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

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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1539 by gezelter, Fri Jan 14 22:31:31 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1895 by gezelter, Mon Jul 1 21:09:37 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/ForceDecomposition.hpp"
42	<	#include "parallel/Communicator.hpp"
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	<	void ForceDecomposition::distributeInitialData() {
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
50	–	int nAtoms;
51	–	int nGroups;
88
89	<	AtomCommRealI = new Comm<I,RealType>(nAtoms);
90	<	AtomCommVectorI = new Comm<I,Vector3d>(nAtoms);
91	<	AtomCommMatrixI = new Comm<I,Mat3x3d>(nAtoms);
89	>	/**
90	>	* distributeInitialData is essentially a copy of the older fortran
91	>	* SimulationSetup
92	>	*/
93	>	void ForceMatrixDecomposition::distributeInitialData() {
94	>	snap_ = sman_->getCurrentSnapshot();
95	>	storageLayout_ = sman_->getStorageLayout();
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	<	AtomCommRealJ = new Comm<J,RealType>(nAtoms);
58	<	AtomCommVectorJ = new Comm<J,Vector3d>(nAtoms);
59	<	AtomCommMatrixJ = new Comm<J,Mat3x3d>(nAtoms);
106	>	massFactors = info_->getMassFactors();
107
108	<	cgCommVectorI = new Comm<I,Vector3d>(nGroups);
109	<	cgCommVectorJ = new Comm<J,Vector3d>(nGroups);
110	<	// more to come
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	>	MPI::Intracomm row = rowComm.getComm();
122	>	MPI::Intracomm col = colComm.getComm();
123	>
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	>	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	>	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_);
149	>	atomColData.resize(nAtomsInCol_);
150	>	atomColData.setStorageLayout(storageLayout_);
151	>	cgRowData.resize(nGroupsInRow_);
152	>	cgRowData.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	>	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	>	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++) {
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	<	void ForceDecomposition::distributeData()  {
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	<	Snapshot* snap = sman_->getCurrentSnapshot();
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	<	AtomCommVectorI->gather(snap->atomData.position,
604	<	snap->atomIData.position);
605	<	AtomCommVectorJ->gather(snap->atomData.position,
606	<	snap->atomJData.position);
603	>	AtomPlanVectorRow->gather(snap_->atomData.position,
604	>	atomRowData.position);
605	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
606	>	atomColData.position);
607
608		// gather up the cutoff group positions
609	<	cgCommVectorI->gather(snap->cgData.position,
610	<	snap->cgIData.position);
611	<	cgCommVectorJ->gather(snap->cgData.position,
612	<	snap->cgJData.position);
609	>
610	>	cgPlanVectorRow->gather(snap_->cgData.position,
611	>	cgRowData.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 (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
630	<	AtomCommMatrixI->gather(snap->atomData.aMat,
631	<	snap->atomIData.aMat);
632	<	AtomCommMatrixJ->gather(snap->atomData.aMat,
633	<	snap->atomJData.aMat);
629	>	if (storageLayout_ & DataStorage::dslAmat) {
630	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
631	>	atomRowData.aMat);
632	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
633	>	atomColData.aMat);
634		}
635	<
636	<	// if needed, gather the atomic eletrostatic frames
637	<	if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
638	<	AtomCommMatrixI->gather(snap->atomData.electroFrame,
639	<	snap->atomIData.electroFrame);
640	<	AtomCommMatrixJ->gather(snap->atomData.electroFrame,
641	<	snap->atomJData.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	<	void ForceDecomposition::collectIntermediateData() {
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();
668		#ifdef IS_MPI
105	–	Snapshot* snap = sman_->getCurrentSnapshot();
106	–	// gather up the atomic positions
669
670	<	if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
671	<	AtomCommRealI->scatter(snap->atomIData.density,
672	<	snap->atomData.density);
673	<	std::vector<RealType> rho_tmp;
674	<	int n = snap->getNumberOfAtoms();
675	<	rho_tmp.reserve( n );
676	<	AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
670	>	if (storageLayout_ & DataStorage::dslDensity) {
671	>
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	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
678		for (int i = 0; i < n; i++)
679	<	snap->atomData.density[i] += rho_tmp[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	<
699	<	void ForceDecomposition::distributeIntermediateData() {
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	<	Snapshot* snap = sman_->getCurrentSnapshot();
