	// find xyz-indices of cell that cutoffGroup is in.
1421	+	whichCell.x() = nCells_.x() * scaled.x();
1422	+	whichCell.y() = nCells_.y() * scaled.y();
1423	+	whichCell.z() = nCells_.z() * scaled.z();
1424	+
1425	+	// find single index of this cell:
1426	+	cellIndex = Vlinear(whichCell, nCells_);
1427	+
1428	+	// add this cutoff group to the list of groups in this cell;
1429	+	cellListCol_[cellIndex].push_back(i);
1430	+	}
1431	+
1432	+	#else
1433	+	for (int i = 0; i < nGroups_; i++) {
1434	+	rs = snap_->cgData.position[i];
1435	+
1436	+	// scaled positions relative to the box vectors
1437	+	scaled = invBox * rs;
1438	+
1439	+	// wrap the vector back into the unit box by subtracting integer box
1440	+	// numbers
1441	+	for (int j = 0; j < 3; j++) {
1442	+	scaled[j] -= roundMe(scaled[j]);
1443	+	scaled[j] += 0.5;
1444	+	// Handle the special case when an object is exactly on the
1445	+	// boundary (a scaled coordinate of 1.0 is the same as
1446	+	// scaled coordinate of 0.0)
1447	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1448	+	}
1449	+
1450	+	// find xyz-indices of cell that cutoffGroup is in.
1451	+	whichCell.x() = nCells_.x() * scaled.x();
1452	+	whichCell.y() = nCells_.y() * scaled.y();
1453	+	whichCell.z() = nCells_.z() * scaled.z();
1454	+
1455	+	// find single index of this cell:
1456	+	cellIndex = Vlinear(whichCell, nCells_);
1457	+
1458	+	// add this cutoff group to the list of groups in this cell;
1459	+	cellList_[cellIndex].push_back(i);
1460	+	}
1461	+
1462	+	#endif
1463	+
1464	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1465	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1466	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1467	+	Vector3i m1v(m1x, m1y, m1z);
1468	+	int m1 = Vlinear(m1v, nCells_);
1469	+
1470	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1471	+	os != cellOffsets_.end(); ++os) {
1472	+
1473	+	Vector3i m2v = m1v + (*os);
1474	+
1475	+
1476	+	if (m2v.x() >= nCells_.x()) {
1477	+	m2v.x() = 0;
1478	+	} else if (m2v.x() < 0) {
1479	+	m2v.x() = nCells_.x() - 1;
1480	+	}
1481	+
1482	+	if (m2v.y() >= nCells_.y()) {
1483	+	m2v.y() = 0;
1484	+	} else if (m2v.y() < 0) {
1485	+	m2v.y() = nCells_.y() - 1;
1486	+	}
1487	+
1488	+	if (m2v.z() >= nCells_.z()) {
1489	+	m2v.z() = 0;
1490	+	} else if (m2v.z() < 0) {
1491	+	m2v.z() = nCells_.z() - 1;
1492	+	}
1493	+
1494	+	int m2 = Vlinear (m2v, nCells_);
1495	+
1496	+	#ifdef IS_MPI
1497	+	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1498	+	j1 != cellListRow_[m1].end(); ++j1) {
1499	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1500	+	j2 != cellListCol_[m2].end(); ++j2) {
1501	+
1502	+	// In parallel, we need to visit *all* pairs of row
1503	+	// & column indicies and will divide labor in the
1504	+	// force evaluation later.
1505	+	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1506	+	if (usePeriodicBoundaryConditions_) {
1507	+	snap_->wrapVector(dr);
1508	+	}
1509	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1510	+	if (dr.lengthSquare() < cuts.third) {
1511	+	neighborList.push_back(make_pair((*j1), (*j2)));
1512	+	}
1513	+	}
1514	+	}
1515	+	#else
1516	+	for (vector<int>::iterator j1 = cellList_[m1].begin();
1517	+	j1 != cellList_[m1].end(); ++j1) {
1518	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1519	+	j2 != cellList_[m2].end(); ++j2) {
1520	+
1521	+	// Always do this if we're in different cells or if
1522	+	// we're in the same cell and the global index of
1523	+	// the j2 cutoff group is greater than or equal to
1524	+	// the j1 cutoff group.  Note that Rappaport's code
1525	+	// has a "less than" conditional here, but that
1526	+	// deals with atom-by-atom computation.  OpenMD
1527	+	// allows atoms within a single cutoff group to
1528	+	// interact with each other.
1529	+
1530	+	if (m2 != m1 || (*j2) >= (*j1) ) {
1531	+
1532	+	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1533	+	if (usePeriodicBoundaryConditions_) {
1534	+	snap_->wrapVector(dr);
1535	+	}
1536	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1537	+	if (dr.lengthSquare() < cuts.third) {
1538	+	neighborList.push_back(make_pair((*j1), (*j2)));
1539	+	}
1540	+	}
1541	+	}
1542	+	}
1543	+	#endif
1544	+	}
1545	+	}
1546	+	}
1547	+	}
1548	+	} else {
1549	+	// branch to do all cutoff group pairs
1550	+	#ifdef IS_MPI
1551	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1552	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1553	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1554	+	if (usePeriodicBoundaryConditions_) {
1555	+	snap_->wrapVector(dr);
1556	+	}
1557	+	cuts = getGroupCutoffs( j1, j2 );
1558	+	if (dr.lengthSquare() < cuts.third) {
1559	+	neighborList.push_back(make_pair(j1, j2));
1560	+	}
1561	+	}
1562	+	}
1563	+	#else
1564	+	// include all groups here.
1565	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1566	+	// include self group interactions j2 == j1
1567	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1568	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1569	+	if (usePeriodicBoundaryConditions_) {
1570	+	snap_->wrapVector(dr);
1571	+	}
1572	+	cuts = getGroupCutoffs( j1, j2 );
1573	+	if (dr.lengthSquare() < cuts.third) {
1574	+	neighborList.push_back(make_pair(j1, j2));
1575	+	}
1576	+	}
1577	+	}
1578	+	#endif
1579	+	}
1580	+
1581	+	// save the local cutoff group positions for the check that is
1582	+	// done on each loop:
1583	+	saved_CG_positions_.clear();
1584	+	for (int i = 0; i < nGroups_; i++)
1585	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1586	+
1587	+	return neighborList;
1588	+	}
1589		} //end namespace OpenMD

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