708	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
709	<	AtomCommRealI->gather(snap->atomData.functional,
710	<	snap->atomIData.functional);
711	<	AtomCommRealJ->gather(snap->atomData.functional,
128	<	snap->atomJData.functional);
707	>	if (storageLayout_ & DataStorage::dslFunctional) {
708	>	AtomPlanRealRow->gather(snap_->atomData.functional,
709	>	atomRowData.functional);
710	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
711	>	atomColData.functional);
712		}
713
714	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
715	<	AtomCommRealI->gather(snap->atomData.functionalDerivative,
716	<	snap->atomIData.functionalDerivative);
717	<	AtomCommRealJ->gather(snap->atomData.functionalDerivative,
718	<	snap->atomJData.functionalDerivative);
714	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
715	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
716	>	atomRowData.functionalDerivative);
717	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
718	>	atomColData.functionalDerivative);
719		}
720		#endif
721		}
722
723
724	<	void ForceDecomposition::collectData() {
724	>	void ForceMatrixDecomposition::collectData() {
725	>	snap_ = sman_->getCurrentSnapshot();
726	>	storageLayout_ = sman_->getStorageLayout();
727	>	#ifdef IS_MPI
728	>	int n = snap_->atomData.force.size();
729	>	vector<Vector3d> frc_tmp(n, V3Zero);
730	>
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	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
738	>	for (int i = 0; i < n; i++) {
739	>	snap_->atomData.force[i] += frc_tmp[i];
740	>	}
741	>
742	>	if (storageLayout_ & DataStorage::dslTorque) {
743	>
744	>	int nt = snap_->atomData.torque.size();
745	>	vector<Vector3d> trq_tmp(nt, V3Zero);
746	>
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	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
754	>	for (int i = 0; i < nt; i++)
755	>	snap_->atomData.torque[i] += trq_tmp[i];
756	>	}
757	>
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	>	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;
971	+
972	+	#ifdef IS_MPI
973	+	d = cgColData.position[cg2] - cgRowData.position[cg1];
974	+	#else
975	+	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
976	+	#endif
977	+
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;
1004	+
1005	+	#ifdef IS_MPI
1006	+	d = cgRowData.position[cg1] - atomRowData.position[atom1];
1007	+	#else
1008	+	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1009	+	#endif
1010	+	if (usePeriodicBoundaryConditions_) {
1011	+	snap_->wrapVector(d);
1012	+	}
1013	+	return d;
1014	+	}
1015	+
1016	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
1017	+	Vector3d d;
1018	+
1019	+	#ifdef IS_MPI
1020	+	d = cgColData.position[cg2] - atomColData.position[atom2];
1021	+	#else
1022	+	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1023	+	#endif
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;
1049	+
1050	+	#ifdef IS_MPI
1051	+	d = atomColData.position[atom2] - atomRowData.position[atom1];
1052	+	#else
1053	+	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1054	+	#endif
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;
1131	+	#else
1132	+	snap_->atomData.force[atom1] += fg;
1133	+	#endif
1134	+	}
1135	+
1136	+	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
1137	+	#ifdef IS_MPI
1138	+	atomColData.force[atom2] += fg;
1139	+	#else
1140	+	snap_->atomData.force[atom2] += fg;
1141	+	#endif
1142	+	}
1143	+
1144	+	// filling interaction blocks with pointers
1145	+	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1146	+	int atom1, int atom2) {
1147	+
1148	+	idat.excluded = excludeAtomPair(atom1, atom2);
1149	+
1150	+	#ifdef IS_MPI
1151	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1152	+	idat.atid1 = identsRow[atom1];
1153	+	idat.atid2 = identsCol[atom2];
1154	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1155	+	//                         ff_->getAtomType(identsCol[atom2]) );
1156	+
1157	+	if (storageLayout_ & DataStorage::dslAmat) {
1158	+	idat.A1 = &(atomRowData.aMat[atom1]);
1159	+	idat.A2 = &(atomColData.aMat[atom2]);
1160	+	}
1161	+
1162	+	if (storageLayout_ & DataStorage::dslTorque) {
1163	+	idat.t1 = &(atomRowData.torque[atom1]);
1164	+	idat.t2 = &(atomColData.torque[atom2]);
1165	+	}
1166	+
1167	+	if (storageLayout_ & DataStorage::dslDipole) {
1168	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1169	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1170	+	}
1171	+
1172	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1173	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1174	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1175	+	}
1176	+
1177	+	if (storageLayout_ & DataStorage::dslDensity) {
1178	+	idat.rho1 = &(atomRowData.density[atom1]);
1179	+	idat.rho2 = &(atomColData.density[atom2]);
1180	+	}
1181	+
1182	+	if (storageLayout_ & DataStorage::dslFunctional) {
1183	+	idat.frho1 = &(atomRowData.functional[atom1]);
1184	+	idat.frho2 = &(atomColData.functional[atom2]);
1185	+	}
1186	+
1187	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1188	+	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1189	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1190	+	}
1191	+
1192	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1193	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1194	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1195	+	}
1196	+
1197	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1198	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1199	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1200	+	}
1201	+
1202	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1203	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1204	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1205	+	}
1206	+
1207	+	#else
1208	+
1209	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1210	+	idat.atid1 = idents[atom1];
1211	+	idat.atid2 = idents[atom2];
1212	+
1213	+	if (storageLayout_ & DataStorage::dslAmat) {
1214	+	idat.A1 = &(snap_->atomData.aMat[atom1]);
1215	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1216	+	}
1217	+
1218	+	if (storageLayout_ & DataStorage::dslTorque) {
1219	+	idat.t1 = &(snap_->atomData.torque[atom1]);
1220	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1221	+	}
1222	+
1223	+	if (storageLayout_ & DataStorage::dslDipole) {
1224	+	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1225	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1226	+	}
1227	+
1228	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1229	+	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1230	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1231	+	}
1232	+
1233	+	if (storageLayout_ & DataStorage::dslDensity) {
1234	+	idat.rho1 = &(snap_->atomData.density[atom1]);
1235	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1236	+	}
1237	+
1238	+	if (storageLayout_ & DataStorage::dslFunctional) {
1239	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1240	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1241	+	}
1242	+
1243	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1244	+	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1245	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1246	+	}
1247	+
1248	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1249	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1250	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1251	+	}
1252	+
1253	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1254	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1255	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1256	+	}
1257	+
1258	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1259	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1260	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1261	+	}
1262	+
1263	+	#endif
1264	+	}
1265	+
1266	+
1267	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1268	+	#ifdef IS_MPI
1269	+	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1270	+	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1271	+	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1272	+	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1273	+
1274	+	atomRowData.force[atom1] += *(idat.f1);
1275	+	atomColData.force[atom2] -= *(idat.f1);
1276	+
1277	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1278	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1279	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1280	+	}
1281	+
1282	+	if (storageLayout_ & DataStorage::dslElectricField) {
1283	+	atomRowData.electricField[atom1] += *(idat.eField1);
1284	+	atomColData.electricField[atom2] += *(idat.eField2);
1285	+	}
1286	+
1287	+	#else
1288	+	pairwisePot += *(idat.pot);
1289	+	excludedPot += *(idat.excludedPot);
1290	+
1291	+	snap_->atomData.force[atom1] += *(idat.f1);
1292	+	snap_->atomData.force[atom2] -= *(idat.f1);
1293	+
1294	+	if (idat.doParticlePot) {
1295	+	// This is the pairwise contribution to the particle pot.  The
1296	+	// embedding contribution is added in each of the low level
1297	+	// non-bonded routines.  In parallel, this calculation is done
1298	+	// in collectData, not in unpackInteractionData.
1299	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1300	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1301	+	}
1302	+
1303	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1304	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1305	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1306	+	}
1307	+
1308	+	if (storageLayout_ & DataStorage::dslElectricField) {
1309	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1310	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1311	+	}
1312	+
1313	+	#endif
1314	+
1315	+	}
1316	+
1317	+	/*
1318	+	* buildNeighborList
1319	+	*
1320	+	* first element of pair is row-indexed CutoffGroup
1321	+	* second element of pair is column-indexed CutoffGroup
1322	+	*/
1323	+	void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1324	+
1325	+	neighborList.clear();
1326	+	groupCutoffs cuts;
1327	+	bool doAllPairs = false;
1328	+
1329	+	RealType rList_ = (largestRcut_ + skinThickness_);
1330	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1331	+	Mat3x3d box;
1332	+	Mat3x3d invBox;
1333	+
1334	+	Vector3d rs, scaled, dr;
1335	+	Vector3i whichCell;
1336	+	int cellIndex;
1337	+
1338	+	#ifdef IS_MPI
1339	+	cellListRow_.clear();
1340	+	cellListCol_.clear();
1341	+	#else
1342	+	cellList_.clear();
1343	+	#endif
1344	+
1345	+	if (!usePeriodicBoundaryConditions_) {
1346	+	box = snap_->getBoundingBox();
1347	+	invBox = snap_->getInvBoundingBox();
1348	+	} else {
1349	+	box = snap_->getHmat();
1350	+	invBox = snap_->getInvHmat();
1351	+	}
1352	+
1353	+	Vector3d boxX = box.getColumn(0);
1354	+	Vector3d boxY = box.getColumn(1);
1355	+	Vector3d boxZ = box.getColumn(2);
1356	+
1357	+	nCells_.x() = (int) ( boxX.length() )/ rList_;
1358	+	nCells_.y() = (int) ( boxY.length() )/ rList_;
1359	+	nCells_.z() = (int) ( boxZ.length() )/ rList_;
1360	+
1361	+	// handle small boxes where the cell offsets can end up repeating cells
1362	+
1363	+	if (nCells_.x() < 3) doAllPairs = true;
1364	+	if (nCells_.y() < 3) doAllPairs = true;
1365	+	if (nCells_.z() < 3) doAllPairs = true;
1366	+
1367	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1368	+
1369	+	#ifdef IS_MPI
1370	+	cellListRow_.resize(nCtot);
1371	+	cellListCol_.resize(nCtot);
1372	+	#else
1373	+	cellList_.resize(nCtot);
1374	+	#endif
1375	+
1376	+	if (!doAllPairs) {
1377	+	#ifdef IS_MPI
1378	+
1379	+	for (int i = 0; i < nGroupsInRow_; i++) {
1380	+	rs = cgRowData.position[i];
1381	+
1382	+	// scaled positions relative to the box vectors
1383	+	scaled = invBox * rs;
1384	+
1385	+	// wrap the vector back into the unit box by subtracting integer box
1386	+	// numbers
1387	+	for (int j = 0; j < 3; j++) {
1388	+	scaled[j] -= roundMe(scaled[j]);
1389	+	scaled[j] += 0.5;
1390	+	// Handle the special case when an object is exactly on the
1391	+	// boundary (a scaled coordinate of 1.0 is the same as
1392	+	// scaled coordinate of 0.0)
1393	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1394	+	}
1395	+
1396	+	// find xyz-indices of cell that cutoffGroup is in.
1397	+	whichCell.x() = nCells_.x() * scaled.x();
1398	+	whichCell.y() = nCells_.y() * scaled.y();
1399	+	whichCell.z() = nCells_.z() * scaled.z();
1400	+
1401	+	// find single index of this cell:
1402	+	cellIndex = Vlinear(whichCell, nCells_);
1403	+
1404	+	// add this cutoff group to the list of groups in this cell;
1405	+	cellListRow_[cellIndex].push_back(i);
1406	+	}
1407	+	for (int i = 0; i < nGroupsInCol_; i++) {
1408	+	rs = cgColData.position[i];
1409	+
1410	+	// scaled positions relative to the box vectors
1411	+	scaled = invBox * rs;
1412	+
1413	+	// wrap the vector back into the unit box by subtracting integer box
1414	+	// numbers
1415	+	for (int j = 0; j < 3; j++) {
1416	+	scaled[j] -= roundMe(scaled[j]);
1417	+	scaled[j] += 0.5;
1418	+	// Handle the special case when an object is exactly on the
1419	+	// boundary (a scaled coordinate of 1.0 is the same as
1420	+	// scaled coordinate of 0.0)
1421	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1422	+	}
1423	+
1424	+	// find xyz-indices of cell that cutoffGroup is in.
1425	+	whichCell.x() = nCells_.x() * scaled.x();
1426	+	whichCell.y() = nCells_.y() * scaled.y();
1427	+	whichCell.z() = nCells_.z() * scaled.z();
1428	+
1429	+	// find single index of this cell:
1430	+	cellIndex = Vlinear(whichCell, nCells_);
1431	+
1432	+	// add this cutoff group to the list of groups in this cell;
1433	+	cellListCol_[cellIndex].push_back(i);
1434	+	}
1435	+
1436	+	#else
1437	+	for (int i = 0; i < nGroups_; i++) {
1438	+	rs = snap_->cgData.position[i];
1439	+
1440	+	// scaled positions relative to the box vectors
1441	+	scaled = invBox * rs;
1442	+
1443	+	// wrap the vector back into the unit box by subtracting integer box
1444	+	// numbers
1445	+	for (int j = 0; j < 3; j++) {
1446	+	scaled[j] -= roundMe(scaled[j]);
1447	+	scaled[j] += 0.5;
1448	+	// Handle the special case when an object is exactly on the
1449	+	// boundary (a scaled coordinate of 1.0 is the same as
1450	+	// scaled coordinate of 0.0)
1451	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1452	+	}
1453	+
1454	+	// find xyz-indices of cell that cutoffGroup is in.
1455	+	whichCell.x() = nCells_.x() * scaled.x();
1456	+	whichCell.y() = nCells_.y() * scaled.y();
1457	+	whichCell.z() = nCells_.z() * scaled.z();
1458	+
1459	+	// find single index of this cell:
1460	+	cellIndex = Vlinear(whichCell, nCells_);
1461	+
1462	+	// add this cutoff group to the list of groups in this cell;
1463	+	cellList_[cellIndex].push_back(i);
1464	+	}
1465	+
1466	+	#endif
1467	+
1468	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1469	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1470	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1471	+	Vector3i m1v(m1x, m1y, m1z);
1472	+	int m1 = Vlinear(m1v, nCells_);
1473	+
1474	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1475	+	os != cellOffsets_.end(); ++os) {
1476	+
1477	+	Vector3i m2v = m1v + (*os);
1478	+
1479	+
1480	+	if (m2v.x() >= nCells_.x()) {
1481	+	m2v.x() = 0;
1482	+	} else if (m2v.x() < 0) {
1483	+	m2v.x() = nCells_.x() - 1;
1484	+	}
1485	+
1486	+	if (m2v.y() >= nCells_.y()) {
1487	+	m2v.y() = 0;
1488	+	} else if (m2v.y() < 0) {
1489	+	m2v.y() = nCells_.y() - 1;
1490	+	}
1491	+
1492	+	if (m2v.z() >= nCells_.z()) {
1493	+	m2v.z() = 0;
1494	+	} else if (m2v.z() < 0) {
1495	+	m2v.z() = nCells_.z() - 1;
1496	+	}
1497	+
1498	+	int m2 = Vlinear (m2v, nCells_);
1499	+
1500	+	#ifdef IS_MPI
1501	+	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1502	+	j1 != cellListRow_[m1].end(); ++j1) {
1503	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1504	+	j2 != cellListCol_[m2].end(); ++j2) {
1505	+
1506	+	// In parallel, we need to visit *all* pairs of row
1507	+	// & column indicies and will divide labor in the
1508	+	// force evaluation later.
1509	+	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1510	+	if (usePeriodicBoundaryConditions_) {
1511	+	snap_->wrapVector(dr);
1512	+	}
1513	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1514	+	if (dr.lengthSquare() < cuts.third) {
1515	+	neighborList.push_back(make_pair((*j1), (*j2)));
1516	+	}
1517	+	}
1518	+	}
1519	+	#else
1520	+	for (vector<int>::iterator j1 = cellList_[m1].begin();
1521	+	j1 != cellList_[m1].end(); ++j1) {
1522	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1523	+	j2 != cellList_[m2].end(); ++j2) {
1524	+
1525	+	// Always do this if we're in different cells or if
1526	+	// we're in the same cell and the global index of
1527	+	// the j2 cutoff group is greater than or equal to
1528	+	// the j1 cutoff group.  Note that Rappaport's code
1529	+	// has a "less than" conditional here, but that
1530	+	// deals with atom-by-atom computation.  OpenMD
1531	+	// allows atoms within a single cutoff group to
1532	+	// interact with each other.
1533	+
1534	+	if (m2 != m1 || (*j2) >= (*j1) ) {
1535	+
1536	+	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1537	+	if (usePeriodicBoundaryConditions_) {
1538	+	snap_->wrapVector(dr);
1539	+	}
1540	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1541	+	if (dr.lengthSquare() < cuts.third) {
1542	+	neighborList.push_back(make_pair((*j1), (*j2)));
1543	+	}
1544	+	}
1545	+	}
1546	+	}
1547	+	#endif
1548	+	}
1549	+	}
1550	+	}
1551	+	}
1552	+	} else {
1553	+	// branch to do all cutoff group pairs
1554	+	#ifdef IS_MPI
1555	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1556	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1557	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1558	+	if (usePeriodicBoundaryConditions_) {
1559	+	snap_->wrapVector(dr);
1560	+	}
1561	+	cuts = getGroupCutoffs( j1, j2 );
1562	+	if (dr.lengthSquare() < cuts.third) {
1563	+	neighborList.push_back(make_pair(j1, j2));
1564	+	}
1565	+	}
1566	+	}
1567	+	#else
1568	+	// include all groups here.
1569	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1570	+	// include self group interactions j2 == j1
1571	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1572	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1573	+	if (usePeriodicBoundaryConditions_) {
1574	+	snap_->wrapVector(dr);
1575	+	}
1576	+	cuts = getGroupCutoffs( j1, j2 );
1577	+	if (dr.lengthSquare() < cuts.third) {
1578	+	neighborList.push_back(make_pair(j1, j2));
1579	+	}
1580	+	}
1581	+	}
1582	+	#endif
1583	+	}
1584	+
1585	+	// save the local cutoff group positions for the check that is
1586	+	// done on each loop:
1587	+	saved_CG_positions_.clear();
1588	+	for (int i = 0; i < nGroups_; i++)
1589	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1590	+	}
1591		} //end namespace OpenMD

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